repo stringclasses 1k
values | file_url stringlengths 96 373 | file_path stringlengths 11 294 | content stringlengths 0 32.8k | language stringclasses 1
value | license stringclasses 6
values | commit_sha stringclasses 1k
values | retrieved_at stringdate 2026-01-04 14:45:56 2026-01-04 18:30:23 | truncated bool 2
classes |
|---|---|---|---|---|---|---|---|---|
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/util/DataSourceDTOParserTest.java | src/test/java/org/ohdsi/webapi/util/DataSourceDTOParserTest.java | package org.ohdsi.webapi.util;
import com.odysseusinc.arachne.commons.types.DBMSType;
import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.DataSourceUnsecuredDTO;
import org.junit.Test;
import org.ohdsi.webapi.source.Source;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.nullValue;
import static org.junit.Assert.*;
public class DataSourceDTOParserTest {
public static final String PGSQL_CONN_STR = "jdbc:postgresql://localhost:5432/ohdsi?ssl=true&user=user&password=secret";
public static final String PGSQL_WO_PWD_CONN_STR = "jdbc:postgresql://localhost:5432/ohdsi?ssl=true";
public static final String MSSQL_CONN_STR = "jdbc:sqlserver://localhost:1433;databaseName=ohdsi;user=msuser;password=password";
public static final String PDW_CONN_STR = "jdbc:sqlserver://yourserver.database.windows.net:1433;database=yourdatabase;user=pdw_user;password=pdw_password;" +
"encrypt=true;trustServerCertificate=false;hostNameInCertificate=*.database.windows.net;loginTimeout=30;";
public static final String REDSHIFT_CONN_STR = "jdbc:redshift://examplecluster.abc123xyz789.us-west-2.redshift.amazonaws.com:5439/" +
"dev?ssl=true&UID=your_username&PWD=your_password";
public static final String NETEZZA_CONN_STR = "jdbc:netezza://main:5490/sales;user=admin;password=password;loglevel=2;logdirpath=C:\\";
public static final String IMPALA_AUTH3_CONN_STR = "jdbc:impala://node1.example.com:18000/default2;AuthMech=3;UID=cloudera;PWD=cloudera";
public static final String IMPALA_AUTH0_CONN_STR = "jdbc:impala://localhost:21050;AuthMech=0;";
public static final String IMPALA_AUTH1_CONN_STR = "jdbc:impala://node1.example.com:21050;AuthMech=1;" +
"KrbRealm=EXAMPLE.COM;KrbHostFQDN=node1.example.com;KrbServiceName=impala";
private static final String BIGQUERY_CONN_STR = "jdbc:bigquery://https://www.googleapis.com/bigquery/v2:443;" +
"ProjectId=MyBigQueryProject;OAuthType=0;OAuthServiceAcctEmail==bqtest1@data-driver-testing.iam.gserviceaccount.com;" +
"OAuthPvtKeyPath=C:\\SecureFiles\\ServiceKeyFile.p12;";
public static final String ORACLE_WO_PWD_CONN_STR = "jdbc:oracle:thin:@myhost:1521:orcl";
public static final String ORACLE_WITH_PWD_CONN_STR = "jdbc:oracle:thin:scott/tiger@myhost:1521:orcl";
public static final String HIVE_CONN_STR = "jdbc:hive2://sandbox-hdp.hortonworks.com:2181/synpuf_531_orc;serviceDiscoveryMode=zooKeeper;zooKeeperNamespace=hiveserver2";
public static final String IRIS_CONN_STR = "jdbc:IRIS://localhost:1972/USER";
@Test
public void parseDTO() {
DataSourceUnsecuredDTO dto;
dto = DataSourceDTOParser.parseDTO(getPostgreSQLSource());
assertThat(dto.getType(), is(DBMSType.POSTGRESQL));
assertThat(dto.getConnectionString(), is(PGSQL_CONN_STR));
assertThat(dto.getUsername(), is("user"));
assertThat(dto.getPassword(), is("secret"));
dto = DataSourceDTOParser.parseDTO(getPostgreSQLPasswordSource());
assertThat(dto.getType(), is(DBMSType.POSTGRESQL));
assertThat(dto.getConnectionString(), is(PGSQL_WO_PWD_CONN_STR));
assertThat(dto.getUsername(), is("user"));
assertThat(dto.getPassword(), is("password"));
dto = DataSourceDTOParser.parseDTO(getMSSQLSource());
assertThat(dto.getType(), is(DBMSType.MS_SQL_SERVER));
assertThat(dto.getConnectionString(), is((MSSQL_CONN_STR)));
assertThat(dto.getUsername(), is("msuser"));
assertThat(dto.getPassword(), is("password"));
dto = DataSourceDTOParser.parseDTO(getPDWSource());
assertThat(dto.getType(), is(DBMSType.PDW));
assertThat(dto.getConnectionString(), is(PDW_CONN_STR));
assertThat(dto.getUsername(), is("pdw_user"));
assertThat(dto.getPassword(), is("pdw_password"));
dto = DataSourceDTOParser.parseDTO(getRedshiftSource());
assertThat(dto.getType(), is(DBMSType.REDSHIFT));
assertThat(dto.getConnectionString(), is(REDSHIFT_CONN_STR));
assertThat(dto.getUsername(), is("your_username"));
assertThat(dto.getPassword(), is("your_password"));
dto = DataSourceDTOParser.parseDTO(getNetezzaSource());
assertThat(dto.getType(), is(DBMSType.NETEZZA));
assertThat(dto.getConnectionString(), is(NETEZZA_CONN_STR));
assertThat(dto.getUsername(), is("admin"));
assertThat(dto.getPassword(), is("password"));
dto = DataSourceDTOParser.parseDTO(getImpalaAuth3Source());
assertThat(dto.getType(), is(DBMSType.IMPALA));
assertThat(dto.getConnectionString(), is(IMPALA_AUTH3_CONN_STR));
assertThat(dto.getUsername(), is("cloudera"));
assertThat(dto.getPassword(), is("cloudera"));
dto = DataSourceDTOParser.parseDTO(getImpalaAuth0Source());
assertThat(dto.getType(), is(DBMSType.IMPALA));
assertThat(dto.getConnectionString(), is(IMPALA_AUTH0_CONN_STR));
assertThat(dto.getUsername(), is(nullValue()));
assertThat(dto.getPassword(), is(nullValue()));
dto = DataSourceDTOParser.parseDTO(getImpalaAuth1Source());
assertThat(dto.getType(), is(DBMSType.IMPALA));
assertThat(dto.getConnectionString(), is(IMPALA_AUTH1_CONN_STR));
assertThat(dto.getUsername(), is(nullValue()));
assertThat(dto.getPassword(), is(nullValue()));
dto = DataSourceDTOParser.parseDTO(getBigQuerySource());
assertThat(dto.getType(), is(DBMSType.BIGQUERY));
assertThat(dto.getConnectionString(), is(BIGQUERY_CONN_STR));
assertThat(dto.getUsername(), is(nullValue()));
assertThat(dto.getPassword(), is(nullValue()));
dto = DataSourceDTOParser.parseDTO(getOracleWOPwdSource());
assertThat(dto.getType(), is(DBMSType.ORACLE));
assertThat(dto.getConnectionString(), is(ORACLE_WO_PWD_CONN_STR));
assertThat(dto.getUsername(), is(nullValue()));
assertThat(dto.getPassword(), is(nullValue()));
dto = DataSourceDTOParser.parseDTO(getOracleWithPwdSource());
assertThat(dto.getType(), is(DBMSType.ORACLE));
assertThat(dto.getConnectionString(), is(ORACLE_WITH_PWD_CONN_STR));
assertThat(dto.getUsername(), is("scott"));
assertThat(dto.getPassword(), is("tiger"));
dto = DataSourceDTOParser.parseDTO(getHiveSource());
assertThat(dto.getType(), is(DBMSType.HIVE));
assertThat(dto.getConnectionString(), is(HIVE_CONN_STR));
assertThat(dto.getUsername(), is(nullValue()));
assertThat(dto.getPassword(), is(nullValue()));
dto = DataSourceDTOParser.parseDTO(getIRISSource());
assertThat(dto.getType(), is(DBMSType.IRIS));
assertThat(dto.getConnectionString(), is(IRIS_CONN_STR));
assertThat(dto.getUsername(), is(nullValue()));
assertThat(dto.getPassword(), is(nullValue()));
}
private Source getPostgreSQLPasswordSource() {
Source source = new Source();
source.setSourceDialect("postgresql");
source.setSourceConnection(PGSQL_WO_PWD_CONN_STR);
source.setUsername("user");
source.setPassword("password");
return source;
}
private Source getOracleWithPwdSource() {
Source source = new Source();
source.setSourceDialect("oracle");
source.setSourceConnection(ORACLE_WITH_PWD_CONN_STR);
return source;
}
private Source getOracleWOPwdSource() {
Source source = new Source();
source.setSourceDialect("oracle");
source.setSourceConnection(ORACLE_WO_PWD_CONN_STR);
return source;
}
private Source getBigQuerySource() {
Source source = new Source();
source.setSourceDialect("bigquery");
source.setSourceConnection(BIGQUERY_CONN_STR);
return source;
}
private Source getImpalaAuth1Source() {
Source source = new Source();
source.setSourceDialect("impala");
source.setSourceConnection(IMPALA_AUTH1_CONN_STR);
return source;
}
private Source getImpalaAuth0Source() {
Source source = new Source();
source.setSourceDialect("impala");
source.setSourceConnection(IMPALA_AUTH0_CONN_STR);
return source;
}
private Source getImpalaAuth3Source() {
Source source = new Source();
source.setSourceDialect("impala");
source.setSourceConnection(IMPALA_AUTH3_CONN_STR);
return source;
}
private Source getNetezzaSource() {
Source source = new Source();
source.setSourceDialect("netezza");
source.setSourceConnection(NETEZZA_CONN_STR);
return source;
}
private Source getRedshiftSource() {
Source source = new Source();
source.setSourceDialect("redshift");
source.setSourceConnection(REDSHIFT_CONN_STR);
return source;
}
private Source getPDWSource() {
Source source = new Source();
source.setSourceDialect("pdw");
source.setSourceConnection(PDW_CONN_STR);
return source;
}
private Source getMSSQLSource() {
Source source = new Source();
source.setSourceDialect("sql server");
source.setSourceConnection(MSSQL_CONN_STR);
return source;
}
private Source getPostgreSQLSource() {
Source source = new Source();
source.setSourceDialect("postgresql");
source.setSourceConnection(PGSQL_CONN_STR);
return source;
}
private Source getHiveSource() {
Source source = new Source();
source.setSourceDialect("hive");
source.setSourceConnection(HIVE_CONN_STR);
return source;
}
private Source getIRISSource() {
Source source = new Source();
source.setSourceDialect("iris");
source.setSourceConnection(IRIS_CONN_STR);
return source;
}
} | java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/util/JsonMappingTest.java | src/test/java/org/ohdsi/webapi/util/JsonMappingTest.java | package org.ohdsi.webapi.util;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.Date;
import org.aspectj.lang.JoinPoint;
import org.junit.Test;
public class JsonMappingTest {
@Test
public void testJsonMapping() throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
Exception e = new Exception("some exception");
StringWriter sw = new StringWriter();
PrintWriter pw = new PrintWriter(sw);
e.printStackTrace(pw);
String s = sw.toString();
Result r = new Result();
r.setStatus("success");
r.setErrorString(s);
r.setReturnedValueType(null);
r.setInvocationDate(new Date().toString());
s = mapper.writeValueAsString(r);
System.out.println(s);
}
class Result {
private String status;
private String returnedValueType;
private String signature;
private String signatureName;
private String invocationDate;
private String errorString;
public Result() {
super();
}
public void Result(JoinPoint joinPoint, Throwable returnedThrowable, Date invocationDate) {
setState(joinPoint, returnedThrowable, invocationDate);
}
protected void setState(JoinPoint joinPoint,
Throwable returnedThrowable, Date invocationDate) {
this.signatureName = joinPoint.getSignature().getName();
this.signature = joinPoint.getSignature().toLongString();
this.status = "failed";
this.returnedValueType = "no return value since operation failed";
/// set error string
StringWriter sw = new StringWriter();
PrintWriter pw = new PrintWriter(sw);
returnedThrowable.printStackTrace(pw);
errorString = sw.toString();
setInvocationDate(invocationDate.toString());
}
protected void setState(JoinPoint joinPoint, Object returnedValue, Date invocationDate) {
this.signatureName = joinPoint.getSignature().getName();
this.signature = joinPoint.getSignature().toLongString();
this.status = "succeeded";
if (returnedValue == null) {
this.returnedValueType = "null";
} else {
this.returnedValueType = returnedValue.getClass().getName();
}
errorString = "";
setInvocationDate(invocationDate.toString());
}
public String getInvocationDate() {
return invocationDate;
}
public void setInvocationDate(String date) {
this.invocationDate = date;
}
public String getStatus() {
return status;
}
public void setStatus(String status) {
this.status = status;
}
public String getErrorString() {
return errorString;
}
public void setErrorString(String stringException) {
this.errorString = stringException;
}
public String getReturnedValueType() {
return returnedValueType;
}
public void setReturnedValueType(String returnedValueType) {
this.returnedValueType = returnedValueType;
}
public String getSignature() {
return signature;
}
public void setSignature(String signature) {
this.signature = signature;
}
public String getSignatureName() {
return signatureName;
}
public void setSignatureName(String signatureName) {
this.signatureName = signatureName;
}
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/service/VocabularyServiceTest.java | src/test/java/org/ohdsi/webapi/service/VocabularyServiceTest.java | package org.ohdsi.webapi.service;
import static org.junit.Assert.assertEquals;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import java.io.IOException;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.source.Source;
import org.ohdsi.webapi.source.SourceDaimon;
import org.ohdsi.webapi.util.PreparedStatementRenderer;
import org.ohdsi.webapi.vocabulary.ConceptSearch;
import org.ohdsi.webapi.vocabulary.DescendentOfAncestorSearch;
import org.ohdsi.webapi.vocabulary.RelatedConceptSearch;
import org.springframework.beans.factory.annotation.Autowired;
public class VocabularyServiceTest extends AbstractServiceTest {
@Autowired
private VocabularyService vocabularyService;
@Before
public void before() {
if (vocabularyService == null) {
vocabularyService = new VocabularyService();
}
}
@Test
public void prepareExecuteSearch() throws IOException {
Source mockSource = mock(Source.class);
when(mockSource.getTableQualifier(SourceDaimon.DaimonType.Vocabulary)).thenReturn("omop_v5");
when(mockSource.getSourceDialect()).thenReturn("sql server");
ConceptSearch search = new ConceptSearch();
search.query = "conceptABC";
int domainIdCount = 5;
search.domainId = new String[domainIdCount];
for (int i = 0; i < domainIdCount; i++) {
search.domainId[i] = "domainId" + i;
}
int vocabularyIdCount = 10;
search.vocabularyId = new String[vocabularyIdCount];
for (int i = 0; i < vocabularyIdCount; i++) {
search.vocabularyId[i] = "vocabularyId" + i;
}
int conceptClassIdCount = 15;
search.conceptClassId = new String[conceptClassIdCount];
for (int i = 0; i < conceptClassIdCount; i++) {
search.conceptClassId[i] = "conceptClassId" + i;
}
search.invalidReason = "V";
search.standardConcept = "Y";
PreparedStatementRenderer psr = vocabularyService.prepareExecuteSearch(search, mockSource);
assertSqlEquals("/vocabulary/sql/search-expected-2.sql", psr);
}
@Test
public void prepareExecuteSearchWithQuery() throws IOException {
String query = "ConceptXYZ";
Source mockSource = mock(Source.class);
when(mockSource.getTableQualifier(SourceDaimon.DaimonType.Vocabulary)).thenReturn("omop_v5");
when(mockSource.getSourceDialect()).thenReturn("sql server");
PreparedStatementRenderer psr = vocabularyService.prepareExecuteSearchWithQuery(query, mockSource);
assertSqlEquals("/vocabulary/sql/search-expected.sql", psr);
assertEquals("%" + query.toLowerCase() + "%", psr.getOrderedParamsList().get(0));
assertEquals("%" + query.toLowerCase() + "%", psr.getOrderedParamsList().get(1));
}
@Test
public void prepareExecuteSearchWithQueryOptionalConceptId() throws IOException {
String query = "12345"; // this looks like a conceptID so add it to the query
Source mockSource = mock(Source.class);
when(mockSource.getTableQualifier(SourceDaimon.DaimonType.Vocabulary)).thenReturn("omop_v5");
when(mockSource.getSourceDialect()).thenReturn("sql server");
PreparedStatementRenderer psr = vocabularyService.prepareExecuteSearchWithQuery(query, mockSource);
assertSqlEquals("/vocabulary/sql/search-expected-3.sql", psr);
assertEquals("%" + query.toLowerCase() + "%", psr.getOrderedParamsList().get(0));
assertEquals("%" + query.toLowerCase() + "%", psr.getOrderedParamsList().get(1));
assertEquals(query, psr.getOrderedParamsList().get(2));
}
@Test
public void prepareGetRelatedConcepts2() throws IOException {
RelatedConceptSearch search = new RelatedConceptSearch();
search.vocabularyId = null; // new String[]{"0","1","2"};//null; was
search.conceptClassId = new String[]{"4", "5"};
search.conceptId = new long[]{(long) 0};
PreparedStatementRenderer psr = vocabularyService.prepareGetRelatedConcepts(search, getSource());
assertSqlEquals("/vocabulary/sql/getRelatedConceptsFiltered-expected-2.sql", psr);
assertEquals(6, psr.getOrderedParamsList().size());
/// the first 4 arguments are the conceptId repeated
for (int i = 0; i < 4; i++) {
long expectedValue = search.conceptId[0];
assertEquals(expectedValue, psr.getOrderedParamsList().get(i));
}
/// the next two arguments are the conceptClassId id
for (int i = 0; i < 2; i++) {
String expectedValue = "" + (i + 4);
assertEquals(expectedValue, psr.getOrderedParamsList().get(i + 4));
}
}
@Test
public void prepareGetRelatedConcepts() throws IOException {
RelatedConceptSearch search = new RelatedConceptSearch();
search.vocabularyId = new String[]{"0", "1", "2"};
search.conceptClassId = new String[]{"4", "5", "6"};
search.conceptId = new long[]{0, 1, 2, 3, 4};
PreparedStatementRenderer psr = vocabularyService.prepareGetRelatedConcepts(search, getSource());
assertSqlEquals("/vocabulary/sql/getRelatedConceptsFiltered-expected-1.sql", psr);
assertEquals(26, psr.getOrderedParamsList().size());
/// the first 20 arguments are the conceptId repeated
for (int i = 0; i < 20; i++) {
int expectedIndex = i % 5;
long expectedValue = search.conceptId[expectedIndex];
assertEquals(expectedValue, psr.getOrderedParamsList().get(i));
}
/// the next three arguments are the vocabulary id
for (int i = 20; i < 23; i++) {
int expectedIndex = i - 20;
String expectedValue = search.vocabularyId[expectedIndex];
assertEquals(expectedValue, psr.getOrderedParamsList().get(i));
}
/// the next three arguments are the vocabulary id
for (int i = 23; i < 26; i++) {
int expectedIndex = i - 23;
String expectedValue = search.conceptClassId[expectedIndex];
assertEquals(expectedValue, psr.getOrderedParamsList().get(i));
}
}
@Test
public void prepareGetCommonAncestors() throws IOException {
Object[] identifiers = {"1"};
PreparedStatementRenderer psr = vocabularyService.prepareGetCommonAncestors(identifiers, getSource());
assertSqlEquals("/vocabulary/sql/getCommonAncestors-expected.sql", psr);
assertEquals(identifiers[0], psr.getOrderedParamsList().get(0));
}
@Test
public void prepareExecuteMappedLookup() throws IOException {
long[] identifiers = new long[]{0L, 1L, 2L, 3L, 4L, 5L, 6L};
PreparedStatementRenderer psr = vocabularyService.prepareExecuteMappedLookup(identifiers, getSource());
assertSqlEquals("/vocabulary/sql/getMappedSourcecodes-expected.sql", psr);
for (int i = 0; i < identifiers.length * 3; i++) {
assertEquals((long) (i % 7), psr.getOrderedParamsList().get(i));
}
}
@Test
public void prepareExecuteSourcecodeLookup() throws IOException {
String[] sourcecodes = new String[]{"a", "b", "c", "d", "e"};
PreparedStatementRenderer psr = vocabularyService.prepareExecuteSourcecodeLookup(sourcecodes, getSource());
assertSqlEquals("/vocabulary/sql/lookupSourcecodes-expected.sql", psr);
assertEquals("a", psr.getOrderedParamsList().get(0));
assertEquals("b", psr.getOrderedParamsList().get(1));
assertEquals("c", psr.getOrderedParamsList().get(2));
assertEquals("d", psr.getOrderedParamsList().get(3));
assertEquals("e", psr.getOrderedParamsList().get(4));
}
@Test
public void prepareExecuteIdentifierLookup() throws IOException {
long[] identifiers = {(long) 11, (long) 5, (long) 8};
PreparedStatementRenderer psr = vocabularyService.prepareExecuteIdentifierLookup(identifiers, getSource());
assertSqlEquals("/vocabulary/sql/lookupIdentifiers-expected.sql", psr);
assertEquals(11L, psr.getOrderedParamsList().get(0));
assertEquals(5L, psr.getOrderedParamsList().get(1));
assertEquals(8L, psr.getOrderedParamsList().get(2));
}
@Test
public void prepareGetDescendantOfAncestorConcepts() throws IOException {
DescendentOfAncestorSearch search = new DescendentOfAncestorSearch();
search.conceptId = "1";
search.ancestorVocabularyId = "2";
search.ancestorClassId = "3";
search.siblingVocabularyId = "4";
search.siblingClassId = "5";
PreparedStatementRenderer psr = vocabularyService.prepareGetDescendantOfAncestorConcepts(search, getSource());
assertSqlEquals("/vocabulary/sql/getDescendentOfAncestorConcepts-expected.sql", psr);
assertEquals(1, psr.getOrderedParamsList().get(0));
assertEquals("2", psr.getOrderedParamsList().get(1));
assertEquals("3", psr.getOrderedParamsList().get(2));
assertEquals("4", psr.getOrderedParamsList().get(3));
assertEquals("5", psr.getOrderedParamsList().get(4));
}
@Test
public void prepareGetDescendantConceptsByList() throws IOException {
String[] conceptList = new String[]{"0", "1", "2", "3", "4"};
PreparedStatementRenderer psr = vocabularyService.prepareGetDescendantConceptsByList(conceptList, getSource());
assertSqlEquals("/vocabulary/sql/getDescendantConceptsMultipleConcepts-expected.sql", psr);
/// verify that the params are ordered correctly
for (int i = 0; i < psr.getOrderedParamsList().size(); i++) {
assertEquals(i, psr.getOrderedParamsList().get(i));
}
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/service/EvidenceServiceTest.java | src/test/java/org/ohdsi/webapi/service/EvidenceServiceTest.java | package org.ohdsi.webapi.service;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.io.IOException;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.evidence.EvidenceSearch;
import org.ohdsi.webapi.util.PreparedStatementRenderer;
import org.springframework.beans.factory.annotation.Autowired;
public class EvidenceServiceTest extends AbstractServiceTest {
@Autowired
EvidenceService evidenceService;
@Before
public void before() {
if (evidenceService == null) evidenceService = new EvidenceService();
}
@Test
public void prepareGetDrugHoiEvidence() throws IOException {
String drugId = "4444";
String hoiId = "5555";
String key = drugId + "-" + hoiId;
PreparedStatementRenderer psr = evidenceService.prepareGetDrugHoiEvidence(key, getSource());
assertSqlEquals("/evidence/sql/getDrugHoiEvidence-expected.sql", psr);
assertTrue(psr.getOrderedParamsList().contains(4444));
assertTrue(psr.getOrderedParamsList().contains(5555));
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/service/TherapyPathResultsServiceTest.java | src/test/java/org/ohdsi/webapi/service/TherapyPathResultsServiceTest.java | package org.ohdsi.webapi.service;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import java.io.IOException;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.util.PreparedStatementRenderer;
import org.springframework.beans.factory.annotation.Autowired;
public class TherapyPathResultsServiceTest extends AbstractServiceTest {
@Autowired
private TherapyPathResultsService therapyPathResultsService;
@Before
public void before() {
if (therapyPathResultsService == null) {
therapyPathResultsService = new TherapyPathResultsService();
}
}
@Test
public void prepareGetReports() throws IOException {
PreparedStatementRenderer psr = therapyPathResultsService.prepareGetReports(getSource());
assertSqlEquals("/therapypathresults/sql/getTherapyPathReports-expected.sql", psr);
}
@Test
public void prepareGetTherapyVectors() throws IOException {
String id = "5555";
PreparedStatementRenderer psr = therapyPathResultsService.prepareGetTherapyVectors(id, getSource());
assertSqlEquals("/therapypathresults/sql/getTherapyPathVectors-expected.sql", psr);
assertEquals(5555, psr.getOrderedParamsList().get(0));
assertEquals(1, psr.getOrderedParamsList().size());
}
@Test
public void prepareGetSummaries() throws IOException {
String[] identifiers = new String[]{"1111"};
PreparedStatementRenderer psr = therapyPathResultsService.prepareGetSummaries(identifiers, getSource());
assertSqlEquals("/therapypathresults/sql/getTherapySummaries-expected.sql", psr);
assertNotNull(psr.getSetter());
assertEquals(1111, psr.getOrderedParamsList().get(0));
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/service/CohortResultsServiceTest.java | src/test/java/org/ohdsi/webapi/service/CohortResultsServiceTest.java | package org.ohdsi.webapi.service;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.io.IOException;
import java.util.regex.Pattern;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.cohortresults.ExposureCohortSearch;
import org.ohdsi.webapi.util.PreparedStatementRenderer;
import org.springframework.beans.factory.annotation.Autowired;
public class CohortResultsServiceTest extends AbstractSpringBootServiceTest {
@Autowired
private CohortResultsService cohortResultsService;
@Before
public void before() {
if (cohortResultsService == null) {
cohortResultsService = new CohortResultsService();
}
}
@Test(expected = Exception.class)
public void getCohortSpecificResultsRefreshIsTrue() {
cohortResultsService.getCohortSpecificResults(-1, null, null, null, true);
}
@Test(expected = Exception.class)
public void getCohortSpecificResultsRefreshIsFalse() {
cohortResultsService.getCohortSpecificResults(-1, null, null, null, false);
}
@Test(expected = Exception.class)
public void getDashboardRefreshIsTrue() {
cohortResultsService.getDashboard(-1, null, null, true, null, true);
}
@Test(expected = Exception.class)
public void getDashboardRefreshIsFalse() {
cohortResultsService.getDashboard(-1, null, null, true, null, false);
}
@Test
public void prepareGetRawDistinctPersonCount() throws IOException {
String id = "1230";
PreparedStatementRenderer psr = cohortResultsService.prepareGetRawDistinctPersonCount(id, getSource());
assertSqlEquals("/cohortresults/sql/raw/getTotalDistinctPeople-expected.sql", psr);
assertEquals(Integer.parseInt(id), psr.getOrderedParamsList().get(0));
}
@Test
public void prepareGetCompletedAnalyses() throws IOException {
String id = "1230";
PreparedStatementRenderer psr = cohortResultsService.prepareGetCompletedAnalysis(id, getSource().getSourceId());
assertSqlEquals("/cohortresults/sql/raw/getCompletedAnalyses-expected.sql", psr);
assertEquals(2, psr.getOrderedParamsList().size());
}
@Test
public void prepareGetExposureOutcomeCohortPredictors() throws IOException {
ExposureCohortSearch search = new ExposureCohortSearch();
search.minCellCount = 5;
search.exposureCohortList = new String[]{"1"};
search.outcomeCohortList = new String[]{"2"};
PreparedStatementRenderer psr = cohortResultsService.prepareGetExposureOutcomeCohortPredictors(search, getSource());
assertSqlEquals("/cohortresults/sql/cohortSpecific/getExposureOutcomePredictors-expected.sql", psr);
}
@Test
public void prepareGetTimeToEventDrilldown() throws IOException {
ExposureCohortSearch search = new ExposureCohortSearch();
search.exposureCohortList = new String[]{"1"};
search.outcomeCohortList = new String[]{"2"};
PreparedStatementRenderer psr = cohortResultsService.prepareGetTimeToEventDrilldown(search, getSource());
assertSqlEquals("/cohortresults/sql/cohortSpecific/getTimeToEventDrilldown-expected.sql", psr);
for (Object param : psr.getOrderedParamsList()) {
assertTrue("1".equals(param) || "2".equals(param));
}
}
@Test
public void prepareGetExposureOutcomeCohortRates() throws IOException {
ExposureCohortSearch search = new ExposureCohortSearch();
search.exposureCohortList = new String[]{"1"};
search.outcomeCohortList = new String[]{"1"};
PreparedStatementRenderer psr = cohortResultsService.prepareGetExposureOutcomeCohortRates(search, getSource());
assertSqlEquals("/cohortresults/sql/cohortSpecific/getExposureOutcomeCohortRates-expected.sql", psr);
for (Object object : psr.getOrderedParamsList()) {
assertTrue("1".equals(object));
}
}
@Test
public void prepareGetCohortMembers() throws IOException {
int id = 111998;
String gender = "M";
String age = "15";
String conditions = "2,3,4";
String drugs = "45,61";
int rows = 5;
PreparedStatementRenderer psr = cohortResultsService.prepareGetCohortMembers(id, gender, age, conditions, drugs, rows, getSource());
assertSqlEquals("/cohortresults/sql/raw/getCohortBreakdownPeople-expected.sql", psr);
assertEquals(id, psr.getOrderedParamsList().get(0));
assertEquals(gender, psr.getOrderedParamsList().get(1));
assertEquals(age, psr.getOrderedParamsList().get(2));
assertEquals(2, psr.getOrderedParamsList().get(3));
assertEquals(3, psr.getOrderedParamsList().get(4));
assertEquals(4, psr.getOrderedParamsList().get(5));
assertEquals(45, psr.getOrderedParamsList().get(6));
assertEquals(61, psr.getOrderedParamsList().get(7));
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/service/SqlRenderServiceTest.java | src/test/java/org/ohdsi/webapi/service/SqlRenderServiceTest.java | package org.ohdsi.webapi.service;
import static org.junit.Assert.*;
import static org.mockito.Mockito.verify;
import static org.ohdsi.webapi.Constants.SqlSchemaPlaceholders.TEMP_DATABASE_SCHEMA_PLACEHOLDER;
import java.util.Collections;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.Mockito;
import org.mockito.Spy;
import org.mockito.runners.MockitoJUnitRunner;
import org.ohdsi.webapi.Constants;
import org.ohdsi.webapi.sqlrender.SourceStatement;
import org.ohdsi.webapi.sqlrender.TranslatedStatement;
@RunWith(MockitoJUnitRunner.class)
public class SqlRenderServiceTest {
public static final String TEST_SQL = "select cast(field as int) from table; ";
@Spy
private SqlRenderService sqlRenderService;
@Captor
private ArgumentCaptor<SourceStatement> sourceStatementCaptor;
@Test
public void translateSQLFromSourceStatement() {
SourceStatement statement = createSourceStatement(TEST_SQL, "oracle");
statement.setOracleTempSchema(null);
sqlRenderService.translateSQLFromSourceStatement(statement);
verify(sqlRenderService).translatedStatement(sourceStatementCaptor.capture());
assertEquals(TEMP_DATABASE_SCHEMA_PLACEHOLDER, sourceStatementCaptor.getValue().getOracleTempSchema());
}
@Test
public void translateSQL_sourceStatementIsNull() {
assertEquals(new TranslatedStatement(), SqlRenderService.translateSQL(null));
}
@Test
public void translateSQL() {
SourceStatement statement = createSourceStatement(TEST_SQL, "oracle");
TranslatedStatement translatedStatement = SqlRenderService.translateSQL(statement);
assertNotNull(translatedStatement.getTargetSQL());
assertNotEquals(TEST_SQL, translatedStatement.getTargetSQL());
}
@Test
public void translateSQL_defaultDialect() {
SourceStatement statement = createSourceStatement(TEST_SQL, Constants.DEFAULT_DIALECT);
TranslatedStatement translatedStatement = SqlRenderService.translateSQL(statement);
assertEquals(TEST_SQL, translatedStatement.getTargetSQL());
}
private SourceStatement createSourceStatement(String testExpression, String dialect) {
SourceStatement statement = new SourceStatement();
statement.setTargetDialect(dialect) ;
statement.setOracleTempSchema("schema");
statement.setSql(testExpression);
statement.getParameters().putAll(Collections.emptyMap());
return statement;
}
} | java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/service/AbstractSpringBootServiceTest.java | src/test/java/org/ohdsi/webapi/service/AbstractSpringBootServiceTest.java | package org.ohdsi.webapi.service;
import org.junit.runner.RunWith;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.context.junit4.SpringRunner;
@SpringBootTest
@RunWith(SpringRunner.class)
@TestPropertySource(locations = "/application-test.properties")
public abstract class AbstractSpringBootServiceTest extends AbstractServiceTest {
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/service/AbstractServiceTest.java | src/test/java/org/ohdsi/webapi/service/AbstractServiceTest.java | package org.ohdsi.webapi.service;
import static org.junit.Assert.assertEquals;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import java.io.IOException;
import org.junit.Before;
import org.ohdsi.circe.helper.ResourceHelper;
import org.ohdsi.webapi.source.Source;
import org.ohdsi.webapi.source.SourceDaimon;
import org.ohdsi.webapi.util.PreparedStatementRenderer;
import org.springframework.util.StringUtils;
public abstract class AbstractServiceTest {
private Source source;
@Before
public void setupMockedSource() {
source = mock(Source.class);
when(getSource().getSourceDialect()).thenReturn("sql server");
when(getSource().getTableQualifier(SourceDaimon.DaimonType.Results)).thenReturn("result_schema");
when(getSource().getTableQualifier(SourceDaimon.DaimonType.Vocabulary)).thenReturn("vocab_schema");
when(getSource().getTableQualifier(SourceDaimon.DaimonType.CDM)).thenReturn("cdm_schema");
when(getSource().getTableQualifier(SourceDaimon.DaimonType.CEM)).thenReturn("evidence_schema");
}
public static void assertSqlEquals(String expectedPath, PreparedStatementRenderer psr) throws IOException {
String expectedSql = StringUtils.trimAllWhitespace(ResourceHelper.GetResourceAsString(expectedPath)).toLowerCase();
assertEquals(expectedSql, StringUtils.trimAllWhitespace(psr.getSql()).toLowerCase());
}
public Source getSource() {
return source;
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/service/CohortDefinitionServiceTest.java | src/test/java/org/ohdsi/webapi/service/CohortDefinitionServiceTest.java | package org.ohdsi.webapi.service;
import java.util.Arrays;
import java.util.List;
import javax.cache.Cache;
import javax.cache.CacheManager;
import javax.cache.management.CacheStatisticsMXBean;
import org.apache.shiro.subject.SimplePrincipalCollection;
import org.apache.shiro.subject.Subject;
import org.apache.shiro.util.ThreadContext;
import org.apache.shiro.web.mgt.DefaultWebSecurityManager;
import static org.assertj.core.api.Assertions.assertThat;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.ohdsi.webapi.cohortdefinition.dto.CohortDTO;
import org.ohdsi.webapi.cohortdefinition.dto.CohortMetadataDTO;
import org.springframework.beans.factory.annotation.Autowired;
import org.ohdsi.webapi.util.CacheHelper;
public class CohortDefinitionServiceTest extends AbstractDatabaseTest {
@Autowired
private CohortDefinitionService cdService;
@Autowired
protected CohortDefinitionRepository cdRepository;
@Autowired(required = false)
private CacheManager cacheManager ;
@Autowired
private DefaultWebSecurityManager securityManager;
// in JUnit 4 it's impossible to mark methods inside interface with annotations, it was implemented in JUnit 5. After upgrade it's needed
// to mark interface methods with @Test, @Before, @After and to remove them from this class
@After
public void tearDownDB() {
cdRepository.deleteAll();
}
@Before
public void setup() {
// Set the SecurityManager for the current thread
SimplePrincipalCollection principalCollection = new SimplePrincipalCollection();
principalCollection.addAll(Arrays.asList("permsTest"), "testRealm");
Subject subject = new Subject.Builder(securityManager)
.authenticated(true)
.principals(principalCollection)
.buildSubject();
ThreadContext.bind(subject);
}
private CohortDTO createEntity(String name) {
CohortDTO dto = new CohortDTO();
dto.setName(name);
return cdService.createCohortDefinition(dto);
}
@Test
public void cohortDefinitionListCacheTest() throws Exception {
if (cacheManager == null) return; // cache is disabled, so nothing to test
CacheStatisticsMXBean cacheStatistics = CacheHelper.getCacheStats(cacheManager , CohortDefinitionService.CachingSetup.COHORT_DEFINITION_LIST_CACHE);
Cache cohortListCache = cacheManager.getCache(CohortDefinitionService.CachingSetup.COHORT_DEFINITION_LIST_CACHE);
// reset the cache and statistics for this test
cacheStatistics.clear();
cohortListCache.clear();
int cacheHits = 0;
int cacheMisses = 0;
List<CohortMetadataDTO> cohortDefList;
cohortDefList = cdService.getCohortDefinitionList();
cacheMisses++;
assertThat(cacheStatistics.getCacheMisses()).isEqualTo(cacheMisses);
assertThat(cacheStatistics.getCacheHits()).isEqualTo(cacheHits);
cohortDefList = cdService.getCohortDefinitionList();
cacheHits++;
assertThat(cacheStatistics.getCacheMisses()).isEqualTo(cacheMisses);
assertThat(cacheStatistics.getCacheHits()).isEqualTo(cacheHits);
}
@Test
public void cohortDefinitionListEvictTest() throws Exception {
if (cacheManager == null) return; // cache is disabled, so nothing to test
CacheStatisticsMXBean cacheStatistics = CacheHelper.getCacheStats(cacheManager , CohortDefinitionService.CachingSetup.COHORT_DEFINITION_LIST_CACHE);
Cache cohortListCache = cacheManager.getCache(CohortDefinitionService.CachingSetup.COHORT_DEFINITION_LIST_CACHE);
// reset the cache and statistics for this test
cacheStatistics.clear();
cohortListCache.clear();
int cacheHits = 0;
int cacheMisses = 0;
List<CohortMetadataDTO> cohortDefList;
cohortDefList = cdService.getCohortDefinitionList();
cacheMisses++;
assertThat(cacheStatistics.getCacheMisses()).isEqualTo(cacheMisses);
assertThat(cacheStatistics.getCacheHits()).isEqualTo(cacheHits);
CohortDTO c = createEntity("Cohort 1");
cohortDefList = cdService.getCohortDefinitionList();
cacheMisses++;
assertThat(cacheStatistics.getCacheMisses()).isEqualTo(cacheMisses);
assertThat(cacheStatistics.getCacheHits()).isEqualTo(cacheHits);
c = cdService.saveCohortDefinition(c.getId(), c);
cohortDefList = cdService.getCohortDefinitionList();
cacheMisses++;
assertThat(cacheStatistics.getCacheMisses()).isEqualTo(cacheMisses);
assertThat(cacheStatistics.getCacheHits()).isEqualTo(cacheHits);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/service/PersonServiceTest.java | src/test/java/org/ohdsi/webapi/service/PersonServiceTest.java | package org.ohdsi.webapi.service;
import java.io.IOException;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.util.PreparedStatementRenderer;
import org.springframework.beans.factory.annotation.Autowired;
public class PersonServiceTest extends AbstractServiceTest {
@Autowired
private PersonService personService;
@Before
public void before() {
if (personService == null) {
personService = new PersonService();
}
}
@Test
public void prepareGetPersonProfile() throws IOException {
String personId = "5555";
PreparedStatementRenderer psr = personService.prepareGetPersonProfile(personId, getSource());
String actualSql = psr.getSql();
Assert.assertNotNull(actualSql);
Assert.assertNotNull(psr.getSetter());
assertSqlEquals("/person/sql/getRecords-expected.sql", psr);
//// count the number of question marks in the sql, make sure it matches the orderedParamsList size
int qmarkCount = 0;
int startIndex = 0;
while ((startIndex = actualSql.indexOf("?", startIndex)) != -1) {
qmarkCount++;
startIndex++;
}
Assert.assertEquals(qmarkCount, psr.getOrderedParamsList().size());
/// make sure that all of the parameters are equivalent to personId value
for (Object param : psr.getOrderedParamsList()) {
Assert.assertEquals(param, 5555L);
}
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/service/CDMResultsServiceTest.java | src/test/java/org/ohdsi/webapi/service/CDMResultsServiceTest.java | package org.ohdsi.webapi.service;
import static org.junit.Assert.assertEquals;
import java.io.IOException;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.util.PreparedStatementRenderer;
import org.springframework.beans.factory.annotation.Autowired;
public class CDMResultsServiceTest extends AbstractServiceTest {
@Autowired
private CDMResultsService cdmResultsService;
@Before
public void before() {
if (cdmResultsService == null) cdmResultsService = new CDMResultsService();
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/service/annotations/SearchDataTransformerTest.java | src/test/java/org/ohdsi/webapi/service/annotations/SearchDataTransformerTest.java | package org.ohdsi.webapi.service.annotations;
import org.json.JSONObject;
import org.junit.Before;
import org.junit.Test;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.isEmptyString;
public class SearchDataTransformerTest {
private SearchDataTransformer sut;
@Before
public void setUp() {
sut = new SearchDataTransformer();
}
@Test
public void shouldReturnEmptyStringWhenInputIsEmpty() {
JSONObject emptyJson = new JSONObject();
String transformed = sut.convertJsonToReadableFormat(emptyJson.toString());
assertThat(transformed, isEmptyString());
}
@Test
public void shouldHandleSearchText() {
String input = "{\"filterData\":{\"searchText\":\"testSearch\"}}";
String result = sut.convertJsonToReadableFormat(input);
assertThat(result, is("Search, \"testSearch\""));
}
@Test
public void shouldHandleFilterSource() {
String input = "{\"filterSource\":\"Search\"}";
String result = sut.convertJsonToReadableFormat(input);
assertThat(result, is("Search"));
}
@Test
public void shouldHandleFilterColumns() {
String input = "{\"filterData\":{\"filterColumns\":[{\"title\":\"Domain\",\"key\":\"Drug\"}]} }";
String result = sut.convertJsonToReadableFormat(input);
assertThat(result, is("Search, \"\", Filtered By: \"Domain: \"Drug\"\""));
}
@Test
public void shouldCombineFilterDataAndFilterSource() {
String input = "{\"filterData\":{\"searchText\":\"testSearch\",\"filterColumns\":[{\"title\":\"Domain\",\"key\":\"Drug\"}]},\"filterSource\":\"Search\"}";
String result = sut.convertJsonToReadableFormat(input);
String expected = "Search, \"testSearch\", Filtered By: \"Domain: \"Drug\"\"";
assertThat(result, is(expected));
}
@Test
public void shouldHandleMultipleFilterColumns() {
String input = "{\"filterData\":{\"filterColumns\":[{\"title\":\"Domain\",\"key\":\"Drug\"},{\"title\":\"Class\",\"key\":\"Medication\"}]}}";
String result = sut.convertJsonToReadableFormat(input);
String expected = "Search, \"\", Filtered By: \"Domain: \"Drug\"" + ", Class: \"Medication\"\"";
assertThat(result, is(expected));
}
@Test
public void shouldHandleNullValuesGracefully() {
String input = "{\"filterData\":{\"filterColumns\":[{\"title\":null,\"key\":null}], \"searchText\":null}, \"filterSource\":null}";
String result = sut.convertJsonToReadableFormat(input);
assertThat(result, is("Search, \"\", Filtered By: \": \"\"\""));
}
} | java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/shiny/CohortPathwaysShinyPackagingServiceTest.java | src/test/java/org/ohdsi/webapi/shiny/CohortPathwaysShinyPackagingServiceTest.java | package org.ohdsi.webapi.shiny;
import com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Answers;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.Spy;
import org.mockito.runners.MockitoJUnitRunner;
import org.ohdsi.webapi.pathway.PathwayService;
import org.ohdsi.webapi.pathway.domain.PathwayAnalysisGenerationEntity;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisDTO;
import org.ohdsi.webapi.pathway.dto.PathwayPopulationResultsDTO;
import org.ohdsi.webapi.pathway.dto.internal.PathwayAnalysisResult;
import java.util.Collections;
import static org.junit.Assert.assertEquals;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyString;
import static org.mockito.Matchers.eq;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
@RunWith(MockitoJUnitRunner.class)
public class CohortPathwaysShinyPackagingServiceTest {
private static final int GENERATION_ID = 1;
private static final String SOURCE_KEY = "SynPuf110k";
@Mock
private PathwayService pathwayService;
@Spy
private ManifestUtils manifestUtils;
@Spy
private FileWriter fileWriter;
@InjectMocks
private CohortPathwaysShinyPackagingService sut;
@Test
public void shouldGetBrief() {
when(pathwayService.getByGenerationId(eq(GENERATION_ID))).thenReturn(createPathwayAnalysisDTO());
when(pathwayService.getResultingPathways(eq((long) GENERATION_ID))).thenReturn(createPathwayAnalysisResult());
ApplicationBrief brief = sut.getBrief(GENERATION_ID, SOURCE_KEY);
assertEquals(brief.getName(), "txp_" + GENERATION_ID + "_" + SOURCE_KEY);
assertEquals(brief.getTitle(), "Pathway_8_gv1x_SynPuf110k");
assertEquals(brief.getDescription(), "desc");
}
@Test
public void shouldPopulateAppData() {
when(pathwayService.findDesignByGenerationId(eq((long) GENERATION_ID))).thenReturn("design json");
when(pathwayService.getGenerationResults(eq((long) GENERATION_ID))).thenReturn(createPathwayGenerationResults());
PathwayAnalysisDTO pathwayAnalysisDTO = Mockito.mock(PathwayAnalysisDTO.class);
PathwayAnalysisGenerationEntity generationEntity = Mockito.mock(PathwayAnalysisGenerationEntity.class);
when(pathwayService.getByGenerationId(eq(GENERATION_ID))).thenReturn(pathwayAnalysisDTO);
when(pathwayService.getGeneration(eq((long) GENERATION_ID))).thenReturn(generationEntity);
CommonShinyPackagingService.ShinyAppDataConsumers dataConsumers = Mockito.mock(CommonShinyPackagingService.ShinyAppDataConsumers.class, Answers.RETURNS_DEEP_STUBS.get());
sut.populateAppData(GENERATION_ID, SOURCE_KEY, dataConsumers);
verify(dataConsumers.getTextFiles(), times(1)).accept(eq("design.json"), anyString());
verify(dataConsumers.getJsonObjects(), times(1)).accept(eq("chartData.json"), any(PathwayPopulationResultsDTO.class));
}
private PathwayPopulationResultsDTO createPathwayGenerationResults() {
return new PathwayPopulationResultsDTO(Collections.emptyList(), Collections.emptyList());
}
@Test
public void shouldReturnIncidenceType() {
assertEquals(sut.getType(), CommonAnalysisType.COHORT_PATHWAY);
}
private PathwayAnalysisResult createPathwayAnalysisResult() {
return new PathwayAnalysisResult();
}
private PathwayAnalysisDTO createPathwayAnalysisDTO() {
PathwayAnalysisDTO pathwayAnalysisDTO = new PathwayAnalysisDTO();
pathwayAnalysisDTO.setId(8);
pathwayAnalysisDTO.setName("pathwayAnalysis");
pathwayAnalysisDTO.setDescription("desc");
return pathwayAnalysisDTO;
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/shiny/IncidenceRatesShinyPackagingServiceTest.java | src/test/java/org/ohdsi/webapi/shiny/IncidenceRatesShinyPackagingServiceTest.java | package org.ohdsi.webapi.shiny;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Answers;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.Spy;
import org.mockito.runners.MockitoJUnitRunner;
import org.ohdsi.webapi.cohortdefinition.dto.CohortDTO;
import org.ohdsi.webapi.ircalc.AnalysisReport;
import org.ohdsi.webapi.ircalc.IncidenceRateAnalysis;
import org.ohdsi.webapi.ircalc.IncidenceRateAnalysisDetails;
import org.ohdsi.webapi.ircalc.IncidenceRateAnalysisExportExpression;
import org.ohdsi.webapi.ircalc.IncidenceRateAnalysisRepository;
import org.ohdsi.webapi.service.IRAnalysisResource;
import org.ohdsi.webapi.source.Source;
import org.ohdsi.webapi.source.SourceRepository;
import static org.junit.Assert.assertEquals;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
@RunWith(MockitoJUnitRunner.class)
public class IncidenceRatesShinyPackagingServiceTest {
@Mock
private IncidenceRateAnalysisRepository repository;
@Spy
private ManifestUtils manifestUtils;
@Spy
private FileWriter fileWriter;
@Mock
private IRAnalysisResource irAnalysisResource;
@Mock
private SourceRepository sourceRepository;
@Spy
private ObjectMapper objectMapper;
@InjectMocks
private IncidenceRatesShinyPackagingService sut;
private final Integer analysisId = 1;
private final String sourceKey = "sourceKey";
@Test
public void shouldGetBrief() {
IncidenceRateAnalysis incidenceRateAnalysis = createIncidenceRateAnalysis();
when(repository.findOne(analysisId)).thenReturn(incidenceRateAnalysis);
Source source = new Source();
source.setSourceId(3);
when(sourceRepository.findBySourceKey("sourceKey")).thenReturn(source);
ApplicationBrief brief = sut.getBrief(analysisId, sourceKey);
assertEquals(brief.getName(), "ir_" + analysisId + "_" + sourceKey);
assertEquals(brief.getTitle(), "Incidence_1_gv1x3_sourceKey");
assertEquals(brief.getDescription(), incidenceRateAnalysis.getDescription());
}
@Test
public void shouldPopulateAppDataWithValidData() throws JsonProcessingException {
Integer generationId = 1;
String sourceKey = "source";
Source source = new Source();
source.setSourceId(3);
when(sourceRepository.findBySourceKey("source")).thenReturn(source);
IncidenceRateAnalysis analysis = Mockito.mock(IncidenceRateAnalysis.class, Answers.RETURNS_DEEP_STUBS.get());
when(analysis.getDetails().getExpression()).thenReturn("{}");
when(repository.findOne(generationId)).thenReturn(analysis);
CohortDTO targetCohort = new CohortDTO();
targetCohort.setId(101);
targetCohort.setName("Target Cohort");
CohortDTO outcomeCohort = new CohortDTO();
outcomeCohort.setId(201);
outcomeCohort.setName("Outcome Cohort");
IncidenceRateAnalysisExportExpression expression = new IncidenceRateAnalysisExportExpression();
expression.outcomeCohorts.add(outcomeCohort);
expression.targetCohorts.add(targetCohort);
when(objectMapper.readValue("{}", IncidenceRateAnalysisExportExpression.class)).thenReturn(expression);
AnalysisReport analysisReport = new AnalysisReport();
analysisReport.summary = new AnalysisReport.Summary();
when(irAnalysisResource.getAnalysisReport(1, "source", 101, 201)).thenReturn(analysisReport);
CommonShinyPackagingService.ShinyAppDataConsumers dataConsumers = mock(CommonShinyPackagingService.ShinyAppDataConsumers.class, Answers.RETURNS_DEEP_STUBS.get());
sut.populateAppData(generationId, sourceKey, dataConsumers);
verify(dataConsumers.getAppProperties(), times(11)).accept(anyString(), anyString());
verify(dataConsumers.getTextFiles(), times(1)).accept(anyString(), anyString());
verify(dataConsumers.getJsonObjects(), times(1)).accept(anyString(), any());
}
@Test
public void shouldReturnIncidenceType() {
assertEquals(sut.getType(), CommonAnalysisType.INCIDENCE);
}
private IncidenceRateAnalysis createIncidenceRateAnalysis() {
IncidenceRateAnalysis incidenceRateAnalysis = new IncidenceRateAnalysis();
IncidenceRateAnalysisDetails incidenceRateAnalysisDetails = new IncidenceRateAnalysisDetails(incidenceRateAnalysis);
incidenceRateAnalysisDetails.setExpression("{\"ConceptSets\":[],\"targetIds\":[11,7],\"outcomeIds\":[12,6],\"timeAtRisk\":{\"start\":{\"DateField\":\"StartDate\",\"Offset\":0},\"end\":{\"DateField\":\"EndDate\",\"Offset\":0}},\"studyWindow\":null,\"strata\":[{\"name\":\"Male\",\"description\":null,\"expression\":{\"Type\":\"ALL\",\"Count\":null,\"CriteriaList\":[],\"DemographicCriteriaList\":[{\"Age\":null,\"Gender\":[{\"CONCEPT_ID\":8507,\"CONCEPT_NAME\":\"MALE\",\"STANDARD_CONCEPT\":null,\"STANDARD_CONCEPT_CAPTION\":\"Unknown\",\"INVALID_REASON\":null,\"INVALID_REASON_CAPTION\":\"Unknown\",\"CONCEPT_CODE\":\"M\",\"DOMAIN_ID\":\"Gender\",\"VOCABULARY_ID\":\"Gender\",\"CONCEPT_CLASS_ID\":null}],\"Race\":null,\"Ethnicity\":null,\"OccurrenceStartDate\":null,\"OccurrenceEndDate\":null}],\"Groups\":[]}},{\"name\":\"Female\",\"description\":null,\"expression\":{\"Type\":\"ALL\",\"Count\":null,\"CriteriaList\":[],\"DemographicCriteriaList\":[{\"Age\":null,\"Gender\":[{\"CONCEPT_ID\":8532,\"CONCEPT_NAME\":\"FEMALE\",\"STANDARD_CONCEPT\":null,\"STANDARD_CONCEPT_CAPTION\":\"Unknown\",\"INVALID_REASON\":null,\"INVALID_REASON_CAPTION\":\"Unknown\",\"CONCEPT_CODE\":\"F\",\"DOMAIN_ID\":\"Gender\",\"VOCABULARY_ID\":\"Gender\",\"CONCEPT_CLASS_ID\":null}],\"Race\":null,\"Ethnicity\":null,\"OccurrenceStartDate\":null,\"OccurrenceEndDate\":null}],\"Groups\":[]}}],\"targetCohorts\":[{\"id\":11,\"name\":\"All population-IR\",\"hasWriteAccess\":false,\"hasReadAccess\":false,\"expression\":{\"cdmVersionRange\":\">=5.0.0\",\"PrimaryCriteria\":{\"CriteriaList\":[{\"ConditionOccurrence\":{\"ConditionTypeExclude\":false}},{\"DrugExposure\":{\"DrugTypeExclude\":false}}],\"ObservationWindow\":{\"PriorDays\":0,\"PostDays\":0},\"PrimaryCriteriaLimit\":{\"Type\":\"First\"}},\"ConceptSets\":[],\"QualifiedLimit\":{\"Type\":\"First\"},\"ExpressionLimit\":{\"Type\":\"First\"},\"InclusionRules\":[],\"CensoringCriteria\":[],\"CollapseSettings\":{\"CollapseType\":\"ERA\",\"EraPad\":0},\"CensorWindow\":{}}},{\"id\":7,\"name\":\"Test Cohort 4\",\"hasWriteAccess\":false,\"hasReadAccess\":false,\"expressionType\":\"SIMPLE_EXPRESSION\",\"expression\":{\"cdmVersionRange\":\">=5.0.0\",\"PrimaryCriteria\":{\"CriteriaList\":[{\"DrugExposure\":{\"CodesetId\":0,\"DrugTypeExclude\":false}}],\"ObservationWindow\":{\"PriorDays\":30,\"PostDays\":0},\"PrimaryCriteriaLimit\":{\"Type\":\"First\"}},\"ConceptSets\":[{\"id\":0,\"name\":\"celecoxib\",\"expression\":{\"items\":[{\"concept\":{\"CONCEPT_ID\":1118084,\"CONCEPT_NAME\":\"celecoxib\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"140587\",\"DOMAIN_ID\":\"Drug\",\"VOCABULARY_ID\":\"RxNorm\",\"CONCEPT_CLASS_ID\":\"Ingredient\"},\"isExcluded\":false,\"includeDescendants\":true,\"includeMapped\":true}]}},{\"id\":1,\"name\":\"Major gastrointestinal (GI) bleeding\",\"expression\":{\"items\":[{\"concept\":{\"CONCEPT_ID\":4280942,\"CONCEPT_NAME\":\"Acute gastrojejunal ulcer with perforation\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"66636001\",\"DOMAIN_ID\":\"Condition\",\"VOCABULARY_ID\":\"SNOMED\",\"CONCEPT_CLASS_ID\":\"Clinical Finding\"},\"isExcluded\":false,\"includeDescendants\":true,\"includeMapped\":false},{\"concept\":{\"CONCEPT_ID\":28779,\"CONCEPT_NAME\":\"Bleeding esophageal varices\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"17709002\",\"DOMAIN_ID\":\"Condition\",\"VOCABULARY_ID\":\"SNOMED\",\"CONCEPT_CLASS_ID\":\"Clinical Finding\"},\"isExcluded\":false,\"includeDescendants\":true,\"includeMapped\":false},{\"concept\":{\"CONCEPT_ID\":198798,\"CONCEPT_NAME\":\"Dieulafoy's vascular malformation\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"109558001\",\"DOMAIN_ID\":\"Condition\",\"VOCABULARY_ID\":\"SNOMED\",\"CONCEPT_CLASS_ID\":\"Clinical Finding\"},\"isExcluded\":false,\"includeDescendants\":true,\"includeMapped\":false},{\"concept\":{\"CONCEPT_ID\":4112183,\"CONCEPT_NAME\":\"Esophageal varices with bleeding, associated with another disorder\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"195475003\",\"DOMAIN_ID\":\"Condition\",\"VOCABULARY_ID\":\"SNOMED\",\"CONCEPT_CLASS_ID\":\"Clinical Finding\"},\"isExcluded\":false,\"includeDescendants\":true,\"includeMapped\":false},{\"concept\":{\"CONCEPT_ID\":194382,\"CONCEPT_NAME\":\"External hemorrhoids\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"23913003\",\"DOMAIN_ID\":\"Condition\",\"VOCABULARY_ID\":\"SNOMED\",\"CONCEPT_CLASS_ID\":\"Clinical Finding\"},\"isExcluded\":false,\"includeDescendants\":false,\"includeMapped\":false},{\"concept\":{\"CONCEPT_ID\":192671,\"CONCEPT_NAME\":\"Gastrointestinal hemorrhage\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"74474003\",\"DOMAIN_ID\":\"Condition\",\"VOCABULARY_ID\":\"SNOMED\",\"CONCEPT_CLASS_ID\":\"Clinical Finding\"},\"isExcluded\":false,\"includeDescendants\":true,\"includeMapped\":false},{\"concept\":{\"CONCEPT_ID\":196436,\"CONCEPT_NAME\":\"Internal hemorrhoids\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"90458007\",\"DOMAIN_ID\":\"Condition\",\"VOCABULARY_ID\":\"SNOMED\",\"CONCEPT_CLASS_ID\":\"Clinical Finding\"},\"isExcluded\":false,\"includeDescendants\":false,\"includeMapped\":false},{\"concept\":{\"CONCEPT_ID\":4338225,\"CONCEPT_NAME\":\"Peptic ulcer with perforation\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"88169003\",\"DOMAIN_ID\":\"Condition\",\"VOCABULARY_ID\":\"SNOMED\",\"CONCEPT_CLASS_ID\":\"Clinical Finding\"},\"isExcluded\":false,\"includeDescendants\":true,\"includeMapped\":false},{\"concept\":{\"CONCEPT_ID\":194158,\"CONCEPT_NAME\":\"Perinatal gastrointestinal hemorrhage\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"48729005\",\"DOMAIN_ID\":\"Condition\",\"VOCABULARY_ID\":\"SNOMED\",\"CONCEPT_CLASS_ID\":\"Clinical Finding\"},\"isExcluded\":false,\"includeDescendants\":true,\"includeMapped\":false}]}}],\"QualifiedLimit\":{\"Type\":\"All\"},\"ExpressionLimit\":{\"Type\":\"First\"},\"InclusionRules\":[{\"name\":\"No prior GI\",\"expression\":{\"Type\":\"ALL\",\"CriteriaList\":[{\"Criteria\":{\"ConditionOccurrence\":{\"CodesetId\":1}},\"StartWindow\":{\"Start\":{\"Coeff\":-1},\"End\":{\"Days\":0,\"Coeff\":1},\"UseIndexEnd\":false,\"UseEventEnd\":false},\"RestrictVisit\":false,\"IgnoreObservationPeriod\":false,\"Occurrence\":{\"Type\":1,\"Count\":0,\"IsDistinct\":false}}],\"DemographicCriteriaList\":[],\"Groups\":[]}}],\"CensoringCriteria\":[],\"CollapseSettings\":{\"CollapseType\":\"ERA\",\"EraPad\":0},\"CensorWindow\":{\"StartDate\":\"2010-04-01\",\"EndDate\":\"2010-12-01\"}}}],\"outcomeCohorts\":[{\"id\":12,\"name\":\"Diabetes-IR\",\"hasWriteAccess\":false,\"hasReadAccess\":false,\"expression\":{\"cdmVersionRange\":\">=5.0.0\",\"PrimaryCriteria\":{\"CriteriaList\":[{\"ConditionOccurrence\":{\"CodesetId\":0,\"First\":true,\"ConditionTypeExclude\":false}}],\"ObservationWindow\":{\"PriorDays\":365,\"PostDays\":0},\"PrimaryCriteriaLimit\":{\"Type\":\"First\"}},\"ConceptSets\":[{\"id\":0,\"name\":\"Diabetes-IR\",\"expression\":{\"items\":[{\"concept\":{\"CONCEPT_ID\":201826,\"CONCEPT_NAME\":\"Type 2 diabetes mellitus\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"44054006\",\"DOMAIN_ID\":\"Condition\",\"VOCABULARY_ID\":\"SNOMED\",\"CONCEPT_CLASS_ID\":\"Clinical Finding\"},\"isExcluded\":false,\"includeDescendants\":true,\"includeMapped\":false}]}}],\"QualifiedLimit\":{\"Type\":\"First\"},\"ExpressionLimit\":{\"Type\":\"First\"},\"InclusionRules\":[{\"name\":\"Age over 18\",\"expression\":{\"Type\":\"ALL\",\"CriteriaList\":[],\"DemographicCriteriaList\":[{\"Age\":{\"Value\":18,\"Op\":\"gte\"}}],\"Groups\":[]}}],\"CensoringCriteria\":[],\"CollapseSettings\":{\"CollapseType\":\"ERA\",\"EraPad\":0},\"CensorWindow\":{}}},{\"id\":6,\"name\":\"TEST COHORT 2\",\"hasWriteAccess\":false,\"hasReadAccess\":false,\"expressionType\":\"SIMPLE_EXPRESSION\",\"expression\":{\"cdmVersionRange\":\">=5.0.0\",\"PrimaryCriteria\":{\"CriteriaList\":[{\"DrugEra\":{\"CodesetId\":0}}],\"ObservationWindow\":{\"PriorDays\":0,\"PostDays\":0},\"PrimaryCriteriaLimit\":{\"Type\":\"All\"}},\"ConceptSets\":[{\"id\":0,\"name\":\"Simvastatin1\",\"expression\":{\"items\":[{\"concept\":{\"CONCEPT_ID\":1539403,\"CONCEPT_NAME\":\"Simvastatin\",\"STANDARD_CONCEPT\":\"S\",\"STANDARD_CONCEPT_CAPTION\":\"Standard\",\"INVALID_REASON\":\"V\",\"INVALID_REASON_CAPTION\":\"Valid\",\"CONCEPT_CODE\":\"36567\",\"DOMAIN_ID\":\"Drug\",\"VOCABULARY_ID\":\"RxNorm\",\"CONCEPT_CLASS_ID\":\"Ingredient\"},\"isExcluded\":false,\"includeDescendants\":true,\"includeMapped\":false}]}}],\"QualifiedLimit\":{\"Type\":\"First\"},\"ExpressionLimit\":{\"Type\":\"All\"},\"InclusionRules\":[],\"EndStrategy\":{\"DateOffset\":{\"DateField\":\"EndDate\",\"Offset\":0}},\"CensoringCriteria\":[],\"CollapseSettings\":{\"CollapseType\":\"ERA\",\"EraPad\":0},\"CensorWindow\":{}}}]}");
incidenceRateAnalysis.setId(analysisId);
incidenceRateAnalysis.setName("Analysis Name");
incidenceRateAnalysis.setDescription("Analysis Description");
incidenceRateAnalysis.setDetails(incidenceRateAnalysisDetails);
return incidenceRateAnalysis;
}
private AnalysisReport createAnalysisReport(int targetId, int outcomeId) {
AnalysisReport analysisReport = new AnalysisReport();
analysisReport.summary = new AnalysisReport.Summary();
analysisReport.summary.targetId = targetId;
analysisReport.summary.outcomeId = outcomeId;
return analysisReport;
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/generationcache/GenerationCacheTest.java | src/test/java/org/ohdsi/webapi/generationcache/GenerationCacheTest.java | package org.ohdsi.webapi.generationcache;
import com.odysseusinc.arachne.commons.types.DBMSType;
import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.KerberosAuthMechanism;
import net.lingala.zip4j.ZipFile;
import net.lingala.zip4j.exception.ZipException;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.analysis.Utils;
import org.ohdsi.circe.cohortdefinition.CohortExpression;
import org.ohdsi.circe.helper.ResourceHelper;
import org.ohdsi.sql.SqlRender;
import org.ohdsi.sql.SqlSplit;
import org.ohdsi.sql.SqlTranslate;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.Constants;
import org.ohdsi.webapi.cohortdefinition.CohortDefinition;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionDetails;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.ohdsi.webapi.cohortdefinition.CohortGenerationRequestBuilder;
import org.ohdsi.webapi.source.Source;
import org.ohdsi.webapi.source.SourceDaimon;
import org.ohdsi.webapi.source.SourceRepository;
import org.ohdsi.webapi.util.SessionUtils;
import org.ohdsi.webapi.util.SourceUtils;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.sql.SQLException;
import java.util.Arrays;
import java.util.Collection;
import java.util.Map;
import java.util.concurrent.atomic.AtomicBoolean;
import java.util.stream.Collectors;
import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
import static org.ohdsi.webapi.Constants.Params.DESIGN_HASH;
import static org.ohdsi.webapi.Constants.Params.RESULTS_DATABASE_SCHEMA;
import org.springframework.beans.factory.annotation.Value;
public class GenerationCacheTest extends AbstractDatabaseTest {
private static final String CDM_SQL = ResourceHelper.GetResourceAsString("/cdm-postgresql-ddl.sql");
private static final String COHORT_JSON = ResourceHelper.GetResourceAsString("/generationcache/cohort/cohortIbuprofenOlder50.json");
private static final String INSERT_COHORT_RESULTS_SQL = ResourceHelper.GetResourceAsString("/generationcache/cohort/insertCohortResults.sql");
private static final String COHORT_COUNTS_SQL = ResourceHelper.GetResourceAsString("/generationcache/cohort/queryCohortCounts.sql");
private static final String EUNOMIA_CSV_ZIP = "/eunomia.csv.zip";
private static final String CDM_SCHEMA_NAME = "cdm";
private static final String RESULT_SCHEMA_NAME = "results";
private static final String SOURCE_KEY = "Embedded_PG";
private static boolean isSetup = false;
private int cohortId; // will be set to the test cohort for each test excution
@Autowired
private GenerationCacheService generationCacheService;
@Autowired
private GenerationCacheRepository generationCacheRepository;
@Autowired
private GenerationCacheHelper generationCacheHelper;
@Autowired
private SourceRepository sourceRepository;
@Autowired
private CohortDefinitionRepository cohortDefinitionRepository;
@Value("${datasource.ohdsi.schema}")
private String ohdsiSchema;
private static final Collection<String> COHORT_DDL_FILE_PATHS = Arrays.asList(
// cohort generation results
"/ddl/results/cohort.sql",
"/ddl/results/cohort_censor_stats.sql",
"/ddl/results/cohort_inclusion.sql",
"/ddl/results/cohort_inclusion_result.sql",
"/ddl/results/cohort_inclusion_stats.sql",
"/ddl/results/cohort_summary_stats.sql",
// cohort generation cache
"/ddl/results/cohort_cache.sql",
"/ddl/results/cohort_censor_stats_cache.sql",
"/ddl/results/cohort_inclusion_result_cache.sql",
"/ddl/results/cohort_inclusion_stats_cache.sql",
"/ddl/results/cohort_summary_stats_cache.sql"
);
private CohortGenerationRequestBuilder cohortGenerationRequestBuilder;
@Before
public void setUp() throws SQLException {
if (!isSetup) { // one-time setup per class here
truncateTable(String.format("%s.%s", ohdsiSchema, "source"));
resetSequence(String.format("%s.%s", ohdsiSchema,"source_sequence"));
sourceRepository.saveAndFlush(getCdmSource());
isSetup = true;
}
// reset cohort tables
truncateTable(String.format("%s.%s", ohdsiSchema, "cohort_definition_details"));
truncateTable(String.format("%s.%s", ohdsiSchema, "cohort_definition"));
resetSequence(String.format("%s.%s", ohdsiSchema, "cohort_definition_sequence"));
cohortId = cohortDefinitionRepository.save(getCohortDefinition()).getId();
cohortGenerationRequestBuilder = getCohortGenerationRequestBuilder(sourceRepository.findBySourceKey(SOURCE_KEY));
generationCacheRepository.deleteAll();
prepareResultSchema();
}
@Test
public void generateCohort() {
AtomicBoolean isSqlExecuted = new AtomicBoolean();
CohortDefinition cohortDefinition = cohortDefinitionRepository.findOneWithDetail(cohortId);
Source source = sourceRepository.findBySourceKey(SOURCE_KEY);
// Run first-time generation
GenerationCacheHelper.CacheResult res = generationCacheHelper.computeCacheIfAbsent(
cohortDefinition,
source,
cohortGenerationRequestBuilder,
(resId, sqls) -> executeCohort(isSqlExecuted, resId)
);
Assert.assertTrue("Cohort SQL is executed in case of empty cache", isSqlExecuted.get());
Map<String, Long> counts = retrieveCohortGenerationCounts(res.getIdentifier());
Assert.assertTrue("Cohort generation properly fills tables", checkCohortCounts(counts));
// Second time generation. Cached results
isSqlExecuted.set(false);
res = generationCacheHelper.computeCacheIfAbsent(
cohortDefinition,
source,
cohortGenerationRequestBuilder,
(resId, sqls) -> isSqlExecuted.set(true)
);
Assert.assertFalse("Cohort results are retrieved from cache", isSqlExecuted.get());
// Generation after results were corrupted
jdbcTemplate.execute(String.format("DELETE FROM %s.cohort_cache;", RESULT_SCHEMA_NAME));
isSqlExecuted.set(false);
res = generationCacheHelper.computeCacheIfAbsent(
cohortDefinition,
source,
cohortGenerationRequestBuilder,
(resId, sqls) -> executeCohort(isSqlExecuted, resId)
);
Assert.assertTrue("Cohort SQL is executed in case of invalid cache", isSqlExecuted.get());
counts = retrieveCohortGenerationCounts(res.getIdentifier());
Assert.assertTrue("Cohort generation properly fills tables after invalid cache", checkCohortCounts(counts));
}
@Test
public void checkCachingWithEmptyResultSet() {
CacheableGenerationType type = CacheableGenerationType.COHORT;
CohortDefinition cohortDefinition = cohortDefinitionRepository.findOneWithDetail(cohortId);
Source source = sourceRepository.findBySourceKey(SOURCE_KEY);
generationCacheHelper.computeCacheIfAbsent(
cohortDefinition,
source,
cohortGenerationRequestBuilder,
(resId, sqls) -> {}
);
GenerationCache generationCache = generationCacheService.getCacheOrEraseInvalid(type, generationCacheService.getDesignHash(type, cohortDefinition.getDetails().getExpression()), source.getSourceId());
Assert.assertNotNull("Empty result set is cached", generationCache);
}
@Test
public void checkHashEquivalence() {
CohortDefinition cohortDefinition = cohortDefinitionRepository.findOneWithDetail(cohortId);
Integer originalHash = generationCacheHelper.computeHash(cohortDefinition.getDetails().getExpression());
// modify the inclusion rule name/description, but should lead to same hash result
CohortExpression expression = CohortExpression.fromJson(cohortDefinition.getDetails().getExpression());
expression.inclusionRules.get(0).name += "...updated name";
expression.inclusionRules.get(0).description += "..updated description";
Integer updatedHash = generationCacheHelper.computeHash(Utils.serialize(expression));
Assert.assertEquals("Expression with different name and descritpion results in same hash", originalHash,updatedHash);
}
private void executeCohort(AtomicBoolean isSqlExecuted, Integer resId) {
String mockSqlList = SqlRender.renderSql(
INSERT_COHORT_RESULTS_SQL,
new String[]{RESULTS_DATABASE_SCHEMA, DESIGN_HASH},
new String[]{RESULT_SCHEMA_NAME, resId.toString()}
);
String[] mockSqls = SqlSplit.splitSql(mockSqlList);
jdbcTemplate.batchUpdate(mockSqls);
isSqlExecuted.set(true);
}
private Map<String, Long> retrieveCohortGenerationCounts(Integer generationId) {
String cohortCountsSql = SqlRender.renderSql(
COHORT_COUNTS_SQL,
new String[]{RESULTS_DATABASE_SCHEMA, DESIGN_HASH},
new String[]{RESULT_SCHEMA_NAME, generationId.toString()}
);
return jdbcTemplate.queryForMap(cohortCountsSql)
.entrySet()
.stream()
.collect(Collectors.toMap(Map.Entry::getKey, e -> (Long) e.getValue()));
}
private boolean checkCohortCounts(Map<String, Long> counts) {
return counts.get("cohort_record_count") == 1
&& counts.get("cohort_inclusion_result_count") == 1
&& counts.get("cohort_inclusion_stats_count") == 1
&& counts.get("cohort_summary_stats_count") == 1
&& counts.get("cohort_censor_stats_count") == 0;
}
private CohortDefinition getCohortDefinition() {
CohortDefinitionDetails cohortDefinitionDetails = new CohortDefinitionDetails();
cohortDefinitionDetails.setExpression(COHORT_JSON);
CohortDefinition cohortDefinition = new CohortDefinition();
cohortDefinition.setName("Unit test");
cohortDefinition.setDetails(cohortDefinitionDetails);
cohortDefinitionDetails.setCohortDefinition(cohortDefinition);
return cohortDefinition;
}
private Source getCdmSource() throws SQLException {
Source source = new Source();
source.setSourceName("Embedded PG");
source.setSourceKey(SOURCE_KEY);
source.setSourceDialect(DBMSType.POSTGRESQL.getOhdsiDB());
source.setSourceConnection(getDataSource().getConnection().getMetaData().getURL());
source.setUsername("postgres");
source.setPassword("postgres");
source.setKrbAuthMethod(KerberosAuthMechanism.PASSWORD);
SourceDaimon cdmDaimon = new SourceDaimon();
cdmDaimon.setPriority(1);
cdmDaimon.setDaimonType(SourceDaimon.DaimonType.CDM);
cdmDaimon.setTableQualifier(CDM_SCHEMA_NAME);
cdmDaimon.setSource(source);
SourceDaimon vocabDaimon = new SourceDaimon();
vocabDaimon.setPriority(1);
vocabDaimon.setDaimonType(SourceDaimon.DaimonType.Vocabulary);
vocabDaimon.setTableQualifier(CDM_SCHEMA_NAME);
vocabDaimon.setSource(source);
SourceDaimon resultsDaimon = new SourceDaimon();
resultsDaimon.setPriority(1);
resultsDaimon.setDaimonType(SourceDaimon.DaimonType.Results);
resultsDaimon.setTableQualifier(RESULT_SCHEMA_NAME);
resultsDaimon.setSource(source);
source.setDaimons(Arrays.asList(cdmDaimon, vocabDaimon, resultsDaimon));
return source;
}
private CohortGenerationRequestBuilder getCohortGenerationRequestBuilder(Source source) {
return new CohortGenerationRequestBuilder(
SessionUtils.sessionId(),
SourceUtils.getResultsQualifier(source)
);
}
// NOTE:
// Not used in the current test set. Will be utilized for cohort generation testing
private static void prepareCdmSchema() throws IOException, ZipException {
String cdmSql = getCdmSql();
jdbcTemplate.batchUpdate("CREATE SCHEMA cdm;", cdmSql);
}
private static void prepareResultSchema() {
String resultSql = getResultTablesSql();
jdbcTemplate.batchUpdate(SqlSplit.splitSql(resultSql));
}
private static String getCdmSql() throws IOException, ZipException {
StringBuilder cdmSqlBuilder = new StringBuilder(CDM_SQL);
cdmSqlBuilder.append("ALTER TABLE @cdm_database_schema.vocabulary ALTER COLUMN vocabulary_reference DROP NOT NULL;\n");
cdmSqlBuilder.append("ALTER TABLE @cdm_database_schema.vocabulary ALTER COLUMN vocabulary_version DROP NOT NULL;\n");
Path tempDir = Files.createTempDirectory("");
tempDir.toFile().deleteOnExit();
// Direct Files.copy into new file in the temp folder throws Access Denied
File eunomiaZip = File.createTempFile("eunomia", "", tempDir.toFile());
try (InputStream is = GenerationCacheTest.class.getResourceAsStream(EUNOMIA_CSV_ZIP)) {
Files.copy(is, eunomiaZip.toPath(), REPLACE_EXISTING);
}
ZipFile zipFile = new ZipFile(eunomiaZip);
zipFile.extractAll(tempDir.toAbsolutePath().toString());
for (final File file : tempDir.toFile().listFiles()) {
if (file.getName().endsWith(".csv")) {
String tableName = file.getName().replace(".csv", "");
String sql = String.format("INSERT INTO @cdm_database_schema.%s SELECT * FROM CSVREAD('%s');", tableName, file.getAbsolutePath());
cdmSqlBuilder.append(sql).append("\n\n");
}
}
return cdmSqlBuilder.toString().replaceAll(Constants.SqlSchemaPlaceholders.CDM_DATABASE_SCHEMA_PLACEHOLDER, CDM_SCHEMA_NAME);
}
private static String getResultTablesSql() {
StringBuilder ddl = new StringBuilder();
ddl.append(String.format("DROP SCHEMA IF EXISTS %s CASCADE;", RESULT_SCHEMA_NAME)).append("\n");
ddl.append(String.format("CREATE SCHEMA %s;", RESULT_SCHEMA_NAME)).append("\n");
COHORT_DDL_FILE_PATHS.forEach(sqlPath -> ddl.append(ResourceHelper.GetResourceAsString(sqlPath)).append("\n"));
String resultSql = SqlRender.renderSql(ddl.toString(), new String[]{"results_schema"}, new String[]{RESULT_SCHEMA_NAME});
return SqlTranslate.translateSql(resultSql, DBMSType.POSTGRESQL.getOhdsiDB());
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/pathway/PathwayAnalysisTest.java | src/test/java/org/ohdsi/webapi/pathway/PathwayAnalysisTest.java | /*
* Copyright 2020 cknoll1.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ohdsi.webapi.pathway;
import com.github.mjeanroy.dbunit.core.dataset.DataSetFactory;
import com.odysseusinc.arachne.commons.types.DBMSType;
import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.KerberosAuthMechanism;
import java.sql.SQLException;
import java.util.Arrays;
import java.util.Collection;
import org.dbunit.Assertion;
import org.dbunit.DatabaseUnitException;
import org.dbunit.database.IDatabaseConnection;
import org.dbunit.dataset.CompositeDataSet;
import org.dbunit.dataset.IDataSet;
import org.dbunit.dataset.ITable;
import org.dbunit.operation.DatabaseOperation;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
import static org.junit.Assert.assertEquals;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.circe.helper.ResourceHelper;
import org.ohdsi.sql.SqlRender;
import org.ohdsi.sql.SqlSplit;
import org.ohdsi.sql.SqlTranslate;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.job.JobExecutionResource;
import org.ohdsi.webapi.pathway.converter.PathwayAnalysisToPathwayVersionConverter;
import org.ohdsi.webapi.pathway.converter.PathwayVersionToPathwayVersionFullDTOConverter;
import org.ohdsi.webapi.pathway.converter.SerializedPathwayAnalysisToPathwayAnalysisConverter;
import org.ohdsi.webapi.pathway.domain.PathwayAnalysisEntity;
import org.ohdsi.webapi.pathway.domain.PathwayAnalysisGenerationEntity;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisExportDTO;
import org.ohdsi.webapi.source.Source;
import org.ohdsi.webapi.source.SourceDaimon;
import org.ohdsi.webapi.source.SourceRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.convert.ConversionService;
import org.springframework.core.convert.support.DefaultConversionService;
/**
*
* @author cknoll1
*/
public class PathwayAnalysisTest extends AbstractDatabaseTest {
private static final Collection<String> CDM_DDL_FILE_PATHS = Arrays.asList("/cdm-postgresql-ddl.sql");
private static final String CDM_SCHEMA_NAME = "cdm";
private static boolean isSourceInitialized = false;
private static final String SOURCE_KEY = "Embedded_PG";
private static Integer SOURCE_ID;
private static final String RESULT_SCHEMA_NAME = "results";
private static final Collection<String> RESULTS_DDL_FILE_PATHS = Arrays.asList(
"/ddl/results/cohort.sql",
"/ddl/results/cohort_cache.sql",
"/ddl/results/cohort_inclusion.sql",
"/ddl/results/cohort_inclusion_result.sql",
"/ddl/results/cohort_inclusion_stats.sql",
"/ddl/results/cohort_inclusion_result_cache.sql",
"/ddl/results/cohort_inclusion_stats_cache.sql",
"/ddl/results/cohort_summary_stats.sql",
"/ddl/results/cohort_summary_stats_cache.sql",
"/ddl/results/cohort_censor_stats.sql",
"/ddl/results/cohort_censor_stats_cache.sql",
"/ddl/results/pathway_analysis_codes.sql",
"/ddl/results/pathway_analysis_events.sql",
"/ddl/results/pathway_analysis_paths.sql",
"/ddl/results/pathway_analysis_stats.sql"
);
@Autowired
private SourceRepository sourceRepository;
@Autowired
private PathwayService pathwayService;
@Autowired
private ConversionService conversionService;
@Value("${datasource.ohdsi.schema}")
private String ohdsiSchema;
private static SerializedPathwayAnalysisToPathwayAnalysisConverter converter = new SerializedPathwayAnalysisToPathwayAnalysisConverter();
@Before
public void setUp() throws Exception {
if (!isSourceInitialized) {
// one-time setup of CDM source
truncateTable(String.format("%s.%s", ohdsiSchema, "source"));
resetSequence(String.format("%s.%s", ohdsiSchema, "source_sequence"));
Source s = sourceRepository.saveAndFlush(getCdmSource());
SOURCE_ID = s.getSourceId();
isSourceInitialized = true;
}
// perform the following before each test
truncateTable(String.format("%s.%s", ohdsiSchema, "cohort_definition"));
resetSequence(String.format("%s.%s", ohdsiSchema, "cohort_definition_sequence"));
truncateTable(String.format("%s.%s", ohdsiSchema, "pathway_analysis"));
resetSequence(String.format("%s.%s", ohdsiSchema, "pathway_analysis_sequence"));
truncateTable(String.format("%s.%s", ohdsiSchema, "generation_cache"));
prepareCdmSchema();
prepareResultSchema();
SerializedPathwayAnalysisToPathwayAnalysisConverter.setConversionService(conversionService);
}
@After
public void tearDownDB() {
truncateTable(String.format("%s.%s", ohdsiSchema, "cohort_definition"));
resetSequence(String.format("%s.%s", ohdsiSchema, "cohort_definition_sequence"));
truncateTable(String.format("%s.%s", ohdsiSchema, "pathway_analysis"));
resetSequence(String.format("%s.%s", ohdsiSchema, "pathway_analysis_sequence"));
}
private static void prepareResultSchema() {
prepareSchema(RESULT_SCHEMA_NAME, "results_schema", RESULTS_DDL_FILE_PATHS);
}
private static void prepareCdmSchema() {
prepareSchema(CDM_SCHEMA_NAME, "cdm_database_schema", CDM_DDL_FILE_PATHS);
}
private static void prepareSchema(final String schemaName, final String schemaToken, final Collection<String> schemaPaths) {
StringBuilder ddl = new StringBuilder();
ddl.append(String.format("DROP SCHEMA IF EXISTS %s CASCADE;", schemaName));
ddl.append(String.format("CREATE SCHEMA %s;", schemaName));
schemaPaths.forEach(sqlPath -> ddl.append(ResourceHelper.GetResourceAsString(sqlPath)).append("\n"));
String resultSql = SqlRender.renderSql(ddl.toString(), new String[]{schemaToken}, new String[]{schemaName});
String ddlSql = SqlTranslate.translateSql(resultSql, DBMSType.POSTGRESQL.getOhdsiDB());
jdbcTemplate.batchUpdate(SqlSplit.splitSql(ddlSql));
}
private Source getCdmSource() throws SQLException {
Source source = new Source();
source.setSourceName("Embedded PG");
source.setSourceKey(SOURCE_KEY);
source.setSourceDialect(DBMSType.POSTGRESQL.getOhdsiDB());
source.setSourceConnection(getDataSource().getConnection().getMetaData().getURL());
source.setUsername("postgres");
source.setPassword("postgres");
source.setKrbAuthMethod(KerberosAuthMechanism.PASSWORD);
SourceDaimon cdmDaimon = new SourceDaimon();
cdmDaimon.setPriority(1);
cdmDaimon.setDaimonType(SourceDaimon.DaimonType.CDM);
cdmDaimon.setTableQualifier(CDM_SCHEMA_NAME);
cdmDaimon.setSource(source);
SourceDaimon vocabDaimon = new SourceDaimon();
vocabDaimon.setPriority(1);
vocabDaimon.setDaimonType(SourceDaimon.DaimonType.Vocabulary);
vocabDaimon.setTableQualifier(CDM_SCHEMA_NAME);
vocabDaimon.setSource(source);
SourceDaimon resultsDaimon = new SourceDaimon();
resultsDaimon.setPriority(1);
resultsDaimon.setDaimonType(SourceDaimon.DaimonType.Results);
resultsDaimon.setTableQualifier(RESULT_SCHEMA_NAME);
resultsDaimon.setSource(source);
source.setDaimons(Arrays.asList(cdmDaimon, vocabDaimon, resultsDaimon));
return source;
}
private void generateAnalysis(PathwayAnalysisEntity entity) throws Exception {
JobExecutionResource executionResource = pathwayService.generatePathways(entity.getId(), SOURCE_ID);
PathwayAnalysisGenerationEntity generationEntity;
while (true) {
generationEntity = pathwayService.getGeneration(executionResource.getExecutionId());
if (generationEntity.getStatus().equals("FAILED") || generationEntity.getStatus().equals("COMPLETED")) {
break;
}
Thread.sleep(2000L);
}
assertEquals("COMPLETED", generationEntity.getStatus());
}
/**
* Basic test that defines a pathway analysis with a Target cohort of the observation period start-end,
* and 2 event cohorts that are constructed from the drug eras of 2 distinct drug concepts:
* Child 1 [Parent 1] (ID=2) and Child 2 [Parent 1] (ID=3) creating the following overlapping periods:
* <pre>{@code
* Target: |-------------------------------------------------|
* EC1: |---| |------|
* EC2: |-----------| |---| |-------|
*
* Final pathway: EC1 -> EC1+EC2 -> EC2
* combo_id: 1 3 2
*
* }</pre>
*
* References:
* /pathway/vocabulary.json: simple vocabulary with 1 parent, 5 children (of parent 1)
* /pathway/simpleTest_PREP.json: the person, drug_era, and observation_period data needed to produce the above cohorts.
*
* @throws Exception
*/
@Test
public void test01_simplePathway() throws Exception {
final String[] testDataSetsPaths = new String[] { "/pathway/vocabulary.json", "/pathway/simpleTest_PREP.json" };
loadPrepData(testDataSetsPaths);
// CDM data loaded, generate pathways
PathwayAnalysisEntity entity = converter.convertToEntityAttribute(ResourceHelper.GetResourceAsString("/pathway/simpleTest_design.json"));
entity = pathwayService.importAnalysis(entity);
generateAnalysis(entity);
// Validate results
// Load actual records from cohort table
final IDatabaseConnection dbUnitCon = getConnection();
final ITable pathwayCodes = dbUnitCon.createQueryTable(RESULT_SCHEMA_NAME + ".pathway_analysis_codes",
String.format("SELECT code, name, is_combo from %s ORDER BY code, name, is_combo", RESULT_SCHEMA_NAME + ".pathway_analysis_codes"));
final ITable pathwayPaths = dbUnitCon.createQueryTable(RESULT_SCHEMA_NAME + ".pathway_analysis_paths",
String.format("SELECT target_cohort_id, step_1, step_2, step_3, step_4, step_5, step_6, step_7, step_8, step_9, step_10, count_value from %s ORDER BY target_cohort_id, step_1, step_2, step_3, step_4, step_5", RESULT_SCHEMA_NAME + ".pathway_analysis_paths"));
final ITable pathwayStats = dbUnitCon.createQueryTable(RESULT_SCHEMA_NAME + ".pathway_analysis_stats",
String.format("SELECT target_cohort_id, target_cohort_count, pathways_count from %s ORDER BY target_cohort_id", RESULT_SCHEMA_NAME + ".pathway_analysis_stats"));
final IDataSet actualDataSet = new CompositeDataSet(new ITable[] {pathwayCodes, pathwayPaths, pathwayStats});
// Load expected data from an XML dataset
final String[] testDataSetsVerify = new String[] {"/pathway/simpleTest_VERIFY.json"};
final IDataSet expectedDataSet = DataSetFactory.createDataSet(testDataSetsVerify);
// Assert actual database table match expected table
Assertion.assertEquals(expectedDataSet, actualDataSet);
}
/**
* A more advanced test that defines a pathway analysis with a Target cohort of the observation period start-end,
* and 2 event cohorts that are constructed from the drug eras of 2 distinct drug concepts, with a gap window of 15d:
* Child 1 [Parent 1] (ID=2) and Child 2 [Parent 1] (ID=3) creating the following overlapping periods:
* <pre>{@code
* Target: |-------------------------------------------------|
* EC1: |---| |------|
* EC2: |-----------| |---| |-------|
*
* With 15d collapse (and re-arranged to show the overlapping periods:
* Target: |-------------------------------------------------|
* EC1: |---|
* EC1: |-------------|
* EC2: |-------------|
* EC2: |---|
* EC2: |----------|
*
* Note: EC1 gets collapse to cause an overlap between the first EC1 episode and second EC2 Episode
* Final pathway: EC1+EC2 -> EC2
* combo_id: 3 2
*
* }</pre>
*
* References:
* /pathway/vocabulary.json: simple vocabulary with 1 parent, 5 children (of parent 1)
* /pathway/collapseTest_PREP.json: the person, drug_era, and observation_period data needed to produce the above cohorts.
*
* @throws Exception
*/
@Test
public void test02_collapseWindow() throws Exception {
final String[] testDataSetsPaths = new String[] { "/pathway/vocabulary.json", "/pathway/collapseTest_PREP.json" };
loadPrepData(testDataSetsPaths);
// CDM data loaded, generate pathways
PathwayAnalysisEntity entity = converter.convertToEntityAttribute(ResourceHelper.GetResourceAsString("/pathway/collapseTest_design.json"));
entity = pathwayService.importAnalysis(entity);
generateAnalysis(entity);
// Validate results
// Load actual records from cohort table
final IDatabaseConnection dbUnitCon = getConnection();
final ITable pathwayCodes = dbUnitCon.createQueryTable(RESULT_SCHEMA_NAME + ".pathway_analysis_codes",
String.format("SELECT code, name, is_combo from %s ORDER BY code, name, is_combo", RESULT_SCHEMA_NAME + ".pathway_analysis_codes"));
final ITable pathwayPaths = dbUnitCon.createQueryTable(RESULT_SCHEMA_NAME + ".pathway_analysis_paths",
String.format("SELECT target_cohort_id, step_1, step_2, step_3, step_4, step_5, step_6, step_7, step_8, step_9, step_10, count_value from %s ORDER BY target_cohort_id, step_1, step_2, step_3, step_4, step_5", RESULT_SCHEMA_NAME + ".pathway_analysis_paths"));
final ITable pathwayStats = dbUnitCon.createQueryTable(RESULT_SCHEMA_NAME + ".pathway_analysis_stats",
String.format("SELECT target_cohort_id, target_cohort_count, pathways_count from %s ORDER BY target_cohort_id", RESULT_SCHEMA_NAME + ".pathway_analysis_stats"));
final IDataSet actualDataSet = new CompositeDataSet(new ITable[] {pathwayCodes, pathwayPaths, pathwayStats});
// Load expected data from an XML dataset
final String[] testDataSetsVerify = new String[] {"/pathway/collapseTest_VERIFY.json"};
final IDataSet expectedDataSet = DataSetFactory.createDataSet(testDataSetsVerify);
// Assert actual database table match expected table
Assertion.assertEquals(expectedDataSet, actualDataSet);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/pathway/PathwayServiceTest.java | src/test/java/org/ohdsi/webapi/pathway/PathwayServiceTest.java | package org.ohdsi.webapi.pathway;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Answers;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.runners.MockitoJUnitRunner;
import org.ohdsi.webapi.pathway.domain.PathwayAnalysisEntity;
import org.ohdsi.webapi.pathway.domain.PathwayAnalysisGenerationEntity;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisDTO;
import org.ohdsi.webapi.pathway.repository.PathwayAnalysisGenerationRepository;
import org.springframework.core.convert.support.GenericConversionService;
import static org.junit.Assert.assertEquals;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyLong;
import static org.mockito.Matchers.eq;
import static org.mockito.Mockito.when;
@RunWith(MockitoJUnitRunner.class)
public class PathwayServiceTest {
@Mock
private PathwayAnalysisGenerationRepository pathwayAnalysisGenerationRepository;
@Mock
private GenericConversionService genericConversionService;
@Mock
private PathwayAnalysisGenerationEntity pathwayAnalysisGenerationEntity;
@Mock(answer = Answers.RETURNS_DEEP_STUBS)
private PathwayAnalysisDTO pathwayAnalysisDTO;
@Mock
private PathwayAnalysisEntity pathwayAnalysisEntity;
@InjectMocks
private PathwayServiceImpl sut;
@Test
public void shouldGetByGenerationId() {
when(pathwayAnalysisGenerationRepository.findOne(anyLong(), any())).thenReturn(pathwayAnalysisGenerationEntity);
when(pathwayAnalysisGenerationEntity.getPathwayAnalysis()).thenReturn(pathwayAnalysisEntity);
when(genericConversionService.convert(eq(pathwayAnalysisEntity), eq(PathwayAnalysisDTO.class))).thenReturn(pathwayAnalysisDTO);
PathwayAnalysisDTO result = sut.getByGenerationId(1);
assertEquals(result, pathwayAnalysisDTO);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/versioning/ConceptSetVersioningTest.java | src/test/java/org/ohdsi/webapi/versioning/ConceptSetVersioningTest.java | package org.ohdsi.webapi.versioning;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.ohdsi.circe.vocabulary.ConceptSetExpression;
import org.ohdsi.webapi.conceptset.ConceptSetItem;
import org.ohdsi.webapi.conceptset.ConceptSetRepository;
import org.ohdsi.webapi.conceptset.dto.ConceptSetVersionFullDTO;
import org.ohdsi.webapi.service.ConceptSetService;
import org.ohdsi.webapi.service.dto.ConceptSetDTO;
import org.ohdsi.webapi.versioning.dto.VersionDTO;
import org.ohdsi.webapi.versioning.dto.VersionUpdateDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.stream.StreamSupport;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNull;
public class ConceptSetVersioningTest extends BaseVersioningTest<ConceptSetDTO, ConceptSetVersionFullDTO, Integer> {
private static final String JSON_PATH = "/versioning/conceptset.json";
@Autowired
private ConceptSetService service;
@Autowired
private ConceptSetRepository repository;
@Autowired
private ObjectMapper mapper;
@Override
public void doCreateInitialData() throws IOException {
ConceptSetDTO dto = new ConceptSetDTO();
dto.setName("test dto name");
initialDTO = service.createConceptSet(dto);
String expression = getExpression(getExpressionPath());
ConceptSetExpression.ConceptSetItem[] expressionItems;
try {
ConceptSetExpression conceptSetExpression = mapper.readValue(expression, ConceptSetExpression.class);
expressionItems = conceptSetExpression.items;
} catch (JsonProcessingException e) {
throw new RuntimeException(e);
}
ConceptSetItem[] items = Arrays.stream(expressionItems)
.map(i -> conversionService.convert(i, ConceptSetItem.class))
.toArray(ConceptSetItem[]::new);
service.saveConceptSetItems(initialDTO.getId(), items);
}
protected void checkClientDTOEquality(ConceptSetVersionFullDTO fullDTO) {
ConceptSetDTO dto = fullDTO.getEntityDTO();
checkEquality(dto);
assertEquals(dto.getTags().size(), 0);
}
protected void checkServerDTOEquality(ConceptSetDTO dto) {
checkEquality(dto);
assertNull(dto.getTags());
}
private void checkEquality(ConceptSetDTO dto) {
assertNotEquals(dto.getName(), initialDTO.getName());
Iterable<ConceptSetItem> initialItems = service.getConceptSetItems(initialDTO.getId());
long initialSize = StreamSupport.stream(initialItems.spliterator(), false).count();
Iterable<ConceptSetItem> newItems = service.getConceptSetItems(dto.getId());
long newSize = StreamSupport.stream(newItems.spliterator(), false).count();
assertEquals(newSize, initialSize);
}
@Override
protected ConceptSetDTO getEntity(Integer id) {
return service.getConceptSet(id);
}
@Override
protected ConceptSetDTO updateEntity(ConceptSetDTO dto) throws Exception {
return service.updateConceptSet(dto.getId(), dto);
}
@Override
protected ConceptSetDTO copyAssetFromVersion(Integer id, int version) {
return service.copyAssetFromVersion(id, version);
}
@Override
protected Integer getId(ConceptSetDTO dto) {
return dto.getId();
}
@Override
protected String getExpressionPath() {
return JSON_PATH;
}
@Override
protected List<VersionDTO> getVersions(Integer id) {
return service.getVersions(id);
}
@Override
protected ConceptSetVersionFullDTO getVersion(Integer id, int version) {
return service.getVersion(id, version);
}
@Override
protected void updateVersion(Integer id, int version, VersionUpdateDTO updateDTO) {
service.updateVersion(id, version, updateDTO);
}
@Override
protected void deleteVersion(Integer id, int version) {
service.deleteVersion(id, version);
}
@Override
public void doClear() {
repository.deleteAll();
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/versioning/ReusableVersioningTest.java | src/test/java/org/ohdsi/webapi/versioning/ReusableVersioningTest.java | package org.ohdsi.webapi.versioning;
import org.ohdsi.webapi.reusable.ReusableService;
import org.ohdsi.webapi.reusable.dto.ReusableDTO;
import org.ohdsi.webapi.reusable.dto.ReusableVersionFullDTO;
import org.ohdsi.webapi.reusable.repository.ReusableRepository;
import org.ohdsi.webapi.versioning.dto.VersionDTO;
import org.ohdsi.webapi.versioning.dto.VersionUpdateDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.List;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
public class ReusableVersioningTest extends BaseVersioningTest<ReusableDTO, ReusableVersionFullDTO, Integer> {
@Autowired
private ReusableService service;
@Autowired
private ReusableRepository repository;
@Override
public void doCreateInitialData() throws IOException {
ReusableDTO dto = new ReusableDTO();
dto.setData("test data");
dto.setName("test name");
dto.setDescription("test description");
initialDTO = service.create(dto);
}
protected void checkClientDTOEquality(ReusableVersionFullDTO fullDTO) {
ReusableDTO dto = fullDTO.getEntityDTO();
checkEquality(dto);
}
protected void checkServerDTOEquality(ReusableDTO dto) {
checkEquality(dto);
}
private void checkEquality(ReusableDTO dto) {
assertNotEquals(dto.getName(), initialDTO.getName());
assertEquals(dto.getTags().size(), 0);
}
@Override
protected ReusableDTO getEntity(Integer id) {
return service.getDTOById(id);
}
@Override
protected ReusableDTO updateEntity(ReusableDTO dto) {
return service.update(dto.getId(), dto);
}
@Override
protected ReusableDTO copyAssetFromVersion(Integer id, int version) {
return service.copyAssetFromVersion(id, version);
}
@Override
protected Integer getId(ReusableDTO dto) {
return dto.getId();
}
@Override
protected String getExpressionPath() {
return null;
}
@Override
protected List<VersionDTO> getVersions(Integer id) {
return service.getVersions(id);
}
@Override
protected ReusableVersionFullDTO getVersion(Integer id, int version) {
return service.getVersion(id, version);
}
@Override
protected void updateVersion(Integer id, int version, VersionUpdateDTO updateDTO) {
service.updateVersion(id, version, updateDTO);
}
@Override
protected void deleteVersion(Integer id, int version) {
service.deleteVersion(id, version);
}
@Override
public void doClear() {
repository.deleteAll();
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/versioning/BaseVersioningTest.java | src/test/java/org/ohdsi/webapi/versioning/BaseVersioningTest.java | package org.ohdsi.webapi.versioning;
import org.apache.commons.io.FileUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.service.dto.CommonEntityExtDTO;
import org.ohdsi.webapi.shiro.Entities.UserEntity;
import org.ohdsi.webapi.shiro.Entities.UserRepository;
import org.ohdsi.webapi.versioning.dto.VersionDTO;
import org.ohdsi.webapi.versioning.dto.VersionFullDTO;
import org.ohdsi.webapi.versioning.dto.VersionUpdateDTO;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.convert.ConversionService;
import org.springframework.util.ResourceUtils;
import java.io.File;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.List;
import java.util.Objects;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
public abstract class BaseVersioningTest<S extends CommonEntityExtDTO,
T extends VersionFullDTO<?>, ID extends Number> extends AbstractDatabaseTest {
protected S initialDTO;
@Autowired
protected UserRepository userRepository;
@Autowired
protected ConversionService conversionService;
protected String getExpression(String path) throws IOException {
File ple_spec = ResourceUtils.getFile(Objects.requireNonNull(this.getClass().getResource(path)));
return FileUtils.readFileToString(ple_spec, StandardCharsets.UTF_8);
}
@Before
public void createInitialData() throws IOException {
UserEntity user = new UserEntity();
user.setLogin("anonymous");
userRepository.save(user);
doCreateInitialData();
}
protected abstract void doCreateInitialData() throws IOException;
@After
public void clear() {
doClear();
userRepository.deleteAll();
}
@Test
public void createAndGetVersion() throws Exception {
S dto = getEntity(getId(initialDTO));
dto.setName(dto.getName() + "__copy");
updateEntity(dto);
List<VersionDTO> versions = getVersions(getId(dto));
assertEquals(1, versions.size());
VersionDTO version = versions.get(0);
T fullDTO = getVersion(getId(dto), version.getVersion());
assertNotNull(fullDTO);
checkClientDTOEquality(fullDTO);
}
@Test
public void deleteVersion() throws Exception {
S dto = getEntity(getId(initialDTO));
dto.setName(dto.getName() + "__copy");
updateEntity(dto);
List<VersionDTO> versions = getVersions(getId(dto));
assertEquals(1, versions.size());
VersionDTO version = versions.get(0);
deleteVersion(getId(dto), version.getVersion());
versions = getVersions(getId(dto));
assertTrue(versions.get(0).isArchived());
}
@Test
public void createAndGetMultipleVersions() throws Exception {
S dto = getEntity(getId(initialDTO));
int count = 3;
for (int i = 0; i < count; i++) {
updateEntity(dto);
}
List<VersionDTO> versions = getVersions(getId(dto));
assertEquals(count, versions.size());
}
@Test
public void updateVersion() throws Exception {
S dto = getEntity(getId(initialDTO));
dto.setName(dto.getName() + "__copy");
updateEntity(dto);
List<VersionDTO> versions = getVersions(getId(dto));
VersionDTO version = versions.get(0);
VersionUpdateDTO updateDTO = new VersionUpdateDTO();
updateDTO.setVersion(version.getVersion());
updateDTO.setArchived(true);
updateDTO.setComment("test comment");
updateVersion(getId(dto), version.getVersion(), updateDTO);
T fullDTO = getVersion(getId(dto), version.getVersion());
version = fullDTO.getVersionDTO();
assertEquals(version.getComment(), updateDTO.getComment());
assertEquals(version.isArchived(), updateDTO.isArchived());
}
@Test
public void copyAssetFromVersion() throws Exception {
S dto = getEntity(getId(initialDTO));
dto.setName(dto.getName() + "__copy");
updateEntity(dto);
List<VersionDTO> versions = getVersions(getId(dto));
VersionDTO version = versions.get(0);
S newDTO = copyAssetFromVersion(getId(dto), version.getVersion());
checkServerDTOEquality(newDTO);
}
protected abstract void doClear();
protected abstract void checkServerDTOEquality(S dto);
protected abstract void checkClientDTOEquality(T dto);
protected abstract List<VersionDTO> getVersions(ID id);
protected abstract T getVersion(ID id, int version);
protected abstract String getExpressionPath();
protected abstract S getEntity(ID id);
protected abstract S updateEntity(S dto) throws Exception;
protected abstract S copyAssetFromVersion(ID id, int version);
protected abstract void updateVersion(ID id, int version, VersionUpdateDTO updateDTO);
protected abstract void deleteVersion(ID id, int version);
protected abstract ID getId(S dto);
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/versioning/CohortVersioningTest.java | src/test/java/org/ohdsi/webapi/versioning/CohortVersioningTest.java | package org.ohdsi.webapi.versioning;
import org.ohdsi.webapi.cohortdefinition.CohortDefinition;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.ohdsi.webapi.cohortdefinition.dto.CohortDTO;
import org.ohdsi.webapi.cohortdefinition.dto.CohortMetadataDTO;
import org.ohdsi.webapi.cohortdefinition.dto.CohortRawDTO;
import org.ohdsi.webapi.cohortdefinition.dto.CohortVersionFullDTO;
import org.ohdsi.webapi.service.CohortDefinitionService;
import org.ohdsi.webapi.versioning.dto.VersionDTO;
import org.ohdsi.webapi.versioning.dto.VersionUpdateDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.List;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNull;
public class CohortVersioningTest extends BaseVersioningTest<CohortDTO, CohortVersionFullDTO, Integer> {
private static final String JSON_PATH = "/versioning/cohort.json";
@Autowired
private CohortDefinitionService service;
@Autowired
private CohortDefinitionRepository repository;
private CohortDTO deserializeExpression(String expression) {
CohortRawDTO rawDTO = new CohortRawDTO();
rawDTO.setExpression(expression);
CohortDTO dto = conversionService.convert(rawDTO, CohortDTO.class);
dto.setName("test dto name");
dto.setDescription("test dto description");
return dto;
}
@Override
public void doCreateInitialData() throws IOException {
String expression = getExpression(getExpressionPath());
CohortDTO dto = deserializeExpression(expression);
initialDTO = service.createCohortDefinition(dto);
}
protected void checkClientDTOEquality(CohortVersionFullDTO fullDTO) {
CohortRawDTO dto = fullDTO.getEntityDTO();
checkEquality(dto);
assertEquals(dto.getTags().size(), 0);
CohortDefinition def = conversionService.convert(initialDTO, CohortDefinition.class);
CohortRawDTO rawDTO = conversionService.convert(def, CohortRawDTO.class);
assertEquals(dto.getExpression(), rawDTO.getExpression());
}
protected void checkServerDTOEquality(CohortDTO dto) {
checkEquality(dto);
assertNull(dto.getTags());
CohortDefinition def = conversionService.convert(initialDTO, CohortDefinition.class);
CohortRawDTO rawDTO = conversionService.convert(def, CohortRawDTO.class);
CohortDefinition newDef = conversionService.convert(dto, CohortDefinition.class);
CohortRawDTO newRawDTO = conversionService.convert(newDef, CohortRawDTO.class);
assertEquals(newRawDTO.getExpression(), rawDTO.getExpression());
}
private void checkEquality(CohortMetadataDTO dto) {
assertNotEquals(dto.getName(), initialDTO.getName());
assertEquals(dto.getDescription(), initialDTO.getDescription());
}
@Override
protected CohortDTO getEntity(Integer id) {
return service.getCohortDefinition(id);
}
@Override
protected CohortDTO updateEntity(CohortDTO dto) {
return service.saveCohortDefinition(dto.getId(), dto);
}
@Override
protected CohortDTO copyAssetFromVersion(Integer id, int version) {
return service.copyAssetFromVersion(id, version);
}
@Override
protected Integer getId(CohortDTO dto) {
return dto.getId();
}
@Override
protected String getExpressionPath() {
return JSON_PATH;
}
@Override
protected List<VersionDTO> getVersions(Integer id) {
return service.getVersions(id);
}
@Override
protected CohortVersionFullDTO getVersion(Integer id, int version) {
return service.getVersion(id, version);
}
@Override
protected void updateVersion(Integer id, int version, VersionUpdateDTO updateDTO) {
service.updateVersion(id, version, updateDTO);
}
@Override
protected void deleteVersion(Integer id, int version) {
service.deleteVersion(id, version);
}
@Override
public void doClear() {
repository.deleteAll();
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/versioning/CcVersioningTest.java | src/test/java/org/ohdsi/webapi/versioning/CcVersioningTest.java | package org.ohdsi.webapi.versioning;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.cohortcharacterization.CcController;
import org.ohdsi.webapi.cohortcharacterization.domain.CohortCharacterizationEntity;
import org.ohdsi.webapi.cohortcharacterization.dto.CcExportDTO;
import org.ohdsi.webapi.cohortcharacterization.dto.CcVersionFullDTO;
import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
import org.ohdsi.webapi.cohortcharacterization.repository.CcRepository;
import org.ohdsi.webapi.cohortcharacterization.specification.CohortCharacterizationImpl;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.ohdsi.webapi.versioning.dto.VersionDTO;
import org.ohdsi.webapi.versioning.dto.VersionUpdateDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.List;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
public class CcVersioningTest extends BaseVersioningTest<CohortCharacterizationDTO, CcVersionFullDTO, Long> {
private static final String JSON_PATH = "/versioning/characterization.json";
@Autowired
private CcController service;
@Autowired
private CcRepository repository;
@Autowired
private CohortDefinitionRepository cohortRepository;
@Override
public void doCreateInitialData() throws IOException {
String expression = getExpression(getExpressionPath());
CohortCharacterizationImpl characterizationImpl =
Utils.deserialize(expression, CohortCharacterizationImpl.class);
CohortCharacterizationEntity entity = conversionService.convert(characterizationImpl, CohortCharacterizationEntity.class);
CcExportDTO exportDTO = conversionService.convert(entity, CcExportDTO.class);
exportDTO.setName("test dto name");
initialDTO = service.doImport(exportDTO);
}
protected void checkClientDTOEquality(CcVersionFullDTO fullDTO) {
CohortCharacterizationDTO dto = fullDTO.getEntityDTO();
checkEquality(dto);
assertEquals(dto.getCohorts().size(), initialDTO.getCohorts().size());
assertEquals(dto.getParameters().size(), initialDTO.getParameters().size());
assertEquals(dto.getFeatureAnalyses().size(), initialDTO.getFeatureAnalyses().size());
}
protected void checkServerDTOEquality(CohortCharacterizationDTO dto) {
checkEquality(dto);
}
private void checkEquality(CohortCharacterizationDTO dto) {
assertNotEquals(dto.getName(), initialDTO.getName());
assertEquals(dto.getCohorts().size(), initialDTO.getCohorts().size());
assertEquals(dto.getParameters().size(), initialDTO.getParameters().size());
assertEquals(dto.getFeatureAnalyses().size(), initialDTO.getFeatureAnalyses().size());
assertEquals(dto.getTags().size(), 0);
}
@Override
protected CohortCharacterizationDTO getEntity(Long id) {
return service.getDesign(id);
}
@Override
protected CohortCharacterizationDTO updateEntity(CohortCharacterizationDTO dto) {
return service.update(dto.getId(), dto);
}
@Override
protected CohortCharacterizationDTO copyAssetFromVersion(Long id, int version) {
return service.copyAssetFromVersion(id, version);
}
@Override
protected Long getId(CohortCharacterizationDTO dto) {
return dto.getId();
}
@Override
protected String getExpressionPath() {
return JSON_PATH;
}
@Override
protected List<VersionDTO> getVersions(Long id) {
return service.getVersions(id);
}
@Override
protected CcVersionFullDTO getVersion(Long id, int version) {
return service.getVersion(id, version);
}
@Override
protected void updateVersion(Long id, int version, VersionUpdateDTO updateDTO) {
service.updateVersion(id, version, updateDTO);
}
@Override
protected void deleteVersion(Long id, int version) {
service.deleteVersion(id, version);
}
@Override
public void doClear() {
repository.deleteAll();
cohortRepository.deleteAll();
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/versioning/IRVersioningTest.java | src/test/java/org/ohdsi/webapi/versioning/IRVersioningTest.java | package org.ohdsi.webapi.versioning;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.ohdsi.webapi.ircalc.IncidenceRateAnalysisRepository;
import org.ohdsi.webapi.ircalc.dto.IRVersionFullDTO;
import org.ohdsi.webapi.service.IRAnalysisService;
import org.ohdsi.webapi.service.dto.IRAnalysisDTO;
import org.ohdsi.webapi.versioning.dto.VersionDTO;
import org.ohdsi.webapi.versioning.dto.VersionUpdateDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.List;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNull;
public class IRVersioningTest extends BaseVersioningTest<IRAnalysisDTO, IRVersionFullDTO, Integer> {
private static final String JSON_PATH = "/versioning/ir.json";
@Autowired
private IRAnalysisService service;
@Autowired
private IncidenceRateAnalysisRepository repository;
@Autowired
private CohortDefinitionRepository cohortRepository;
private IRAnalysisDTO deserializeExpression(String expression) {
IRAnalysisDTO dto =
Utils.deserialize(expression, IRAnalysisDTO.class);
dto.setName("test dto name");
dto.setDescription("test dto description");
return dto;
}
@Override
public void doCreateInitialData() throws IOException {
String expression = getExpression(getExpressionPath());
IRAnalysisDTO dto = deserializeExpression(expression);
initialDTO = service.doImport(dto);
}
protected void checkClientDTOEquality(IRVersionFullDTO fullDTO) {
IRAnalysisDTO dto = fullDTO.getEntityDTO();
checkEquality(dto);
assertEquals(dto.getTags().size(), 0);
}
protected void checkServerDTOEquality(IRAnalysisDTO dto) {
checkEquality(dto);
assertNull(dto.getTags());
}
private void checkEquality(IRAnalysisDTO dto) {
assertNotEquals(dto.getName(), initialDTO.getName());
assertEquals(dto.getDescription(), initialDTO.getDescription());
assertEquals(dto.getExpression(), initialDTO.getExpression());
}
@Override
protected IRAnalysisDTO getEntity(Integer id) {
return service.getAnalysis(id);
}
@Override
protected IRAnalysisDTO updateEntity(IRAnalysisDTO dto) {
return service.saveAnalysis(dto.getId(), dto);
}
@Override
protected IRAnalysisDTO copyAssetFromVersion(Integer id, int version) {
return service.copyAssetFromVersion(id, version);
}
@Override
protected Integer getId(IRAnalysisDTO dto) {
return dto.getId();
}
@Override
protected String getExpressionPath() {
return JSON_PATH;
}
@Override
protected List<VersionDTO> getVersions(Integer id) {
return service.getVersions(id);
}
@Override
protected IRVersionFullDTO getVersion(Integer id, int version) {
return service.getVersion(id, version);
}
@Override
protected void updateVersion(Integer id, int version, VersionUpdateDTO updateDTO) {
service.updateVersion(id, version, updateDTO);
}
@Override
protected void deleteVersion(Integer id, int version) {
service.deleteVersion(id, version);
}
@Override
public void doClear() {
repository.deleteAll();
cohortRepository.deleteAll();
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/versioning/PathwayVersioningTest.java | src/test/java/org/ohdsi/webapi/versioning/PathwayVersioningTest.java | package org.ohdsi.webapi.versioning;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.ohdsi.webapi.pathway.PathwayController;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisDTO;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisExportDTO;
import org.ohdsi.webapi.pathway.dto.PathwayVersionFullDTO;
import org.ohdsi.webapi.pathway.repository.PathwayAnalysisEntityRepository;
import org.ohdsi.webapi.versioning.dto.VersionDTO;
import org.ohdsi.webapi.versioning.dto.VersionUpdateDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.List;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
public class PathwayVersioningTest extends BaseVersioningTest<PathwayAnalysisDTO, PathwayVersionFullDTO, Integer> {
private static final String JSON_PATH = "/versioning/pathway.json";
@Autowired
private PathwayController service;
@Autowired
private PathwayAnalysisEntityRepository repository;
@Autowired
private CohortDefinitionRepository cohortRepository;
@Override
public void doCreateInitialData() throws IOException {
String expression = getExpression(getExpressionPath());
PathwayAnalysisExportDTO dto = Utils.deserialize(expression, PathwayAnalysisExportDTO.class);
dto.setName("test dto name");
initialDTO = service.importAnalysis(dto);
}
protected void checkClientDTOEquality(PathwayVersionFullDTO fullDTO) {
PathwayAnalysisDTO dto = fullDTO.getEntityDTO();
checkEquality(dto);
}
protected void checkServerDTOEquality(PathwayAnalysisDTO dto) {
checkEquality(dto);
}
private void checkEquality(PathwayAnalysisDTO dto) {
assertNotEquals(dto.getName(), initialDTO.getName());
assertEquals(dto.getEventCohorts().size(), initialDTO.getEventCohorts().size());
assertEquals(dto.getTargetCohorts().size(), initialDTO.getTargetCohorts().size());
assertEquals(dto.getTags().size(), 0);
}
@Override
protected PathwayAnalysisDTO getEntity(Integer id) {
return service.get(id);
}
@Override
protected PathwayAnalysisDTO updateEntity(PathwayAnalysisDTO dto) {
return service.update(dto.getId(), dto);
}
@Override
protected PathwayAnalysisDTO copyAssetFromVersion(Integer id, int version) {
return service.copyAssetFromVersion(id, version);
}
@Override
protected Integer getId(PathwayAnalysisDTO dto) {
return dto.getId();
}
@Override
protected String getExpressionPath() {
return JSON_PATH;
}
@Override
protected List<VersionDTO> getVersions(Integer id) {
return service.getVersions(id);
}
@Override
protected PathwayVersionFullDTO getVersion(Integer id, int version) {
return service.getVersion(id, version);
}
@Override
protected void updateVersion(Integer id, int version, VersionUpdateDTO updateDTO) {
service.updateVersion(id, version, updateDTO);
}
@Override
protected void deleteVersion(Integer id, int version) {
service.deleteVersion(id, version);
}
@Override
public void doClear() {
repository.deleteAll();
cohortRepository.deleteAll();
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/test/SecurityIT.java | src/test/java/org/ohdsi/webapi/test/SecurityIT.java | package org.ohdsi.webapi.test;
import com.github.springtestdbunit.DbUnitTestExecutionListener;
import com.github.springtestdbunit.annotation.DatabaseOperation;
import com.github.springtestdbunit.annotation.DatabaseTearDown;
import com.github.springtestdbunit.annotation.DbUnitConfiguration;
import com.google.common.collect.ImmutableMap;
import org.apache.catalina.webresources.TomcatURLStreamHandlerFactory;
import org.glassfish.jersey.server.model.Parameter;
import org.glassfish.jersey.server.model.Resource;
import org.glassfish.jersey.server.model.ResourceMethod;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.ErrorCollector;
import org.junit.runner.RunWith;
import org.ohdsi.webapi.JerseyConfig;
import org.ohdsi.webapi.WebApi;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.test.web.client.TestRestTemplate;
import org.springframework.http.*;
import org.springframework.test.context.ActiveProfiles;
import org.springframework.test.context.TestExecutionListeners;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.context.junit4.SpringRunner;
import org.springframework.web.util.UriComponentsBuilder;
import javax.ws.rs.core.MediaType;
import java.io.IOException;
import java.net.URI;
import java.util.*;
import static org.assertj.core.api.Java6Assertions.assertThat;
import static org.springframework.test.context.TestExecutionListeners.MergeMode.MERGE_WITH_DEFAULTS;
@RunWith(SpringRunner.class)
@SpringBootTest(classes = {WebApi.class, WebApiIT.DbUnitConfiguration.class}, webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
@ActiveProfiles("test")
@DbUnitConfiguration(databaseConnection = "dbUnitDatabaseConnection")
@TestExecutionListeners(value = {DbUnitTestExecutionListener.class}, mergeMode = MERGE_WITH_DEFAULTS)
@DatabaseTearDown(value = "/database/empty.xml", type = DatabaseOperation.DELETE_ALL)
@TestPropertySource(properties = {"security.provider=AtlasRegularSecurity"})
public class SecurityIT {
private final Map<String, HttpStatus> EXPECTED_RESPONSE_CODES = ImmutableMap.<String, HttpStatus>builder()
.put("/info/", HttpStatus.OK)
.put("/i18n/", HttpStatus.OK)
.put("/i18n/locales", HttpStatus.OK)
.put("/ddl/results", HttpStatus.OK)
.put("/ddl/cemresults", HttpStatus.OK)
.put("/ddl/achilles", HttpStatus.OK)
.put("/saml/saml-metadata", HttpStatus.OK)
.put("/saml/slo", HttpStatus.TEMPORARY_REDIRECT)
.build();
@Autowired
private TestRestTemplate restTemplate;
@Autowired
private JerseyConfig jerseyConfig;
@Value("${baseUri}")
private String baseUri;
@Rule
public ErrorCollector collector = new ErrorCollector();
private final Logger LOG = LoggerFactory.getLogger(SecurityIT.class);
@BeforeClass
public static void before() throws IOException {
TomcatURLStreamHandlerFactory.disable();
ITStarter.before();
}
@AfterClass
public static void after() {
ITStarter.tearDownSubject();
}
@Test
public void testServiceSecurity() {
Map<String, List<ServiceInfo>> serviceMap = getServiceMap();
for (String servicePrefix : serviceMap.keySet()) {
List<ServiceInfo> serviceInfos = serviceMap.get(servicePrefix);
for (ServiceInfo serviceInfo : serviceInfos) {
if (!serviceInfo.pathPrefix.startsWith("/")) {
serviceInfo.pathPrefix = "/" + serviceInfo.pathPrefix;
}
serviceInfo.pathPrefix = serviceInfo.pathPrefix.replaceAll("//", "/");
String rawUrl = baseUri + serviceInfo.pathPrefix;
URI uri = null;
try {
Map<String, String> parametersMap = prepareParameters(serviceInfo.parameters);
HttpEntity<?> entity = new HttpEntity<>(new HttpHeaders());
uri = UriComponentsBuilder.fromUriString(rawUrl)
.buildAndExpand(parametersMap).encode().toUri();
LOG.info("testing service {}:{}", serviceInfo.httpMethod, uri);
ResponseEntity<?> response = this.restTemplate.exchange(uri, serviceInfo.httpMethod, entity,
getResponseType(serviceInfo));
LOG.info("tested service {}:{} with code {}", serviceInfo.httpMethod, uri, response.getStatusCode());
HttpStatus expectedStatus = EXPECTED_RESPONSE_CODES.getOrDefault(serviceInfo.pathPrefix, HttpStatus.UNAUTHORIZED);
assertThat(response.getStatusCode()).isEqualTo(expectedStatus);
} catch (Throwable t) {
LOG.info("failed service {}:{}", serviceInfo.httpMethod, uri);
collector.addError(new ThrowableEx(t, rawUrl));
}
}
}
}
private Class<?> getResponseType(ServiceInfo serviceInfo) {
if (serviceInfo.mediaTypes.contains(MediaType.TEXT_PLAIN_TYPE)) {
return String.class;
} else if (serviceInfo.pathPrefix.equalsIgnoreCase("/saml/saml-metadata")) {
return Void.class;
}
return Object.class;
}
private Map<String, String> prepareParameters(List<Parameter> parameters) {
Map<String, String> parametersMap = new HashMap<>();
if (parameters != null && !parameters.isEmpty()) {
for (Parameter parameter : parameters) {
String value = "0";
// if parameter has classloader then it is of object type, else it is primitive type
if (parameter.getRawType().getClassLoader() != null) {
value = null;
}
parametersMap.put(parameter.getSourceName(), value);
}
}
return parametersMap;
}
/*
* Retrieve information about rest services (path prefixes, http methods, parameters)
*/
private Map<String, List<ServiceInfo>> getServiceMap() {
//
Set<Class<?>> classes = this.jerseyConfig.getClasses();
Map<String, List<ServiceInfo>> serviceMap = new HashMap<>();
for (Class<?> clazz : classes) {
Map<String, List<ServiceInfo>> map = scan(clazz);
if (map != null) {
serviceMap.putAll(map);
}
}
return serviceMap;
}
private Map<String, List<ServiceInfo>> scan(Class<?> baseClass) {
Resource.Builder builder = Resource.builder(baseClass);
if (null == builder)
return null;
Resource resource = builder.build();
String uriPrefix = "";
Map<String, List<ServiceInfo>> info = new TreeMap<>();
return process(uriPrefix, resource, info);
}
private Map<String, List<ServiceInfo>> process(String uriPrefix, Resource resource, Map<String, List<ServiceInfo>> info) {
String pathPrefix = uriPrefix;
List<Resource> resources = new ArrayList<>(resource.getChildResources());
if (resource.getPath() != null) {
pathPrefix = pathPrefix + resource.getPath();
}
for (ResourceMethod method : resource.getAllMethods()) {
List<ServiceInfo> serviceInfos = info.computeIfAbsent(pathPrefix, k -> new ArrayList<>());
ServiceInfo serviceInfo = new ServiceInfo();
serviceInfo.pathPrefix = pathPrefix;
serviceInfo.httpMethod = HttpMethod.resolve(method.getHttpMethod());
serviceInfo.parameters = method.getInvocable().getParameters();
serviceInfo.mediaTypes = method.getProducedTypes();
serviceInfos.add(serviceInfo);
}
for (Resource childResource : resources) {
process(pathPrefix, childResource, info);
}
return info;
}
private static class ServiceInfo {
public String pathPrefix;
public HttpMethod httpMethod;
public List<Parameter> parameters;
public List<MediaType> mediaTypes;
}
private static class ThrowableEx extends Throwable {
private final String serviceName;
public ThrowableEx(Throwable throwable, String serviceName) {
super(throwable);
this.serviceName = serviceName;
}
@Override
public String getMessage() {
return serviceName + ": " + super.getMessage();
}
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/test/TestConstants.java | src/test/java/org/ohdsi/webapi/test/TestConstants.java | package org.ohdsi.webapi.test;
public class TestConstants {
public final static String COPY_PREFIX = "COPY OF ";
public final static String NEW_TEST_ENTITY = "New test entity";
public final static String SOME_UNIQUE_TEST_NAME = "Some unique test name";
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/test/WebApiIT.java | src/test/java/org/ohdsi/webapi/test/WebApiIT.java | package org.ohdsi.webapi.test;
import static org.junit.Assert.assertEquals;
import static org.springframework.test.context.TestExecutionListeners.MergeMode.MERGE_WITH_DEFAULTS;
import com.github.springtestdbunit.DbUnitTestExecutionListener;
import com.github.springtestdbunit.annotation.DbUnitConfiguration;
import java.io.IOException;
import java.sql.SQLException;
import java.util.Arrays;
import java.util.Collection;
import com.github.springtestdbunit.bean.DatabaseDataSourceConnectionFactoryBean;
import com.odysseusinc.arachne.commons.types.DBMSType;
import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.KerberosAuthMechanism;
import org.apache.catalina.webresources.TomcatURLStreamHandlerFactory;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.runner.RunWith;
import org.ohdsi.circe.helper.ResourceHelper;
import org.ohdsi.sql.SqlRender;
import org.ohdsi.sql.SqlSplit;
import org.ohdsi.sql.SqlTranslate;
import org.ohdsi.webapi.WebApi;
import org.ohdsi.webapi.source.Source;
import org.ohdsi.webapi.source.SourceDaimon;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.test.context.TestConfiguration;
import org.springframework.context.annotation.Bean;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.test.context.TestExecutionListeners;
import org.springframework.test.context.junit4.SpringRunner;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.test.context.ActiveProfiles;
import org.springframework.boot.test.web.client.TestRestTemplate;
import javax.sql.DataSource;
@RunWith(SpringRunner.class)
@SpringBootTest(classes = {WebApi.class, WebApiIT.DbUnitConfiguration.class}, webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
@ActiveProfiles("test")
@DbUnitConfiguration(databaseConnection = "dbUnitDatabaseConnection")
@TestExecutionListeners(value = {DbUnitTestExecutionListener.class}, mergeMode = MERGE_WITH_DEFAULTS)
public abstract class WebApiIT {
protected final Logger log = LoggerFactory.getLogger(getClass());
protected final String SOURCE_KEY = "Embedded_PG";
protected static final String CDM_SCHEMA_NAME = "cdm";
protected static final String RESULT_SCHEMA_NAME = "results";
private static final Collection<String> CDM_DDL_FILE_PATHS = Arrays.asList("/cdm-postgresql-ddl.sql");
private static final Collection<String> RESULTS_DDL_FILE_PATHS = Arrays.asList(
"/ddl/results/cohort.sql",
"/ddl/results/cohort_cache.sql",
"/ddl/results/cohort_inclusion.sql",
"/ddl/results/cohort_inclusion_result.sql",
"/ddl/results/cohort_inclusion_stats.sql",
"/ddl/results/cohort_inclusion_result_cache.sql",
"/ddl/results/cohort_inclusion_stats_cache.sql",
"/ddl/results/cohort_summary_stats.sql",
"/ddl/results/cohort_summary_stats_cache.sql",
"/ddl/results/cohort_censor_stats.sql",
"/ddl/results/cohort_censor_stats_cache.sql",
"/ddl/results/pathway_analysis_codes.sql",
"/ddl/results/pathway_analysis_events.sql",
"/ddl/results/pathway_analysis_paths.sql",
"/ddl/results/pathway_analysis_stats.sql",
"/ddl/results/achilles_result_concept_count.sql"
);
@TestConfiguration
public static class DbUnitConfiguration {
@Bean
DatabaseDataSourceConnectionFactoryBean dbUnitDatabaseConnection(DataSource primaryDataSource) {
DatabaseDataSourceConnectionFactoryBean dbUnitDatabaseConnection = new DatabaseDataSourceConnectionFactoryBean(primaryDataSource);
dbUnitDatabaseConnection.setSchema("public");
return dbUnitDatabaseConnection;
}
}
@Value("${baseUri}")
private String baseUri;
private final TestRestTemplate restTemplate = new TestRestTemplate();
protected static JdbcTemplate jdbcTemplate;
@BeforeClass
public static void before() throws IOException {
TomcatURLStreamHandlerFactory.disable();
ITStarter.before();
jdbcTemplate = new JdbcTemplate(ITStarter.getDataSource());
}
@AfterClass
public static void after() {
ITStarter.tearDownSubject();
}
public TestRestTemplate getRestTemplate() {
return this.restTemplate;
}
public String getBaseUri() {
return this.baseUri;
}
public void setBaseUri(final String baseUri) {
this.baseUri = baseUri;
}
public void assertOK(ResponseEntity<?> entity) {
assertEquals(HttpStatus.OK, entity.getStatusCode());
if (log.isDebugEnabled()) {
log.debug("Body: {}", entity.getBody());
}
}
protected void truncateTable(final String tableName) {
jdbcTemplate.execute(String.format("TRUNCATE %s CASCADE",tableName));
}
protected void resetSequence(final String sequenceName) {
jdbcTemplate.execute(String.format("ALTER SEQUENCE %s RESTART WITH 1", sequenceName));
}
protected Source getCdmSource() throws SQLException {
Source source = new Source();
source.setSourceName("Embedded PG");
source.setSourceKey(SOURCE_KEY);
source.setSourceDialect(DBMSType.POSTGRESQL.getOhdsiDB());
source.setSourceConnection(ITStarter.getDataSource().getConnection().getMetaData().getURL());
source.setUsername("postgres");
source.setPassword("postgres");
source.setKrbAuthMethod(KerberosAuthMechanism.PASSWORD);
SourceDaimon cdmDaimon = new SourceDaimon();
cdmDaimon.setPriority(1);
cdmDaimon.setDaimonType(SourceDaimon.DaimonType.CDM);
cdmDaimon.setTableQualifier(CDM_SCHEMA_NAME);
cdmDaimon.setSource(source);
SourceDaimon vocabDaimon = new SourceDaimon();
vocabDaimon.setPriority(1);
vocabDaimon.setDaimonType(SourceDaimon.DaimonType.Vocabulary);
vocabDaimon.setTableQualifier(CDM_SCHEMA_NAME);
vocabDaimon.setSource(source);
SourceDaimon resultsDaimon = new SourceDaimon();
resultsDaimon.setPriority(1);
resultsDaimon.setDaimonType(SourceDaimon.DaimonType.Results);
resultsDaimon.setTableQualifier(RESULT_SCHEMA_NAME);
resultsDaimon.setSource(source);
source.setDaimons(Arrays.asList(cdmDaimon, vocabDaimon, resultsDaimon));
return source;
}
protected void prepareResultSchema() {
prepareSchema(RESULT_SCHEMA_NAME, "results_schema", RESULTS_DDL_FILE_PATHS);
}
protected void prepareCdmSchema() {
prepareSchema(CDM_SCHEMA_NAME, "cdm_database_schema", CDM_DDL_FILE_PATHS);
}
private void prepareSchema(final String schemaName, final String schemaToken, final Collection<String> schemaPaths) {
StringBuilder ddl = new StringBuilder();
ddl.append(String.format("DROP SCHEMA IF EXISTS %s CASCADE;", schemaName));
ddl.append(String.format("CREATE SCHEMA %s;", schemaName));
schemaPaths.forEach(sqlPath -> ddl.append(ResourceHelper.GetResourceAsString(sqlPath)).append("\n"));
String resultSql = SqlRender.renderSql(ddl.toString(), new String[]{schemaToken}, new String[]{schemaName});
String ddlSql = SqlTranslate.translateSql(resultSql, DBMSType.POSTGRESQL.getOhdsiDB());
jdbcTemplate.batchUpdate(SqlSplit.splitSql(ddlSql));
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/test/AbstractShiro.java | src/test/java/org/ohdsi/webapi/test/AbstractShiro.java | package org.ohdsi.webapi.test;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.UnavailableSecurityManagerException;
import org.apache.shiro.subject.Subject;
import org.apache.shiro.subject.support.SubjectThreadState;
import org.apache.shiro.util.LifecycleUtils;
import org.apache.shiro.util.ThreadState;
import org.apache.shiro.mgt.SecurityManager;
import org.junit.AfterClass;
/**
* Abstract test case enabling Shiro in test environments.
*/
public abstract class AbstractShiro {
private static ThreadState subjectThreadState;
public AbstractShiro() {
}
/**
* Allows subclasses to set the currently executing {@link Subject} instance.
*
* @param subject the Subject instance
*/
protected static void setSubject(Subject subject) {
clearSubject();
subjectThreadState = createThreadState(subject);
subjectThreadState.bind();
}
protected Subject getSubject() {
return SecurityUtils.getSubject();
}
protected static ThreadState createThreadState(Subject subject) {
return new SubjectThreadState(subject);
}
/**
* Clears Shiro's thread state, ensuring the thread remains clean for future test execution.
*/
protected static void clearSubject() {
doClearSubject();
}
private static void doClearSubject() {
if (subjectThreadState != null) {
subjectThreadState.clear();
subjectThreadState = null;
}
}
protected static void setSecurityManager(SecurityManager securityManager) {
SecurityUtils.setSecurityManager(securityManager);
}
protected static SecurityManager getSecurityManager() {
return SecurityUtils.getSecurityManager();
}
@AfterClass
public static void tearDownShiro() {
doClearSubject();
try {
SecurityManager securityManager = getSecurityManager();
LifecycleUtils.destroy(securityManager);
} catch (UnavailableSecurityManagerException e) {
//we don't care about this when cleaning up the test environment
//(for example, maybe the subclass is a unit test and it didn't
// need a SecurityManager instance because it was using only
// mock Subject instances)
}
setSecurityManager(null);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/test/JobServiceIT.java | src/test/java/org/ohdsi/webapi/test/JobServiceIT.java | package org.ohdsi.webapi.test;
import static org.junit.Assert.assertEquals;
import com.github.springtestdbunit.annotation.DatabaseOperation;
import com.github.springtestdbunit.annotation.DatabaseSetup;
import com.github.springtestdbunit.annotation.DatabaseTearDown;
import java.util.HashMap;
import java.util.Map;
import org.junit.Assert;
import org.junit.Ignore;
import org.junit.Test;
import org.ohdsi.webapi.exampleapplication.ExampleApplicationWithJobService;
import org.ohdsi.webapi.job.JobExecutionResource;
import org.ohdsi.webapi.job.JobInstanceResource;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.retry.RetryCallback;
import org.springframework.retry.RetryContext;
import org.springframework.retry.policy.TimeoutRetryPolicy;
import org.springframework.retry.support.RetryTemplate;
@DatabaseTearDown(value = "/database/empty.xml", type = DatabaseOperation.DELETE_ALL)
public class JobServiceIT extends WebApiIT {
@Value("${exampleservice.endpoint}")
private String endpointExample;
@Value("${jobservice.endpoint.job}")
private String endpointJob;
@Value("${jobservice.endpoint.jobexecution}")
private String endpointJobExecution;
@Value("${jobservice.endpoint.jobexecution.alt}")
private String endpointJobExecutionAlternative;
/* The test is ignored, because it is failing with current xstream version com.thoughtworks.xstream:xstream:1.4.19.
* see https://github.com/OHDSI/WebAPI/issues/2109 for details. */
@Test
@Ignore
public void createAndFindJob() {
//create/queue job
final ResponseEntity<JobExecutionResource> postEntity = getRestTemplate().postForEntity(this.endpointExample, null,
JobExecutionResource.class);
assertOk(postEntity);
final JobExecutionResource postExecution = postEntity.getBody();
assertJobExecution(postExecution);
//check on status of job
final Map<String, Object> params = new HashMap<String, Object>();
params.put("instanceId", postExecution.getJobInstanceResource().getInstanceId());
params.put("executionId", postExecution.getExecutionId());
//retry until asynchronous job is complete
final RetryTemplate template = new RetryTemplate();
final TimeoutRetryPolicy policy = new TimeoutRetryPolicy();
policy.setTimeout(30000L);
template.setRetryPolicy(policy);
final ResponseEntity<JobExecutionResource> getEntityExecution = template
.execute((RetryCallback<ResponseEntity<JobExecutionResource>, IllegalStateException>) context -> {
// Do stuff that might fail, e.g. webservice operation
final ResponseEntity<JobExecutionResource> getEntityExecution1 = getRestTemplate().getForEntity(
JobServiceIT.this.endpointJobExecution, JobExecutionResource.class, params);
final JobExecutionResource getExecution = getEntityExecution1.getBody();
assertJobExecution(getExecution);
if (!"COMPLETED".equals(getExecution.getStatus())) {
JobServiceIT.this.log.debug("Incomplete job, trying again...");
throw new IllegalStateException("Incomplete job");
}
return getEntityExecution1;
});
//end retry
final JobExecutionResource getExecution = getEntityExecution.getBody();
assertJobExecution(getExecution);
final ResponseEntity<JobInstanceResource> getEntityInstance = getRestTemplate().getForEntity(this.endpointJob,
JobInstanceResource.class, params);
assertOk(getEntityInstance);
assertJobInstance(getEntityInstance.getBody());
assertEquals(postExecution.getExecutionId(), getExecution.getExecutionId());
//Check alternate endpoint
final ResponseEntity<JobExecutionResource> getEntityExecutionAlt = getRestTemplate().getForEntity(
this.endpointJobExecutionAlternative, JobExecutionResource.class, params);
final JobExecutionResource getExecutionAlt = getEntityExecutionAlt.getBody();
assertJobExecution(getExecution);
assertEquals(postExecution.getExecutionId(), getExecutionAlt.getExecutionId());
}
private void assertJobInstance(final JobInstanceResource instance) {
Assert.assertNotNull(instance.getInstanceId());
assertEquals(ExampleApplicationWithJobService.EXAMPLE_JOB_NAME, instance.getName());
}
private void assertOk(final ResponseEntity<?> entity) {
assertEquals(entity.getStatusCode(), HttpStatus.OK);
}
private void assertJobExecution(final JobExecutionResource execution) {
Assert.assertNotNull(execution);
Assert.assertNotNull(execution.getExecutionId());
Assert.assertNotNull(execution.getJobInstanceResource().getInstanceId());
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/test/CDMResultsServiceIT.java | src/test/java/org/ohdsi/webapi/test/CDMResultsServiceIT.java | package org.ohdsi.webapi.test;
import com.odysseusinc.arachne.commons.types.DBMSType;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.circe.helper.ResourceHelper;
import org.ohdsi.sql.SqlRender;
import org.ohdsi.sql.SqlTranslate;
import org.ohdsi.webapi.achilles.service.AchillesCacheService;
import org.ohdsi.webapi.cdmresults.service.CDMCacheService;
import org.ohdsi.webapi.source.SourceRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.ResponseEntity;
public class CDMResultsServiceIT extends WebApiIT {
private static final String CDM_RESULTS_FILE_PATH = "/database/cdm_results.sql";
@Value("${cdmResultsService.endpoint.conceptRecordCount}")
private String conceptRecordCountEndpoint;
@Value("${cdmResultsService.endpoint.clearCache}")
private String clearCacheEndpoint;
@Autowired
private SourceRepository sourceRepository;
@Autowired
private AchillesCacheService achillesService;
@Autowired
private CDMCacheService cdmCacheService;
@Before
public void init() throws Exception {
truncateTable(String.format("%s.%s", "public", "source"));
resetSequence(String.format("%s.%s", "public", "source_sequence"));
sourceRepository.saveAndFlush(getCdmSource());
prepareCdmSchema();
prepareResultSchema();
addCDMResults();
}
private void addCDMResults() {
String resultSql = SqlRender.renderSql(ResourceHelper.GetResourceAsString(
CDM_RESULTS_FILE_PATH),
new String[] { "results_schema" }, new String[] { RESULT_SCHEMA_NAME });
String sql = SqlTranslate.translateSql(resultSql, DBMSType.POSTGRESQL.getOhdsiDB());
jdbcTemplate.execute(sql);
}
@Test
public void requestConceptRecordCounts_firstTime_returnsResults() {
// Arrange
List<Integer> conceptIds = Arrays.asList(1);
Map<String, String> queryParameters = new HashMap<String, String>();
queryParameters.put("sourceName", SOURCE_KEY);
List<LinkedHashMap<String, List<Integer>>> list = new ArrayList<>();
@SuppressWarnings("unchecked")
Class<List<LinkedHashMap<String, List<Integer>>>> returnClass = (Class<List<LinkedHashMap<String, List<Integer>>>>)list.getClass();
// Act
final ResponseEntity<List<LinkedHashMap<String, List<Integer>>>> entity = getRestTemplate().postForEntity(this.conceptRecordCountEndpoint, conceptIds,
returnClass, queryParameters );
// Assert
assertOK(entity);
List<LinkedHashMap<String, List<Integer>>> results = entity.getBody();
assertEquals(1, results.size());
LinkedHashMap<String, List<Integer>> resultHashMap = results.get(0);
assertEquals(1, resultHashMap.size());
assertTrue(resultHashMap.containsKey("1"));
List<Integer> counts = resultHashMap.get("1");
assertEquals(100, counts.get(0).intValue());
assertEquals(101, counts.get(1).intValue());
assertEquals(102, counts.get(2).intValue());
assertEquals(103, counts.get(3).intValue());
}
@Test
public void achillesService_clearCache_nothingInCache_doesNothing() {
// Arrange
// Act
achillesService.clearCache();
// Assert
String sql = "SELECT COUNT(*) FROM achilles_cache";
Integer count = jdbcTemplate.queryForObject(sql, Integer.class);
assertEquals(0, count.intValue());
}
@Test
public void achillesService_clearCache_somethingInCache_clearsAllRowsForSource() {
// Arrange
String insertSqlRow1 = "INSERT INTO achilles_cache (id, source_id, cache_name, cache) VALUES (1, 1, 'cache1', 'cache1')";
jdbcTemplate.execute(insertSqlRow1);
String insertSqlRow2 = "INSERT INTO achilles_cache (id, source_id, cache_name, cache) VALUES (2, 1, 'cache2', 'cache2')";
jdbcTemplate.execute(insertSqlRow2);
// Act
achillesService.clearCache();
// Assert
String sql = "SELECT COUNT(*) FROM achilles_cache";
Integer count = jdbcTemplate.queryForObject(sql, Integer.class);
assertEquals(0, count.intValue());
}
@Test
public void cdmCacheService_clearCache_nothingInCache_doesNothing() {
// Arrange
// Act
cdmCacheService.clearCache();
// Assert
String sql = "SELECT COUNT(*) FROM cdm_cache";
Integer count = jdbcTemplate.queryForObject(sql, Integer.class);
assertEquals(0, count.intValue());
}
@Test
public void cdmCacheService_clearCache_somethingInCache_clearsAllRowsForSource() {
// Arrange
String insertSqlRow1 = "INSERT INTO cdm_cache (id, concept_id, source_id, record_count, descendant_record_count, person_count, descendant_person_count) VALUES (1, 1, 1, 100, 101, 102, 103)";
jdbcTemplate.execute(insertSqlRow1);
String insertSqlRow2 = "INSERT INTO cdm_cache (id, concept_id, source_id, record_count, descendant_record_count, person_count, descendant_person_count) VALUES (2, 2, 1, 200, 201, 202, 203)";
jdbcTemplate.execute(insertSqlRow2);
// Act
cdmCacheService.clearCache();
// Assert
String sql = "SELECT COUNT(*) FROM cdm_cache";
Integer count = jdbcTemplate.queryForObject(sql, Integer.class);
assertEquals(0, count.intValue());
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/test/VocabularyServiceIT.java | src/test/java/org/ohdsi/webapi/test/VocabularyServiceIT.java | package org.ohdsi.webapi.test;
import com.odysseusinc.arachne.commons.types.DBMSType;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.circe.helper.ResourceHelper;
import org.ohdsi.sql.SqlRender;
import org.ohdsi.sql.SqlTranslate;
import org.ohdsi.webapi.source.SourceRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.ResponseEntity;
public class VocabularyServiceIT extends WebApiIT {
private static final String CONCEPT_FILE_PATH = "/database/concept.sql";
@Value("${vocabularyservice.endpoint.vocabularies}")
private String endpointVocabularies;
@Value("${vocabularyservice.endpoint.concept}")
private String endpointConcept;
@Value("${vocabularyservice.endpoint.domains}")
private String endpointDomains;
@Autowired
private SourceRepository sourceRepository;
@Before
public void init() throws Exception {
truncateTable(String.format("%s.%s", "public", "source"));
resetSequence(String.format("%s.%s", "public", "source_sequence"));
sourceRepository.saveAndFlush(getCdmSource());
prepareCdmSchema();
prepareResultSchema();
addConcept();
}
private void addConcept() {
String resultSql = SqlRender.renderSql(ResourceHelper.GetResourceAsString(CONCEPT_FILE_PATH),
new String[]{"cdm_database_schema"}, new String[]{CDM_SCHEMA_NAME});
String sql = SqlTranslate.translateSql(resultSql, DBMSType.POSTGRESQL.getOhdsiDB());
jdbcTemplate.execute(sql);
}
@Test
public void canGetConcept() {
//Action
final ResponseEntity<String> entity = getRestTemplate().getForEntity(this.endpointConcept, String.class);
//Assertion
assertOK(entity);
}
@Test
public void canGetVocabularies() {
//Action
final ResponseEntity<String> entity = getRestTemplate().getForEntity(this.endpointVocabularies, String.class);
//Assertion
assertOK(entity);
}
@Test
public void canGetDomains() {
//Action
final ResponseEntity<String> entity = getRestTemplate().getForEntity(this.endpointDomains, String.class);
//Assertion
assertOK(entity);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/test/ITStarter.java | src/test/java/org/ohdsi/webapi/test/ITStarter.java | package org.ohdsi.webapi.test;
import io.zonky.test.db.postgres.embedded.EmbeddedPostgres;
import org.apache.shiro.subject.SimplePrincipalCollection;
import org.apache.shiro.subject.Subject;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.mockito.Mockito;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.test.context.TestPropertySource;
import javax.sql.DataSource;
import java.io.IOException;
import java.sql.SQLException;
@RunWith(Suite.class)
@Suite.SuiteClasses({
SecurityIT.class,
JobServiceIT.class,
CohortAnalysisServiceIT.class,
VocabularyServiceIT.class,
CDMResultsServiceIT.class
})
@TestPropertySource(locations = "/application-test.properties")
public class ITStarter extends AbstractShiro {
private static EmbeddedPostgres pg;
private static final Logger log = LoggerFactory.getLogger(ITStarter.class);
@BeforeClass
public static void before() throws IOException {
if (pg == null) {
pg = EmbeddedPostgres.start();
try {
System.setProperty("datasource.url", pg.getPostgresDatabase().getConnection().getMetaData().getURL());
} catch (SQLException e) {
throw new RuntimeException(e);
}
System.setProperty("flyway.datasource.url", System.getProperty("datasource.url"));
System.setProperty("security.db.datasource.url", System.getProperty("datasource.url"));
System.setProperty("security.db.datasource.username", "postgres");
System.setProperty("security.db.datasource.password", "postgres");
System.setProperty("security.db.datasource.schema", "public");
//set up shiro
Subject subjectUnderTest = Mockito.mock(Subject.class);
SimplePrincipalCollection principalCollection = Mockito.mock(SimplePrincipalCollection.class);
Mockito.when(subjectUnderTest.isAuthenticated()).thenReturn(true);
Mockito.when(subjectUnderTest.getPrincipals()).thenReturn(principalCollection);
Mockito.when(principalCollection.getPrimaryPrincipal()).thenReturn("admin@odysseusinc.com");
//bind the subject to the current thread
setSubject(subjectUnderTest);
}
}
public static DataSource getDataSource() {
return pg.getPostgresDatabase();
}
@AfterClass
public static void tearDownSubject() {
String callerClassName = Thread.currentThread().getStackTrace()[2].getClassName();
String currentClassName = Thread.currentThread().getStackTrace()[1].getClassName();
if (pg != null && currentClassName.equalsIgnoreCase(callerClassName)) {
try {
//unbind the subject from the current thread
clearSubject();
pg.close();
} catch (Exception ex) {
log.warn("Error while stopping the embedded PostgreSQL instance", ex);
}
}
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/test/CohortAnalysisServiceIT.java | src/test/java/org/ohdsi/webapi/test/CohortAnalysisServiceIT.java | /*
* The contents of this file are subject to the Regenstrief Public License
* Version 1.0 (the "License"); you may not use this file except in compliance with the License.
* Please contact Regenstrief Institute if you would like to obtain a copy of the license.
* <p>
* Software distributed under the License is distributed on an "AS IS"
* basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
* License for the specific language governing rights and limitations
* under the License.
* <p>
* Copyright (C) Regenstrief Institute. All Rights Reserved.
*/
package org.ohdsi.webapi.test;
import com.github.springtestdbunit.annotation.DatabaseOperation;
import com.github.springtestdbunit.annotation.DatabaseSetup;
import com.github.springtestdbunit.annotation.DatabaseTearDown;
import java.util.Collections;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.cohortanalysis.CohortAnalysisTask;
import org.ohdsi.webapi.job.JobExecutionResource;
import org.ohdsi.webapi.source.SourceRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.ResponseEntity;
@DatabaseSetup("/database/cohort.xml")
@DatabaseTearDown(value = "/database/empty.xml", type = DatabaseOperation.DELETE_ALL)
public class CohortAnalysisServiceIT extends WebApiIT {
@Value("${cohortanalysis.endpoint}")
private String endpointCohortAnalysis;
@Autowired
private SourceRepository sourceRepository;
@Before
public void init() throws Exception {
truncateTable(String.format("%s.%s", "public", "source"));
resetSequence(String.format("%s.%s", "public", "source_sequence"));
sourceRepository.saveAndFlush(getCdmSource());
prepareCdmSchema();
prepareResultSchema();
}
@Test
public void canCreateAnalysis() {
//Arrange
CohortAnalysisTask task = new CohortAnalysisTask();
task.setAnalysisIds(Collections.singletonList("0"));
task.setCohortDefinitionIds(Collections.singletonList("1"));
task.setSourceKey(SOURCE_KEY);
//Action
final ResponseEntity<JobExecutionResource> entity = getRestTemplate().postForEntity(this.endpointCohortAnalysis,
task, JobExecutionResource.class);
//Assert
assertOK(entity);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/test/feasibility/StudyInfoTest.java | src/test/java/org/ohdsi/webapi/test/feasibility/StudyInfoTest.java | /*
* Copyright 2015 Observational Health Data Sciences and Informatics [OHDSI.org].
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ohdsi.webapi.test.feasibility;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import org.junit.Ignore;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.feasibility.FeasibilityStudy;
import org.ohdsi.webapi.feasibility.FeasibilityStudyRepository;
import org.ohdsi.webapi.feasibility.StudyGenerationInfo;
import org.ohdsi.webapi.GenerationStatus;
import org.ohdsi.webapi.source.Source;
import org.ohdsi.webapi.source.SourceRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.test.annotation.Rollback;
import org.springframework.transaction.annotation.Transactional;
/**
*
* @author Chris Knoll <cknoll@ohdsi.org>
*/
@SpringBootTest
@Rollback
public class StudyInfoTest extends AbstractDatabaseTest {
@Autowired
private FeasibilityStudyRepository studyRepository;
@Autowired
private SourceRepository sourceRepository;
@PersistenceContext
protected EntityManager entityManager;
@Ignore
@Test
@Transactional(transactionManager="transactionManager")
public void testStudyCRUD() {
Source source = new Source();
source.setSourceId(1);
FeasibilityStudy newStudy = new FeasibilityStudy();
newStudy.setName("Test Info Study");
newStudy = this.studyRepository.save(newStudy);
StudyGenerationInfo info = new StudyGenerationInfo(newStudy, source); // for testing, assume a sourceId of 1 exists.
info.setStatus(GenerationStatus.PENDING);
newStudy.getStudyGenerationInfoList().add(info);
this.studyRepository.save(newStudy);
newStudy.getStudyGenerationInfoList().clear();
this.studyRepository.save(newStudy);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/test/feasibility/FeasibilityTests.java | src/test/java/org/ohdsi/webapi/test/feasibility/FeasibilityTests.java | /*
* Copyright 2015 Observational Health Data Sciences and Informatics [OHDSI.org].
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ohdsi.webapi.test.feasibility;
import java.util.ArrayList;
import java.util.List;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.WebApi;
import org.ohdsi.webapi.feasibility.InclusionRule;
import org.ohdsi.webapi.feasibility.FeasibilityStudy;
import org.ohdsi.webapi.feasibility.FeasibilityStudyRepository;
import org.ohdsi.webapi.cohortdefinition.CohortDefinition;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionDetails;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.test.annotation.Rollback;
import org.springframework.transaction.annotation.Transactional;
/**
*
* @author Chris Knoll <cknoll@ohdsi.org>
*/
@SpringBootTest(classes = WebApi.class)
@Rollback
public class FeasibilityTests extends AbstractDatabaseTest {
@Autowired
private CohortDefinitionRepository cohortDefinitionRepository;
@Autowired
private FeasibilityStudyRepository studyRepository;
@PersistenceContext
protected EntityManager entityManager;
public int doCreate()
{
// create a new study, using CohortDefinition:1 as the index rule, and associate 3 inclusion rules.
FeasibilityStudy newStudy = new FeasibilityStudy();
CohortDefinition def = new CohortDefinition();
CohortDefinitionDetails defDetails = new CohortDefinitionDetails();
def.setName("Index Rule for Test Study");
this.cohortDefinitionRepository.save(def);
// assign details
defDetails.setCohortDefinition(def);
def.setDetails(defDetails);
defDetails.setExpression("{\"DefinitionExpression\": \"{ some epression }\"}");
this.cohortDefinitionRepository.save(def);
newStudy.setName("Test Study")
.setIndexRule(def);
ArrayList<InclusionRule> inclusionRules = new ArrayList<>();
inclusionRules.add(new InclusionRule()
.setName("Inclusion Rule 1")
.setDescription("Description for Inclusion Rule 1")
.setExpression("{\"CriteriaExpression\": \"{Rule 1}\"}"));
inclusionRules.add(new InclusionRule()
.setName("Inclusion Rule 2")
.setDescription("Description for Inclusion Rule 2")
.setExpression("{\"CriteriaExpression\": \"{Rule 2}\"}"));
inclusionRules.add(new InclusionRule()
.setName("Inclusion Rule 3")
.setDescription("Description for Inclusion Rule 3")
.setExpression("{\"CriteriaExpression\": \"{Rule 3}\"}"));
newStudy.setInclusionRules(inclusionRules);
studyRepository.save(newStudy);
return newStudy.getId();
}
public void doUpdate(int id)
{
FeasibilityStudy updatedStudy = studyRepository.findOneWithDetail(id);
CohortDefinition updatedDef = updatedStudy.getIndexRule();
updatedDef.setName("Updated By StudyTest");
// try removing the first inclusion rule
List<InclusionRule> updatedRules = updatedStudy.getInclusionRules();
updatedRules.add(new InclusionRule()
.setName("Inclusion Rule 4")
.setDescription("Description for Inclusion Rule 4")
.setExpression("{\"CriteriaExpression\": \"{Rule 4}\"}"));
updatedStudy.setInclusionRules(updatedRules);
this.studyRepository.save(updatedStudy);
}
@Test
@Transactional(transactionManager="transactionManager")
public void testStudyCRUD() {
int newStudyId = doCreate();
doUpdate(newStudyId);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/executionengine/service/ScriptExecutionServiceImplTest.java | src/test/java/org/ohdsi/webapi/executionengine/service/ScriptExecutionServiceImplTest.java | package org.ohdsi.webapi.executionengine.service;
import static org.mockito.Matchers.*;
import static org.mockito.Mockito.doNothing;
import static org.mockito.Mockito.doReturn;
import static org.mockito.Mockito.spy;
import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import net.lingala.zip4j.ZipFile;
import net.lingala.zip4j.model.FileHeader;
import org.apache.commons.compress.utils.IOUtils;
import org.hamcrest.MatcherAssert;
import org.hamcrest.Matchers;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.Spy;
import org.mockito.runners.MockitoJUnitRunner;
import org.ohdsi.webapi.executionengine.entity.AnalysisResultFile;
import org.ohdsi.webapi.executionengine.entity.ExecutionEngineAnalysisStatus;
import org.ohdsi.webapi.executionengine.entity.ExecutionEngineGenerationEntity;
import org.ohdsi.webapi.executionengine.repository.ExecutionEngineGenerationRepository;
import org.ohdsi.webapi.shiro.management.datasource.SourceAccessor;
@RunWith(MockitoJUnitRunner.class)
public class ScriptExecutionServiceImplTest {
public static final long EXECUTION_ID = 1L;
@Mock
private ExecutionEngineGenerationRepository executionEngineGenerationRepository;
@Mock
private SourceAccessor sourceAccessor;
@InjectMocks
@Spy
private ScriptExecutionServiceImpl scriptExecutionService;
@Spy
private ExecutionEngineAnalysisStatus executionEngineAnalysisStatus = new ExecutionEngineAnalysisStatus();
@Spy
private ExecutionEngineGenerationEntity executionEngineGenerationEntity = new DummyExecutionEngineGenerationEntity();
@Before
public void setUp() throws Exception {
doReturn(executionEngineAnalysisStatus)
.when(executionEngineGenerationEntity)
.getAnalysisExecution();
doReturn(Optional.of(executionEngineGenerationEntity))
.when(executionEngineGenerationRepository)
.findById(eq(EXECUTION_ID));
doNothing()
.when(sourceAccessor)
.checkAccess(any());
}
@Test
public void getExecutionResultWithMultivalueZip() throws Exception {
executionEngineAnalysisStatus.setResultFiles(Arrays.asList(
createAnalysisResultFile("/analysisresult/stdout.txt"),
createAnalysisResultFile("/analysisresult/file1.txt"),
createAnalysisResultFile("/analysisresult/multivalue/analysis_result.zip"),
createAnalysisResultFile("/analysisresult/multivalue/analysis_result.z01"),
createAnalysisResultFile("/analysisresult/multivalue/analysis_result.z02"),
createAnalysisResultFile("/analysisresult/multivalue/analysis_result.z03"),
createAnalysisResultFile("/analysisresult/multivalue/analysis_result.z04")
));
File executionResult = scriptExecutionService.getExecutionResult(EXECUTION_ID);
ZipFile zipFile = new ZipFile(executionResult);
List<String> fileNamesInZip = ((List<FileHeader>) zipFile.getFileHeaders()).stream().map(FileHeader::getFileName).collect(Collectors.toList());
MatcherAssert.assertThat(fileNamesInZip, Matchers.containsInAnyOrder(
"stdout.txt", "file1.txt",
"analysis/CohortCharacterization.zip", "analysis/runAnalysis.R", "analysis/.Rhistory"));
}
@Test
public void getExecutionResultWithoutMultivolumeZip() throws Exception {
executionEngineAnalysisStatus.setResultFiles(Arrays.asList(
createAnalysisResultFile("/analysisresult/stdout.txt"),
createAnalysisResultFile("/analysisresult/file1.txt"),
createAnalysisResultFile("/analysisresult/analysis_result.zip")
));
File executionResult = scriptExecutionService.getExecutionResult(EXECUTION_ID);
ZipFile zipFile = new ZipFile(executionResult);
List<String> fileNamesInZip = ((List<FileHeader>) zipFile.getFileHeaders()).stream().map(FileHeader::getFileName).collect(Collectors.toList());
MatcherAssert.assertThat(fileNamesInZip, Matchers.containsInAnyOrder(
"stdout.txt", "file1.txt",
"analysis/", //for some reason getFileHeaders returns directories for a normal zip, and dont for multivalue zip
"analysis/CohortCharacterization.zip", "analysis/runAnalysis.R", "analysis/.Rhistory"));
}
@Test
public void getExecutionResultWithoutZip() throws Exception {
executionEngineAnalysisStatus.setResultFiles(Arrays.asList(
createAnalysisResultFile("/analysisresult/stdout.txt"),
createAnalysisResultFile("/analysisresult/file1.txt"),
createAnalysisResultFile("/analysisresult/file2.txt")
));
File executionResult = scriptExecutionService.getExecutionResult(EXECUTION_ID);
ZipFile zipFile = new ZipFile(executionResult);
List<String> fileNamesInZip = ((List<FileHeader>) zipFile.getFileHeaders()).stream().map(FileHeader::getFileName).collect(Collectors.toList());
MatcherAssert.assertThat(fileNamesInZip, Matchers.containsInAnyOrder("stdout.txt", "file1.txt", "file2.txt"));
}
private AnalysisResultFile createAnalysisResultFile(String fileName) throws IOException {
AnalysisResultFile analysisResultFile = spy(new AnalysisResultFile());
analysisResultFile.setFileName(new File(fileName).getName());
analysisResultFile.setMediaType("Application");
doReturn(IOUtils.toByteArray(this.getClass().getResourceAsStream(fileName)))
.when(analysisResultFile)
.getContents();
return analysisResultFile;
}
public static class DummyExecutionEngineGenerationEntity extends ExecutionEngineGenerationEntity {
}
} | java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/executionengine/service/AnalysisZipRepackServiceTest.java | src/test/java/org/ohdsi/webapi/executionengine/service/AnalysisZipRepackServiceTest.java | package org.ohdsi.webapi.executionengine.service;
import static org.hamcrest.CoreMatchers.is;
import static org.junit.Assert.assertThat;
import java.io.IOException;
import java.io.InputStream;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.compress.utils.IOUtils;
import org.hamcrest.Matchers;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.executionengine.entity.AnalysisResultFileContent;
import org.ohdsi.webapi.executionengine.entity.ExecutionEngineAnalysisStatus;
public class AnalysisZipRepackServiceTest {
private AnalysisZipRepackService analysisZipRepackService = new AnalysisZipRepackService();
private AnalysisResultFileContentSensitiveInfoServiceImpl sensitiveInfoService = new AnalysisResultFileContentSensitiveInfoServiceImpl();
private ExecutionEngineAnalysisStatus execution;
private List<AnalysisResultFileContent> resultFileContents;
@Before
public void setUp() throws Exception {
execution = new ExecutionEngineAnalysisStatus();
sensitiveInfoService = new AnalysisResultFileContentSensitiveInfoServiceImpl();
sensitiveInfoService.init();
resultFileContents = Arrays.asList(
new AnalysisResultFileContent(execution, "analysis_result.zip", "application", getTestArchive("/analysisresult/analysis_result.zip")),
new AnalysisResultFileContent(execution, "stdout.txt", "text/plain", getTestArchive("/analysisresult/stdout.txt"))
);
}
@Test
public void processArchivesIsBigEnoughToSplitIntoMultiplyVolumes() {
List<AnalysisResultFileContent> analysisRepackResult = analysisZipRepackService.process(this.resultFileContents, 1);
List<String> fileNamesAfterRepack = analysisRepackResult.stream().map(f -> f.getAnalysisResultFile().getFileName()).collect(Collectors.toList());
assertThat(
fileNamesAfterRepack,
Matchers.containsInAnyOrder("analysis_result.zip", "analysis_result.z01", "analysis_result.z02", "analysis_result.z03", "analysis_result.z04", "stdout.txt")
);
}
@Test
public void processArchivesIsNotBigEnoughToSplitIntoMultiplyVolumes() {
List<AnalysisResultFileContent> analysisRepackResult = analysisZipRepackService.process(this.resultFileContents, 5);
List<String> fileNamesAfterRepack = analysisRepackResult.stream().map(f -> f.getAnalysisResultFile().getFileName()).collect(Collectors.toList());
assertThat(
fileNamesAfterRepack,
Matchers.containsInAnyOrder("analysis_result.zip", "stdout.txt")
);
}
@Test
public void processThereIsNotArchiveToSplit() throws IOException {
resultFileContents = Arrays.asList(
new AnalysisResultFileContent(execution, "stdout.txt", "text/plain", getTestArchive("/analysisresult/stdout.txt")),
new AnalysisResultFileContent(execution, "file1.txt", "text/plain", getTestArchive("/analysisresult/stdout.txt")),
new AnalysisResultFileContent(execution, "file2.txt", "text/plain", getTestArchive("/analysisresult/stdout.txt"))
);
List<AnalysisResultFileContent> analysisRepackResult = analysisZipRepackService.process(this.resultFileContents, 5);
List<String> fileNamesAfterRepack = analysisRepackResult.stream().map(f -> f.getAnalysisResultFile().getFileName()).collect(Collectors.toList());
assertThat(
fileNamesAfterRepack,
Matchers.containsInAnyOrder("file1.txt", "file2.txt", "stdout.txt")
);
}
private byte[] getTestArchive(String file) throws IOException {
InputStream resourceAsStream = this.getClass().getResourceAsStream(file);
return IOUtils.toByteArray(resourceAsStream);
}
} | java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/check/checker/EstimationCheckerTest.java | src/test/java/org/ohdsi/webapi/check/checker/EstimationCheckerTest.java | package org.ohdsi.webapi.check.checker;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.check.CheckResult;
import org.ohdsi.webapi.check.Checker;
import org.ohdsi.webapi.check.checker.characterization.CharacterizationChecker;
import org.ohdsi.webapi.check.checker.estimation.EstimationChecker;
import org.ohdsi.webapi.check.warning.Warning;
import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
import org.ohdsi.webapi.estimation.dto.EstimationDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.Optional;
import static org.junit.Assert.*;
public class EstimationCheckerTest extends BaseCheckerTest {
private static final String JSON_VALID = "/check/checker/estimation-valid.json";
private static final String JSON_NO_ANALYSIS_SETTINGS = "/check/checker/estimation-no-analysis-settings.json";
private static final String JSON_POSITIVE_CONTROL_INVALID_VALUES = "/check/checker/estimation-positive-control-invalid-values.json";
@Autowired
private EstimationChecker checker;
@Test
public void checkValid() throws IOException {
String json = getJsonFromFile(JSON_VALID);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
Assert.assertEquals(0, result.getWarnings().size());
}
@Test
public void checkNoSpecification() throws IOException {
String json = getJsonFromFile(JSON_VALID);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification - null or empty");
}
@Test
public void checkNoAnalysisSettings() throws IOException {
String json = getJsonFromFile(JSON_NO_ANALYSIS_SETTINGS);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification - null or empty");
}
@Test
public void checkPositiveControlInvalidWindowStart() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: positive control synthesis :: time-at-risk window start - must be greater or equal to 0");
}
@Test
public void checkPositiveControlInvalidWindowEnd() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: positive control synthesis :: time-at-risk window end - must be greater or equal to 0");
}
@Test
public void checkPositiveControlInvalidWashout() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: positive control synthesis :: minimum required continuous observation time - must be greater or equal to 0");
}
@Test
public void checkPositiveControlInvalidMaxSubjects() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: positive control synthesis :: maximum number of people used to fit an outcome model - must be greater or equal to 0");
}
@Test
public void checkPositiveControlInvalidRatioBetweenTargetAndInjected() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: positive control synthesis :: allowed ratio between target and injected signal size - must be greater or equal to 0");
}
@Test
public void checkPositiveControlInvaliOutcomeIdOffset() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: positive control synthesis :: first new outcome ID that is to be created - must be greater or equal to 0");
}
@Test
public void checkPositiveControlInvalidMinOutcomeCountForModel() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: positive control synthesis :: minimum number of outcome events required to build a model - must be greater or equal to 0");
}
@Test
public void checkPositiveControlInvalidMinOutcomeCountForInjection() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: positive control synthesis :: minimum number of outcome events required to inject a signal - must be greater or equal to 0");
}
@Test
public void checkNegativeControlInvalidOccurrenceType() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: negative control outcome :: type of occurrence of the event when selecting from the domain - null or empty");
}
@Test
public void checkNegativeControlInvalidDetectOnDescendants() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: negative control outcome :: using of descendant concepts for the negative control outcome - null or empty");
}
@Test
public void checkNegativeControlInvalidDomains() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: negative control outcome :: domains to detect negative control outcomes - null or empty");
}
@Test
public void checkInvalidNegativeControl() throws IOException {
String json = getJsonFromFile(JSON_POSITIVE_CONTROL_INVALID_VALUES);
EstimationDTO dto = Utils.deserialize(json, EstimationDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: negative control - invalid");
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/check/checker/CharacterizationCheckerTest.java | src/test/java/org/ohdsi/webapi/check/checker/CharacterizationCheckerTest.java | package org.ohdsi.webapi.check.checker;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.check.CheckResult;
import org.ohdsi.webapi.check.Checker;
import org.ohdsi.webapi.check.checker.characterization.CharacterizationChecker;
import org.ohdsi.webapi.check.checker.tag.helper.TagHelper;
import org.ohdsi.webapi.check.warning.Warning;
import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
import org.ohdsi.webapi.service.dto.IRAnalysisDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.Optional;
public class CharacterizationCheckerTest extends BaseCheckerTest {
private static final String JSON_VALID = "/check/checker/characterization-valid.json";
private static final String JSON_NO_COHORTS = "/check/checker/characterization-no-cohorts.json";
private static final String JSON_NO_FEATURE_ANALYSES = "/check/checker/characterization-no-fa.json";
@Autowired
private CharacterizationChecker checker;
@Test
public void checkValid() throws IOException {
String json = getJsonFromFile(JSON_VALID);
CohortCharacterizationDTO dto = Utils.deserialize(json, CohortCharacterizationDTO.class);
Checker<CohortCharacterizationDTO> checker = this.checker;
CheckResult result = new CheckResult(checker.check(dto));
Assert.assertEquals(0, result.getWarnings().size());
}
@Test
public void checkNoCohorts() throws IOException {
String json = getJsonFromFile(JSON_NO_COHORTS);
CohortCharacterizationDTO dto = Utils.deserialize(json, CohortCharacterizationDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "cohorts - null or empty");
}
@Test
public void checkNoFeatureAnalyses() throws IOException {
String json = getJsonFromFile(JSON_NO_FEATURE_ANALYSES);
CohortCharacterizationDTO dto = Utils.deserialize(json, CohortCharacterizationDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "feature analyses - null or empty");
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/check/checker/IRCheckerTest.java | src/test/java/org/ohdsi/webapi/check/checker/IRCheckerTest.java | package org.ohdsi.webapi.check.checker;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.check.CheckResult;
import org.ohdsi.webapi.check.Checker;
import org.ohdsi.webapi.check.checker.ir.IRChecker;
import org.ohdsi.webapi.check.checker.tag.helper.TagHelper;
import org.ohdsi.webapi.check.warning.Warning;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisDTO;
import org.ohdsi.webapi.service.dto.IRAnalysisDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.Optional;
public class IRCheckerTest extends BaseCheckerTest {
private static final String JSON_VALID = "/check/checker/ir-valid.json";
private static final String JSON_NO_EXPRESSION = "/check/checker/ir-no-expression.json";
private static final String JSON_NO_COHORTS = "/check/checker/ir-no-cohorts.json";
@Autowired
private IRChecker checker;
@Test
public void checkValid() throws IOException {
String json = getJsonFromFile(JSON_VALID);
IRAnalysisDTO dto = Utils.deserialize(json, IRAnalysisDTO.class);
Checker<IRAnalysisDTO> checker = this.checker;
CheckResult result = new CheckResult(checker.check(dto));
Assert.assertEquals(0, result.getWarnings().size());
}
@Test
public void checkEmptyExpression() throws IOException {
String json = getJsonFromFile(JSON_NO_EXPRESSION);
IRAnalysisDTO dto = Utils.deserialize(json, IRAnalysisDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "expression - null or empty");
}
@Test
public void checkNoOutcomeCohorts() throws IOException {
String json = getJsonFromFile(JSON_NO_COHORTS);
IRAnalysisDTO dto = Utils.deserialize(json, IRAnalysisDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "outcome cohorts - null or empty");
}
@Test
public void checkNoTargetCohorts() throws IOException {
String json = getJsonFromFile(JSON_NO_COHORTS);
IRAnalysisDTO dto = Utils.deserialize(json, IRAnalysisDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "target cohorts - null or empty");
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/check/checker/PredictionCheckerTest.java | src/test/java/org/ohdsi/webapi/check/checker/PredictionCheckerTest.java | package org.ohdsi.webapi.check.checker;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.check.CheckResult;
import org.ohdsi.webapi.check.Checker;
import org.ohdsi.webapi.check.checker.characterization.CharacterizationChecker;
import org.ohdsi.webapi.check.checker.pathway.PathwayChecker;
import org.ohdsi.webapi.check.checker.prediction.PredictionChecker;
import org.ohdsi.webapi.check.warning.Warning;
import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisDTO;
import org.ohdsi.webapi.prediction.dto.PredictionAnalysisDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.Optional;
import static org.junit.Assert.*;
public class PredictionCheckerTest extends BaseCheckerTest {
private static final String JSON_VALID = "/check/checker/prediction-valid.json";
private static final String JSON_INVALID_VALUES = "/check/checker/prediction-invalid-values.json";
private static final String JSON_NO_VALUES = "/check/checker/prediction-no-values.json";
@Autowired
private PredictionChecker checker;
@Test
public void checkValid() throws IOException {
String json = getJsonFromFile(JSON_VALID);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
Checker<PredictionAnalysisDTO> checker = this.checker;
CheckResult result = new CheckResult(checker.check(dto));
Assert.assertEquals(0, result.getWarnings().size());
}
@Test
public void checkNoSpecification() throws IOException {
String json = getJsonFromFile(JSON_VALID);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification - null or empty");
}
@Test
public void checkNoRunPplArgs() throws IOException {
String json = getJsonFromFile(JSON_NO_VALUES);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: settings - null or empty");
}
@Test
public void checkInvalidRunPplArgsTestFraction() throws IOException {
String json = getJsonFromFile(JSON_INVALID_VALUES);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: settings :: test fraction - must be between 0 and 100");
}
@Test
public void checkInvalidRunPplArgsMinFraction() throws IOException {
String json = getJsonFromFile(JSON_INVALID_VALUES);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: settings :: minimum covariate fraction - must be greater or equal to 0");
}
@Test
public void checkNoOutcomeCohorts() throws IOException {
String json = getJsonFromFile(JSON_NO_VALUES);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: outcome cohorts - null or empty");
}
@Test
public void checkNoTargetCohorts() throws IOException {
String json = getJsonFromFile(JSON_NO_VALUES);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: target cohorts - null or empty");
}
@Test
public void checkNoModelSettings() throws IOException {
String json = getJsonFromFile(JSON_NO_VALUES);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: model settings - null or empty");
}
@Test
public void checkInvalidModelSettings() throws IOException {
String json = getJsonFromFile(JSON_INVALID_VALUES);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: model settings - duplicate values");
}
@Test
public void checkNoCovariateSettings() throws IOException {
String json = getJsonFromFile(JSON_NO_VALUES);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: covariate settings - null or empty");
}
@Test
public void checkInvalidCovariateSettings() throws IOException {
String json = getJsonFromFile(JSON_INVALID_VALUES);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: covariate settings - duplicate values");
}
@Test
public void checkNoPopulationSettings() throws IOException {
String json = getJsonFromFile(JSON_NO_VALUES);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: population settings - null or empty");
}
@Test
public void checkInvalidPopulationSettings() throws IOException {
String json = getJsonFromFile(JSON_INVALID_VALUES);
PredictionAnalysisDTO dto = Utils.deserialize(json, PredictionAnalysisDTO.class);
dto.setSpecification(json);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "specification :: population settings - duplicate values");
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/check/checker/PathwayCheckerTest.java | src/test/java/org/ohdsi/webapi/check/checker/PathwayCheckerTest.java | package org.ohdsi.webapi.check.checker;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.check.CheckResult;
import org.ohdsi.webapi.check.Checker;
import org.ohdsi.webapi.check.checker.pathway.PathwayChecker;
import org.ohdsi.webapi.check.checker.tag.helper.TagHelper;
import org.ohdsi.webapi.check.warning.Warning;
import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.Optional;
public class PathwayCheckerTest extends BaseCheckerTest {
private static final String JSON_VALID = "/check/checker/pathway-valid.json";
private static final String JSON_INVALID = "/check/checker/pathway-invalid.json";
@Autowired
private PathwayChecker checker;
@Test
public void checkValid() throws IOException {
String json = getJsonFromFile(JSON_VALID);
PathwayAnalysisDTO dto = Utils.deserialize(json, PathwayAnalysisDTO.class);
Checker<PathwayAnalysisDTO> checker = this.checker;
CheckResult result = new CheckResult(checker.check(dto));
Assert.assertEquals(0, result.getWarnings().size());
}
@Test
public void checkNoTargetCohorts() throws IOException {
String json = getJsonFromFile(JSON_INVALID);
PathwayAnalysisDTO dto = Utils.deserialize(json, PathwayAnalysisDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "target cohorts - null or empty");
}
@Test
public void checkNoEventCohorts() throws IOException {
String json = getJsonFromFile(JSON_INVALID);
PathwayAnalysisDTO dto = Utils.deserialize(json, PathwayAnalysisDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "event cohorts - null or empty");
}
@Test
public void checkInvalidMaxPathLength() throws IOException {
String json = getJsonFromFile(JSON_INVALID);
PathwayAnalysisDTO dto = Utils.deserialize(json, PathwayAnalysisDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "maximum path length - must be between 1 and 10");
}
@Test
public void checkInvalidMinCellCount() throws IOException {
String json = getJsonFromFile(JSON_INVALID);
PathwayAnalysisDTO dto = Utils.deserialize(json, PathwayAnalysisDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "minimum cell count - must be greater or equal to 0");
}
@Test
public void checkInvalidCombinationWindow() throws IOException {
String json = getJsonFromFile(JSON_INVALID);
PathwayAnalysisDTO dto = Utils.deserialize(json, PathwayAnalysisDTO.class);
CheckResult result = new CheckResult(checker.check(dto));
checkWarning(result, "combination window - must be greater or equal to 0");
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/check/checker/BaseCheckerTest.java | src/test/java/org/ohdsi/webapi/check/checker/BaseCheckerTest.java | package org.ohdsi.webapi.check.checker;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.io.FileUtils;
import org.hamcrest.Matchers;
import org.junit.Assert;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.check.CheckResult;
import org.ohdsi.webapi.check.Checker;
import org.ohdsi.webapi.check.checker.characterization.CharacterizationChecker;
import org.ohdsi.webapi.check.warning.Warning;
import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.context.junit4.SpringRunner;
import org.springframework.util.ResourceUtils;
import java.io.File;
import java.io.IOException;
import java.nio.charset.Charset;
import java.util.Optional;
public abstract class BaseCheckerTest extends AbstractDatabaseTest {
protected String getJsonFromFile(String path) throws IOException {
File file = ResourceUtils.getFile(this.getClass().getResource(path));
return FileUtils.readFileToString(file, Charset.defaultCharset());
}
protected void checkWarning(CheckResult result, String message) {
List<String> warningMessages = result.getWarnings().stream().map(Warning::toMessage).collect(Collectors.toList());
Assert.assertThat(warningMessages, Matchers.hasItem(message));
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/entity/PathwayEntityTest.java | src/test/java/org/ohdsi/webapi/entity/PathwayEntityTest.java | package org.ohdsi.webapi.entity;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.model.CommonEntity;
import org.ohdsi.webapi.pathway.PathwayController;
import org.ohdsi.webapi.pathway.PathwayService;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisDTO;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisExportDTO;
import org.ohdsi.webapi.pathway.repository.PathwayAnalysisEntityRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.convert.ConversionService;
import org.springframework.transaction.annotation.Transactional;
import java.util.ArrayList;
import static org.ohdsi.webapi.test.TestConstants.NEW_TEST_ENTITY;
public class PathwayEntityTest extends AbstractDatabaseTest implements TestCreate, TestCopy<PathwayAnalysisDTO>, TestImport<PathwayAnalysisDTO, PathwayAnalysisExportDTO> {
@Autowired
protected ConversionService conversionService;
@Autowired
protected PathwayController pwController;
@Autowired
protected PathwayAnalysisEntityRepository pwRepository;
@Autowired
protected PathwayService pwService;
private PathwayAnalysisDTO firstSavedDTO;
// in JUnit 4 it's impossible to mark methods inside interface with annotations, it was implemented in JUnit 5. After upgrade it's needed
// to mark interface methods with @Test, @Before, @After and to remove them from this class
@After
@Override
public void tearDownDB() {
pwRepository.deleteAll();
}
@Before
@Override
public void init() throws Exception {
TestCreate.super.init();
}
@Test
@Override
public void shouldNotCreateEntityWithDuplicateName() {
TestCreate.super.shouldNotCreateEntityWithDuplicateName();
}
@Test
@Override
public void shouldCopyWithUniqueName() throws Exception {
TestCopy.super.shouldCopyWithUniqueName();
}
@Test
@Override
public void shouldCopyFromCopy() throws Exception {
TestCopy.super.shouldCopyFromCopy();
}
@Test
@Override
public void shouldCopySeveralTimesOriginal() throws Exception {
TestCopy.super.shouldCopySeveralTimesOriginal();
}
@Test
@Override
public void shouldCopyOfPartlySameName() throws Exception {
TestCopy.super.shouldCopyOfPartlySameName();
}
@Test
@Override
@Transactional
public void shouldImportUniqueName() throws Exception {
TestImport.super.shouldImportUniqueName();
}
@Test
@Override
@Transactional
public void shouldImportWithTheSameName() throws Exception {
TestImport.super.shouldImportWithTheSameName();
}
@Test
@Override
@Transactional
public void shouldImportWhenEntityWithNameExists() throws Exception {
TestImport.super.shouldImportWhenEntityWithNameExists();
}
@Override
public PathwayAnalysisDTO createCopy(PathwayAnalysisDTO dto) {
return pwController.copy(dto.getId());
}
@Override
public void initFirstDTO() {
firstSavedDTO = createEntity(NEW_TEST_ENTITY);
}
@Override
public PathwayAnalysisDTO getFirstSavedDTO() {
return firstSavedDTO;
}
@Override
public PathwayAnalysisDTO createEntity(String name) {
return createEntity(createAndInitIncomingEntity(name));
}
@Override
public PathwayAnalysisDTO createEntity(PathwayAnalysisDTO dto) {
return pwController.create(dto);
}
@Override
public PathwayAnalysisDTO createAndInitIncomingEntity(String name) {
PathwayAnalysisDTO dto = new PathwayAnalysisDTO();
dto.setName(name);
dto.setEventCohorts(new ArrayList<>());
dto.setTargetCohorts(new ArrayList<>());
return dto;
}
@Override
public String getConstraintName() {
return "uq_pw_name";
}
@Override
public CommonEntity getEntity(int id) {
return pwService.getById(id);
}
@Override
public PathwayAnalysisExportDTO getExportEntity(CommonEntity entity) {
return conversionService.convert(entity, PathwayAnalysisExportDTO.class);
}
@Override
public PathwayAnalysisDTO doImport(PathwayAnalysisExportDTO dto) {
return pwController.importAnalysis(dto);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/entity/EntityMethods.java | src/test/java/org/ohdsi/webapi/entity/EntityMethods.java | package org.ohdsi.webapi.entity;
import org.ohdsi.webapi.CommonDTO;
import org.springframework.test.context.TestContextManager;
public interface EntityMethods<T extends CommonDTO> {
void initFirstDTO() throws Exception;
T createEntity(String name) throws Exception;
default void init() throws Exception {
TestContextManager testContextManager = new TestContextManager(getClass());
testContextManager.prepareTestInstance(this);
initFirstDTO();
}
void tearDownDB();
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/entity/ConceptSetEntityTest.java | src/test/java/org/ohdsi/webapi/entity/ConceptSetEntityTest.java | package org.ohdsi.webapi.entity;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.conceptset.ConceptSetRepository;
import org.ohdsi.webapi.service.ConceptSetService;
import org.ohdsi.webapi.service.dto.ConceptSetDTO;
import org.springframework.beans.factory.annotation.Autowired;
import static org.ohdsi.webapi.service.ConceptSetService.COPY_NAME;
import static org.ohdsi.webapi.test.TestConstants.NEW_TEST_ENTITY;
public class ConceptSetEntityTest extends AbstractDatabaseTest implements TestCreate, TestCopy<ConceptSetDTO> {
@Autowired
protected ConceptSetService csService;
@Autowired
protected ConceptSetRepository csRepository;
private ConceptSetDTO firstSavedDTO;
// in JUnit 4 it's impossible to mark methods inside interface with annotations, it was implemented in JUnit 5. After upgrade it's needed
// to mark interface methods with @Test, @Before, @After and to remove them from this class
@After
@Override
public void tearDownDB() {
csRepository.deleteAll();
}
@Before
@Override
public void init() throws Exception {
TestCreate.super.init();
}
@Test
@Override
public void shouldNotCreateEntityWithDuplicateName() {
TestCreate.super.shouldNotCreateEntityWithDuplicateName();
}
@Test
@Override
public void shouldCopyWithUniqueName() throws Exception {
TestCopy.super.shouldCopyWithUniqueName();
}
@Test
@Override
public void shouldCopyFromCopy() throws Exception {
TestCopy.super.shouldCopyFromCopy();
}
@Test
@Override
public void shouldCopySeveralTimesOriginal() throws Exception {
TestCopy.super.shouldCopySeveralTimesOriginal();
}
@Test
@Override
public void shouldCopyOfPartlySameName() throws Exception {
TestCopy.super.shouldCopyOfPartlySameName();
}
@Override
public ConceptSetDTO createCopy(ConceptSetDTO dto) {
dto.setName(csService.getNameForCopy(dto.getId()).get(COPY_NAME));
return csService.createConceptSet(dto);
}
@Override
public void initFirstDTO() {
firstSavedDTO = createEntity(NEW_TEST_ENTITY);
}
@Override
public ConceptSetDTO getFirstSavedDTO() {
return firstSavedDTO;
}
@Override
public ConceptSetDTO createEntity(String name) {
ConceptSetDTO dto = new ConceptSetDTO();
dto.setName(name);
return csService.createConceptSet(dto);
}
@Override
public String getConstraintName() {
return "uq_cs_name";
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/entity/CohortDefinitionEntityTest.java | src/test/java/org/ohdsi/webapi/entity/CohortDefinitionEntityTest.java | package org.ohdsi.webapi.entity;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.ohdsi.webapi.cohortdefinition.dto.CohortDTO;
import org.ohdsi.webapi.service.CohortDefinitionService;
import org.springframework.beans.factory.annotation.Autowired;
import static org.ohdsi.webapi.test.TestConstants.NEW_TEST_ENTITY;
public class CohortDefinitionEntityTest extends AbstractDatabaseTest implements TestCreate, TestCopy<CohortDTO> {
@Autowired
private CohortDefinitionService cdService;
@Autowired
protected CohortDefinitionRepository cdRepository;
private CohortDTO firstSavedDTO;
// in JUnit 4 it's impossible to mark methods inside interface with annotations, it was implemented in JUnit 5. After upgrade it's needed
// to mark interface methods with @Test, @Before, @After and to remove them from this class
@After
@Override
public void tearDownDB() {
cdRepository.deleteAll();
}
@Before
@Override
public void init() throws Exception {
TestCreate.super.init();
}
@Test
@Override
public void shouldNotCreateEntityWithDuplicateName() {
TestCreate.super.shouldNotCreateEntityWithDuplicateName();
}
@Test
@Override
public void shouldCopyWithUniqueName() throws Exception {
TestCopy.super.shouldCopyWithUniqueName();
}
@Test
@Override
public void shouldCopyFromCopy() throws Exception {
TestCopy.super.shouldCopyFromCopy();
}
@Test
@Override
public void shouldCopySeveralTimesOriginal() throws Exception {
TestCopy.super.shouldCopySeveralTimesOriginal();
}
@Test
@Override
public void shouldCopyOfPartlySameName() throws Exception {
TestCopy.super.shouldCopyOfPartlySameName();
}
@Override
public CohortDTO createCopy(CohortDTO dto) {
return cdService.copy(dto.getId());
}
@Override
public void initFirstDTO() {
firstSavedDTO = createEntity(NEW_TEST_ENTITY);
}
@Override
public CohortDTO getFirstSavedDTO() {
return firstSavedDTO;
}
@Override
public String getConstraintName() {
return "uq_cd_name";
}
@Override
public CohortDTO createEntity(String name) {
CohortDTO dto = new CohortDTO();
dto.setName(name);
return cdService.createCohortDefinition(dto);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/entity/TestImport.java | src/test/java/org/ohdsi/webapi/entity/TestImport.java | package org.ohdsi.webapi.entity;
import org.ohdsi.webapi.CommonDTO;
import org.ohdsi.webapi.model.CommonEntity;
import static org.junit.Assert.assertEquals;
import static org.ohdsi.webapi.test.TestConstants.NEW_TEST_ENTITY;
import static org.ohdsi.webapi.test.TestConstants.SOME_UNIQUE_TEST_NAME;
public interface TestImport<T extends CommonDTO, U extends CommonDTO> extends EntityMethods {
CommonEntity getEntity(int id);
U getExportEntity(CommonEntity entity);
T doImport(U dto) throws Exception;
T createAndInitIncomingEntity(String name);
T createEntity(T dto) throws Exception;
T getFirstSavedDTO();
default void shouldImportUniqueName() throws Exception {
//Arrange
CommonEntity savedEntity = getEntity(getFirstSavedDTO().getId().intValue());
U exportedEntity = getExportEntity(savedEntity);
exportedEntity.setName(SOME_UNIQUE_TEST_NAME);
//Action
T firstImport = doImport(exportedEntity);
//Assert
assertEquals(SOME_UNIQUE_TEST_NAME, firstImport.getName());
}
default void shouldImportWithTheSameName() throws Exception {
//Arrange
CommonEntity savedEntity = getEntity(getFirstSavedDTO().getId().intValue());
U exportDTO = getExportEntity(savedEntity);
//Action
T firstImport = doImport(exportDTO);
//reset dto
exportDTO = getExportEntity(savedEntity);
T secondImport = doImport(exportDTO);
//Assert
assertEquals(NEW_TEST_ENTITY + " (1)", firstImport.getName());
assertEquals(NEW_TEST_ENTITY + " (2)", secondImport.getName());
}
default void shouldImportWhenEntityWithNameExists() throws Exception {
//Arrange
CommonEntity firstCreatedEntity = getEntity(getFirstSavedDTO().getId().intValue());
U firstExportDTO = getExportEntity(firstCreatedEntity);
T secondIncomingEntity = createAndInitIncomingEntity(NEW_TEST_ENTITY + " (1)");
//save "New test entity (1)" to DB
createEntity(secondIncomingEntity);
T thirdIncomingEntity = createAndInitIncomingEntity(NEW_TEST_ENTITY + " (1) (2)");
//save "New test entity (1) (2)" to DB
T thirdSavedDTO = createEntity(thirdIncomingEntity);
CommonEntity thirdCreatedEntity = getEntity(thirdSavedDTO.getId().intValue());
U thirdExportDTO = getExportEntity(thirdCreatedEntity);
//Action
//import of "New test entity"
T firstImport = doImport(firstExportDTO);
//import of "New test entity (1) (2)"
T secondImport = doImport(thirdExportDTO);
T fourthIncomingEntity = createAndInitIncomingEntity(NEW_TEST_ENTITY + " (1) (2) (2)");
//save "New test entity (1) (2) (2)" to DB
createEntity(fourthIncomingEntity);
//reset dto
thirdExportDTO = getExportEntity(thirdCreatedEntity);
//import of "New test entity (1) (2)"
T thirdImport = doImport(thirdExportDTO);
//Assert
assertEquals(NEW_TEST_ENTITY + " (2)", firstImport.getName());
assertEquals(NEW_TEST_ENTITY + " (1) (2) (1)", secondImport.getName());
assertEquals(NEW_TEST_ENTITY + " (1) (2) (3)", thirdImport.getName());
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/entity/EstimationEntityTest.java | src/test/java/org/ohdsi/webapi/entity/EstimationEntityTest.java | package org.ohdsi.webapi.entity;
import com.odysseusinc.arachne.commons.types.DBMSType;
import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.KerberosAuthMechanism;
import org.apache.commons.io.FileUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.analysis.AnalysisCohortDefinition;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionDetailsRepository;
import org.ohdsi.webapi.estimation.Estimation;
import org.ohdsi.webapi.estimation.EstimationController;
import org.ohdsi.webapi.estimation.EstimationService;
import org.ohdsi.webapi.estimation.dto.EstimationDTO;
import org.ohdsi.webapi.estimation.repository.EstimationRepository;
import org.ohdsi.webapi.estimation.specification.EstimationAnalysisImpl;
import org.ohdsi.webapi.model.CommonEntity;
import org.ohdsi.webapi.source.Source;
import org.ohdsi.webapi.source.SourceDaimon;
import org.ohdsi.webapi.source.SourceRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.convert.ConversionService;
import java.io.File;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.sql.SQLException;
import java.util.Arrays;
import java.util.List;
import static org.junit.Assert.assertEquals;
import static org.ohdsi.analysis.estimation.design.EstimationTypeEnum.COMPARATIVE_COHORT_ANALYSIS;
import static org.ohdsi.webapi.test.TestConstants.NEW_TEST_ENTITY;
public class EstimationEntityTest extends AbstractDatabaseTest implements TestCreate, TestCopy<EstimationDTO>, TestImport<EstimationDTO, EstimationAnalysisImpl> {
@Autowired
protected ConversionService conversionService;
@Autowired
protected EstimationController pleController;
@Autowired
protected EstimationRepository pleRepository;
@Autowired
protected EstimationService pleService;
@Autowired
protected CohortDefinitionDetailsRepository cdRepository;
@Autowired
private SourceRepository sourceRepository;
private EstimationDTO firstSavedDTO;
private static String PLE_SPECIFICATION;
@BeforeClass
public static void setPleSpecification() throws IOException {
File ple_spec = new File("src/test/resources/ple-specification.json");
PLE_SPECIFICATION = FileUtils.readFileToString(ple_spec, StandardCharsets.UTF_8);
}
// in JUnit 4 it's impossible to mark methods inside interface with annotations, it was implemented in JUnit 5. After upgrade it's needed
// to mark interface methods with @Test, @Before, @After and to remove them from this class
@After
@Override
public void tearDownDB() {
pleRepository.deleteAll();
}
@Before
@Override
public void init() throws Exception {
TestCreate.super.init();
truncateTable(String.format("%s.%s", "public", "source"));
resetSequence(String.format("%s.%s", "public", "source_sequence"));
sourceRepository.saveAndFlush(getCdmSource());
}
@Test
@Override
public void shouldNotCreateEntityWithDuplicateName() {
TestCreate.super.shouldNotCreateEntityWithDuplicateName();
}
@Test
@Override
public void shouldCopyWithUniqueName() throws Exception {
TestCopy.super.shouldCopyWithUniqueName();
}
@Test
@Override
public void shouldCopyFromCopy() throws Exception {
TestCopy.super.shouldCopyFromCopy();
}
@Test
@Override
public void shouldCopySeveralTimesOriginal() throws Exception {
TestCopy.super.shouldCopySeveralTimesOriginal();
}
@Test
@Override
public void shouldCopyOfPartlySameName() throws Exception {
TestCopy.super.shouldCopyOfPartlySameName();
}
@Test
@Override
public void shouldImportUniqueName() throws Exception {
TestImport.super.shouldImportUniqueName();
}
@Test
@Override
public void shouldImportWithTheSameName() throws Exception {
TestImport.super.shouldImportWithTheSameName();
}
@Test
@Override
public void shouldImportWhenEntityWithNameExists() throws Exception {
TestImport.super.shouldImportWhenEntityWithNameExists();
}
@Test
public void shouldImportWhenHashcodesOfCDsAndCSsAreDifferent() throws Exception {
//Arrange
File pleFile = new File("src/test/resources/ple-example-for-import.json");
String pleStr = FileUtils.readFileToString(pleFile, StandardCharsets.UTF_8);
EstimationAnalysisImpl ple = Utils.deserialize(pleStr, EstimationAnalysisImpl.class);
//Action
pleController.importAnalysis(ple);
cdRepository.findAll().forEach(cd -> {
cd.setExpression(cd.getExpression().replaceAll("5.0.0", "6.0.0"));
cdRepository.save(cd);
});
EstimationDTO importedEs = pleController.importAnalysis(ple);
//Assert
assertEquals("Comparative effectiveness of ACE inhibitors vs Thiazide diuretics as first-line monotherapy for hypertension (1)",
pleController.getAnalysis(importedEs.getId()).getName());
EstimationAnalysisImpl importedExpression = pleService.getAnalysisExpression(importedEs.getId());
List<AnalysisCohortDefinition> cds = importedExpression.getCohortDefinitions();
assertEquals("New users of ACE inhibitors as first-line monotherapy for hypertension (1)", cds.get(0).getName());
assertEquals("New users of Thiazide-like diuretics as first-line monotherapy for hypertension (1)", cds.get(1).getName());
assertEquals("Acute myocardial infarction events (1)", cds.get(2).getName());
assertEquals("Angioedema events (1)", cds.get(3).getName());
}
@Override
public EstimationDTO createCopy(EstimationDTO dto) throws Exception {
return pleController.copy(dto.getId());
}
@Override
public void initFirstDTO() throws Exception {
firstSavedDTO = createEntity(NEW_TEST_ENTITY);
}
@Override
public EstimationDTO getFirstSavedDTO() {
return firstSavedDTO;
}
@Override
public EstimationDTO createEntity(String name) throws Exception {
return createEntity(createAndInitIncomingEntity(name));
}
@Override
public EstimationDTO createEntity(EstimationDTO dto) throws Exception {
Estimation estimation = createEstimation(dto.getName());
return pleController.createEstimation(estimation);
}
@Override
public EstimationDTO createAndInitIncomingEntity(String name) {
Estimation estimation = createEstimation(name);
return conversionService.convert(estimation, EstimationDTO.class);
}
private Estimation createEstimation(String name) {
Estimation estimation = new Estimation();
estimation.setName(name);
estimation.setType(COMPARATIVE_COHORT_ANALYSIS);
estimation.setSpecification(PLE_SPECIFICATION);
return estimation;
}
@Override
public String getConstraintName() {
return "uq_es_name";
}
@Override
public CommonEntity getEntity(int id) {
return pleService.getAnalysis(id);
}
@Override
public EstimationAnalysisImpl getExportEntity(CommonEntity entity) {
return pleController.exportAnalysis(entity.getId().intValue());
}
@Override
public EstimationDTO doImport(EstimationAnalysisImpl dto) throws Exception {
return pleController.importAnalysis(dto);
}
private Source getCdmSource() throws SQLException {
Source source = new Source();
source.setSourceName("Embedded PG");
source.setSourceKey("Embedded_PG");
source.setSourceDialect(DBMSType.POSTGRESQL.getOhdsiDB());
source.setSourceConnection(getDataSource().getConnection().getMetaData().getURL());
source.setUsername("postgres");
source.setPassword("postgres");
source.setKrbAuthMethod(KerberosAuthMechanism.PASSWORD);
SourceDaimon cdmDaimon = new SourceDaimon();
cdmDaimon.setPriority(1);
cdmDaimon.setDaimonType(SourceDaimon.DaimonType.CDM);
cdmDaimon.setTableQualifier("cdm");
cdmDaimon.setSource(source);
SourceDaimon vocabDaimon = new SourceDaimon();
vocabDaimon.setPriority(1);
vocabDaimon.setDaimonType(SourceDaimon.DaimonType.Vocabulary);
vocabDaimon.setTableQualifier("cdm");
vocabDaimon.setSource(source);
SourceDaimon resultsDaimon = new SourceDaimon();
resultsDaimon.setPriority(1);
resultsDaimon.setDaimonType(SourceDaimon.DaimonType.Results);
resultsDaimon.setTableQualifier("results");
resultsDaimon.setSource(source);
source.setDaimons(Arrays.asList(cdmDaimon, vocabDaimon, resultsDaimon));
return source;
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/entity/CCEntityTest.java | src/test/java/org/ohdsi/webapi/entity/CCEntityTest.java | package org.ohdsi.webapi.entity;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.cohortcharacterization.CcController;
import org.ohdsi.webapi.cohortcharacterization.CcService;
import org.ohdsi.webapi.cohortcharacterization.domain.CohortCharacterizationEntity;
import org.ohdsi.webapi.cohortcharacterization.dto.CcExportDTO;
import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
import org.ohdsi.webapi.cohortcharacterization.repository.CcRepository;
import org.ohdsi.webapi.model.CommonEntity;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.convert.ConversionService;
import org.springframework.transaction.annotation.Transactional;
import static org.ohdsi.webapi.test.TestConstants.NEW_TEST_ENTITY;
public class CCEntityTest extends AbstractDatabaseTest implements TestCreate, TestCopy<CohortCharacterizationDTO>, TestImport<CohortCharacterizationDTO, CcExportDTO> {
@Autowired
protected ConversionService conversionService;
@Autowired
protected CcController ccController;
@Autowired
protected CcRepository ccRepository;
@Autowired
protected CcService ccService;
private CohortCharacterizationDTO firstSavedDTO;
// in JUnit 4 it's impossible to mark methods inside interface with annotations, it was implemented in JUnit 5. After upgrade it's needed
// to mark interface methods with @Test, @Before, @After and to remove them from this class
@Before
@Override
public void init() throws Exception {
TestCreate.super.init();
}
@After
@Override
public void tearDownDB() {
ccRepository.deleteAll();
}
@Test
@Override
public void shouldNotCreateEntityWithDuplicateName() {
TestCreate.super.shouldNotCreateEntityWithDuplicateName();
}
@Test
@Override
public void shouldCopyWithUniqueName() throws Exception {
TestCopy.super.shouldCopyWithUniqueName();
}
@Test
@Override
public void shouldCopyFromCopy() throws Exception {
TestCopy.super.shouldCopyFromCopy();
}
@Test
@Override
public void shouldCopySeveralTimesOriginal() throws Exception {
TestCopy.super.shouldCopySeveralTimesOriginal();
}
@Test
@Override
public void shouldCopyOfPartlySameName() throws Exception {
TestCopy.super.shouldCopyOfPartlySameName();
}
@Test
@Override
@Transactional
public void shouldImportUniqueName() throws Exception {
TestImport.super.shouldImportUniqueName();
}
@Test
@Override
@Transactional
public void shouldImportWithTheSameName() throws Exception {
TestImport.super.shouldImportWithTheSameName();
}
@Test
@Override
@Transactional
public void shouldImportWhenEntityWithNameExists() throws Exception {
TestImport.super.shouldImportWhenEntityWithNameExists();
}
@Override
public CohortCharacterizationDTO createCopy(CohortCharacterizationDTO dto) {
return ccController.copy(dto.getId());
}
@Override
public void initFirstDTO() {
firstSavedDTO = createEntity(NEW_TEST_ENTITY);
}
@Override
public CohortCharacterizationDTO getFirstSavedDTO() {
return firstSavedDTO;
}
@Override
public String getConstraintName() {
return "uq_cc_name";
}
@Override
public CohortCharacterizationDTO createEntity(String name) {
return createEntity(createAndInitIncomingEntity(name));
}
@Override
public CohortCharacterizationDTO createEntity(CohortCharacterizationDTO dto) {
return ccController.create(dto);
}
@Override
public CohortCharacterizationDTO createAndInitIncomingEntity(String name) {
CohortCharacterizationDTO dto = new CohortCharacterizationDTO();
dto.setName(name);
return dto;
}
@Override
public CohortCharacterizationEntity getEntity(int id) {
return ccService.findByIdWithLinkedEntities((long) id);
}
@Override
public CcExportDTO getExportEntity(CommonEntity entity) {
return conversionService.convert(entity, CcExportDTO.class);
}
@Override
public CohortCharacterizationDTO doImport(CcExportDTO dto) {
return ccController.doImport(dto);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/entity/IREntityTest.java | src/test/java/org/ohdsi/webapi/entity/IREntityTest.java | package org.ohdsi.webapi.entity;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.ircalc.IncidenceRateAnalysisRepository;
import org.ohdsi.webapi.service.IRAnalysisResource;
import org.ohdsi.webapi.service.dto.IRAnalysisDTO;
import org.springframework.beans.factory.annotation.Autowired;
import static org.ohdsi.webapi.test.TestConstants.NEW_TEST_ENTITY;
public class IREntityTest extends AbstractDatabaseTest implements TestCreate, TestCopy<IRAnalysisDTO> {
@Autowired
protected IRAnalysisResource irAnalysisResource;
@Autowired
protected IncidenceRateAnalysisRepository irRepository;
private IRAnalysisDTO firstSavedDTO;
// in JUnit 4 it's impossible to mark methods inside interface with annotations, it was implemented in JUnit 5. After upgrade it's needed
// to mark interface methods with @Test, @Before, @After and to remove them from this class
@After
@Override
public void tearDownDB() {
irRepository.deleteAll();
}
@Before
@Override
public void init() throws Exception {
TestCreate.super.init();
}
@Test
@Override
public void shouldNotCreateEntityWithDuplicateName() {
TestCreate.super.shouldNotCreateEntityWithDuplicateName();
}
@Test
@Override
public void shouldCopyWithUniqueName() throws Exception {
TestCopy.super.shouldCopyWithUniqueName();
}
@Test
@Override
public void shouldCopyFromCopy() throws Exception {
TestCopy.super.shouldCopyFromCopy();
}
@Test
@Override
public void shouldCopySeveralTimesOriginal() throws Exception {
TestCopy.super.shouldCopySeveralTimesOriginal();
}
@Test
@Override
public void shouldCopyOfPartlySameName() throws Exception {
TestCopy.super.shouldCopyOfPartlySameName();
}
@Override
public IRAnalysisDTO createCopy(IRAnalysisDTO dto) {
return irAnalysisResource.copy(dto.getId());
}
@Override
public void initFirstDTO() {
firstSavedDTO = createEntity(NEW_TEST_ENTITY);
}
@Override
public IRAnalysisDTO getFirstSavedDTO() {
return firstSavedDTO;
}
@Override
public IRAnalysisDTO createEntity(String name) {
IRAnalysisDTO dto = new IRAnalysisDTO();
dto.setName(name);
return irAnalysisResource.createAnalysis(dto);
}
@Override
public String getConstraintName() {
return "uq_ir_name";
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/entity/TestCopy.java | src/test/java/org/ohdsi/webapi/entity/TestCopy.java | package org.ohdsi.webapi.entity;
import org.ohdsi.webapi.CommonDTO;
import static org.junit.Assert.assertEquals;
import static org.ohdsi.webapi.test.TestConstants.COPY_PREFIX;
import static org.ohdsi.webapi.test.TestConstants.NEW_TEST_ENTITY;
public interface TestCopy<T extends CommonDTO> extends EntityMethods {
T createCopy(T dto) throws Exception;
T createEntity(String name) throws Exception;
T getFirstSavedDTO();
default void shouldCopyWithUniqueName() throws Exception {
//Action
T copy = createCopy(getFirstSavedDTO());
//Assert
assertEquals(COPY_PREFIX + NEW_TEST_ENTITY, copy.getName());
}
default void shouldCopyFromCopy() throws Exception {
//Action
T firstCopy = createCopy(getFirstSavedDTO());
T secondCopy = createCopy(firstCopy);
//Assert
assertEquals(COPY_PREFIX + COPY_PREFIX + NEW_TEST_ENTITY, secondCopy.getName());
}
default void shouldCopySeveralTimesOriginal() throws Exception {
//Action
T firstCopy = createCopy(getFirstSavedDTO());
T secondCopy = createCopy(getFirstSavedDTO());
//Assert
assertEquals(COPY_PREFIX + NEW_TEST_ENTITY, firstCopy.getName());
assertEquals(COPY_PREFIX + NEW_TEST_ENTITY + " (1)", secondCopy.getName());
}
default void shouldCopyOfPartlySameName() throws Exception {
String firstName = "abcde, abc, abc";
String secondName = "abcde (1), abcde, abcde (2)";
//Arrange
createEntity(COPY_PREFIX + firstName);
T savedDTO = createEntity(secondName);
//Action
T copy = createCopy(savedDTO);
//Assert
assertEquals(COPY_PREFIX + secondName, copy.getName());
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/entity/PredictionEntityTest.java | src/test/java/org/ohdsi/webapi/entity/PredictionEntityTest.java | package org.ohdsi.webapi.entity;
import com.odysseusinc.arachne.commons.types.DBMSType;
import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.KerberosAuthMechanism;
import org.apache.commons.io.FileUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.model.CommonEntity;
import org.ohdsi.webapi.prediction.PredictionAnalysis;
import org.ohdsi.webapi.prediction.PredictionController;
import org.ohdsi.webapi.prediction.PredictionService;
import org.ohdsi.webapi.prediction.dto.PredictionAnalysisDTO;
import org.ohdsi.webapi.prediction.repository.PredictionAnalysisRepository;
import org.ohdsi.webapi.prediction.specification.PatientLevelPredictionAnalysisImpl;
import org.ohdsi.webapi.source.Source;
import org.ohdsi.webapi.source.SourceDaimon;
import org.ohdsi.webapi.source.SourceRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.convert.ConversionService;
import java.io.File;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.sql.SQLException;
import java.util.Arrays;
import static org.ohdsi.webapi.test.TestConstants.NEW_TEST_ENTITY;
public class PredictionEntityTest extends AbstractDatabaseTest implements TestCreate, TestCopy<PredictionAnalysisDTO>, TestImport<PredictionAnalysisDTO, PatientLevelPredictionAnalysisImpl> {
@Autowired
protected ConversionService conversionService;
@Autowired
protected PredictionController plpController;
@Autowired
protected PredictionAnalysisRepository plpRepository;
@Autowired
private SourceRepository sourceRepository;
@Autowired
protected PredictionService plpService;
private PredictionAnalysisDTO firstSavedDTO;
private static String PLP_SPECIFICATION;
@BeforeClass
public static void setPlpSpecification() throws IOException {
File plp_spec = new File("src/test/resources/plp-specification.json");
PLP_SPECIFICATION = FileUtils.readFileToString(plp_spec, StandardCharsets.UTF_8);
}
// in JUnit 4 it's impossible to mark methods inside interface with annotations, it was implemented in JUnit 5. After upgrade it's needed
// to mark interface methods with @Test, @Before, @After and to remove them from this class
@After
@Override
public void tearDownDB() {
plpRepository.deleteAll();
}
@Before
@Override
public void init() throws Exception {
TestCreate.super.init();
truncateTable(String.format("%s.%s", "public", "source"));
resetSequence(String.format("%s.%s", "public", "source_sequence"));
sourceRepository.saveAndFlush(getCdmSource());
}
@Test
@Override
public void shouldNotCreateEntityWithDuplicateName() {
TestCreate.super.shouldNotCreateEntityWithDuplicateName();
}
@Test
@Override
public void shouldCopyWithUniqueName() throws Exception {
TestCopy.super.shouldCopyWithUniqueName();
}
@Test
@Override
public void shouldCopyFromCopy() throws Exception {
TestCopy.super.shouldCopyFromCopy();
}
@Test
@Override
public void shouldCopySeveralTimesOriginal() throws Exception {
TestCopy.super.shouldCopySeveralTimesOriginal();
}
@Test
@Override
public void shouldCopyOfPartlySameName() throws Exception {
TestCopy.super.shouldCopyOfPartlySameName();
}
@Test
@Override
public void shouldImportUniqueName() throws Exception {
TestImport.super.shouldImportUniqueName();
}
@Test
@Override
public void shouldImportWithTheSameName() throws Exception {
TestImport.super.shouldImportWithTheSameName();
}
@Test
@Override
public void shouldImportWhenEntityWithNameExists() throws Exception {
TestImport.super.shouldImportWhenEntityWithNameExists();
}
@Override
public PredictionAnalysisDTO createCopy(PredictionAnalysisDTO dto) {
return plpController.copy(dto.getId());
}
@Override
public void initFirstDTO() {
firstSavedDTO = createEntity(NEW_TEST_ENTITY);
}
@Override
public PredictionAnalysisDTO getFirstSavedDTO() {
return firstSavedDTO;
}
@Override
public PredictionAnalysisDTO createEntity(String name) {
return createEntity(createAndInitIncomingEntity(name));
}
@Override
public PredictionAnalysisDTO createEntity(PredictionAnalysisDTO dto) {
PredictionAnalysis prediction = createPrediction(dto.getName());
return plpController.createAnalysis(prediction);
}
@Override
public PredictionAnalysisDTO createAndInitIncomingEntity(String name) {
PredictionAnalysis predictionAnalysis = createPrediction(name);
return conversionService.convert(predictionAnalysis, PredictionAnalysisDTO.class);
}
private PredictionAnalysis createPrediction(String name) {
PredictionAnalysis prediction = new PredictionAnalysis();
prediction.setName(name);
prediction.setSpecification(PLP_SPECIFICATION);
return prediction;
}
@Override
public String getConstraintName() {
return "uq_pd_name";
}
@Override
public CommonEntity getEntity(int id) {
return plpService.getAnalysis(id);
}
@Override
public PatientLevelPredictionAnalysisImpl getExportEntity(CommonEntity entity) {
return plpController.exportAnalysis(entity.getId().intValue());
}
@Override
public PredictionAnalysisDTO doImport(PatientLevelPredictionAnalysisImpl dto) throws Exception {
return plpController.importAnalysis(dto);
}
private Source getCdmSource() throws SQLException {
Source source = new Source();
source.setSourceName("Embedded PG");
source.setSourceKey("Embedded_PG");
source.setSourceDialect(DBMSType.POSTGRESQL.getOhdsiDB());
source.setSourceConnection(getDataSource().getConnection().getMetaData().getURL());
source.setUsername("postgres");
source.setPassword("postgres");
source.setKrbAuthMethod(KerberosAuthMechanism.PASSWORD);
SourceDaimon cdmDaimon = new SourceDaimon();
cdmDaimon.setPriority(1);
cdmDaimon.setDaimonType(SourceDaimon.DaimonType.CDM);
cdmDaimon.setTableQualifier("cdm");
cdmDaimon.setSource(source);
SourceDaimon vocabDaimon = new SourceDaimon();
vocabDaimon.setPriority(1);
vocabDaimon.setDaimonType(SourceDaimon.DaimonType.Vocabulary);
vocabDaimon.setTableQualifier("cdm");
vocabDaimon.setSource(source);
SourceDaimon resultsDaimon = new SourceDaimon();
resultsDaimon.setPriority(1);
resultsDaimon.setDaimonType(SourceDaimon.DaimonType.Results);
resultsDaimon.setTableQualifier("results");
resultsDaimon.setSource(source);
source.setDaimons(Arrays.asList(cdmDaimon, vocabDaimon, resultsDaimon));
return source;
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/entity/TestCreate.java | src/test/java/org/ohdsi/webapi/entity/TestCreate.java | package org.ohdsi.webapi.entity;
import org.apache.commons.lang3.exception.ExceptionUtils;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.ohdsi.webapi.test.TestConstants.NEW_TEST_ENTITY;
public interface TestCreate extends EntityMethods {
String getConstraintName();
default void shouldNotCreateEntityWithDuplicateName() {
//Action
try {
createEntity(NEW_TEST_ENTITY);
fail();
} catch (Exception e) {
//Assert
assertTrue(ExceptionUtils.getRootCauseMessage(e).contains(getConstraintName()));
}
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/tagging/CohortTaggingTest.java | src/test/java/org/ohdsi/webapi/tagging/CohortTaggingTest.java | package org.ohdsi.webapi.tagging;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.ohdsi.webapi.cohortdefinition.dto.CohortDTO;
import org.ohdsi.webapi.cohortdefinition.dto.CohortRawDTO;
import org.ohdsi.webapi.service.CohortDefinitionService;
import org.ohdsi.webapi.tag.domain.Tag;
import org.ohdsi.webapi.tag.dto.TagNameListRequestDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.List;
public class CohortTaggingTest extends BaseTaggingTest<CohortDTO, Integer> {
private static final String JSON_PATH = "/tagging/cohort.json";
@Autowired
private CohortDefinitionService service;
@Autowired
private CohortDefinitionRepository repository;
@Override
public void doCreateInitialData() throws IOException {
String expression = getExpression(getExpressionPath());
CohortDTO dto = deserializeExpression(expression);
initialDTO = service.createCohortDefinition(dto);
}
@Override
protected CohortDTO doCopyData(CohortDTO def) {
return service.copy(def.getId());
}
private CohortDTO deserializeExpression(String expression) {
CohortRawDTO rawDTO = new CohortRawDTO();
rawDTO.setExpression(expression);
CohortDTO dto = conversionService.convert(rawDTO, CohortDTO.class);
dto.setName("test dto name");
dto.setDescription("test dto description");
return dto;
}
@Override
protected void doClear() {
repository.deleteAll();
}
@Override
protected String getExpressionPath() {
return JSON_PATH;
}
@Override
protected void assignTag(Integer id, boolean isPermissionProtected) {
service.assignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignTag(Integer id, boolean isPermissionProtected) {
service.unassignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void assignProtectedTag(Integer id, boolean isPermissionProtected) {
service.assignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignProtectedTag(Integer id, boolean isPermissionProtected) {
service.unassignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected CohortDTO getDTO(Integer id) {
return service.getCohortDefinition(id);
}
@Override
protected Integer getId(CohortDTO dto) {
return dto.getId();
}
@Override
protected void assignTags(Integer id, Tag...tags) {
for (Tag tag : tags) {
service.assignTag(id, tag.getId());
}
}
@Override
protected List<CohortDTO> getDTOsByTag(List<String> tagNames) {
TagNameListRequestDTO requestDTO = new TagNameListRequestDTO();
requestDTO.setNames(tagNames);
return service.listByTags(requestDTO);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/tagging/IRTaggingTest.java | src/test/java/org/ohdsi/webapi/tagging/IRTaggingTest.java | package org.ohdsi.webapi.tagging;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.ohdsi.webapi.ircalc.IncidenceRateAnalysisRepository;
import org.ohdsi.webapi.service.IRAnalysisService;
import org.ohdsi.webapi.service.dto.IRAnalysisDTO;
import org.ohdsi.webapi.tag.domain.Tag;
import org.ohdsi.webapi.tag.dto.TagNameListRequestDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.List;
public class IRTaggingTest extends BaseTaggingTest<IRAnalysisDTO, Integer> {
private static final String JSON_PATH = "/tagging/ir.json";
@Autowired
private IRAnalysisService service;
@Autowired
private IncidenceRateAnalysisRepository repository;
@Autowired
private CohortDefinitionRepository cohortRepository;
@Override
public void doCreateInitialData() throws IOException {
String expression = getExpression(getExpressionPath());
IRAnalysisDTO dto = deserializeExpression(expression);
initialDTO = service.doImport(dto);
}
@Override
protected IRAnalysisDTO doCopyData(IRAnalysisDTO def) {
return service.copy(def.getId());
}
private IRAnalysisDTO deserializeExpression(String expression) {
IRAnalysisDTO dto =
Utils.deserialize(expression, IRAnalysisDTO.class);
dto.setName("test dto name");
dto.setDescription("test dto description");
return dto;
}
@Override
protected void doClear() {
repository.deleteAll();
cohortRepository.deleteAll();
}
@Override
protected String getExpressionPath() {
return JSON_PATH;
}
@Override
protected void assignTag(Integer id, boolean isPermissionProtected) {
service.assignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignTag(Integer id, boolean isPermissionProtected) {
service.unassignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void assignProtectedTag(Integer id, boolean isPermissionProtected) {
service.assignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignProtectedTag(Integer id, boolean isPermissionProtected) {
service.unassignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected IRAnalysisDTO getDTO(Integer id) {
return service.getAnalysis(id);
}
@Override
protected Integer getId(IRAnalysisDTO dto) {
return dto.getId();
}
@Override
protected void assignTags(Integer id, Tag...tags) {
for (Tag tag : tags) {
service.assignTag(id, tag.getId());
}
}
@Override
protected List<IRAnalysisDTO> getDTOsByTag(List<String> tagNames) {
TagNameListRequestDTO requestDTO = new TagNameListRequestDTO();
requestDTO.setNames(tagNames);
return service.listByTags(requestDTO);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/tagging/ReusableTaggingTest.java | src/test/java/org/ohdsi/webapi/tagging/ReusableTaggingTest.java | package org.ohdsi.webapi.tagging;
import org.ohdsi.webapi.reusable.ReusableController;
import org.ohdsi.webapi.reusable.dto.ReusableDTO;
import org.ohdsi.webapi.reusable.repository.ReusableRepository;
import org.ohdsi.webapi.tag.domain.Tag;
import org.ohdsi.webapi.tag.dto.TagNameListRequestDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.List;
public class ReusableTaggingTest extends BaseTaggingTest<ReusableDTO, Integer> {
@Autowired
private ReusableController controller;
@Autowired
private ReusableRepository repository;
@Override
public void doCreateInitialData() throws IOException {
ReusableDTO dto = new ReusableDTO();
dto.setData("test data");
dto.setName("test name");
dto.setDescription("test description");
initialDTO = controller.create(dto);
}
@Override
protected ReusableDTO doCopyData(ReusableDTO def) {
return controller.copy(def.getId());
}
@Override
protected void doClear() {
repository.deleteAll();
}
@Override
protected String getExpressionPath() {
return null;
}
@Override
protected void assignTag(Integer id, boolean isPermissionProtected) {
controller.assignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignTag(Integer id, boolean isPermissionProtected) {
controller.unassignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void assignProtectedTag(Integer id, boolean isPermissionProtected) {
controller.assignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignProtectedTag(Integer id, boolean isPermissionProtected) {
controller.unassignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected ReusableDTO getDTO(Integer id) {
return controller.get(id);
}
@Override
protected Integer getId(ReusableDTO dto) {
return dto.getId();
}
@Override
protected void assignTags(Integer id, Tag...tags) {
for (Tag tag : tags) {
controller.assignTag(id, tag.getId());
}
}
@Override
protected List<ReusableDTO> getDTOsByTag(List<String> tagNames) {
TagNameListRequestDTO requestDTO = new TagNameListRequestDTO();
requestDTO.setNames(tagNames);
return controller.listByTags(requestDTO);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/tagging/PathwayTaggingTest.java | src/test/java/org/ohdsi/webapi/tagging/PathwayTaggingTest.java | package org.ohdsi.webapi.tagging;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.ohdsi.webapi.pathway.PathwayController;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisDTO;
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisExportDTO;
import org.ohdsi.webapi.pathway.repository.PathwayAnalysisEntityRepository;
import org.ohdsi.webapi.tag.domain.Tag;
import org.ohdsi.webapi.tag.dto.TagNameListRequestDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.List;
public class PathwayTaggingTest extends BaseTaggingTest<PathwayAnalysisDTO, Integer> {
private static final String JSON_PATH = "/tagging/pathway.json";
@Autowired
private PathwayController service;
@Autowired
private PathwayAnalysisEntityRepository repository;
@Autowired
private CohortDefinitionRepository cohortRepository;
@Override
public void doCreateInitialData() throws IOException {
String expression = getExpression(getExpressionPath());
PathwayAnalysisExportDTO dto = Utils.deserialize(expression, PathwayAnalysisExportDTO.class);
dto.setName("test dto name");
initialDTO = service.importAnalysis(dto);
}
@Override
protected PathwayAnalysisDTO doCopyData(PathwayAnalysisDTO def) {
return service.copy(def.getId());
}
@Override
protected void doClear() {
repository.deleteAll();
cohortRepository.deleteAll();
}
@Override
protected String getExpressionPath() {
return JSON_PATH;
}
@Override
protected void assignTag(Integer id, boolean isPermissionProtected) {
service.assignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignTag(Integer id, boolean isPermissionProtected) {
service.unassignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void assignProtectedTag(Integer id, boolean isPermissionProtected) {
service.assignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignProtectedTag(Integer id, boolean isPermissionProtected) {
service.unassignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected PathwayAnalysisDTO getDTO(Integer id) {
return service.get(id);
}
@Override
protected Integer getId(PathwayAnalysisDTO dto) {
return dto.getId();
}
@Override
protected void assignTags(Integer id, Tag...tags) {
for (Tag tag : tags) {
service.assignTag(id, tag.getId());
}
}
@Override
protected List<PathwayAnalysisDTO> getDTOsByTag(List<String> tagNames) {
TagNameListRequestDTO requestDTO = new TagNameListRequestDTO();
requestDTO.setNames(tagNames);
return service.listByTags(requestDTO);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/tagging/ConceptSetTaggingTest.java | src/test/java/org/ohdsi/webapi/tagging/ConceptSetTaggingTest.java | package org.ohdsi.webapi.tagging;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.ohdsi.circe.vocabulary.ConceptSetExpression;
import org.ohdsi.webapi.conceptset.ConceptSetItem;
import org.ohdsi.webapi.conceptset.ConceptSetRepository;
import org.ohdsi.webapi.service.ConceptSetService;
import org.ohdsi.webapi.service.dto.ConceptSetDTO;
import org.ohdsi.webapi.tag.domain.Tag;
import org.ohdsi.webapi.tag.dto.TagNameListRequestDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
public class ConceptSetTaggingTest extends BaseTaggingTest<ConceptSetDTO, Integer> {
private static final String JSON_PATH = "/tagging/conceptset.json";
@Autowired
private ConceptSetService service;
@Autowired
private ConceptSetRepository repository;
@Autowired
private ObjectMapper mapper;
@Override
public void doCreateInitialData() throws IOException {
ConceptSetDTO dto = new ConceptSetDTO();
dto.setName("test dto name");
initialDTO = service.createConceptSet(dto);
String expression = getExpression(getExpressionPath());
ConceptSetExpression.ConceptSetItem[] expressionItems;
try {
ConceptSetExpression conceptSetExpression = mapper.readValue(expression, ConceptSetExpression.class);
expressionItems = conceptSetExpression.items;
} catch (JsonProcessingException e) {
throw new RuntimeException(e);
}
ConceptSetItem[] items = Arrays.stream(expressionItems)
.map(i -> conversionService.convert(i, ConceptSetItem.class))
.toArray(ConceptSetItem[]::new);
service.saveConceptSetItems(initialDTO.getId(), items);
}
@Override
protected ConceptSetDTO doCopyData(ConceptSetDTO def) {
ConceptSetDTO dto = new ConceptSetDTO();
dto.setName("test dto name 2");
return service.createConceptSet(dto);
}
@Override
protected void doClear() {
repository.deleteAll();
}
@Override
protected String getExpressionPath() {
return JSON_PATH;
}
@Override
protected void assignTag(Integer id, boolean isPermissionProtected) {
service.assignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignTag(Integer id, boolean isPermissionProtected) {
service.unassignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void assignProtectedTag(Integer id, boolean isPermissionProtected) {
service.assignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignProtectedTag(Integer id, boolean isPermissionProtected) {
service.unassignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected ConceptSetDTO getDTO(Integer id) {
return service.getConceptSet(id);
}
@Override
protected Integer getId(ConceptSetDTO dto) {
return dto.getId();
}
@Override
protected void assignTags(Integer id, Tag...tags) {
for (Tag tag : tags) {
service.assignTag(id, tag.getId());
}
}
@Override
protected List<ConceptSetDTO> getDTOsByTag(List<String> tagNames) {
TagNameListRequestDTO requestDTO = new TagNameListRequestDTO();
requestDTO.setNames(tagNames);
return service.listByTags(requestDTO);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/tagging/CcTaggingTest.java | src/test/java/org/ohdsi/webapi/tagging/CcTaggingTest.java | package org.ohdsi.webapi.tagging;
import org.ohdsi.analysis.Utils;
import org.ohdsi.webapi.cohortcharacterization.CcController;
import org.ohdsi.webapi.cohortcharacterization.domain.CohortCharacterizationEntity;
import org.ohdsi.webapi.cohortcharacterization.dto.CcExportDTO;
import org.ohdsi.webapi.cohortcharacterization.dto.CcShortDTO;
import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
import org.ohdsi.webapi.cohortcharacterization.repository.CcRepository;
import org.ohdsi.webapi.cohortcharacterization.specification.CohortCharacterizationImpl;
import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
import org.ohdsi.webapi.tag.domain.Tag;
import org.ohdsi.webapi.tag.dto.TagNameListRequestDTO;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.List;
public class CcTaggingTest extends BaseTaggingTest<CcShortDTO, Long> {
private static final String JSON_PATH = "/tagging/characterization.json";
@Autowired
private CcController service;
@Autowired
private CcRepository repository;
@Autowired
private CohortDefinitionRepository cohortRepository;
@Override
public void doCreateInitialData() throws IOException {
String expression = getExpression(getExpressionPath());
CohortCharacterizationImpl characterizationImpl =
Utils.deserialize(expression, CohortCharacterizationImpl.class);
CohortCharacterizationEntity entity = conversionService.convert(characterizationImpl, CohortCharacterizationEntity.class);
CcExportDTO exportDTO = conversionService.convert(entity, CcExportDTO.class);
exportDTO.setName("test dto name");
initialDTO = service.doImport(exportDTO);
}
@Override
protected CcShortDTO doCopyData(CcShortDTO def) {
return service.copy(def.getId());
}
@Override
protected List<CcShortDTO> getDTOsByTag(List<String> tagNames) {
TagNameListRequestDTO requestDTO = new TagNameListRequestDTO();
requestDTO.setNames(tagNames);
return service.listByTags(requestDTO);
}
@Override
protected void doClear() {
repository.deleteAll();
cohortRepository.deleteAll();
}
@Override
protected String getExpressionPath() {
return JSON_PATH;
}
@Override
protected void assignTag(Long id, boolean isPermissionProtected) {
service.assignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignTag(Long id, boolean isPermissionProtected) {
service.unassignTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void assignProtectedTag(Long id, boolean isPermissionProtected) {
service.assignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected void unassignProtectedTag(Long id, boolean isPermissionProtected) {
service.unassignPermissionProtectedTag(id, getTag(isPermissionProtected).getId());
}
@Override
protected CohortCharacterizationDTO getDTO(Long id) {
return service.getDesign(id);
}
@Override
protected Long getId(CcShortDTO dto) {
return dto.getId();
}
@Override
protected void assignTags(Long id, Tag...tags) {
for (Tag tag : tags) {
service.assignTag(id, tag.getId());
}
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/tagging/BaseTaggingTest.java | src/test/java/org/ohdsi/webapi/tagging/BaseTaggingTest.java | package org.ohdsi.webapi.tagging;
import org.apache.commons.io.FileUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.service.dto.CommonEntityExtDTO;
import org.ohdsi.webapi.shiro.Entities.UserEntity;
import org.ohdsi.webapi.shiro.Entities.UserRepository;
import org.ohdsi.webapi.tag.domain.Tag;
import org.ohdsi.webapi.tag.domain.TagType;
import org.ohdsi.webapi.tag.repository.TagRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.convert.ConversionService;
import org.springframework.util.ResourceUtils;
import java.io.File;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import static org.junit.Assert.assertEquals;
public abstract class BaseTaggingTest<T extends CommonEntityExtDTO, ID extends Number> extends AbstractDatabaseTest {
protected T initialDTO;
@Autowired
protected UserRepository userRepository;
@Autowired
protected TagRepository tagRepository;
@Autowired
protected ConversionService conversionService;
private Tag tag1, tag2, tag3, protectedTag;
protected String getExpression(String path) throws IOException {
File ple_spec = ResourceUtils.getFile(Objects.requireNonNull(this.getClass().getResource(path)));
return FileUtils.readFileToString(ple_spec, StandardCharsets.UTF_8);
}
@Before
public void createInitialData() throws IOException {
UserEntity user = new UserEntity();
user.setLogin("anonymous");
userRepository.save(user);
this.protectedTag = new Tag();
this.protectedTag.setName("protected tag name");
this.protectedTag.setPermissionProtected(true);
this.protectedTag.setType(TagType.SYSTEM);
this.protectedTag.setCreatedDate(new Date());
tagRepository.save(this.protectedTag);
this.tag1 = new Tag();
this.tag1.setName("tag name");
this.tag1.setPermissionProtected(false);
this.tag1.setType(TagType.SYSTEM);
this.tag1.setCreatedDate(new Date());
tagRepository.save(this.tag1);
this.tag2 = new Tag();
this.tag2.setName("tag name 2");
this.tag2.setPermissionProtected(false);
this.tag2.setType(TagType.SYSTEM);
this.tag2.setCreatedDate(new Date());
tagRepository.save(this.tag2);
this.tag3 = new Tag();
this.tag3.setName("tag name 3");
this.tag3.setPermissionProtected(false);
this.tag3.setType(TagType.SYSTEM);
this.tag3.setCreatedDate(new Date());
tagRepository.save(this.tag3);
doCreateInitialData();
}
@After
public void clear() {
doClear();
tagRepository.deleteAll();
userRepository.deleteAll();
}
@Test
public void assignTag() {
assignTag(getId(initialDTO), false);
T dto = getDTO(getId(initialDTO));
assertEquals(dto.getTags().size(), 1);
}
@Test
public void assignProtectedTag() {
assignProtectedTag(getId(initialDTO), true);
T dto = getDTO(getId(initialDTO));
assertEquals(dto.getTags().size(), 1);
}
@Test
public void unassignTag() {
assignTag();
T dto = getDTO(getId(initialDTO));
assertEquals(dto.getTags().size(), 1);
unassignTag(getId(initialDTO), false);
dto = getDTO(getId(initialDTO));
assertEquals(dto.getTags().size(), 0);
}
@Test
public void unassignProtectedTag() {
assignProtectedTag();
T dto = getDTO(getId(initialDTO));
assertEquals(dto.getTags().size(), 1);
unassignProtectedTag(getId(initialDTO), true);
dto = getDTO(getId(initialDTO));
assertEquals(dto.getTags().size(), 0);
}
@Test
public void byTags() {
assignTags(getId(initialDTO), this.tag1, this.tag2);
List<T> dtos = getDTOsByTag(Arrays.asList("tag name", "tag name 2"));
assertEquals(dtos.size(), 1);
dtos = getDTOsByTag(Collections.singletonList("tag name"));
assertEquals(dtos.size(), 1);
dtos = getDTOsByTag(Collections.singletonList("tag name 2"));
assertEquals(dtos.size(), 1);
dtos = getDTOsByTag(Collections.singletonList("tag name 3"));
assertEquals(dtos.size(), 0);
T dto = doCopyData(initialDTO);
assignTags(getId(dto), this.tag3);
dtos = getDTOsByTag(Arrays.asList("tag name", "tag name 2"));
assertEquals(dtos.size(), 1);
dtos = getDTOsByTag(Arrays.asList("tag name", "tag name 2", "tag name 3"));
assertEquals(dtos.size(), 0);
dtos = getDTOsByTag(Collections.singletonList("tag name"));
assertEquals(dtos.size(), 1);
dtos = getDTOsByTag(Collections.singletonList("tag name 2"));
assertEquals(dtos.size(), 1);
dtos = getDTOsByTag(Collections.singletonList("tag name 3"));
assertEquals(dtos.size(), 1);
assignTags(getId(dto), this.tag1, this.tag2);
dtos = getDTOsByTag(Arrays.asList("tag name", "tag name 2"));
assertEquals(dtos.size(), 2);
dtos = getDTOsByTag(Arrays.asList("tag name", "tag name 2", "tag name 3"));
assertEquals(dtos.size(), 1);
}
protected Tag getTag(boolean isProtected) {
return tagRepository.findAll().stream()
.filter(t -> t.isPermissionProtected() == isProtected)
.findFirst()
.orElseThrow(() -> new RuntimeException("cannot get tag"));
}
protected List<Tag> getTags(boolean isProtected) {
return tagRepository.findAll().stream()
.filter(t -> t.isPermissionProtected() == isProtected)
.collect(Collectors.toList());
}
protected abstract void doCreateInitialData() throws IOException;
protected abstract T doCopyData(T def);
protected abstract void doClear();
protected abstract String getExpressionPath();
protected abstract void assignTag(ID id, boolean isPermissionProtected);
protected abstract void assignTags(ID id, Tag...tags);
protected abstract void unassignTag(ID id, boolean isPermissionProtected);
protected abstract void assignProtectedTag(ID id, boolean isPermissionProtected);
protected abstract void unassignProtectedTag(ID id, boolean isPermissionProtected);
protected abstract T getDTO(ID id);
protected abstract ID getId(T dto);
protected abstract List<T> getDTOsByTag(List<String> tagNames);
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/security/PermissionTest.java | src/test/java/org/ohdsi/webapi/security/PermissionTest.java | /*
* Copyright 2024 cknoll1.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ohdsi.webapi.security;
import java.util.Arrays;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.SimplePrincipalCollection;
import org.apache.shiro.subject.Subject;
import org.apache.shiro.util.ThreadContext;
import org.apache.shiro.web.mgt.DefaultWebSecurityManager;
import org.dbunit.operation.DatabaseOperation;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import org.junit.Before;
import org.junit.Test;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.ohdsi.webapi.shiro.PermissionManager;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.test.context.TestPropertySource;
/**
*
* @author cknoll1
*/
@TestPropertySource(properties = {
"security.provider=AtlasRegularSecurity"
})
public class PermissionTest extends AbstractDatabaseTest {
@Autowired
private PermissionManager permissionManager;
@Value("${security.provider}")
String securityProvider;
@Autowired
private DefaultWebSecurityManager securityManager;
private Subject subject;
@Before
public void setup() {
// Set the SecurityManager for the current thread
SimplePrincipalCollection principalCollection = new SimplePrincipalCollection();
principalCollection.addAll(Arrays.asList("permsTest"),"testRealm");
subject = new Subject.Builder(securityManager)
.authenticated(true)
.principals(principalCollection)
.buildSubject();
ThreadContext.bind(subject);
}
@Test
public void permsTest() throws Exception {
// need to clear authorization cache before each test
permissionManager.clearAuthorizationInfoCache();
Subject s = SecurityUtils.getSubject();
String subjetName = permissionManager.getSubjectName();
final String[] testDataSetsPaths = new String[] {"/permission/permsTest_PREP.json" };
loadPrepData(testDataSetsPaths, DatabaseOperation.REFRESH);
// subject can manage printer1 and printer2, can do print and query on any printer.
assertTrue(s.isPermitted("printer:manage:printer1"));
assertTrue(s.isPermitted("printer:manage:printer2"));
assertFalse(s.isPermitted("printer:manage:printer3"));
assertTrue(s.isPermitted("printer:query:printer4"));
assertTrue(s.isPermitted("printer:print:printer5"));
loadPrepData(testDataSetsPaths, DatabaseOperation.DELETE);
}
@Test
public void wildcardTest() throws Exception {
// need to clear authorization cache before each test
permissionManager.clearAuthorizationInfoCache();
Subject s = SecurityUtils.getSubject();
final String[] testDataSetsPaths = new String[] {"/permission/wildcardTest_PREP.json" };
loadPrepData(testDataSetsPaths, DatabaseOperation.REFRESH);
// subject has * permisison, so any permisison test is true
assertTrue(s.isPermitted("printer:manage:printer1"));
assertTrue(s.isPermitted("printer"));
loadPrepData(testDataSetsPaths, DatabaseOperation.DELETE);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/cohortcharacterization/CohortCharacterizationServiceTest.java | src/test/java/org/ohdsi/webapi/cohortcharacterization/CohortCharacterizationServiceTest.java | package org.ohdsi.webapi.cohortcharacterization;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.core.type.TypeReference;
import com.odysseusinc.arachne.commons.types.DBMSType;
import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.KerberosAuthMechanism;
import net.lingala.zip4j.ZipFile;
import net.lingala.zip4j.exception.ZipException;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.ohdsi.analysis.Utils;
import org.ohdsi.circe.helper.ResourceHelper;
import org.ohdsi.sql.SqlRender;
import org.ohdsi.sql.SqlSplit;
import org.ohdsi.sql.SqlTranslate;
import org.ohdsi.webapi.cohortcharacterization.converter.SerializedCcToCcConverter;
import org.ohdsi.webapi.cohortcharacterization.domain.CcGenerationEntity;
import org.ohdsi.webapi.cohortcharacterization.domain.CohortCharacterizationEntity;
import org.ohdsi.webapi.cohortcharacterization.dto.ExportExecutionResultRequest;
import org.ohdsi.webapi.generationcache.GenerationCacheTest;
import org.ohdsi.webapi.job.JobExecutionResource;
import org.ohdsi.webapi.source.Source;
import org.ohdsi.webapi.source.SourceDaimon;
import org.ohdsi.webapi.source.SourceRepository;
import org.ohdsi.webapi.source.SourceService;
import org.springframework.beans.factory.annotation.Autowired;
import javax.ws.rs.core.Response;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.sql.SQLException;
import java.util.*;
import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import org.ohdsi.webapi.AbstractDatabaseTest;
import org.springframework.beans.factory.annotation.Value;
public class CohortCharacterizationServiceTest extends AbstractDatabaseTest {
private static final String CDM_SQL = ResourceHelper.GetResourceAsString("/cdm-postgresql-ddl.sql");
private static final String PARAM_JSON = ResourceHelper.GetResourceAsString("/cohortcharacterization/reportData.json");
private static final String PARAM_JSON_WITH_STRATA = ResourceHelper.GetResourceAsString("/cohortcharacterization/reportDataWithStrata.json");
private static final String CC_JSON = ResourceHelper.GetResourceAsString("/cohortcharacterization/ibuprofenVsAspirin.json");
private static final String CC_WITH_STRATA_JSON = ResourceHelper.GetResourceAsString("/cohortcharacterization/ibuprofenVsAspirinWithStrata.json");
private static final String RESULT_SCHEMA_NAME = "results";
private static final String CDM_SCHEMA_NAME = "cdm";
private static final String SOURCE_KEY = "Embedded_PG";
private static final String EUNOMIA_CSV_ZIP = "/eunomia.csv.zip";
private static boolean isCdmInitialized = false;
@Autowired
private CcService ccService;
@Autowired
private CcController ccController;
@Autowired
private SourceRepository sourceRepository;
@Autowired
private SourceService sourceService;
@Value("${datasource.ohdsi.schema}")
private String ohdsiSchema;
private static final Collection<String> COHORT_DDL_FILE_PATHS = Arrays.asList(
"/ddl/results/cohort.sql",
"/ddl/results/cohort_cache.sql",
"/ddl/results/cohort_inclusion.sql",
"/ddl/results/cohort_inclusion_result.sql",
"/ddl/results/cohort_inclusion_stats.sql",
"/ddl/results/cohort_inclusion_result_cache.sql",
"/ddl/results/cohort_inclusion_stats_cache.sql",
"/ddl/results/cohort_summary_stats.sql",
"/ddl/results/cohort_summary_stats_cache.sql",
"/ddl/results/cohort_censor_stats.sql",
"/ddl/results/cohort_censor_stats_cache.sql",
"/ddl/results/cohort_characterizations.sql"
);
@Before
public void setUp() throws Exception {
if (!isCdmInitialized) {
// one-time setup of CDM and CDM source
truncateTable(String.format("%s.%s", ohdsiSchema, "source"));
resetSequence(String.format("%s.%s", ohdsiSchema,"source_sequence"));
sourceRepository.saveAndFlush(getCdmSource());
prepareCdmSchema();
isCdmInitialized = true;
}
prepareResultSchema();
}
@Ignore
@Test
public void testExportGeneration() throws Exception {
doTestExportGeneration(CC_JSON, PARAM_JSON);
}
@Ignore
@Test
public void testExportGenerationWithStrata() throws Exception {
doTestExportGeneration(CC_WITH_STRATA_JSON, PARAM_JSON_WITH_STRATA);
}
public void doTestExportGeneration(String entityStr, String paramData) throws Exception {
CohortCharacterizationEntity entity = new SerializedCcToCcConverter().convertToEntityAttribute(entityStr);
entity = ccService.importCc(entity);
JobExecutionResource executionResource = ccService.generateCc(entity.getId(), SOURCE_KEY);
CcGenerationEntity generationEntity;
while (true) {
generationEntity = ccService.findGenerationById(executionResource.getExecutionId());
if (generationEntity.getStatus().equals("FAILED") || generationEntity.getStatus().equals("COMPLETED")) {
break;
}
Thread.sleep(2000L);
}
assertEquals("COMPLETED", generationEntity.getStatus());
TypeReference<Data> typeRef = new TypeReference<Data>() {
};
Data data = Utils.deserialize(paramData, typeRef);
for (ParamItem paramItem : data.paramItems) {
checkRequest(entity, generationEntity.getId(), paramItem);
}
}
private void checkRequest(CohortCharacterizationEntity entity, Long generationId, ParamItem paramItem) throws IOException {
String dataItemMessage = String.format("Checking dataitem %s", paramItem.toString());
try {
ZipFile zipFile = getZipFile(generationId, paramItem);
if (paramItem.fileItems.isEmpty()) {
// File is valid
assertTrue(dataItemMessage, zipFile.isValidZipFile());
// but empty
assertTrue(dataItemMessage, zipFile.getFileHeaders().isEmpty());
} else {
// File should not be empty
assertTrue(dataItemMessage, zipFile.isValidZipFile());
Path tempDir = Files.createTempDirectory(String.valueOf(System.currentTimeMillis()));
tempDir.toFile().deleteOnExit();
zipFile.extractAll(tempDir.toAbsolutePath().toString());
assertEquals(dataItemMessage, paramItem.fileItems.size(), tempDir.toFile().listFiles().length);
for (File file : tempDir.toFile().listFiles()) {
String fileMessage = String.format("Checking filename %s for dataitem %s", file.getName(), paramItem.toString());
Optional<FileItem> fileItem = paramItem.fileItems.stream()
.filter(f -> f.fileName.equals(file.getName()))
.findAny();
assertTrue(fileMessage, fileItem.isPresent());
long count = Files.lines(file.toPath()).count();
// include header line
assertEquals(fileMessage, fileItem.get().lineCount + 1, count);
}
}
} catch (IllegalArgumentException e) {
// Exception should be thrown when parameter of feature is invalid
int analysisId = paramItem.analysisIds.stream().filter(
aid -> entity.getFeatureAnalyses().stream().noneMatch(fa -> Objects.equals(fa.getId(), aid))
).findFirst().get();
String expectedMessage = String.format("Feature with id=%s not found in analysis", analysisId);
assertEquals(dataItemMessage, e.getMessage(), expectedMessage);
}
}
private ZipFile getZipFile(Long id, ParamItem paramItem) throws IOException {
ExportExecutionResultRequest request = new ExportExecutionResultRequest();
request.setCohortIds(paramItem.cohortIds);
request.setAnalysisIds(paramItem.analysisIds);
request.setDomainIds(paramItem.domainIds);
request.setSummary(paramItem.isSummary);
request.setComparative(paramItem.isComparative);
Response response = ccController.exportGenerationsResults(id, request);
assertEquals(200, response.getStatus());
ByteArrayOutputStream baos = (ByteArrayOutputStream) response.getEntity();
File tempFile = File.createTempFile("reports", ".zip");
tempFile.deleteOnExit();
try (OutputStream outputStream = new FileOutputStream(tempFile)) {
baos.writeTo(outputStream);
}
return new ZipFile(tempFile);
}
private static void prepareResultSchema() {
String resultSql = getResultTablesSql();
jdbcTemplate.batchUpdate(SqlSplit.splitSql(resultSql));
}
private static void prepareCdmSchema() throws Exception {
String cdmSql = getCdmSql();
jdbcTemplate.batchUpdate(SqlSplit.splitSql(cdmSql));
}
private static String getResultTablesSql() {
StringBuilder ddl = new StringBuilder();
ddl.append(String.format("DROP SCHEMA IF EXISTS %s CASCADE;", RESULT_SCHEMA_NAME)).append("\n");
ddl.append(String.format("CREATE SCHEMA %s;", RESULT_SCHEMA_NAME)).append("\n");
COHORT_DDL_FILE_PATHS.forEach(sqlPath -> ddl.append(ResourceHelper.GetResourceAsString(sqlPath)).append("\n"));
String resultSql = SqlRender.renderSql(ddl.toString(), new String[]{"results_schema"}, new String[]{RESULT_SCHEMA_NAME});
return SqlTranslate.translateSql(resultSql, DBMSType.POSTGRESQL.getOhdsiDB());
}
private Source getCdmSource() throws SQLException {
Source source = new Source();
source.setSourceName("Embedded PG");
source.setSourceKey(SOURCE_KEY);
source.setSourceDialect(DBMSType.POSTGRESQL.getOhdsiDB());
source.setSourceConnection(getDataSource().getConnection().getMetaData().getURL());
source.setUsername("postgres");
source.setPassword("postgres");
source.setKrbAuthMethod(KerberosAuthMechanism.PASSWORD);
SourceDaimon cdmDaimon = new SourceDaimon();
cdmDaimon.setPriority(1);
cdmDaimon.setDaimonType(SourceDaimon.DaimonType.CDM);
cdmDaimon.setTableQualifier(CDM_SCHEMA_NAME);
cdmDaimon.setSource(source);
SourceDaimon vocabDaimon = new SourceDaimon();
vocabDaimon.setPriority(1);
vocabDaimon.setDaimonType(SourceDaimon.DaimonType.Vocabulary);
vocabDaimon.setTableQualifier(CDM_SCHEMA_NAME);
vocabDaimon.setSource(source);
SourceDaimon resultsDaimon = new SourceDaimon();
resultsDaimon.setPriority(1);
resultsDaimon.setDaimonType(SourceDaimon.DaimonType.Results);
resultsDaimon.setTableQualifier(RESULT_SCHEMA_NAME);
resultsDaimon.setSource(source);
source.setDaimons(Arrays.asList(cdmDaimon, vocabDaimon, resultsDaimon));
return source;
}
private static String getCdmSql() throws IOException, ZipException {
StringBuilder cdmSqlBuilder = new StringBuilder(
"DROP SCHEMA IF EXISTS @cdm_database_schema CASCADE; CREATE SCHEMA @cdm_database_schema;");
cdmSqlBuilder.append(CDM_SQL);
cdmSqlBuilder.append("ALTER TABLE @cdm_database_schema.vocabulary ALTER COLUMN vocabulary_reference DROP NOT NULL;\n");
cdmSqlBuilder.append("ALTER TABLE @cdm_database_schema.vocabulary ALTER COLUMN vocabulary_version DROP NOT NULL;\n");
Path tempDir = Files.createTempDirectory("");
tempDir.toFile().deleteOnExit();
// Direct Files.copy into new file in the temp folder throws Access Denied
File eunomiaZip = File.createTempFile("eunomia", "", tempDir.toFile());
try (InputStream is = GenerationCacheTest.class.getResourceAsStream(EUNOMIA_CSV_ZIP)) {
Files.copy(is, eunomiaZip.toPath(), REPLACE_EXISTING);
}
ZipFile zipFile = new ZipFile(eunomiaZip);
zipFile.extractAll(tempDir.toAbsolutePath().toString());
for (final File file : tempDir.toFile().listFiles()) {
if (file.getName().endsWith(".csv")) {
String tableName = file.getName().replace(".csv", "");
String sql = String.format("COPY @cdm_database_schema.%s FROM '%s' DELIMITER ',' CSV HEADER;", tableName, file.getAbsolutePath());
cdmSqlBuilder.append(sql).append("\n\n");
}
}
return cdmSqlBuilder.toString().replaceAll("@cdm_database_schema", CDM_SCHEMA_NAME);
}
public static class Data {
@JsonProperty("Params")
public List<ParamItem> paramItems;
}
public static class ParamItem {
@JsonProperty("analysisIds")
public List<Integer> analysisIds;
@JsonProperty("cohortIds")
public List<Integer> cohortIds;
@JsonProperty("domainIds")
public List<String> domainIds;
@JsonProperty("isSummary")
public Boolean isSummary;
@JsonProperty("fileDatas")
public List<FileItem> fileItems;
@JsonProperty("isComparative")
public Boolean isComparative;
@Override
public String toString() {
return new ToStringBuilder(this)
.append("analysisIds", analysisIds)
.append("cohortIds", cohortIds)
.append("isSummary", isSummary)
.append("isComparative", isComparative)
.toString();
}
}
public static class FileItem {
@JsonProperty("fileName")
public String fileName;
@JsonProperty("lineCount")
public Integer lineCount;
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/cohortcharacterization/SkeletonCohortCharacterizationTest.java | src/test/java/org/ohdsi/webapi/cohortcharacterization/SkeletonCohortCharacterizationTest.java | /*
* Copyright 2020 cknoll1.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ohdsi.webapi.cohortcharacterization;
import static org.hamcrest.Matchers.notNullValue;
import static org.junit.Assert.assertThat;
import org.junit.Test;
import org.ohdsi.cohortcharacterization.CCQueryBuilder;
/**
*
* @author cknoll1
*/
public class SkeletonCohortCharacterizationTest {
@Test
public void ccQueryBuilderTest() {
final Integer sourceId = 1;
final String cohortTable = "cohort";
final String sessionId = "session";
final String tempSchema = "tempSchema";
CCQueryBuilder ccQueryBuilder = new CCQueryBuilder("{}", cohortTable, sessionId, null, null, null, tempSchema, 0);
assertThat(ccQueryBuilder, notNullValue());
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/cohortresults/CohortResultsAnalysisRunnerTest.java | src/test/java/org/ohdsi/webapi/cohortresults/CohortResultsAnalysisRunnerTest.java | package org.ohdsi.webapi.cohortresults;
import org.junit.Test;
public class CohortResultsAnalysisRunnerTest {
@Test(expected = Exception.class)
public void testSaveIsFalseScenarios() {
CohortResultsAnalysisRunner r = new CohortResultsAnalysisRunner(null, null, null);
r.getCohortConditionDrilldown(null, -1, -1, 0, 0, null, false);
r.getCohortDataDensity(null, 0, null, null, null, false);
r.getCohortDeathData(null, 0, null, null, null, false);
r.getCohortDrugDrilldown(null, 0, 0, null, null, null, false);
r.getCohortMeasurementResults(null, 0, null, null, null, false);
r.getCohortMeasurementResultsDrilldown(null, 0, 0, null, null, null, false);
r.getCohortObservationPeriod(null, 0, null, null, null, false);
r.getCohortObservationResults(null, 0, null, null, null, false);
r.getCohortObservationResultsDrilldown(null, 0, 0, null, null, null, false);
r.getCohortProcedureDrilldown(null, 0, 0, null, null, null, false);
r.getCohortProceduresDrilldown(null, 0, 0, null, null, null, false);
r.getCohortSpecificSummary(null, 0, null, null, null, false);
r.getCohortSpecificTreemapResults(null, 0, null, null, null, false);
r.getCohortVisitsDrilldown(null, 0, 0, null, null, null, false);
r.getConditionEraDrilldown(null, 0, 0, null, null, null, false);
r.getConditionEraTreemap(null, 0, null, null, null, false);
r.getConditionResults(null, 0, 0, null, null, null, false);
r.getConditionTreemap(null, 0, null, null, null, false);
r.getDashboard(null, 0, null, null, null, false, false);
r.getDrugEraResults(null, 0, 0, null, null, null, false);
r.getDrugEraTreemap(null, 0, null, null, null, false);
r.getDrugResults(null, 0, 0, null, null, null, false);
r.getDrugTreemap(null, 0, null, null, null, false);
r.getHeraclesHeel(null, 0, null, false);
r.getPersonResults(null, 0, null, null, null, false);
r.getProcedureTreemap(null, 0, null, null, null, false);
r.getVisitTreemap(null, 0, null, null, null, false);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/vocabulary/test/ConceptSetExpressionTests.java | src/test/java/org/ohdsi/webapi/vocabulary/test/ConceptSetExpressionTests.java | /*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ohdsi.webapi.vocabulary.test;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.Assert;
import org.ohdsi.circe.vocabulary.Concept;
import org.ohdsi.circe.vocabulary.ConceptSetExpression;
import org.ohdsi.circe.vocabulary.ConceptSetExpressionQueryBuilder;
/**
*
* @author cknoll1
*/
public class ConceptSetExpressionTests {
private static ConceptSetExpression getTestExpression() {
ConceptSetExpression exp = new ConceptSetExpression();
exp.items = new ConceptSetExpression.ConceptSetItem[8];
exp.items[0] = new ConceptSetExpression.ConceptSetItem();
exp.items[0].concept = new Concept();
exp.items[0].concept.conceptId = 1L;
exp.items[0].concept.conceptName = "First Concept";
exp.items[0].isExcluded = false;
exp.items[0].includeDescendants = false;
exp.items[0].includeMapped = false;
exp.items[1] = new ConceptSetExpression.ConceptSetItem();
exp.items[1].concept = new Concept();
exp.items[1].concept.conceptId = 2L;
exp.items[1].concept.conceptName = "Second Concept";
exp.items[1].isExcluded = false;
exp.items[1].includeDescendants = true;
exp.items[1].includeMapped = false;
exp.items[2] = new ConceptSetExpression.ConceptSetItem();
exp.items[2].concept = new Concept();
exp.items[2].concept.conceptId = 3L;
exp.items[2].concept.conceptName = "Third Concept";
exp.items[2].isExcluded = false;
exp.items[2].includeDescendants = true;
exp.items[2].includeMapped = true;
exp.items[3] = new ConceptSetExpression.ConceptSetItem();
exp.items[3].concept = new Concept();
exp.items[3].concept.conceptId = 4L;
exp.items[3].concept.conceptName = "Forth Concept (Excluded)";
exp.items[3].isExcluded = true;
exp.items[3].includeDescendants = false;
exp.items[3].includeMapped = false;
exp.items[4] = new ConceptSetExpression.ConceptSetItem();
exp.items[4].concept = new Concept();
exp.items[4].concept.conceptId = 5L;
exp.items[4].concept.conceptName = "Fith Concept (Excluded)";
exp.items[4].isExcluded = true;
exp.items[4].includeDescendants = true;
exp.items[4].includeMapped = false;
exp.items[5] = new ConceptSetExpression.ConceptSetItem();
exp.items[5].concept = new Concept();
exp.items[5].concept.conceptId = 6L;
exp.items[5].concept.conceptName = "Sixth Concept (Excluded)";
exp.items[5].isExcluded = true;
exp.items[5].includeDescendants = false;
exp.items[5].includeMapped = true;
exp.items[6] = new ConceptSetExpression.ConceptSetItem();
exp.items[6].concept = new Concept();
exp.items[6].concept.conceptId = 7L;
exp.items[6].concept.conceptName = "Seventh Concept (Excluded)";
exp.items[6].isExcluded = true;
exp.items[6].includeDescendants = true;
exp.items[6].includeMapped = true;
exp.items[7] = new ConceptSetExpression.ConceptSetItem();
exp.items[7].concept = new Concept();
exp.items[7].concept.conceptId = 8L;
exp.items[7].concept.conceptName = "Eigth Concept";
exp.items[7].isExcluded = false;
exp.items[7].includeDescendants = false;
exp.items[7].includeMapped = true;
return exp;
}
@BeforeClass
public static void setUpClass() throws Exception {
}
@AfterClass
public static void tearDownClass() throws Exception {
}
@Test
public void SimpleConceptSetExpressionBuild() {
ConceptSetExpressionQueryBuilder builder = new ConceptSetExpressionQueryBuilder();
ConceptSetExpression testExpression = getTestExpression();
String conceptSetExpressionSql = builder.buildExpressionQuery(testExpression);
// included concepts should have (1,2,3,8)
Assert.assertTrue(conceptSetExpressionSql.indexOf("(1,2,3,8)") > 0);
// included descendants should have (2,3)
Assert.assertTrue(conceptSetExpressionSql.indexOf("(2,3)") > 0);
// excluded concepts should have (4,5,6,7)
Assert.assertTrue(conceptSetExpressionSql.indexOf("(4,5,6,7)") > 0);
// excluded descendants should have (5,7)
Assert.assertTrue(conceptSetExpressionSql.indexOf("(5,7)") > 0);
// mapped concepts should have (3,8)
Assert.assertTrue(conceptSetExpressionSql.indexOf("(3,8)") > 0);
// mapped descendants should have 3
Assert.assertTrue(conceptSetExpressionSql.indexOf("(3)") > 0);
// mapped excludes should have (6,7)
Assert.assertTrue(conceptSetExpressionSql.indexOf("(6,7)") > 0);
// mapped exclude descendants should have (7)
Assert.assertTrue(conceptSetExpressionSql.indexOf("(7)") > 0);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/test/java/org/ohdsi/webapi/cdmresults/cache/CDMResultsCacheTest.java | src/test/java/org/ohdsi/webapi/cdmresults/cache/CDMResultsCacheTest.java | package org.ohdsi.webapi.cdmresults.cache;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.only;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.runners.MockitoJUnitRunner;
import org.ohdsi.webapi.cdmresults.DescendantRecordCount;
@RunWith(MockitoJUnitRunner.class)
public class CDMResultsCacheTest {
private CDMResultsCache cache = new CDMResultsCache();
@Mock
private Function<List<Integer>, List<DescendantRecordCount>> function;
@Captor
private ArgumentCaptor<List<Integer>> idForRequestCaptor;
@Test
public void warm() {
assertFalse(cache.isWarm());
cache.warm();
assertTrue(cache.isWarm());
}
@Test
public void findAndCache_nothingCached() {
List<Integer> ids = Arrays.asList(1, 2, 3, 4);
when(function.apply(any())).thenReturn(
ids.stream().map(CDMResultsCacheTest.this::createDescendantRecordCount).collect(Collectors.toList())
);
Collection<DescendantRecordCount> records = cache.findAndCache(ids, function);
assertEquals(4, records.size());
assertEquals(ids, records.stream().map(DescendantRecordCount::getId).collect(Collectors.toList()));
}
@Test
public void findAndCache_getAllDataFromCache() {
List<Integer> ids = Arrays.asList(1, 2, 3, 4);
when(function.apply(any())).thenReturn(
ids.stream().map(CDMResultsCacheTest.this::createDescendantRecordCount).collect(Collectors.toList())
);
cache.findAndCache(ids, function);
cache.findAndCache(ids, function);
Collection<DescendantRecordCount> records = cache.findAndCache(ids, function);
verify(function, only()).apply(any());
assertEquals(ids, records.stream().map(DescendantRecordCount::getId).collect(Collectors.toList()));
}
@Test
public void findAndCache_getOnlySomeDataFromCache() {
List<Integer> ids1 = Arrays.asList(1, 2);
List<Integer> ids2 = Arrays.asList(1, 2, 3, 4);
when(function.apply(any())).then(invocation -> {
List<Integer> ids = invocation.getArgumentAt(0, List.class);
return ids.stream().map(CDMResultsCacheTest.this::createDescendantRecordCount).collect(Collectors.toList());
}
);
cache.findAndCache(ids1, function);
cache.findAndCache(ids2, function);
verify(function, times(2)).apply(idForRequestCaptor.capture());
assertEquals(Arrays.asList(1, 2), idForRequestCaptor.getAllValues().get(0));
assertEquals(Arrays.asList(3, 4), idForRequestCaptor.getAllValues().get(1));
}
@Test
public void findAndCache_idFromRequestThatDoesNotPresentInStorage() {
List<Integer> ids1 = Arrays.asList(1, 2, 3, 4);
List<Integer> ids2 = Arrays.asList(1, 2);
when(function.apply(any())).then(invocation -> {
List<Integer> ids = invocation.getArgumentAt(0, List.class);
return ids2.stream().map(CDMResultsCacheTest.this::createDescendantRecordCount).collect(Collectors.toList());
}
);
cache.findAndCache(ids1, function);
cache.findAndCache(ids1, function);
verify(function, only()).apply(idForRequestCaptor.capture());
assertEquals(ids1, idForRequestCaptor.getAllValues().get(0));
assertNotNull(cache.get(1));
assertNotNull(cache.get(2));
assertNull(cache.get(3));
assertNull(cache.get(4));
}
@Test
public void addValue() {
cache.cacheValue(createDescendantRecordCount(1));
cache.cacheValue(createDescendantRecordCount(2));
assertEquals(new Long(1_001L), cache.get(1).getRecordCount());
assertEquals(new Long(1_000_001L), cache.get(1).getDescendantRecordCount());
assertEquals(new Long(1_002L), cache.get(2).getRecordCount());
assertEquals(new Long(1_000_002L), cache.get(2).getDescendantRecordCount());
}
@Test
public void addValues() {
final List<DescendantRecordCount> records = IntStream.range(1, 10).boxed()
.map(this::createDescendantRecordCount)
.collect(Collectors.toList());
cache.cacheValues(records);
records.forEach(record ->
assertNotNull(cache.get(record.getId()))
);
}
@Test
public void get() {
cache.cacheValue(createDescendantRecordCount(1));
assertEquals(new Long(1_001L), cache.get(1).getRecordCount());
assertEquals(new Long(1_000_001L), cache.get(1).getDescendantRecordCount());
}
@Test
public void cacheRequestedIds() {
final List<Integer> ids = IntStream.range(1, 5).boxed()
.collect(Collectors.toList());
cache.cacheRequestedIds(ids);
ids.forEach(id ->
assertTrue(cache.isRequested(id))
);
}
@Test
public void cacheRequestedId() {
cache.cacheRequestedId(1);
cache.cacheRequestedId(2);
assertTrue(cache.isRequested(1));
assertTrue(cache.isRequested(2));
assertFalse(cache.isRequested(3));
}
@Test
public void isRequested() {
cache.cacheRequestedId(1);
assertTrue(cache.isRequested(1));
}
@Test
public void notRequested() {
cache.cacheRequestedId(1);
assertFalse(cache.isRequested(2));
}
@Test
public void isWarm() {
cache.warm();
assertTrue(cache.isWarm());
assertFalse(cache.notWarm());
}
private DescendantRecordCount createDescendantRecordCount(int id) {
long recordCount = 1_000 + id;
long descendantRecordCount = 1_000_000 + id;
DescendantRecordCount value = new DescendantRecordCount();
value.setId(id);
value.setRecordCount(recordCount);
value.setDescendantRecordCount(descendantRecordCount);
return value;
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/JdbcExceptionMapper.java | src/main/java/org/ohdsi/webapi/JdbcExceptionMapper.java | package org.ohdsi.webapi;
import com.odysseusinc.logging.event.FailedDbConnectEvent;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationEventPublisher;
import org.springframework.jdbc.CannotGetJdbcConnectionException;
import javax.ws.rs.core.Response;
import javax.ws.rs.ext.ExceptionMapper;
import javax.ws.rs.ext.Provider;
@Provider
public class JdbcExceptionMapper implements ExceptionMapper<CannotGetJdbcConnectionException> {
@Autowired
private ApplicationEventPublisher eventPublisher;
@Override
public Response toResponse(CannotGetJdbcConnectionException exception) {
eventPublisher.publishEvent(new FailedDbConnectEvent(this, exception.getMessage()));
return Response.ok().build();
}
} | java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/ConverterConfiguration.java | src/main/java/org/ohdsi/webapi/ConverterConfiguration.java | package org.ohdsi.webapi;
import com.odysseusinc.arachne.commons.utils.ConverterUtils;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.convert.support.DefaultConversionService;
import org.springframework.core.convert.support.GenericConversionService;
@Configuration
public class ConverterConfiguration {
@Bean
public GenericConversionService conversionService(){
return new DefaultConversionService();
}
@Bean
public ConverterUtils converterUtils(final GenericConversionService conversionService) {
return new ConverterUtils(conversionService);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/IExecutionInfo.java | src/main/java/org/ohdsi/webapi/IExecutionInfo.java | package org.ohdsi.webapi;
import java.util.Date;
public interface IExecutionInfo<T extends IExecutionInfo> {
Date getStartTime();
Integer getExecutionDuration();
GenerationStatus getStatus();
boolean getIsValid();
boolean getIsCanceled();
String getMessage();
T setStartTime(Date startTime);
T setExecutionDuration(Integer executionDuration);
T setStatus(GenerationStatus status);
T setIsValid(boolean valid);
T setMessage(String message);
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/LogConfiguration.java | src/main/java/org/ohdsi/webapi/LogConfiguration.java | package org.ohdsi.webapi;
import com.odysseusinc.logging.LoggingEventMessageFactory;
import com.odysseusinc.logging.LoggingService;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@Configuration
public class LogConfiguration {
@Bean
public LoggingEventMessageFactory loggingEventMessageFactory(){
return new LoggingEventMessageFactory();
}
@Bean
public LoggingService loggingService(LoggingEventMessageFactory factory){
return new LoggingService(factory);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/Pagination.java | src/main/java/org/ohdsi/webapi/Pagination.java | package org.ohdsi.webapi;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
@Target(ElementType.PARAMETER)
@Retention(RetentionPolicy.RUNTIME)
public @interface Pagination {
} | java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/CacheConfig.java | src/main/java/org/ohdsi/webapi/CacheConfig.java | package org.ohdsi.webapi;
import org.springframework.cache.annotation.EnableCaching;
import org.springframework.context.annotation.Configuration;
@Configuration
@EnableCaching
public class CacheConfig {
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/JerseyConfig.java | src/main/java/org/ohdsi/webapi/JerseyConfig.java | package org.ohdsi.webapi;
import org.glassfish.hk2.utilities.binding.AbstractBinder;
import org.glassfish.jersey.media.multipart.MultiPartFeature;
import org.glassfish.jersey.message.GZipEncoder;
import org.glassfish.jersey.server.ResourceConfig;
import org.glassfish.jersey.server.filter.EncodingFilter;
import org.glassfish.jersey.server.spi.internal.ValueFactoryProvider;
import org.ohdsi.webapi.cohortcharacterization.CcController;
import org.ohdsi.webapi.executionengine.controller.ScriptExecutionCallbackController;
import org.ohdsi.webapi.executionengine.controller.ScriptExecutionController;
import org.ohdsi.webapi.info.InfoService;
import org.ohdsi.webapi.security.PermissionController;
import org.ohdsi.webapi.security.SSOController;
import org.ohdsi.webapi.service.ActivityService;
import org.ohdsi.webapi.service.CDMResultsService;
import org.ohdsi.webapi.service.CohortAnalysisService;
import org.ohdsi.webapi.service.CohortDefinitionService;
import org.ohdsi.webapi.service.CohortResultsService;
import org.ohdsi.webapi.service.CohortService;
import org.ohdsi.webapi.service.ConceptSetService;
import org.ohdsi.webapi.service.DDLService;
import org.ohdsi.webapi.service.EvidenceService;
import org.ohdsi.webapi.service.FeasibilityService;
import org.ohdsi.webapi.service.FeatureExtractionService;
import org.ohdsi.webapi.service.IRAnalysisResource;
import org.ohdsi.webapi.service.JobService;
import org.ohdsi.webapi.service.PersonService;
import org.ohdsi.webapi.service.SqlRenderService;
import org.ohdsi.webapi.service.TherapyPathResultsService;
import org.ohdsi.webapi.service.UserService;
import org.ohdsi.webapi.service.VocabularyService;
import org.ohdsi.webapi.shiny.ShinyController;
import org.ohdsi.webapi.source.SourceController;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Component;
import javax.inject.Singleton;
import javax.ws.rs.ext.RuntimeDelegate;
import org.ohdsi.webapi.cache.CacheService;
/**
*
*/
@Component
public class JerseyConfig extends ResourceConfig implements InitializingBean {
@Value("${jersey.resources.root.package}")
private String rootPackage;
@Value("${shiny.enabled:false}")
private Boolean shinyEnabled;
public JerseyConfig() {
RuntimeDelegate.setInstance(new org.glassfish.jersey.internal.RuntimeDelegateImpl());
EncodingFilter.enableFor(this, GZipEncoder.class);
}
/* (non-Jsdoc)
* @see org.springframework.beans.factory.InitializingBean#afterPropertiesSet()
*/
@Override
public void afterPropertiesSet() throws Exception {
packages(this.rootPackage);
register(ActivityService.class);
register(CacheService.class);
register(CcController.class);
register(CDMResultsService.class);
register(CohortAnalysisService.class);
register(CohortDefinitionService.class);
register(CohortResultsService.class);
register(CohortService.class);
register(ConceptSetService.class);
register(DDLService.class);
register(EvidenceService.class);
register(FeasibilityService.class);
register(FeatureExtractionService.class);
register(InfoService.class);
register(IRAnalysisResource.class);
register(JobService.class);
register(MultiPartFeature.class);
register(PermissionController.class);
register(PersonService.class);
register(ScriptExecutionController.class);
register(ScriptExecutionCallbackController.class);
register(SourceController.class);
register(SqlRenderService.class);
register(SSOController.class);
register(TherapyPathResultsService.class);
register(UserService.class);
register(VocabularyService.class);
register(new AbstractBinder() {
@Override
protected void configure() {
bind(PageableValueFactoryProvider.class)
.to(ValueFactoryProvider.class)
.in(Singleton.class);
}
});
if (shinyEnabled) {
register(ShinyController.class);
}
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/SchedulerConfiguration.java | src/main/java/org/ohdsi/webapi/SchedulerConfiguration.java | package org.ohdsi.webapi;
import com.cronutils.model.definition.CronDefinition;
import com.cronutils.model.definition.CronDefinitionBuilder;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.scheduling.TaskScheduler;
import org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler;
import static com.cronutils.model.CronType.QUARTZ;
@Configuration
public class SchedulerConfiguration {
@Bean
public TaskScheduler taskScheduler() {
final ThreadPoolTaskScheduler taskScheduler = new ThreadPoolTaskScheduler();
taskScheduler.setPoolSize(20);
taskScheduler.initialize();
return taskScheduler;
}
@Bean
public CronDefinition cronDefinition() {
return CronDefinitionBuilder.instanceDefinitionFor(QUARTZ);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/WebApi.java | src/main/java/org/ohdsi/webapi/WebApi.java | package org.ohdsi.webapi;
import org.apache.catalina.webresources.TomcatURLStreamHandlerFactory;
import org.springframework.boot.autoconfigure.SpringBootApplication;
import org.springframework.boot.autoconfigure.orm.jpa.HibernateJpaAutoConfiguration;
import org.springframework.boot.autoconfigure.web.ErrorMvcAutoConfiguration;
import org.springframework.boot.builder.SpringApplicationBuilder;
import org.springframework.boot.web.support.SpringBootServletInitializer;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.EnableAspectJAutoProxy;
import org.springframework.scheduling.annotation.EnableScheduling;
import javax.annotation.PostConstruct;
import java.util.TimeZone;
import org.springframework.boot.autoconfigure.solr.SolrAutoConfiguration;
/**
* Launch as java application or deploy as WAR (@link {@link WebApplication}
* will source this file).
*/
@EnableScheduling
@SpringBootApplication(exclude={HibernateJpaAutoConfiguration.class, ErrorMvcAutoConfiguration.class, SolrAutoConfiguration.class})
@EnableAspectJAutoProxy(proxyTargetClass = true)
public class WebApi extends SpringBootServletInitializer {
@Override
protected SpringApplicationBuilder configure(final SpringApplicationBuilder application) {
return application.sources(WebApi.class);
}
public static void main(final String[] args) throws Exception
{
TomcatURLStreamHandlerFactory.disable();
new SpringApplicationBuilder(WebApi.class).run(args);
}
@PostConstruct
public void init() {
TimeZone.setDefault(TimeZone.getTimeZone("UTC"));
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/AuthDataSource.java | src/main/java/org/ohdsi/webapi/AuthDataSource.java | /*
*
* Copyright 2017 Observational Health Data Sciences and Informatics
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
* Authors: Mikhail Mironov, Vitaly Koulakov
*
*/
package org.ohdsi.webapi;
import com.zaxxer.hikari.HikariConfig;
import com.zaxxer.hikari.HikariDataSource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import javax.sql.DataSource;
@Configuration("authDataSourceConfig")
@ConditionalOnProperty(name = "security.provider", havingValue = "AtlasRegularSecurity")
public class AuthDataSource {
private final Logger logger = LoggerFactory.getLogger(AuthDataSource.class);
@Value("${security.db.datasource.driverClassName}")
private String driverClassName;
@Value("${security.db.datasource.url}")
private String url;
@Value("${security.db.datasource.username}")
private String username;
@Value("${security.db.datasource.password}")
private String password;
@Value("${security.db.datasource.schema}")
private String schema;
@Value("${spring.datasource.hikari.connection-test-query}")
private String testQuery;
@Value("${spring.datasource.hikari.connection-test-query-timeout}")
private Long validationTimeout;
@Value("${spring.datasource.hikari.maximum-pool-size}")
private int maxPoolSize;
@Value("${spring.datasource.hikari.minimum-idle}")
private int minPoolIdle;
@Value("${spring.datasource.hikari.connection-timeout}")
private int connectionTimeout;
@Value("${spring.datasource.hikari.register-mbeans}")
private boolean registerMbeans;
@Value("${spring.datasource.hikari.mbean-name}")
private String mbeanName;
@Bean(name = "authDataSource")
public DataSource authDataSource() {
try {
HikariConfig config = new HikariConfig();
config.setDriverClassName(driverClassName);
config.setJdbcUrl(url);
config.setUsername(username);
config.setPassword(password);
config.setSchema(schema);
config.setConnectionTestQuery(testQuery);
config.setConnectionTimeout(connectionTimeout);
config.setMaximumPoolSize(maxPoolSize);
config.setMinimumIdle(minPoolIdle);
config.setValidationTimeout(validationTimeout);
config.setPoolName(mbeanName);
config.setRegisterMbeans(registerMbeans);
return new HikariDataSource(config);
} catch (Exception ex) {
logger.error("Failed to initialize connection to DB used for authentication: {}", ex.getMessage());
return null;
}
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/JMXConfiguration.java | src/main/java/org/ohdsi/webapi/JMXConfiguration.java | package org.ohdsi.webapi;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.EnableMBeanExport;
import org.springframework.jmx.support.RegistrationPolicy;
@Configuration
@EnableMBeanExport(registration = RegistrationPolicy.IGNORE_EXISTING)
public class JMXConfiguration {
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/OidcConfCreator.java | src/main/java/org/ohdsi/webapi/OidcConfCreator.java | /*
*
* Copyright 2017 Observational Health Data Sciences and Informatics
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
* Authors: Mikhail Mironov
*
*/
package org.ohdsi.webapi;
import com.nimbusds.jose.JWSAlgorithm;
import org.pac4j.oidc.config.OidcConfiguration;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Component;
import java.util.HashMap;
import java.util.Map;
@Component
public class OidcConfCreator {
@Value("${security.oid.clientId}")
private String clientId;
@Value("${security.oid.apiSecret}")
private String apiSecret;
@Value("${security.oid.url}")
private String url;
@Value("${security.oid.logoutUrl}")
private String logoutUrl;
@Value("${security.oid.extraScopes}")
private String extraScopes;
@Value("#{${security.oid.customParams:{T(java.util.Collections).emptyMap()}}}")
private Map<String, String> customParams = new HashMap<>();
@Value("${security.oauth.callback.api}")
private String oauthApiCallback;
public OidcConfiguration build() {
OidcConfiguration conf = new OidcConfiguration();
conf.setClientId(clientId);
conf.setSecret(apiSecret);
conf.setDiscoveryURI(url);
conf.setLogoutUrl(logoutUrl);
conf.setWithState(true);
conf.setUseNonce(true);
if (customParams != null) {
customParams.forEach(conf::addCustomParam);
}
String scopes = "openid";
if (extraScopes != null && !extraScopes.isEmpty()){
scopes += " ";
scopes += extraScopes;
}
conf.setScope(scopes);
conf.setPreferredJwsAlgorithm(JWSAlgorithm.RS256);
return conf;
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/JobInvalidator.java | src/main/java/org/ohdsi/webapi/JobInvalidator.java | package org.ohdsi.webapi;
import org.ohdsi.webapi.executionengine.entity.ExecutionEngineAnalysisStatus;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.admin.service.SearchableJobExecutionDao;
import org.springframework.batch.core.BatchStatus;
import org.springframework.batch.core.ExitStatus;
import org.springframework.batch.core.JobExecution;
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.DependsOn;
import org.springframework.stereotype.Component;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct;
import java.util.Calendar;
@Component
@DependsOn("flyway")
public class JobInvalidator {
private static final Logger log = LoggerFactory.getLogger(JobInvalidator.class);
public static final String INVALIDATED_BY_SYSTEM_EXIT_MESSAGE = "Invalidated by system";
private final JobRepository jobRepository;
private final TransactionTemplate transactionTemplateRequiresNew;
private final SearchableJobExecutionDao jobExecutionDao;
@Autowired
public JobInvalidator(JobRepository repository, TransactionTemplate transactionTemplateRequiresNew,
SearchableJobExecutionDao jobExecutionDao) {
this.jobRepository = repository;
this.transactionTemplateRequiresNew = transactionTemplateRequiresNew;
this.jobExecutionDao = jobExecutionDao;
}
@PostConstruct
private void invalidateGenerations() {
transactionTemplateRequiresNew.execute(s -> {
jobExecutionDao.getRunningJobExecutions().forEach(this::invalidationJobExecution);
return null;
});
}
public void invalidateJobExecutionById(ExecutionEngineAnalysisStatus executionEngineAnalysisStatus) {
JobExecution job = jobExecutionDao.getJobExecution(executionEngineAnalysisStatus.getExecutionEngineGeneration().getId());
if (job == null || job.getJobId() == null) {
log.error("Cannot invalidate job. There is no job for execution-engine-analysis-status with id = {}", executionEngineAnalysisStatus.getId());
return;
}
invalidationJobExecution(job);
}
public void invalidationJobExecution(JobExecution job) {
job.setStatus(BatchStatus.FAILED);
job.setExitStatus(new ExitStatus(ExitStatus.FAILED.getExitCode(), INVALIDATED_BY_SYSTEM_EXIT_MESSAGE));
job.setEndTime(Calendar.getInstance().getTime());
jobRepository.update(job);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/ShiroConfiguration.java | src/main/java/org/ohdsi/webapi/ShiroConfiguration.java | package org.ohdsi.webapi;
import java.util.Collection;
import java.util.Set;
import org.apache.shiro.realm.Realm;
import org.apache.shiro.spring.web.ShiroFilterFactoryBean;
import org.apache.shiro.web.mgt.DefaultWebSecurityManager;
import org.ohdsi.webapi.shiro.AtlasWebSecurityManager;
import org.ohdsi.webapi.shiro.lockout.*;
import org.ohdsi.webapi.shiro.management.DataSourceAccessBeanPostProcessor;
import org.ohdsi.webapi.shiro.management.DisabledSecurity;
import org.ohdsi.webapi.shiro.management.Security;
import org.ohdsi.webapi.shiro.management.datasource.DataSourceAccessParameterResolver;
import org.ohdsi.webapi.shiro.realms.JwtAuthRealm;
import org.ohdsi.webapi.shiro.subject.WebDelegatingRunAsSubjectFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression;
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
import org.springframework.context.ApplicationEventPublisher;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import javax.servlet.Filter;
import java.util.Map;
import java.util.stream.Collectors;
/**
* Created by GMalikov on 20.08.2015.
*/
@Configuration
public class ShiroConfiguration {
@Value("${security.maxLoginAttempts}")
private int maxLoginAttempts;
@Value("${security.duration.initial}")
private long initialDuration;
@Value("${security.duration.increment}")
private long increment;
@Value("${spring.aop.proxy-target-class:false}")
private Boolean proxyTargetClass;
@Autowired
protected ApplicationEventPublisher eventPublisher;
@Bean
public ShiroFilterFactoryBean shiroFilter(Security security, LockoutPolicy lockoutPolicy) {
ShiroFilterFactoryBean shiroFilter = new ShiroFilterFactoryBean();
shiroFilter.setSecurityManager(securityManager(security, lockoutPolicy));
Map<String, Filter> filters = security.getFilters().entrySet().stream()
.collect(Collectors.toMap(f -> f.getKey().getTemplateName(), Map.Entry::getValue));
shiroFilter.setFilters(filters);
shiroFilter.setFilterChainDefinitionMap(security.getFilterChain());
return shiroFilter;
}
@Bean
public DefaultWebSecurityManager securityManager(Security security, LockoutPolicy lockoutPolicy) {
Set<Realm> realmsForAuthentication = security.getRealms();
Collection<Realm> realmsForAuthorization = getJwtAuthRealmForAuthorization(security);
final DefaultWebSecurityManager securityManager = new AtlasWebSecurityManager(
lockoutPolicy,
security.getAuthenticator(),
realmsForAuthentication,
realmsForAuthorization
);
securityManager.setSubjectFactory(new WebDelegatingRunAsSubjectFactory());
return securityManager;
}
@Bean
@ConditionalOnExpression("#{!'${security.provider}'.equals('AtlasRegularSecurity')}")
public LockoutPolicy noLockoutPolicy() {
return new NoLockoutPolicy();
}
@Bean
@ConditionalOnProperty(name = "security.provider", havingValue = "AtlasRegularSecurity")
public LockoutPolicy lockoutPolicy() {
return new DefaultLockoutPolicy(lockoutStrategy(), maxLoginAttempts, eventPublisher);
}
@Bean
@ConditionalOnProperty(name = "security.provider", havingValue = "AtlasRegularSecurity")
public LockoutStrategy lockoutStrategy() {
return new ExponentLockoutStrategy(initialDuration, increment, maxLoginAttempts);
}
@Bean
@ConditionalOnMissingBean(value = DisabledSecurity.class)
public DataSourceAccessBeanPostProcessor dataSourceAccessBeanPostProcessor(DataSourceAccessParameterResolver parameterResolver) {
return new DataSourceAccessBeanPostProcessor(parameterResolver, proxyTargetClass);
}
private Collection<Realm> getJwtAuthRealmForAuthorization(Security security) {
return security.getRealms().stream()
.filter(JwtAuthRealm.class::isInstance)
.collect(Collectors.toList());
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/GenerationStatus.java | src/main/java/org/ohdsi/webapi/GenerationStatus.java | /*
* Copyright 2015 Observational Health Data Sciences and Informatics [OHDSI.org].
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ohdsi.webapi;
/**
*
* @author Chris Knoll <cknoll@ohdsi.org>
*/
public enum GenerationStatus {
ERROR,
PENDING,
RUNNING,
COMPLETE
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/DataAccessConfig.java | src/main/java/org/ohdsi/webapi/DataAccessConfig.java | package org.ohdsi.webapi;
import com.cosium.spring.data.jpa.entity.graph.repository.support.EntityGraphJpaRepositoryFactoryBean;
import com.odysseusinc.datasourcemanager.encryption.EncryptorUtils;
import com.odysseusinc.datasourcemanager.encryption.NotEncrypted;
import org.jasypt.encryption.pbe.PBEStringEncryptor;
import org.jasypt.hibernate4.encryptor.HibernatePBEEncryptorRegistry;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.DependsOn;
import org.springframework.context.annotation.Primary;
import org.springframework.core.env.Environment;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.jdbc.datasource.DriverManagerDataSource;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import org.springframework.transaction.support.TransactionTemplate;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import java.sql.Driver;
import java.sql.DriverManager;
import java.sql.SQLException;
import java.util.Properties;
/**
*
*/
@Configuration
@EnableTransactionManagement
@EnableJpaRepositories(repositoryFactoryBeanClass = EntityGraphJpaRepositoryFactoryBean.class)
public class DataAccessConfig {
private final Logger logger = LoggerFactory.getLogger(DataAccessConfig.class);
@Autowired
private Environment env;
@Value("${jasypt.encryptor.enabled}")
private boolean encryptorEnabled;
private Properties getJPAProperties() {
Properties properties = new Properties();
properties.setProperty("hibernate.default_schema", this.env.getProperty("spring.jpa.properties.hibernate.default_schema"));
properties.setProperty("hibernate.dialect", this.env.getProperty("spring.jpa.properties.hibernate.dialect"));
properties.setProperty("hibernate.generate_statistics", this.env.getProperty("spring.jpa.properties.hibernate.generate_statistics"));
properties.setProperty("hibernate.jdbc.batch_size", this.env.getProperty("spring.jpa.properties.hibernate.jdbc.batch_size"));
properties.setProperty("hibernate.order_inserts", this.env.getProperty("spring.jpa.properties.hibernate.order_inserts"));
properties.setProperty("hibernate.id.new_generator_mappings", "true");
return properties;
}
@Bean
@DependsOn("defaultStringEncryptor")
@Primary
public DataSource primaryDataSource() {
logger.info("datasource.url is: " + this.env.getRequiredProperty("datasource.url"));
String driver = this.env.getRequiredProperty("datasource.driverClassName");
String url = this.env.getRequiredProperty("datasource.url");
String user = this.env.getRequiredProperty("datasource.username");
String pass = this.env.getRequiredProperty("datasource.password");
boolean autoCommit = false;
//pooling - currently issues with (at least) oracle with use of temp tables and "on commit preserve rows" instead of "on commit delete rows";
//http://forums.ohdsi.org/t/transaction-vs-session-scope-for-global-temp-tables-statements/333/2
/*final PoolConfiguration pc = new org.apache.tomcat.jdbc.pool.PoolProperties();
pc.setDriverClassName(driver);
pc.setUrl(url);
pc.setUsername(user);
pc.setPassword(pass);
pc.setDefaultAutoCommit(autoCommit);*/
//non-pooling
DriverManagerDataSource ds = new DriverManagerDataSource(url, user, pass);
ds.setDriverClassName(driver);
//note autocommit defaults vary across vendors. use provided @Autowired TransactionTemplate
String[] supportedDrivers;
supportedDrivers = new String[]{"org.postgresql.Driver", "com.microsoft.sqlserver.jdbc.SQLServerDriver", "oracle.jdbc.driver.OracleDriver", "com.amazon.redshift.jdbc.Driver", "com.cloudera.impala.jdbc.Driver", "net.starschema.clouddb.jdbc.BQDriver", "org.netezza.Driver", "com.simba.googlebigquery.jdbc42.Driver", "org.apache.hive.jdbc.HiveDriver", "com.simba.spark.jdbc.Driver", "net.snowflake.client.jdbc.SnowflakeDriver", "com.databricks.client.jdbc.Driver", "com.intersystems.jdbc.IRISDriver"};
for (String driverName : supportedDrivers) {
try {
Class.forName(driverName);
logger.info("driver loaded: {}", driverName);
} catch (Exception ex) {
logger.info("error loading {} driver. {}", driverName, ex.getMessage());
}
}
// Redshift driver can be loaded first because it is mentioned in manifest file -
// put the redshift driver at the end so that it doesn't
// conflict with postgres queries
java.util.Enumeration<Driver> drivers = DriverManager.getDrivers();
while (drivers.hasMoreElements()) {
Driver d = drivers.nextElement();
if (d.getClass().getName().contains("com.amazon.redshift.jdbc")) {
try {
DriverManager.deregisterDriver(d);
DriverManager.registerDriver(d);
} catch (SQLException e) {
throw new RuntimeException("Could not deregister redshift driver", e);
}
}
}
return ds;
//return new org.apache.tomcat.jdbc.pool.DataSource(pc);
}
@Bean
public PBEStringEncryptor defaultStringEncryptor(){
PBEStringEncryptor stringEncryptor = encryptorEnabled ?
EncryptorUtils.buildStringEncryptor(env) :
new NotEncrypted();
HibernatePBEEncryptorRegistry
.getInstance()
.registerPBEStringEncryptor("defaultStringEncryptor", stringEncryptor);
return stringEncryptor;
}
@Bean
public EntityManagerFactory entityManagerFactory(DataSource dataSource) {
HibernateJpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
vendorAdapter.setGenerateDdl(false);
vendorAdapter.setShowSql(Boolean.valueOf(this.env.getRequiredProperty("spring.jpa.show-sql")));
//hibernate.dialect is resolved based on driver
//vendorAdapter.setDatabasePlatform(hibernateDialect);
LocalContainerEntityManagerFactoryBean factory = new LocalContainerEntityManagerFactoryBean();
factory.setJpaVendorAdapter(vendorAdapter);
factory.setJpaProperties(getJPAProperties());
factory.setPackagesToScan("org.ohdsi.webapi");
factory.setDataSource(dataSource);
factory.afterPropertiesSet();
return factory.getObject();
}
@Bean
@Primary
//This is needed so that JpaTransactionManager is used for autowiring, instead of DataSourceTransactionManager
public PlatformTransactionManager jpaTransactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager txManager = new JpaTransactionManager();
txManager.setEntityManagerFactory(entityManagerFactory);
return txManager;
}
@Bean
public TransactionTemplate transactionTemplate(PlatformTransactionManager transactionManager) {
TransactionTemplate transactionTemplate = new TransactionTemplate();
transactionTemplate.setTransactionManager(transactionManager);
return transactionTemplate;
}
@Bean
public TransactionTemplate transactionTemplateRequiresNew(PlatformTransactionManager transactionManager) {
TransactionTemplate transactionTemplate = new TransactionTemplate();
transactionTemplate.setTransactionManager(transactionManager);
transactionTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
return transactionTemplate;
}
@Bean
public TransactionTemplate transactionTemplateNoTransaction(PlatformTransactionManager transactionManager) {
TransactionTemplate transactionTemplate = new TransactionTemplate();
transactionTemplate.setTransactionManager(transactionManager);
transactionTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_NOT_SUPPORTED);
return transactionTemplate;
}
/*
public String getSparqlEndpoint()
{
String sparqlEndpoint = this.env.getRequiredProperty("sparql.endpoint");
return sparqlEndpoint;
}*/
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/GenerationStatusConverter.java | src/main/java/org/ohdsi/webapi/GenerationStatusConverter.java | /*
* Copyright 2015 Observational Health Data Sciences and Informatics [OHDSI.org].
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ohdsi.webapi;
import javax.persistence.AttributeConverter;
import javax.persistence.Converter;
/**
*
* @author Chris Knoll <cknoll@ohdsi.org>
*/
@Converter(autoApply = true)
public class GenerationStatusConverter implements AttributeConverter<GenerationStatus, Integer>{
@Override
public Integer convertToDatabaseColumn(GenerationStatus status) {
switch (status) {
case ERROR:
return -1;
case PENDING:
return 0;
case RUNNING:
return 1;
case COMPLETE:
return 2;
default:
throw new IllegalArgumentException("Unknown value: " + status);
}
}
@Override
public GenerationStatus convertToEntityAttribute(Integer statusValue) {
switch (statusValue) {
case -1: return GenerationStatus.ERROR;
case 0: return GenerationStatus.PENDING;
case 1: return GenerationStatus.RUNNING;
case 2: return GenerationStatus.COMPLETE;
default: throw new IllegalArgumentException("Unknown status value: " + statusValue);
}
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/FlywayConfig.java | src/main/java/org/ohdsi/webapi/FlywayConfig.java | package org.ohdsi.webapi;
import com.odysseusinc.arachne.commons.config.flyway.ApplicationContextAwareSpringJdbcMigrationResolver;
import javax.sql.DataSource;
import org.flywaydb.core.Flyway;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
import org.springframework.boot.autoconfigure.flyway.FlywayDataSource;
import org.springframework.boot.autoconfigure.flyway.FlywayMigrationInitializer;
import org.springframework.boot.autoconfigure.jdbc.DataSourceBuilder;
import org.springframework.boot.context.properties.ConfigurationProperties;
import org.springframework.context.ApplicationContext;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
/**
*
*/
@Configuration
@ConditionalOnProperty(prefix = "flyway", name = "enabled", matchIfMissing = true)
public class FlywayConfig {
@Bean
@ConfigurationProperties(prefix="flyway.datasource")
@FlywayDataSource
public DataSource secondaryDataSource() {
return DataSourceBuilder.create().build();
}
@Bean(initMethod = "migrate", name = "flyway")
@ConfigurationProperties(prefix="flyway")
public Flyway flyway() {
Flyway flyway = new Flyway();
flyway.setDataSource(secondaryDataSource());
return flyway;
}
@Bean
public FlywayMigrationInitializer flywayInitializer(ApplicationContext context, Flyway flyway) {
ApplicationContextAwareSpringJdbcMigrationResolver contextAwareResolver = new ApplicationContextAwareSpringJdbcMigrationResolver(context);
flyway.setResolvers(contextAwareResolver);
return new FlywayMigrationInitializer(flyway, null);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/RLangClassImpl.java | src/main/java/org/ohdsi/webapi/RLangClassImpl.java | package org.ohdsi.webapi;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.ohdsi.analysis.RLangClass;
/**
*
* @author asena5
*/
public abstract class RLangClassImpl implements RLangClass {
/**
*
*/
protected String attrClass = "args";
/**
* Get attrClass
* @return attrClass
**/
@JsonProperty("attr_class")
public String getAttrClass() {
return attrClass;
}
/**
*
* @param attrClass
*/
public void setAttrClass(String attrClass) {
this.attrClass = attrClass;
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/KrbConfiguration.java | src/main/java/org/ohdsi/webapi/KrbConfiguration.java | package org.ohdsi.webapi;
import com.odysseusinc.datasourcemanager.krblogin.KerberosService;
import com.odysseusinc.datasourcemanager.krblogin.KerberosServiceImpl;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@Configuration
public class KrbConfiguration {
@Value("${kerberos.timeout}")
private long timeout;
@Value("${kerberos.kinitPath}")
private String kinitPath;
@Value("${kerberos.configPath}")
private String configPath;
@Bean
public KerberosService kerberosService(){
return new KerberosServiceImpl(timeout, kinitPath, configPath);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/PageableValueFactoryProvider.java | src/main/java/org/ohdsi/webapi/PageableValueFactoryProvider.java | /*
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ohdsi.webapi;
import java.util.ArrayList;
import java.util.List;
import javax.inject.Inject;
import javax.ws.rs.DefaultValue;
import javax.ws.rs.QueryParam;
import org.glassfish.hk2.api.Factory;
import org.glassfish.hk2.api.ServiceLocator;
import org.glassfish.jersey.server.internal.inject.AbstractContainerRequestValueFactory;
import org.glassfish.jersey.server.model.Parameter;
import org.glassfish.jersey.server.spi.internal.ValueFactoryProvider;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Sort;
public class PageableValueFactoryProvider implements ValueFactoryProvider {
private final ServiceLocator locator;
@Inject
public PageableValueFactoryProvider(ServiceLocator locator) {
this.locator = locator;
}
@Override
public Factory<?> getValueFactory(Parameter parameter) {
if (parameter.getRawType() == Pageable.class
&& parameter.isAnnotationPresent(Pagination.class)) {
Factory<?> factory = new PageableValueFactory(locator);
return factory;
}
return null;
}
@Override
public PriorityType getPriority() {
return Priority.NORMAL;
}
private static class PageableValueFactory
extends AbstractContainerRequestValueFactory<Pageable> {
@QueryParam("page") @DefaultValue("0") Integer page;
@QueryParam("size") @DefaultValue("10") Integer size;
@QueryParam("sort") List<String> sort;
private final ServiceLocator locator;
private PageableValueFactory(ServiceLocator locator) {
this.locator = locator;
}
@Override
public Pageable provide() {
locator.inject(this);
List<Sort.Order> orders = new ArrayList<>();
for (String propOrder: sort) {
String[] propOrderSplit = propOrder.split(",");
String property = propOrderSplit[0];
if (propOrderSplit.length == 1) {
orders.add(new Sort.Order(property));
} else {
Sort.Direction direction
= Sort.Direction.fromStringOrNull(propOrderSplit[1]);
orders.add(new Sort.Order(direction, property));
}
}
return new PageRequest(page, size,
orders.isEmpty() ? null : new Sort(orders));
}
}
} | java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/CommonDTO.java | src/main/java/org/ohdsi/webapi/CommonDTO.java | package org.ohdsi.webapi;
public interface CommonDTO {
String getName();
void setName(String name);
Number getId();
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/I18nConfig.java | src/main/java/org/ohdsi/webapi/I18nConfig.java | package org.ohdsi.webapi;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.web.servlet.LocaleResolver;
import org.springframework.web.servlet.config.annotation.InterceptorRegistry;
import org.springframework.web.servlet.config.annotation.WebMvcConfigurerAdapter;
import org.springframework.web.servlet.i18n.AcceptHeaderLocaleResolver;
import org.springframework.web.servlet.i18n.LocaleChangeInterceptor;
import java.util.Locale;
@Configuration
public class I18nConfig {
@Bean
public LocaleResolver localeResolver() {
AcceptHeaderLocaleResolver localeResolver = new AcceptHeaderLocaleResolver();
localeResolver.setDefaultLocale(new Locale("en"));
return localeResolver;
}
public void addInterceptors(InterceptorRegistry registry) {
LocaleChangeInterceptor localeChangeInterceptor = new LocaleChangeInterceptor();
localeChangeInterceptor.setParamName("lang");
registry.addInterceptor(localeChangeInterceptor);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/KerberosUtils.java | src/main/java/org/ohdsi/webapi/KerberosUtils.java | package org.ohdsi.webapi;
import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.DataSourceUnsecuredDTO;
import com.odysseusinc.arachne.execution_engine_common.util.ConnectionParams;
import org.ohdsi.webapi.source.Source;
public final class KerberosUtils {
private KerberosUtils(){}
public static void setKerberosParams(Source source, ConnectionParams connectionParams, DataSourceUnsecuredDTO ds) {
ds.setUseKerberos(Boolean.TRUE);
ds.setKrbAuthMethod(source.getKrbAuthMethod());
ds.setKeyfile(source.getKeyfile());
if (source.getKrbAdminServer() != null) {
ds.setKrbAdminFQDN(source.getKrbAdminServer());
} else {
ds.setKrbAdminFQDN(connectionParams.getKrbFQDN());
}
ds.setKrbFQDN(connectionParams.getKrbFQDN());
ds.setKrbRealm(connectionParams.getKrbRealm());
ds.setKrbPassword(connectionParams.getPassword());
ds.setKrbUser(connectionParams.getUser());
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/Constants.java | src/main/java/org/ohdsi/webapi/Constants.java | package org.ohdsi.webapi;
import com.google.common.collect.ImmutableList;
import org.springframework.batch.core.ExitStatus;
public interface Constants {
String DEFAULT_DIALECT = "sql server";
String GENERATE_COHORT = "generateCohort";
String GENERATE_COHORT_CHARACTERIZATION = "generateCohortCharacterization";
String GENERATE_PATHWAY_ANALYSIS = "generatePathwayAnalysis";
String GENERATE_IR_ANALYSIS = "irAnalysis";
String GENERATE_PREDICTION_ANALYSIS = "generatePredictionAnalysis";
String GENERATE_ESTIMATION_ANALYSIS = "generateEstimationAnalysis";
String WARM_CACHE = "warmCache";
String USERS_IMPORT = "usersImport";
String JOB_IS_ALREADY_SCHEDULED = "Job for provider %s is already scheduled";
String FAILED = ExitStatus.FAILED.getExitCode();
String CANCELED = "CANCELED";
String SYSTEM_USER = "system";
String TEMP_COHORT_TABLE_PREFIX = "temp_cohort_";
Float DEFAULT_THRESHOLD = 0.01f;
ImmutableList<String> ALLOWED_JOB_EXECUTION_PARAMETERS = ImmutableList.of(
"jobName",
"jobAuthor",
"cohort_definition_id",
"cohortId",
"cohortDefinitionIds",
"source_id",
"source_key",
"scriptType",
"analysis_id",
"concept_set_id",
"cohort_characterization_id",
"pathway_analysis_id",
"estimation_analysis_id",
"prediction_analysis_id"
);
String SESSION_ID = "Session-ID";
interface SqlSchemaPlaceholders {
String CDM_DATABASE_SCHEMA_PLACEHOLDER = "@cdm_database_schema";
String RESULTS_DATABASE_SCHEMA_PLACEHOLDER = "@results_database_schema";
String VOCABULARY_DATABASE_SCHEMA_PLACEHOLDER = "@vocabulary_database_schema";
String TEMP_DATABASE_SCHEMA_PLACEHOLDER = "@temp_database_schema";
}
interface Params {
String VOCABULARY_DATABASE_SCHEMA = "vocabulary_database_schema";
String COHORT_DEFINITION_ID = "cohort_definition_id";
String COHORT_CHARACTERIZATION_ID = "cohort_characterization_id";
String PATHWAY_ANALYSIS_ID = "pathway_analysis_id";
String PREDICTION_ANALYSIS_ID = "prediction_analysis_id";
String PREDICTION_SKELETON_VERSION = "v0.0.1";
String ESTIMATION_ANALYSIS_ID = "estimation_analysis_id";
String UPDATE_PASSWORD = "update_password";
String SOURCE_ID = "source_id";
String SOURCE_KEY = "source_key";
String ANALYSIS_ID = "analysis_id";
String CDM_DATABASE_SCHEMA = "cdm_database_schema";
String JOB_NAME = "jobName";
String JOB_AUTHOR = "jobAuthor";
String RESULTS_DATABASE_SCHEMA = "results_database_schema";
String TARGET_DATABASE_SCHEMA = "target_database_schema";
String TEMP_DATABASE_SCHEMA = "temp_database_schema";
String TARGET_DIALECT = "target_dialect";
String TARGET_TABLE = "target_table";
String COHORT_ID_FIELD_NAME = "cohort_id_field_name";
String TARGET_COHORT_ID = "target_cohort_id";
String GENERATE_STATS = "generate_stats";
String JOB_START_TIME = "time";
String USER_IMPORT_ID = "user_import_id";
String USER_ROLES = "userRoles";
String SESSION_ID = "sessionId";
String PACKAGE_NAME = "packageName";
String PACKAGE_FILE_NAME = "packageFilename";
String EXECUTABLE_FILE_NAME = "executableFilename";
String GENERATION_ID = "generation_id";
String DESIGN_HASH = "design_hash";
String DEMOGRAPHIC_STATS = "demographic_stats";
}
interface Variables {
String SOURCE = "source";
}
interface Headers {
String ACCESS_CONTROL_EXPOSE_HEADERS = "Access-Control-Expose-Headers";
String AUTH_PROVIDER = "x-auth-provider";
String USER_LANGAUGE = "User-Language";
String ACTION_LOCATION = "action-location";
String BEARER = "Bearer";
String X_AUTH_ERROR = "x-auth-error";
String CONTENT_DISPOSITION = "Content-Disposition";
}
interface SecurityProviders {
String DISABLED = "DisabledSecurity";
String REGULAR = "AtlasRegularSecurity";
String GOOGLE = "AtlasGoogleSecurity";
}
interface Templates {
String ENTITY_COPY_PREFIX = "COPY OF %s";
}
interface Tables {
String COHORT_CACHE = "cohort_cache";
String COHORT_INCLUSION_RESULT_CACHE = "cohort_inclusion_result_cache";
String COHORT_INCLUSION_STATS_CACHE = "cohort_inclusion_stats_cache";
String COHORT_SUMMARY_STATS_CACHE = "cohort_summary_stats_cache";
String COHORT_CENSOR_STATS_CACHE = "cohort_censor_stats_cache";
}
interface CallbackUrlResolvers {
String QUERY = "query";
String PATH = "path";
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/TerminateJobStepExceptionHandler.java | src/main/java/org/ohdsi/webapi/TerminateJobStepExceptionHandler.java | /*
* Copyright 2015 Observational Health Data Sciences and Informatics [OHDSI.org].
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ohdsi.webapi;
import org.springframework.batch.repeat.RepeatContext;
import org.springframework.batch.repeat.exception.ExceptionHandler;
/**
*
* @author Chris Knoll <cknoll@ohdsi.org>
*/
public class TerminateJobStepExceptionHandler implements ExceptionHandler {
@Override
public void handleException(RepeatContext rc, Throwable thrwbl) throws Throwable {
rc.setTerminateOnly();
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/JobConfig.java | src/main/java/org/ohdsi/webapi/JobConfig.java | package org.ohdsi.webapi;
import javax.annotation.PostConstruct;
import javax.sql.DataSource;
import org.apache.commons.lang3.StringUtils;
import org.ohdsi.webapi.audittrail.listeners.AuditTrailJobListener;
import org.ohdsi.webapi.common.generation.AutoremoveJobListener;
import org.ohdsi.webapi.common.generation.CancelJobListener;
import org.ohdsi.webapi.job.JobTemplate;
import org.ohdsi.webapi.service.JobService;
import org.ohdsi.webapi.shiro.management.Security;
import org.ohdsi.webapi.util.ManagedThreadPoolTaskExecutor;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.admin.service.*;
import org.springframework.batch.core.configuration.BatchConfigurationException;
import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.batch.core.explore.support.JobExplorerFactoryBean;
import org.springframework.batch.core.explore.support.MapJobExplorerFactoryBean;
import org.springframework.batch.core.job.builder.JobBuilder;
import org.springframework.batch.core.launch.JobLauncher;
import org.springframework.batch.core.launch.support.SimpleJobLauncher;
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.batch.core.repository.support.JobRepositoryFactoryBean;
import org.springframework.batch.core.repository.support.MapJobRepositoryFactoryBean;
import org.springframework.batch.support.transaction.ResourcelessTransactionManager;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.DependsOn;
import org.springframework.context.annotation.Primary;
import org.springframework.core.task.TaskExecutor;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import org.springframework.transaction.PlatformTransactionManager;
/**
* Had to copy DefaultBatchConfigurer and include within because jobLauncher config is private.
* https://github.com/spring-projects/spring-boot/issues/1655
*/
@Configuration
@EnableBatchProcessing
@DependsOn({"batchDatabaseInitializer"})
public class JobConfig {
private static final Logger log = LoggerFactory.getLogger(CustomBatchConfigurer.class);
@Value("${spring.batch.repository.tableprefix}")
private String tablePrefix;
@Value("${spring.batch.repository.isolationLevelForCreate}")
private String isolationLevelForCreate;
@Value("${spring.batch.taskExecutor.corePoolSize}")
private Integer corePoolSize;
@Value("${spring.batch.taskExecutor.maxPoolSize}")
private Integer maxPoolSize;
@Value("${spring.batch.taskExecutor.queueCapacity}")
private Integer queueCapacity;
@Value("${spring.batch.taskExecutor.threadGroupName}")
private String threadGroupName;
@Value("${spring.batch.taskExecutor.threadNamePrefix}")
private String threadNamePrefix;
@Autowired
private DataSource dataSource;
@Autowired
private AuditTrailJobListener auditTrailJobListener;
@Bean
public String batchTablePrefix() {
return this.tablePrefix;
}
@Bean
public TaskExecutor taskExecutor() {
final ThreadPoolTaskExecutor taskExecutor = new ManagedThreadPoolTaskExecutor();
taskExecutor.setCorePoolSize(corePoolSize);
taskExecutor.setMaxPoolSize(maxPoolSize);
taskExecutor.setQueueCapacity(queueCapacity);
if (StringUtils.isNotBlank(threadGroupName)) {
taskExecutor.setThreadGroupName(threadGroupName);
}
if (StringUtils.isNotBlank(threadNamePrefix)) {
taskExecutor.setThreadNamePrefix(threadNamePrefix);
}
taskExecutor.afterPropertiesSet();
return taskExecutor;
}
@Bean
public BatchConfigurer batchConfigurer() {
return new CustomBatchConfigurer(this.dataSource);
}
@Bean
public JobTemplate jobTemplate(final JobLauncher jobLauncher, final JobBuilderFactory jobBuilders,
final StepBuilderFactory stepBuilders, final Security security) {
return new JobTemplate(jobLauncher, jobBuilders, stepBuilders, security);
}
@Bean
public SearchableJobExecutionDao searchableJobExecutionDao(DataSource dataSource) {
JdbcSearchableJobExecutionDao dao = new JdbcSearchableJobExecutionDao();
dao.setDataSource(dataSource);
dao.setTablePrefix(JobConfig.this.tablePrefix);
return dao;
}
@Bean
public SearchableJobInstanceDao searchableJobInstanceDao(JdbcTemplate jdbcTemplate) {
JdbcSearchableJobInstanceDao dao = new JdbcSearchableJobInstanceDao();
dao.setJdbcTemplate(jdbcTemplate);//no setDataSource as in SearchableJobExecutionDao
dao.setTablePrefix(JobConfig.this.tablePrefix);
return dao;
}
@Primary
@Bean
public JobBuilderFactory jobBuilders(JobRepository jobRepository) {
return new JobBuilderFactory(jobRepository) {
@Override
public JobBuilder get(String name) {
return super.get(name)
.listener(new CancelJobListener())
.listener(auditTrailJobListener);
}
};
}
class CustomBatchConfigurer implements BatchConfigurer {
private DataSource dataSource;
private PlatformTransactionManager transactionManager;
private JobRepository jobRepository;
private JobLauncher jobLauncher;
private JobExplorer jobExplorer;
@Autowired
public void setDataSource(final DataSource dataSource) {
this.dataSource = dataSource;
// this.transactionManager = new DataSourceTransactionManager(dataSource);
}
@Autowired
public void setTransactionManager(final PlatformTransactionManager transactionManager) {
this.transactionManager = transactionManager;
}
protected CustomBatchConfigurer() {
}
public CustomBatchConfigurer(final DataSource dataSource) {
setDataSource(dataSource);
}
@Override
public JobRepository getJobRepository() {
return this.jobRepository;
}
@Override
public PlatformTransactionManager getTransactionManager() {
return this.transactionManager;
}
@Override
public JobLauncher getJobLauncher() {
return this.jobLauncher;
}
@Override
public JobExplorer getJobExplorer() {
return this.jobExplorer;
}
@PostConstruct
public void initialize() {
try {
if (this.dataSource == null) {
log.warn("No datasource was provided...using a Map based JobRepository");
if (this.transactionManager == null) {
this.transactionManager = new ResourcelessTransactionManager();
}
final MapJobRepositoryFactoryBean jobRepositoryFactory = new MapJobRepositoryFactoryBean(
this.transactionManager);
jobRepositoryFactory.afterPropertiesSet();
this.jobRepository = jobRepositoryFactory.getObject();
final MapJobExplorerFactoryBean jobExplorerFactory = new MapJobExplorerFactoryBean(jobRepositoryFactory);
jobExplorerFactory.afterPropertiesSet();
this.jobExplorer = jobExplorerFactory.getObject();
} else {
this.jobRepository = createJobRepository();
final JobExplorerFactoryBean jobExplorerFactoryBean = new JobExplorerFactoryBean();
jobExplorerFactoryBean.setDataSource(this.dataSource);
jobExplorerFactoryBean.setTablePrefix(JobConfig.this.tablePrefix);
jobExplorerFactoryBean.afterPropertiesSet();
this.jobExplorer = jobExplorerFactoryBean.getObject();
}
this.jobLauncher = createJobLauncher();
} catch (final Exception e) {
throw new BatchConfigurationException(e);
}
}
private JobLauncher createJobLauncher() throws Exception {
final SimpleJobLauncher jobLauncher = new SimpleJobLauncher();
//async TODO
jobLauncher.setTaskExecutor(taskExecutor());
jobLauncher.setJobRepository(this.jobRepository);
jobLauncher.afterPropertiesSet();
return jobLauncher;
}
protected JobRepository createJobRepository() throws Exception {
final JobRepositoryFactoryBean factory = new JobRepositoryFactoryBean();
factory.setDataSource(this.dataSource);
//prevent ISOLATION_DEFAULT setting for oracle (i.e. SERIALIZABLE)
//ISOLATION_REPEATABLE_READ throws READ_COMMITTED and SERIALIZABLE are the only valid transaction levels
factory.setIsolationLevelForCreate(JobConfig.this.isolationLevelForCreate);
factory.setTablePrefix(JobConfig.this.tablePrefix);
factory.setTransactionManager(getTransactionManager());
factory.setValidateTransactionState(false);
factory.afterPropertiesSet();
return factory.getObject();
}
}
}
/*extends DefaultBatchConfigurer {
private static final Log log = LogFactory.getLog(BatchConfig.class);
@Autowired
private JobBuilderFactory jobBuilders;
@Autowired
private StepBuilderFactory stepBuilders;
@Autowired
private DataSource dataSource;
@Value("${spring.batch.repository.tableprefix}")
private String tablePrefix;
@Bean
public String batchTablePrefix() {
return this.tablePrefix;
}
@Override
protected JobRepository createJobRepository() throws Exception {
final JobRepositoryFactoryBean factory = new JobRepositoryFactoryBean();
factory.setDataSource(this.dataSource);
factory.setTablePrefix(this.tablePrefix);
factory.setIsolationLevelForCreate(this.isolationLevel);
factory.setTransactionManager(getTransactionManager());
factory.afterPropertiesSet();
return factory.getObject();
}
@Bean
public TaskExecutor taskExecutor() {
final ThreadPoolTaskExecutor taskExecutor = new ThreadPoolTaskExecutor();
taskExecutor.setMaxPoolSize(2);//TODO
taskExecutor.afterPropertiesSet();
return taskExecutor;
}
}
*/
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/shiro/TokenManager.java | src/main/java/org/ohdsi/webapi/shiro/TokenManager.java | package org.ohdsi.webapi.shiro;
import io.jsonwebtoken.Claims;
import io.jsonwebtoken.JwtException;
import io.jsonwebtoken.Jwts;
import io.jsonwebtoken.SignatureAlgorithm;
import io.jsonwebtoken.SignatureException;
import io.jsonwebtoken.UnsupportedJwtException;
import io.jsonwebtoken.impl.crypto.MacProvider;
import java.security.Key;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import javax.servlet.ServletRequest;
import javax.servlet.http.HttpServletRequest;
import org.apache.shiro.web.util.WebUtils;
import org.ohdsi.webapi.Constants;
import org.ohdsi.webapi.util.ExpiringMultimap;
/**
*
* @author gennadiy.anisimov
*/
public class TokenManager {
private static final String AUTHORIZATION_HEADER = "Authorization";
private static final Map<String, Key> userToKeyMap = new HashMap<>();
private static final ExpiringMultimap<String, Key> gracePeriodInvalidTokens = new ExpiringMultimap<>(30000);
public static String createJsonWebToken(String subject, String sessionId, Date expiration) {
Key key = MacProvider.generateKey();
Key oldKey;
if ((oldKey = userToKeyMap.get(subject)) != null) {
gracePeriodInvalidTokens.put(subject, oldKey);
}
userToKeyMap.put(subject, key);
Map<String, Object> claims = new HashMap<>();
claims.put(Constants.SESSION_ID, sessionId);
return Jwts.builder()
.setClaims(claims)
.setSubject(subject)
.setExpiration(expiration)
.signWith(SignatureAlgorithm.HS512, key)
.compact();
}
public static String getSubject(String jwt) throws JwtException {
return getBody(jwt).getSubject();
}
public static Claims getBody(String jwt) {
// Get untrusted subject for secret key retrieval
String untrustedSubject = getUntrustedSubject(jwt);
if (untrustedSubject == null) {
throw new UnsupportedJwtException("Cannot extract subject from the token");
}
// Pick all secret keys: latest one + previous keys, which were just invalidated (to overcome concurrency issue)
List<Key> keyOptions = gracePeriodInvalidTokens.get(untrustedSubject);
if (userToKeyMap.containsKey(untrustedSubject)) {
keyOptions.add(0, userToKeyMap.get(untrustedSubject));
}
return keyOptions.stream()
.map(key -> {
try {
return Jwts.parser()
.setSigningKey(key)
.parseClaimsJws(jwt)
.getBody();
} catch (Exception ex) {
return null;
}
})
.filter(Objects::nonNull)
.findFirst()
.orElseThrow(() -> new SignatureException("Signing key is not registered for the subject."));
}
protected static String getUntrustedSubject(String jws) {
int i = jws.lastIndexOf('.');
if (i == -1) {
return null;
}
String untrustedJwtString = jws.substring(0, i+1);
return Jwts.parser().parseClaimsJwt(untrustedJwtString).getBody().getSubject();
}
public static Boolean invalidate(String jwt) {
if (jwt == null)
return false;
String subject;
try {
subject = getSubject(jwt);
}
catch(JwtException e) {
return false;
}
if (!userToKeyMap.containsKey(subject))
return false;
userToKeyMap.remove(subject);
return true;
}
public static String extractToken(ServletRequest request) {
HttpServletRequest httpRequest = WebUtils.toHttp(request);
String header = httpRequest.getHeader(AUTHORIZATION_HEADER);
if (header == null || header.isEmpty())
return null;
if (!header.toLowerCase(Locale.ENGLISH).startsWith("bearer"))
return null;
String[] headerParts = header.split(" ");
if (headerParts.length != 2)
return null;
String jwt = headerParts[1];
return jwt;
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/shiro/AtlasWebSecurityManager.java | src/main/java/org/ohdsi/webapi/shiro/AtlasWebSecurityManager.java | package org.ohdsi.webapi.shiro;
import java.util.Collection;
import org.apache.commons.collections.CollectionUtils;
import org.apache.shiro.authc.pam.ModularRealmAuthenticator;
import org.apache.shiro.authz.ModularRealmAuthorizer;
import org.apache.shiro.realm.Realm;
import org.ohdsi.webapi.shiro.lockout.LockoutPolicy;
import org.ohdsi.webapi.shiro.lockout.LockoutWebSecurityManager;
/**
* WebSecurityManger uses the same collection of the realms for authentication and authorization by default.
* In our case only jwtAuthRealm make a real authorization, so for this we create ModularRealmAuthenticator and ModularRealmAuthorizer by hand,
* and override afterRealmsSet, to prevent reassign realms for authenticator and authorizer.
*
*/
public class AtlasWebSecurityManager extends LockoutWebSecurityManager {
public AtlasWebSecurityManager(LockoutPolicy lockoutPolicy, ModularRealmAuthenticator authenticator, Collection<Realm> authenticationRealms, Collection<Realm> authorizationRealms) {
super(lockoutPolicy);
ModularRealmAuthorizer authorizer = new ModularRealmAuthorizer();
Collection realms = CollectionUtils.union(authenticationRealms, authorizationRealms);
if (realms != null && !realms.isEmpty()) {
this.setRealms(realms);
}
authenticator.setRealms(authenticationRealms);
authorizer.setRealms(authorizationRealms);
this.setAuthenticator(authenticator);
this.setAuthorizer(authorizer);
}
@Override
protected void afterRealmsSet() {
//by default this method override realms for authenticator and authorizer. we don't want this.
//do nothing
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/shiro/PermissionManager.java | src/main/java/org/ohdsi/webapi/shiro/PermissionManager.java | package org.ohdsi.webapi.shiro;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.odysseusinc.logging.event.AddUserEvent;
import com.odysseusinc.logging.event.DeleteRoleEvent;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authc.UnknownAccountException;
import org.apache.shiro.subject.Subject;
import org.ohdsi.webapi.helper.Guard;
import org.ohdsi.webapi.security.model.UserSimpleAuthorizationInfo;
import org.ohdsi.webapi.shiro.Entities.PermissionEntity;
import org.ohdsi.webapi.shiro.Entities.PermissionRepository;
import org.ohdsi.webapi.shiro.Entities.RequestStatus;
import org.ohdsi.webapi.shiro.Entities.RoleEntity;
import org.ohdsi.webapi.shiro.Entities.RolePermissionEntity;
import org.ohdsi.webapi.shiro.Entities.RolePermissionRepository;
import org.ohdsi.webapi.shiro.Entities.RoleRepository;
import org.ohdsi.webapi.shiro.Entities.UserEntity;
import org.ohdsi.webapi.shiro.Entities.UserOrigin;
import org.ohdsi.webapi.shiro.Entities.UserRepository;
import org.ohdsi.webapi.shiro.Entities.UserRoleEntity;
import org.ohdsi.webapi.shiro.Entities.UserRoleRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationEventPublisher;
import org.springframework.stereotype.Component;
import org.springframework.transaction.annotation.Transactional;
import java.security.Principal;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.stream.Collectors;
import javax.cache.CacheManager;
import javax.cache.configuration.MutableConfiguration;
import org.apache.commons.lang3.StringUtils;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.authz.permission.WildcardPermission;
import org.ohdsi.circe.helper.ResourceHelper;
import org.ohdsi.webapi.util.CacheHelper;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.autoconfigure.cache.JCacheManagerCustomizer;
import org.springframework.cache.annotation.CacheEvict;
import org.springframework.cache.annotation.Cacheable;
import org.springframework.jdbc.core.JdbcTemplate;
/**
*
* @author gennadiy.anisimov
*/
@Component
@Transactional
public class PermissionManager {
//create cache
@Component
public static class CachingSetup implements JCacheManagerCustomizer {
public static final String AUTH_INFO_CACHE = "authorizationInfo";
@Override
public void customize(CacheManager cacheManager) {
// due to unit tests causing application contexts to reload cache manager caches, we
// have to check for the existance of a cache before creating it
Set<String> cacheNames = CacheHelper.getCacheNames(cacheManager);
// Evict when a user, role or permission is modified/deleted.
if (!cacheNames.contains(AUTH_INFO_CACHE)) {
cacheManager.createCache(AUTH_INFO_CACHE, new MutableConfiguration<String, UserSimpleAuthorizationInfo>()
.setTypes(String.class, UserSimpleAuthorizationInfo.class)
.setStoreByValue(false)
.setStatisticsEnabled(true));
}
}
}
@Value("${datasource.ohdsi.schema}")
private String ohdsiSchema;
@Autowired
private UserRepository userRepository;
@Autowired
private RoleRepository roleRepository;
@Autowired
private PermissionRepository permissionRepository;
@Autowired
private RolePermissionRepository rolePermissionRepository;
@Autowired
private UserRoleRepository userRoleRepository;
@Autowired
private ApplicationEventPublisher eventPublisher;
@Autowired
private JdbcTemplate jdbcTemplate;
private ThreadLocal<ConcurrentHashMap<String, UserSimpleAuthorizationInfo>> authorizationInfoCache = ThreadLocal.withInitial(ConcurrentHashMap::new);
public static class PermissionsDTO {
public Map<String, List<String>> permissions = null;
}
public RoleEntity addRole(String roleName, boolean isSystem) {
Guard.checkNotEmpty(roleName);
checkRoleIsAbsent(roleName, isSystem, "Can't create role - it already exists");
RoleEntity role = new RoleEntity();
role.setName(roleName);
role.setSystemRole(isSystem);
role = this.roleRepository.save(role);
return role;
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, key = "#login")
public String addUserToRole(String roleName, String login) {
return addUserToRole(roleName, login, UserOrigin.SYSTEM);
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, key = "#login")
public String addUserToRole(String roleName, String login, UserOrigin userOrigin) {
Guard.checkNotEmpty(roleName);
Guard.checkNotEmpty(login);
RoleEntity role = this.getSystemRoleByName(roleName);
UserEntity user = this.getUserByLogin(login);
UserRoleEntity userRole = this.addUser(user, role, userOrigin, null);
return userRole.getStatus();
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, key = "#login")
public void removeUserFromRole(String roleName, String login, UserOrigin origin) {
Guard.checkNotEmpty(roleName);
Guard.checkNotEmpty(login);
if (roleName.equalsIgnoreCase(login))
throw new RuntimeException("Can't remove user from personal role");
RoleEntity role = this.getSystemRoleByName(roleName);
UserEntity user = this.getUserByLogin(login);
UserRoleEntity userRole = this.userRoleRepository.findByUserAndRole(user, role);
if (userRole != null && (origin == null || origin.equals(userRole.getOrigin())))
this.userRoleRepository.delete(userRole);
}
public Iterable<RoleEntity> getRoles(boolean includePersonalRoles) {
if (includePersonalRoles) {
return this.roleRepository.findAll();
} else {
return this.roleRepository.findAllBySystemRoleTrue();
}
}
/**
* Return the UserSimpleAuthorizastionInfo which contains the login, roles and permissions for the specified login
*
* @param login The login to fetch the authorization info
* @return A UserSimpleAuthorizationInfo containing roles and permissions.
*/
@Cacheable(cacheNames = CachingSetup.AUTH_INFO_CACHE)
public UserSimpleAuthorizationInfo getAuthorizationInfo(final String login) {
return authorizationInfoCache.get().computeIfAbsent(login, newLogin -> {
final UserSimpleAuthorizationInfo info = new UserSimpleAuthorizationInfo();
final UserEntity userEntity = userRepository.findByLogin(login);
if(userEntity == null) {
throw new UnknownAccountException("Account does not exist");
}
info.setUserId(userEntity.getId());
info.setLogin(userEntity.getLogin());
for (UserRoleEntity userRole: userEntity.getUserRoles()) {
info.addRole(userRole.getRole().getName());
}
// convert permission index from queryUserPermissions() into a map of WildcardPermissions
Map<String, List<String>> permsIdx = this.queryUserPermissions(login).permissions;
Map permissionMap = new HashMap<String, List<Permission>>();
Set<String> permissionNames = new HashSet<>();
for(String permIdxKey : permsIdx.keySet()) {
List<String> perms = permsIdx.get(permIdxKey);
permissionNames.addAll(perms);
// convert raw string permission into Wildcard perm for each element in this key's array.
permissionMap.put(permIdxKey, perms.stream().map(perm -> new WildcardPermission(perm)).collect(Collectors.toList()));
}
info.setStringPermissions(permissionNames);
info.setPermissionIdx(permissionMap);
return info;
});
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
public void clearAuthorizationInfoCache() {
authorizationInfoCache.set(new ConcurrentHashMap<>());
}
@Transactional
public UserEntity registerUser(final String login, final String name, final Set<String> defaultRoles) {
return registerUser(login, name, UserOrigin.SYSTEM, defaultRoles);
}
@Transactional
public UserEntity registerUser(final String login, final String name, final UserOrigin userOrigin,
final Set<String> defaultRoles) {
Guard.checkNotEmpty(login);
UserEntity user = userRepository.findByLogin(login);
if (user != null) {
if (user.getName() == null || !userOrigin.equals(user.getOrigin())) {
String nameToSet = name;
if (name == null) {
nameToSet = login;
}
user.setName(nameToSet);
user.setOrigin(userOrigin);
user = userRepository.save(user);
}
return user;
}
checkRoleIsAbsent(login, false, "User with such login has been improperly removed from the database. " +
"Please contact your system administrator");
user = new UserEntity();
user.setLogin(login);
user.setName(name);
user.setOrigin(userOrigin);
user = userRepository.save(user);
eventPublisher.publishEvent(new AddUserEvent(this, user.getId(), login));
RoleEntity personalRole = this.addRole(login, false);
this.addUser(user, personalRole, userOrigin, null);
if (defaultRoles != null) {
for (String roleName: defaultRoles) {
RoleEntity defaultRole = this.getSystemRoleByName(roleName);
if (defaultRole != null) {
this.addUser(user, defaultRole, userOrigin, null);
}
}
}
user = userRepository.findOne(user.getId());
return user;
}
public Iterable<UserEntity> getUsers() {
return this.userRepository.findAll();
}
public PermissionEntity getOrAddPermission(final String permissionName, final String permissionDescription) {
Guard.checkNotEmpty(permissionName);
PermissionEntity permission = this.permissionRepository.findByValueIgnoreCase(permissionName);
if (permission != null) {
return permission;
}
permission = new PermissionEntity();
permission.setValue(permissionName);
permission.setDescription(permissionDescription);
permission = this.permissionRepository.save(permission);
return permission;
}
public Set<RoleEntity> getUserRoles(Long userId) throws Exception {
UserEntity user = this.getUserById(userId);
Set<RoleEntity> roles = this.getUserRoles(user);
return roles;
}
public Iterable<PermissionEntity> getPermissions() {
return this.permissionRepository.findAll();
}
public Set<PermissionEntity> getUserPermissions(Long userId) {
UserEntity user = this.getUserById(userId);
Set<PermissionEntity> permissions = this.getUserPermissions(user);
return permissions;
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
public void removeRole(Long roleId) {
eventPublisher.publishEvent(new DeleteRoleEvent(this, roleId));
this.roleRepository.delete(roleId);
}
public Set<PermissionEntity> getRolePermissions(Long roleId) {
RoleEntity role = this.getRoleById(roleId);
Set<PermissionEntity> permissions = this.getRolePermissions(role);
return permissions;
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
public void addPermission(Long roleId, Long permissionId) {
PermissionEntity permission = this.getPermissionById(permissionId);
RoleEntity role = this.getRoleById(roleId);
this.addPermission(role, permission, null);
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
public void addPermission(RoleEntity role, PermissionEntity permission) {
this.addPermission(role, permission, null);
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
public void removePermission(Long permissionId, Long roleId) {
RolePermissionEntity rolePermission = this.rolePermissionRepository.findByRoleIdAndPermissionId(roleId, permissionId);
if (rolePermission != null)
this.rolePermissionRepository.delete(rolePermission);
}
public Set<UserEntity> getRoleUsers(Long roleId) {
RoleEntity role = this.getRoleById(roleId);
Set<UserEntity> users = this.getRoleUsers(role);
return users;
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
public void addUser(Long userId, Long roleId) {
UserEntity user = this.getUserById(userId);
RoleEntity role = this.getRoleById(roleId);
this.addUser(user, role, UserOrigin.SYSTEM, null);
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
public void removeUser(Long userId, Long roleId) {
UserRoleEntity userRole = this.userRoleRepository.findByUserIdAndRoleId(userId, roleId);
if (userRole != null)
this.userRoleRepository.delete(userRole);
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
public void removePermission(String value) {
PermissionEntity permission = this.permissionRepository.findByValueIgnoreCase(value);
if (permission != null)
this.permissionRepository.delete(permission);
}
public RoleEntity getUserPersonalRole(String username) {
return this.getRoleByName(username, false);
}
public RoleEntity getCurrentUserPersonalRole() {
String username = this.getSubjectName();
return getUserPersonalRole(username);
}
private void checkRoleIsAbsent(String roleName, boolean isSystem, String message) {
RoleEntity role = this.roleRepository.findByNameAndSystemRole(roleName, isSystem);
if (role != null) {
throw new RuntimeException(message);
}
}
public Set<PermissionEntity> getUserPermissions(UserEntity user) {
Set<RoleEntity> roles = this.getUserRoles(user);
Set<PermissionEntity> permissions = new LinkedHashSet<>();
for (RoleEntity role : roles) {
permissions.addAll(this.getRolePermissions(role));
}
return permissions;
}
public PermissionsDTO queryUserPermissions(final String login) {
String permQuery = StringUtils.replace(
ResourceHelper.GetResourceAsString("/resources/security/getPermissionsForUser.sql"),
"@ohdsi_schema",
this.ohdsiSchema);
final UserEntity user = userRepository.findByLogin(login);
List<String> permissions = this.jdbcTemplate.query(
permQuery,
(ps) -> {
ps.setLong(1, user.getId());
},
(rs, rowNum) -> {
return rs.getString("value");
});
PermissionsDTO permDto = new PermissionsDTO();
permDto.permissions = permsToMap(permissions);
return permDto;
}
/**
* This method takes a list of strings and returns a JSObject representing
* the first element of each permission as a key, and the List<String> of
* permissions that start with the key as the value
*/
private Map<String, List<String>> permsToMap(List<String> permissions) {
Map<String, List<String>> resultMap = new HashMap<>();
// Process each input string
for (String inputString : permissions) {
String[] parts = inputString.split(":");
String key = parts[0];
// Create a new JsonArray for the key if it doesn't exist
resultMap.putIfAbsent(key, new ArrayList<>());
// Add the value to the JsonArray
resultMap.get(key).add(inputString);
}
// Convert the resultMap to a JsonNode
return resultMap;
}
private Set<PermissionEntity> getRolePermissions(RoleEntity role) {
Set<PermissionEntity> permissions = new LinkedHashSet<>();
Set<RolePermissionEntity> rolePermissions = role.getRolePermissions();
for (RolePermissionEntity rolePermission : rolePermissions) {
if (isRelationAllowed(rolePermission.getStatus())) {
PermissionEntity permission = rolePermission.getPermission();
permissions.add(permission);
}
}
return permissions;
}
private Set<RoleEntity> getUserRoles(UserEntity user) {
Set<UserRoleEntity> userRoles = user.getUserRoles();
Set<RoleEntity> roles = new LinkedHashSet<>();
for (UserRoleEntity userRole : userRoles) {
if (isRelationAllowed(userRole.getStatus())) {
RoleEntity role = userRole.getRole();
roles.add(role);
}
}
return roles;
}
private Set<UserEntity> getRoleUsers(RoleEntity role) {
Set<UserEntity> users = new LinkedHashSet<>();
for (UserRoleEntity userRole : role.getUserRoles()) {
if (isRelationAllowed(userRole.getStatus())) {
users.add(userRole.getUser());
}
}
return users;
}
public UserEntity getCurrentUser() {
final String login = this.getSubjectName();
final UserEntity currentUser = this.getUserByLogin(login);
return currentUser;
}
public UserEntity getUserById(Long userId) {
UserEntity user = this.userRepository.findOne(userId);
if (user == null)
throw new RuntimeException("User doesn't exist");
return user;
}
private UserEntity getUserByLogin(final String login) {
final UserEntity user = this.userRepository.findByLogin(login);
if (user == null)
throw new RuntimeException("User doesn't exist");
return user;
}
private RoleEntity getRoleByName(String roleName, Boolean isSystemRole) {
final RoleEntity roleEntity = this.roleRepository.findByNameAndSystemRole(roleName, isSystemRole);
if (roleEntity == null)
throw new RuntimeException("Role doesn't exist");
return roleEntity;
}
public RoleEntity getSystemRoleByName(String roleName) {
return getRoleByName(roleName, true);
}
private RoleEntity getRoleById(Long roleId) {
final RoleEntity roleEntity = this.roleRepository.findById(roleId);
if (roleEntity == null)
throw new RuntimeException("Role doesn't exist");
return roleEntity;
}
private PermissionEntity getPermissionById(Long permissionId) {
final PermissionEntity permission = this.permissionRepository.findById(permissionId);
if (permission == null )
throw new RuntimeException("Permission doesn't exist");
return permission;
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
private RolePermissionEntity addPermission(final RoleEntity role, final PermissionEntity permission, final String status) {
RolePermissionEntity relation = this.rolePermissionRepository.findByRoleAndPermission(role, permission);
if (relation == null) {
relation = new RolePermissionEntity();
relation.setRole(role);
relation.setPermission(permission);
relation.setStatus(status);
relation = this.rolePermissionRepository.save(relation);
}
return relation;
}
private boolean isRelationAllowed(final String relationStatus) {
return relationStatus == null || relationStatus.equals(RequestStatus.APPROVED);
}
private UserRoleEntity addUser(final UserEntity user, final RoleEntity role,
final UserOrigin userOrigin, final String status) {
UserRoleEntity relation = this.userRoleRepository.findByUserAndRole(user, role);
if (relation == null) {
relation = new UserRoleEntity();
relation.setUser(user);
relation.setRole(role);
relation.setStatus(status);
relation.setOrigin(userOrigin);
relation = this.userRoleRepository.save(relation);
}
return relation;
}
public String getSubjectName() {
Subject subject = SecurityUtils.getSubject();
Object principalObject = subject.getPrincipals().getPrimaryPrincipal();
if (principalObject instanceof String)
return (String)principalObject;
if (principalObject instanceof Principal) {
Principal principal = (Principal)principalObject;
return principal.getName();
}
throw new UnsupportedOperationException();
}
public RoleEntity getRole(Long id) {
return this.roleRepository.findById(id);
}
public RoleEntity updateRole(RoleEntity roleEntity) {
return this.roleRepository.save(roleEntity);
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
public void addPermissionsFromTemplate(RoleEntity roleEntity, Map<String, String> template, String value) {
for (Map.Entry<String, String> entry : template.entrySet()) {
String permission = String.format(entry.getKey(), value);
String description = String.format(entry.getValue(), value);
PermissionEntity permissionEntity = this.getOrAddPermission(permission, description);
this.addPermission(roleEntity, permissionEntity);
}
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
public void addPermissionsFromTemplate(Map<String, String> template, String value) {
RoleEntity currentUserPersonalRole = getCurrentUserPersonalRole();
addPermissionsFromTemplate(currentUserPersonalRole, template, value);
}
@CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
public void removePermissionsFromTemplate(Map<String, String> template, String value) {
for (Map.Entry<String, String> entry : template.entrySet()) {
String permission = String.format(entry.getKey(), value);
this.removePermission(permission);
}
}
public boolean roleExists(String roleName) {
return this.roleRepository.existsByName(roleName);
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/shiro/management/FilterTemplates.java | src/main/java/org/ohdsi/webapi/shiro/management/FilterTemplates.java | package org.ohdsi.webapi.shiro.management;
public enum FilterTemplates {
SEND_TOKEN_IN_URL("sendTokenInUrl"),
SEND_TOKEN_IN_HEADER("sendTokenInHeader"),
SEND_TOKEN_IN_REDIRECT("sendTokenInRedirect"),
JWT_AUTHC("jwtAuthc"),
ACCESS_AUTHC("accessAuthc"),
NEGOTIATE_AUTHC("negotiateAuthc"),
GOOGLE_AUTHC("googleAuthc"),
FACEBOOK_AUTHC("facebookAuthc"),
GITHUB_AUTHC("githubAuthc"),
CAS_AUTHC("casAuthc"),
SAML_AUTHC("samlAuthc"),
SAML_AUTHC_FORCE("samlAuthcForce"),
NO_SESSION_CREATION("noSessionCreation"),
FORCE_SESSION_CREATION("forceSessionCreation"),
AUTHZ("authz"),
CORS("cors"),
SSL("ssl"),
NO_CACHE("noCache"),
HIDE_RESOURCE("hideResource"),
LOGOUT("logout"),
UPDATE_TOKEN("updateToken"),
JDBC_FILTER("jdbcFilter"),
KERBEROS_FILTER("kerberosFilter"),
LDAP_FILTER("ldapFilter"),
AD_FILTER("adFilter"),
OIDC_AUTH("oidcAuth"),
OIDC_DIRECT_AUTH("oidcDirectAuth"),
OAUTH_CALLBACK("oauthCallback"),
HANDLE_UNSUCCESSFUL_OAUTH("handleUnsuccessfullOAuth"),
HANDLE_CAS("handleCas"),
HANDLE_SAML("handleSaml"),
RUN_AS("runAs");
private String templateName;
FilterTemplates(String templateName){
this.templateName = templateName;
}
public String getTemplateName() {
return templateName;
}
public static final FilterTemplates[] OAUTH_CALLBACK_FILTERS = new FilterTemplates[]{ SSL, FORCE_SESSION_CREATION, HANDLE_UNSUCCESSFUL_OAUTH, OAUTH_CALLBACK };
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
OHDSI/WebAPI | https://github.com/OHDSI/WebAPI/blob/b22d7bf02d98c0cf78c46801877368d6ecad2245/src/main/java/org/ohdsi/webapi/shiro/management/AtlasRegularSecurity.java | src/main/java/org/ohdsi/webapi/shiro/management/AtlasRegularSecurity.java | package org.ohdsi.webapi.shiro.management;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.buji.pac4j.filter.CallbackFilter;
import io.buji.pac4j.filter.SecurityFilter;
import io.buji.pac4j.realm.Pac4jRealm;
import org.apache.commons.lang3.StringUtils;
import org.apache.shiro.realm.Realm;
import org.apache.shiro.realm.activedirectory.ActiveDirectoryRealm;
import org.apache.shiro.realm.ldap.DefaultLdapRealm;
import org.apache.shiro.realm.ldap.JndiLdapContextFactory;
import org.jasig.cas.client.validation.Cas20ServiceTicketValidator;
import org.ohdsi.webapi.Constants;
import org.ohdsi.webapi.security.model.EntityPermissionSchemaResolver;
import org.ohdsi.webapi.shiro.Entities.UserRepository;
import org.ohdsi.webapi.shiro.PermissionManager;
import org.ohdsi.webapi.shiro.filters.*;
import org.ohdsi.webapi.shiro.filters.auth.ActiveDirectoryAuthFilter;
import org.ohdsi.webapi.shiro.filters.auth.AtlasJwtAuthFilter;
import org.ohdsi.webapi.shiro.filters.auth.JdbcAuthFilter;
import org.ohdsi.webapi.shiro.filters.auth.KerberosAuthFilter;
import org.ohdsi.webapi.shiro.filters.auth.LdapAuthFilter;
import org.ohdsi.webapi.shiro.filters.auth.SamlHandleFilter;
import org.ohdsi.webapi.shiro.mapper.ADUserMapper;
import org.ohdsi.webapi.shiro.mapper.LdapUserMapper;
import org.ohdsi.webapi.shiro.realms.ADRealm;
import org.ohdsi.webapi.shiro.realms.JdbcAuthRealm;
import org.ohdsi.webapi.shiro.realms.JwtAuthRealm;
import org.ohdsi.webapi.shiro.realms.KerberosAuthRealm;
import org.ohdsi.webapi.shiro.realms.LdapRealm;
import org.ohdsi.webapi.user.importer.providers.LdapProvider;
import org.ohdsi.webapi.util.ResourceUtils;
import org.opensaml.saml.common.xml.SAMLConstants;
import org.pac4j.cas.client.CasClient;
import org.pac4j.cas.config.CasConfiguration;
import org.pac4j.core.client.Client;
import org.pac4j.core.client.Clients;
import org.pac4j.core.config.Config;
import org.pac4j.core.http.callback.CallbackUrlResolver;
import org.pac4j.core.http.callback.PathParameterCallbackUrlResolver;
import org.pac4j.core.http.callback.QueryParameterCallbackUrlResolver;
import org.pac4j.http.client.direct.HeaderClient;
import org.pac4j.oauth.client.FacebookClient;
import org.pac4j.oauth.client.GitHubClient;
import org.pac4j.oauth.client.Google2Client;
import org.pac4j.oidc.client.OidcClient;
import org.pac4j.oidc.config.OidcConfiguration;
import org.pac4j.oidc.credentials.authenticator.UserInfoOidcAuthenticator;
import org.pac4j.saml.client.SAML2Client;
import org.pac4j.saml.config.SAML2Configuration;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
import org.springframework.context.ApplicationEventPublisher;
import org.springframework.context.annotation.DependsOn;
import org.springframework.ldap.core.LdapTemplate;
import org.springframework.stereotype.Component;
import org.springframework.web.client.RestTemplate;
import waffle.shiro.negotiate.NegotiateAuthenticationFilter;
import waffle.shiro.negotiate.NegotiateAuthenticationRealm;
import javax.naming.Context;
import javax.servlet.Filter;
import javax.sql.DataSource;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.nio.charset.StandardCharsets;
import java.util.*;
import static com.odysseusinc.arachne.commons.utils.QuoteUtils.dequote;
import static org.ohdsi.webapi.shiro.management.FilterTemplates.*;
@Component
@ConditionalOnProperty(name = "security.provider", havingValue = Constants.SecurityProviders.REGULAR)
@DependsOn("flyway")
public class AtlasRegularSecurity extends AtlasSecurity {
private final Logger logger = LoggerFactory.getLogger(AtlasRegularSecurity.class);
@Value("${security.token.expiration}")
private int tokenExpirationIntervalInSeconds;
@Value("${security.oauth.callback.ui}")
private String oauthUiCallback;
@Value("${security.oauth.callback.api}")
private String oauthApiCallback;
@Value("${security.oauth.callback.urlResolver}")
private String oauthCallbackUrlResolver;
@Value("${security.oauth.google.apiKey}")
private String googleApiKey;
@Value("${security.oauth.google.apiSecret}")
private String googleApiSecret;
@Value("${security.oauth.facebook.apiKey}")
private String facebookApiKey;
@Value("${security.oauth.facebook.apiSecret}")
private String facebookApiSecret;
@Value("${security.oauth.github.apiKey}")
private String githubApiKey;
@Value("${security.oauth.github.apiSecret}")
private String githubApiSecret;
@Value("${security.kerberos.spn}")
private String kerberosSpn;
@Value("${security.kerberos.keytabPath}")
private String kerberosKeytabPath;
@Value("${security.ldap.dn}")
private String userDnTemplate;
@Value("${security.ldap.url}")
private String ldapUrl;
@Value("${security.ldap.searchString}")
private String ldapSearchString;
@Value("${security.ldap.searchBase}")
private String ldapSearchBase;
@Value("${security.ad.url}")
private String adUrl;
@Value("${security.ad.searchBase}")
private String adSearchBase;
@Value("${security.ad.principalSuffix}")
private String adPrincipalSuffix;
@Value("${security.ad.system.username}")
private String adSystemUsername;
@Value("${security.ad.system.password}")
private String adSystemPassword;
@Value("${security.db.datasource.authenticationQuery}")
private String jdbcAuthenticationQuery;
@Value("${security.ad.searchFilter}")
private String adSearchFilter;
@Value("${security.ad.searchString}")
private String adSearchString;
@Value("${security.ad.ignore.partial.result.exception}")
private Boolean adIgnorePartialResultException;
@Value("${security.google.accessToken.enabled}")
private Boolean googleAccessTokenEnabled;
@Value("${security.saml.keyManager.storePassword}")
private String keyStorePassword;
@Value("${security.saml.keyManager.passwords.arachnenetwork}")
private String privateKeyPassword;
@Value("${security.saml.entityId}")
private String identityProviderEntityId;
@Value("${security.saml.idpMetadataLocation}")
private String metadataLocation;
@Value("${security.saml.keyManager.keyStoreFile}")
private String keyStoreFile;
@Value("${security.saml.keyManager.defaultKey}")
private String alias;
@Value("${security.saml.metadataLocation}")
private String spMetadataLocation;
@Value("${security.saml.callbackUrl}")
private String samlCallbackUrl;
@Value("${security.saml.maximumAuthenticationLifetime}")
private int maximumAuthenticationLifetime;
@Autowired
@Qualifier("activeDirectoryProvider")
private LdapProvider adLdapProvider;
@Autowired
@Qualifier("authDataSource")
private DataSource jdbcDataSource;
@Autowired
private UserRepository userRepository;
@Autowired
private ApplicationEventPublisher eventPublisher;
@Autowired
private ADUserMapper adUserMapper;
@Autowired
private LdapUserMapper ldapUserMapper;
@Value("${security.oid.redirectUrl}")
private String redirectUrl;
@Value("${security.cas.loginUrl}")
private String casLoginUrl;
@Value("${security.cas.callbackUrl}")
private String casCallbackUrl;
@Value("${security.cas.serverUrl}")
private String casServerUrl;
@Value("${security.cas.cassvcs}")
private String casSvcs;
@Value("${security.cas.casticket}")
private String casticket;
@Value("${security.saml.enabled:false}")
private boolean samlEnabled;
@Value("${security.auth.windows.enabled}")
private boolean windowsAuthEnabled;
@Value("${security.auth.kerberos.enabled}")
private boolean kerberosAuthEnabled;
@Value("${security.auth.jdbc.enabled}")
private boolean jdbcAuthEnabled;
@Value("${security.auth.ldap.enabled}")
private boolean ldapAuthEnabled;
@Value("${security.auth.ad.enabled}")
private boolean adAuthEnabled;
@Value("${security.auth.cas.enabled}")
private boolean casAuthEnabled;
@Value("${security.auth.openid.enabled}")
private boolean openidAuthEnabled;
@Value("${security.auth.facebook.enabled}")
private boolean facebookAuthEnabled;
@Value("${security.auth.github.enabled}")
private boolean githubAuthEnabled;
@Value("${security.auth.google.enabled}")
private boolean googleAuthEnabled;
private RestTemplate restTemplate = new RestTemplate();
@Autowired
private PermissionManager permissionManager;
@Autowired
private ObjectMapper objectMapper;
public AtlasRegularSecurity(EntityPermissionSchemaResolver permissionSchemaResolver) {
super(permissionSchemaResolver);
}
@Override
public Map<FilterTemplates, Filter> getFilters() {
Map<FilterTemplates, Filter> filters = super.getFilters();
filters.put(LOGOUT, new LogoutFilter(eventPublisher));
filters.put(UPDATE_TOKEN, new UpdateAccessTokenFilter(this.authorizer, this.defaultRoles, this.tokenExpirationIntervalInSeconds,
this.redirectUrl));
filters.put(ACCESS_AUTHC, new GoogleAccessTokenFilter(restTemplate, permissionManager, Collections.emptySet()));
filters.put(JWT_AUTHC, new AtlasJwtAuthFilter());
if (this.jdbcAuthEnabled) {
filters.put(JDBC_FILTER, new JdbcAuthFilter(eventPublisher));
}
if (this.kerberosAuthEnabled) {
filters.put(KERBEROS_FILTER, new KerberosAuthFilter());
}
if (this.ldapAuthEnabled) {
filters.put(LDAP_FILTER, new LdapAuthFilter(eventPublisher));
}
if (this.adAuthEnabled) {
filters.put(AD_FILTER, new ActiveDirectoryAuthFilter(eventPublisher));
}
if (this.windowsAuthEnabled) {
filters.put(NEGOTIATE_AUTHC, new NegotiateAuthenticationFilter());
}
filters.put(SEND_TOKEN_IN_URL, new SendTokenInUrlFilter(this.oauthUiCallback));
filters.put(SEND_TOKEN_IN_HEADER, new SendTokenInHeaderFilter(this.objectMapper));
filters.put(RUN_AS, new RunAsFilter(userRepository));
// OAuth
//
CallbackUrlResolver urlResolver = getCallbackUrlResolver();
List<Client> clients = new ArrayList<>();
if (this.googleAuthEnabled) {
Google2Client googleClient = new Google2Client(this.googleApiKey, this.googleApiSecret);
googleClient.setCallbackUrl(oauthApiCallback);
googleClient.setCallbackUrlResolver(urlResolver);
googleClient.setScope(Google2Client.Google2Scope.EMAIL_AND_PROFILE);
clients.add(googleClient);
}
if (this.facebookAuthEnabled) {
FacebookClient facebookClient = new FacebookClient(this.facebookApiKey, this.facebookApiSecret);
facebookClient.setScope("email");
facebookClient.setFields("email");
clients.add(facebookClient);
}
if (this.githubAuthEnabled) {
GitHubClient githubClient = new GitHubClient(this.githubApiKey, this.githubApiSecret);
githubClient.setScope("user:email");
clients.add(githubClient);
}
if (this.openidAuthEnabled) {
OidcConfiguration configuration = oidcConfCreator.build();
if (StringUtils.isNotBlank(configuration.getClientId())) {
// https://www.pac4j.org/4.0.x/docs/clients/openid-connect.html
// OidcClient allows indirect login through UI with code flow
OidcClient oidcClient = new OidcClient(configuration);
oidcClient.setCallbackUrl(oauthApiCallback);
oidcClient.setCallbackUrlResolver(urlResolver);
clients.add(oidcClient);
// HeaderClient allows api access with a bearer token from the identity provider
UserInfoOidcAuthenticator authenticator = new UserInfoOidcAuthenticator(configuration);
HeaderClient headerClient = new HeaderClient("Authorization", "Bearer ", authenticator);
clients.add(headerClient);
} else {
logger.warn("openidAuth is enabled but no client id is provided");
}
}
if (clients.size() > 0) {
Config cfg =
new Config(
new Clients(
this.oauthApiCallback,
clients
)
);
// assign clients to filters
if (this.googleAuthEnabled) {
SecurityFilter googleOauthFilter = new SecurityFilter();
googleOauthFilter.setConfig(cfg);
googleOauthFilter.setClients("Google2Client");
filters.put(GOOGLE_AUTHC, googleOauthFilter);
}
if (this.facebookAuthEnabled) {
SecurityFilter facebookOauthFilter = new SecurityFilter();
facebookOauthFilter.setConfig(cfg);
facebookOauthFilter.setClients("FacebookClient");
filters.put(FACEBOOK_AUTHC, facebookOauthFilter);
}
if (this.githubAuthEnabled) {
SecurityFilter githubOauthFilter = new SecurityFilter();
githubOauthFilter.setConfig(cfg);
githubOauthFilter.setClients("GitHubClient");
filters.put(GITHUB_AUTHC, githubOauthFilter);
}
if (this.openidAuthEnabled) {
SecurityFilter oidcFilter = new SecurityFilter();
oidcFilter.setConfig(cfg);
oidcFilter.setClients("OidcClient");
filters.put(OIDC_AUTH, oidcFilter);
SecurityFilter oidcDirectFilter = new SecurityFilter();
oidcDirectFilter.setConfig(cfg);
oidcDirectFilter.setClients("HeaderClient");
filters.put(OIDC_DIRECT_AUTH, oidcDirectFilter);
}
CallbackFilter callbackFilter = new CallbackFilter();
callbackFilter.setConfig(cfg);
filters.put(OAUTH_CALLBACK, callbackFilter);
filters.put(HANDLE_UNSUCCESSFUL_OAUTH, new RedirectOnFailedOAuthFilter(this.oauthUiCallback));
}
if (this.casAuthEnabled) {
this.setUpCAS(filters);
}
if (this.samlEnabled) {
this.setUpSaml(filters);
}
return filters;
}
@Override
protected FilterChainBuilder getFilterChainBuilder() {
List<FilterTemplates> authcFilters = googleAccessTokenEnabled ? Arrays.asList(ACCESS_AUTHC, JWT_AUTHC) :
Collections.singletonList(JWT_AUTHC);
// the order does matter - first match wins
FilterChainBuilder filterChainBuilder = new FilterChainBuilder()
.setRestFilters(SSL, NO_SESSION_CREATION, CORS, NO_CACHE)
.setAuthcFilter(authcFilters.toArray(new FilterTemplates[0]))
.setAuthzFilter(AUTHZ)
// login/logout
.addRestPath("/user/refresh", JWT_AUTHC, UPDATE_TOKEN, SEND_TOKEN_IN_HEADER)
.addProtectedRestPath("/user/runas", RUN_AS, UPDATE_TOKEN, SEND_TOKEN_IN_HEADER)
.addRestPath("/user/logout", LOGOUT);
// MUST be called before adding OAuth filters
if (this.openidAuthEnabled || this.googleAuthEnabled || this.facebookAuthEnabled || this.githubAuthEnabled) {
filterChainBuilder
.setBeforeOAuthFilters(SSL, CORS, FORCE_SESSION_CREATION)
.setAfterOAuthFilters(UPDATE_TOKEN, SEND_TOKEN_IN_URL)
.addPath("/user/oauth/callback", OAUTH_CALLBACK_FILTERS)
.addPath("/user/oauth/callback/*", OAUTH_CALLBACK_FILTERS);
}
if (this.openidAuthEnabled) {
filterChainBuilder
.addRestPath("/user/login/openid", FORCE_SESSION_CREATION, OIDC_AUTH, UPDATE_TOKEN, SEND_TOKEN_IN_URL)
.addRestPath("/user/login/openidDirect", FORCE_SESSION_CREATION, OIDC_DIRECT_AUTH, UPDATE_TOKEN, SEND_TOKEN_IN_HEADER);
}
if (this.googleAuthEnabled) {
filterChainBuilder.addOAuthPath("/user/oauth/google", GOOGLE_AUTHC);
}
if (this.facebookAuthEnabled) {
filterChainBuilder.addOAuthPath("/user/oauth/facebook", FACEBOOK_AUTHC);
}
if (this.githubAuthEnabled) {
filterChainBuilder.addOAuthPath("/user/oauth/github", GITHUB_AUTHC);
}
if (this.kerberosAuthEnabled) {
filterChainBuilder.addRestPath("/user/login/kerberos", KERBEROS_FILTER, UPDATE_TOKEN, SEND_TOKEN_IN_HEADER);
}
if (this.windowsAuthEnabled) {
filterChainBuilder.addRestPath("/user/login/windows", NEGOTIATE_AUTHC, UPDATE_TOKEN, SEND_TOKEN_IN_HEADER);
}
if (this.jdbcAuthEnabled) {
filterChainBuilder.addRestPath("/user/login/db", JDBC_FILTER, UPDATE_TOKEN, SEND_TOKEN_IN_HEADER);
}
if (this.ldapAuthEnabled) {
filterChainBuilder.addRestPath("/user/login/ldap", LDAP_FILTER, UPDATE_TOKEN, SEND_TOKEN_IN_HEADER);
}
if (this.adAuthEnabled) {
filterChainBuilder.addRestPath("/user/login/ad", AD_FILTER, UPDATE_TOKEN, SEND_TOKEN_IN_HEADER);
}
if (this.casAuthEnabled) {
filterChainBuilder
.addPath("/user/login/cas", SSL, CORS, FORCE_SESSION_CREATION, CAS_AUTHC, UPDATE_TOKEN, SEND_TOKEN_IN_URL)
.addPath("/user/cas/callback", SSL, HANDLE_CAS, UPDATE_TOKEN, SEND_TOKEN_IN_URL);
}
if (this.samlEnabled) {
filterChainBuilder
.addPath("/user/login/saml", SSL, CORS, FORCE_SESSION_CREATION, SAML_AUTHC, UPDATE_TOKEN, SEND_TOKEN_IN_URL)
.addPath("/user/login/samlForce", SSL, CORS, FORCE_SESSION_CREATION, SAML_AUTHC_FORCE, UPDATE_TOKEN, SEND_TOKEN_IN_URL)
.addPath("/user/saml/callback", SSL, HANDLE_SAML, UPDATE_TOKEN, SEND_TOKEN_IN_URL);
}
setupProtectedPaths(filterChainBuilder);
return filterChainBuilder.addRestPath("/**");
}
@Override
public Set<Realm> getRealms() {
Set<Realm> realms = super.getRealms();
realms.add(new JwtAuthRealm(this.authorizer));
if (this.windowsAuthEnabled) {
realms.add(new NegotiateAuthenticationRealm());
}
realms.add(new Pac4jRealm());
if (jdbcAuthEnabled && jdbcDataSource != null) {
realms.add(new JdbcAuthRealm(jdbcDataSource, jdbcAuthenticationQuery));
}
if (this.kerberosAuthEnabled) {
realms.add(new KerberosAuthRealm(kerberosSpn, kerberosKeytabPath));
}
if (this.ldapAuthEnabled) {
realms.add(ldapRealm());
}
if (this.adAuthEnabled) {
realms.add(activeDirectoryRealm());
}
return realms;
}
private OidcClient getOidcClient() {
OidcConfiguration configuration = oidcConfCreator.build();
return new OidcClient(configuration);
}
private GitHubClient getGitHubClient() {
GitHubClient githubClient = new GitHubClient(this.githubApiKey, this.githubApiSecret);
githubClient.setScope("user:email");
return githubClient;
}
private FacebookClient getFacebookClient() {
FacebookClient facebookClient = new FacebookClient(this.facebookApiKey, this.facebookApiSecret);
facebookClient.setScope("email");
facebookClient.setFields("email");
return facebookClient;
}
private void setUpSaml(Map<FilterTemplates, Filter> filters) {
try {
SAML2Client client = setUpSamlClient(filters, SAML_AUTHC, false);
SAML2Client clientForce = setUpSamlClient(filters, SAML_AUTHC_FORCE, true);
SamlHandleFilter samlHandleFilter = new SamlHandleFilter(client, clientForce, this.oauthUiCallback);
filters.put(HANDLE_SAML, samlHandleFilter);
samlEnabled = true;
} catch (Exception e) {
samlEnabled = false;
filters.remove(SAML_AUTHC_FORCE);
filters.remove(SAML_AUTHC);
filters.remove(HANDLE_SAML);
logger.error("Failed to initlize SAML filters: " + e.getMessage());
}
}
private SAML2Client setUpSamlClient(Map<FilterTemplates, Filter> filters, FilterTemplates template, boolean isForcedAuth) {
final SAML2Configuration cfg = new SAML2Configuration(
ResourceUtils.mapPathToResource(keyStoreFile),
alias,
null,
keyStorePassword,
privateKeyPassword,
ResourceUtils.mapPathToResource(metadataLocation));
cfg.setMaximumAuthenticationLifetime(this.maximumAuthenticationLifetime);
cfg.setServiceProviderEntityId(identityProviderEntityId);
cfg.setForceAuth(isForcedAuth);
cfg.setServiceProviderMetadataPath(spMetadataLocation);
cfg.setAuthnRequestBindingType(SAMLConstants.SAML2_REDIRECT_BINDING_URI);
final SAML2Client saml2Client = new SAML2Client(cfg);
Config samlCfg = new Config(new Clients(samlCallbackUrl, saml2Client));
SecurityFilter samlAuthFilter = new SecurityFilter();
samlAuthFilter.setConfig(samlCfg);
samlAuthFilter.setClients("saml2Client");
filters.put(template, samlAuthFilter);
return saml2Client;
}
private Google2Client getGoogle2Client() {
Google2Client googleClient = new Google2Client(this.googleApiKey, this.googleApiSecret);
googleClient.setScope(Google2Client.Google2Scope.EMAIL);
return googleClient;
}
private DefaultLdapRealm ldapRealm() {
DefaultLdapRealm realm = new LdapRealm(ldapSearchString, ldapSearchBase, ldapUserMapper);
JndiLdapContextFactory contextFactory = new JndiLdapContextFactory();
contextFactory.setUrl(dequote(ldapUrl));
contextFactory.setPoolingEnabled(false);
contextFactory.getEnvironment().put(Context.INITIAL_CONTEXT_FACTORY, "com.sun.jndi.ldap.LdapCtxFactory");
realm.setContextFactory(contextFactory);
if (StringUtils.isNotEmpty(userDnTemplate)) {
realm.setUserDnTemplate(dequote(userDnTemplate));
}
return realm;
}
private ActiveDirectoryRealm activeDirectoryRealm() {
ActiveDirectoryRealm realm = new ADRealm(getLdapTemplate(), adSearchFilter, adSearchString, adUserMapper);
realm.setUrl(dequote(adUrl));
realm.setSearchBase(dequote(adSearchBase));
realm.setPrincipalSuffix(dequote(adPrincipalSuffix));
realm.setSystemUsername(dequote(adSystemUsername));
realm.setSystemPassword(dequote(adSystemPassword));
return realm;
}
private LdapTemplate getLdapTemplate() {
if (StringUtils.isNotBlank(adSearchFilter)) {
return adLdapProvider.getLdapTemplate();
}
return null;
}
private void setUpCAS(Map<FilterTemplates, Filter> filters) {
try {
/**
* CAS config
*/
CasConfiguration casConf = new CasConfiguration();
String casLoginUrlString;
if (casSvcs != null && !"".equals(casSvcs)) {
casLoginUrlString = casLoginUrl + "?cassvc=" + casSvcs + "&casurl="
+ URLEncoder.encode(casCallbackUrl, StandardCharsets.UTF_8.name());
} else {
casLoginUrlString = casLoginUrl + "?casurl="
+ URLEncoder.encode(casCallbackUrl, StandardCharsets.UTF_8.name());
}
casConf.setLoginUrl(casLoginUrlString);
Cas20ServiceTicketValidator cas20Validator = new Cas20ServiceTicketValidator(casServerUrl);
casConf.setDefaultTicketValidator(cas20Validator);
CasClient casClient = new CasClient(casConf);
Config casCfg = new Config(new Clients(casCallbackUrl, casClient));
/**
* CAS filter
*/
SecurityFilter casAuthnFilter = new SecurityFilter();
casAuthnFilter.setConfig(casCfg);
casAuthnFilter.setClients("CasClient");
filters.put(CAS_AUTHC, casAuthnFilter);
/**
* CAS callback filter
*/
CasHandleFilter casHandleFilter = new CasHandleFilter(cas20Validator, casCallbackUrl, casticket);
filters.put(HANDLE_CAS, casHandleFilter);
} catch (UnsupportedEncodingException e) {
this.logger.error("Atlas security filter errors: {}", e);
}
}
private CallbackUrlResolver getCallbackUrlResolver() {
CallbackUrlResolver resolver = new QueryParameterCallbackUrlResolver();
if (Constants.CallbackUrlResolvers.PATH.equals(oauthCallbackUrlResolver)) {
resolver = new PathParameterCallbackUrlResolver();
} else if (!Constants.CallbackUrlResolvers.QUERY.equals(oauthCallbackUrlResolver)) {
this.logger.warn("OAuth Callback Url Resolver {} not supported, ignored and used default QueryParameterUrlResolver", oauthCallbackUrlResolver);
}
return resolver;
}
public boolean isSamlEnabled() {
return samlEnabled;
}
}
| java | Apache-2.0 | b22d7bf02d98c0cf78c46801877368d6ecad2245 | 2026-01-05T02:37:20.475642Z | false |
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