conflict_resolution stringlengths 27 16k |
|---|
<<<<<<<
import org.junit.contrib.truth.subjects.DefaultSubject;
import org.junit.contrib.truth.subjects.IntSubject;
=======
import org.junit.contrib.truth.subjects.IntegerSubject;
>>>>>>>
import org.junit.contrib.truth.subjects.DefaultSubject;
import org.junit.contrib.truth.subjects.IntegerSubject; |
<<<<<<<
public class IntegerSubject extends Subject<IntegerSubject, Long> {
=======
/**
* Propositions for Integral numeric subjects
*
* @author David Saff
* @author Christian Gruber (cgruber@israfil.net)
*/
public class IntegerSubject extends Subject<Long> {
>>>>>>>
/**
* Propositions for Integral numeric su... |
<<<<<<<
EXPECT.that("abc").contains("x")
.and().contains("y")
.and().contains("z");
=======
EXPECT.that("abc").contains("x").contains("y").contains("z");
EXPECT.that(Arrays.asList(new String[]{"a", "b", "c"})).containsAnyOf("a", "c");
>>>>>>>
EXPECT.that("abc").contains("x")
... |
<<<<<<<
public And<IntegerSubject> isInclusivelyInRange(int lower, int upper) {
if (lower > upper) {
throw new IllegalArgumentException(String.format(
RANGE_BOUNDS_OUT_OF_ORDER_MSG, lower, upper));
}
=======
public Subject<Long> isInclusivelyInRange(long lower, long upper) {
ensureOrde... |
<<<<<<<
public class PhotoGridAdapter extends RecyclerView.Adapter<PhotoGridAdapter.PhotoViewHolder> implements View.OnClickListener, View.OnLongClickListener {
=======
public class PhotoGridAdapter extends RecyclerView.Adapter<PhotoGridAdapter.PhotoViewHolder>{
>>>>>>>
public class PhotoGridAdapter extends Recycler... |
<<<<<<<
=======
// non-polymorphic type variables from bindings in closure
YType closureVars[] = NO_PARAM;
int closureVarCount;
void restrictArg(YType type, boolean active) {
if (type.seen)
return;
if (type.field >= FIELD_NON_POLYMORPHIC)
... |
<<<<<<<
shell = new CypherShell(linePrinter, new PrettyConfig(Format.PLAIN, true, 1000), false);
shell.connect(new ConnectionConfig("bolt://", "localhost", 7687, "neo4j", "neo", false, ABSENT_DB_NAME));
=======
shell = new CypherShell(linePrinter, new PrettyConfig(Format.PLAIN, true, 1000));
... |
<<<<<<<
import org.junit.Ignore;
import org.junit.Rule;
=======
import org.junit.Before;
>>>>>>>
import org.junit.Before;
import org.junit.Rule;
<<<<<<<
ShellAndConnection sac = getShell( cliArgs );
CypherShell shell = sac.shell;
ConnectionConfig connectionConfig = sac.connectionConfig;
===... |
<<<<<<<
CopyMode, CopyModeDesc, PatternTerminal, CraftingPattern, ProcessingPattern, Crafts, Creates, And, With, MolecularAssembler,
StoredPower, MaxPower, RequiredPower, Efficiency, InWorldCrafting, inWorldFluix, inWorldPurification, inWorldSingularity,
OfSecondOutput, NoSecondOutput, RFTunnel, Stores, Next, Sele... |
<<<<<<<
public static ItemStack extractItemsByRecipe(IEnergySource energySrc, BaseActionSource mySrc, IMEMonitor<IAEItemStack> src, World w, IRecipe r,
ItemStack output, InventoryCrafting ci, ItemStack providedTemplate, int slot, IItemList<IAEItemStack> aitems)
{
if ( energySrc.extractAEPower( 1, Actionable.SIMU... |
<<<<<<<
AxisAlignedBB axisalignedbb1 = entity1.boundingBox.expand( f1, f1, f1 );
MovingObjectPosition movingobjectposition1 = axisalignedbb1.calculateIntercept( vec3, vec31 );
=======
AxisAlignedBB boundingBox = entity1.boundingBox.expand( (double) f1, (double) f1, (double) f1 );
MovingObjectPosit... |
<<<<<<<
public static ItemStack getContainerItem(ItemStack stackInSlot)
{
if ( stackInSlot == null )
return null;
Item i = stackInSlot.getItem();
if ( i == null || !i.hasContainerItem( stackInSlot ) )
{
if ( stackInSlot.stackSize > 1 )
{
stackInSlot.stackSize--;
return stackInSlot;
}
r... |
<<<<<<<
import com.beust.jcommander.*;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
=======
import com.beust.jcommander.*;
import org.opencb.biodata.models.variant.VariantSource;
import org.opencb.biodata.models.variant.VariantStudy;
>>>>>>>
import com.beust.jc... |
<<<<<<<
import java.util.*;
=======
import java.util.Arrays;
import java.util.Collections;
import java.util.Map;
>>>>>>>
import java.util.*;
import java.util.Arrays;
import java.util.Collections;
import java.util.Map; |
<<<<<<<
public OpenCGAResult<Long> count(Query query, String user, StudyAclEntry.StudyPermissions studyPermission) throws CatalogDBException {
=======
public QueryResult<Long> count(long studyUid, Query query, String user, StudyAclEntry.StudyPermissions studyPermission)
throws CatalogDBException {... |
<<<<<<<
import org.opencb.biodata.models.variant.Variant;
=======
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.VariantSource;
>>>>>>>
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.VariantSource;
<<<<<<<
dbAdaptor ... |
<<<<<<<
configuration.setOpenRegister(true);
configuration.getAdmin().setPassword("demo");
CatalogDemo.createDemoDatabase(configuration, catalogCommandOptions.demoCatalogCommandOptions.force);
CatalogManager catalogManager = new CatalogManager(configuration);
sessionId = catalogM... |
<<<<<<<
import org.apache.commons.lang3.time.StopWatch;
=======
import org.apache.commons.lang3.StringUtils;
>>>>>>>
<<<<<<<
=======
import org.apache.hadoop.hbase.util.Bytes;
import org.apache.hadoop.util.StopWatch;
import org.opencb.commons.datastore.core.ObjectMap;
>>>>>>>
import org.apache.hadoop.util.StopWa... |
<<<<<<<
=======
import com.mongodb.BasicDBObject;
import com.mongodb.DBObject;
import org.junit.Assert;
import org.junit.Rule;
>>>>>>>
import com.mongodb.BasicDBObject;
import com.mongodb.DBObject;
<<<<<<<
=======
import org.opencb.datastore.core.QueryOptions;
import org.opencb.datastore.core.config.DataStoreConf... |
<<<<<<<
int getProjectId(String userId, String project);
String getProjectOwner(int projectId) throws CatalogManagerException;
=======
int getProjectId(String userId, String project) throws CatalogManagerException;
>>>>>>>
int getProjectId(String userId, String project) throws CatalogManagerExcepti... |
<<<<<<<
OpenCGAResult<File> queryResult = fileDBAdaptor.get(finalQuery, options, userId);
auditManager.auditSearch(userId, Enums.Resource.FILE, study.getId(), study.getUuid(), auditParams,
=======
OpenCGAResult<File> queryResult = fileDBAdaptor.get(study.getUid(), finalQuery, optio... |
<<<<<<<
List<String> include = Arrays.asList("chromosome", "start", "end", "alternative", "reference", "sourceEntries");
iteratorQueryOptions.add("include", include); // add() does not overwrite in case a "include" was already specified
=======
List<String> include = Arrays.asList("chromosom... |
<<<<<<<
sampleIndexQuery = SampleIndexQueryParser.parseSampleIndexQuery(query, metadataManager);
StudyMetadata studyMetadata = metadataManager.getStudyMetadata(sampleIndexQuery.getStudy());
=======
SampleIndexQuery sampleIndexQuery = sampleIndexDBAdaptor.getSampleIndexQueryParser().parse(query... |
<<<<<<<
import org.opencb.opencga.catalog.exceptions.CatalogException;
import org.opencb.opencga.catalog.utils.Constants;
import org.opencb.opencga.catalog.utils.UUIDUtils;
import org.opencb.opencga.core.common.Entity;
=======
import org.opencb.opencga.catalog.exceptions.CatalogException;
>>>>>>>
import org.opencb.o... |
<<<<<<<
static class ObjectWrapperMap extends HashMap<String, ObjectWrapper> { }
=======
static class AbstractMapWrapper {
public AbstractMap<String, Integer> values;
}
>>>>>>>
static class ObjectWrapperMap extends HashMap<String, ObjectWrapper> { }
static class AbstractMapWrapp... |
<<<<<<<
OpenCGAResult<ClinicalAnalysis> analysisDataResult = clinicalDBAdaptor.get(queryCopy, queryOptions, user);
if (analysisDataResult.getNumResults() == 0) {
analysisDataResult = clinicalDBAdaptor.get(queryCopy, queryOptions);
if (analysisDataResult.getNumResults() == 0) {
=... |
<<<<<<<
import com.google.common.collect.BiMap;
import com.google.protobuf.InvalidProtocolBufferException;
=======
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java... |
<<<<<<<
+ '.' + DocumentToStudyVariantEntryConverter.FILEID_FIELD, files, studyBuilder, QueryOperation.AND,
queryOperation, t -> t);
=======
+ '.' + DocumentToStudyVariantEntryConverter.FILEID_FIELD, files, builder, Qu... |
<<<<<<<
// assertEquals(1, annotationSetQueryResult.getNumResults());
Map<String, Object> map = sampleQueryResult.first().getAnnotationSets().get(0).getAnnotations();
assertEquals(4, map.size());
=======
// assertEquals(1, annotationSetDataResult.getNumResults());
Map<String, Obj... |
<<<<<<<
Entity.FAMILY);
=======
allFamilyPermissions, collectionName);
>>>>>>>
allFamilyPermissions, Entity.FAMILY); |
<<<<<<<
=======
import org.opencb.opencga.analysis.variant.VariantExportTool;
import org.opencb.opencga.analysis.variant.operations.VariantFileDeleteOperationTool;
>>>>>>>
import org.opencb.opencga.analysis.variant.operations.VariantFileDeleteOperationTool; |
<<<<<<<
return AnalysisJobExecutor.createJob(catalogManager, studyId, jobName,
AnalysisFileIndexer.OPENCGA_ANALYSIS_BIN_NAME, jobDescription, outDir, inputFiles,
=======
return jobFactory.createJob(studyId, jobName,
AnalysisFileIndexer.OPENCGA_ANALYSIS_BIN_NAME, jobDesc... |
<<<<<<<
import org.opencb.opencga.storage.hadoop.variant.archive.ArchiveTableHelper;
import org.opencb.opencga.storage.hadoop.variant.mr.AbstractHBaseVariantMapper;
import org.opencb.opencga.storage.hadoop.variant.mr.AnalysisTableMapReduceHelper;
=======
>>>>>>>
import org.opencb.opencga.storage.hadoop.variant.archi... |
<<<<<<<
public OpenCGAResult<Panel> get(Query query, QueryOptions options, String user)
throws CatalogDBException, CatalogAuthorizationException {
return get(null, query, options, user);
}
OpenCGAResult<Panel> get(ClientSession clientSession, Query query, QueryOptions options, String us... |
<<<<<<<
=======
import org.opencb.commons.datastore.core.QueryResult;
import org.opencb.opencga.catalog.db.api.CatalogFileDBAdaptor;
import org.opencb.opencga.catalog.managers.CatalogManager;
>>>>>>>
import org.opencb.commons.datastore.core.QueryResult; |
<<<<<<<
import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;
import org.opencb.opencga.storage.core.variant.adaptors.iterators.VariantDBIterator;
=======
import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils;
>>>>>>>
import org.opencb.opencga.storage.core.variant.adaptors.Va... |
<<<<<<<
// @Deprecated
// INCLUDE_SRC("include.src", false), //Include original source file on the transformed file and the final db
=======
EXTRA_GENOTYPE_FIELDS_TYPE("include.extra-fields-format", ""), //Other sample information format (String, Integer, Float)
EXTRA_G... |
<<<<<<<
import org.opencb.opencga.analysis.storage.OpenCGATestExternalResource;
import org.opencb.opencga.storage.core.variant.VariantStorageEngine;
=======
import org.opencb.opencga.storage.core.manager.OpenCGATestExternalResource;
import org.opencb.opencga.storage.core.variant.VariantStorageOptions;
>>>>>>>
import... |
<<<<<<<
=======
import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils;
import org.opencb.opencga.storage.core.variant.annotation.DefaultVariantAnnotationManager;
>>>>>>>
import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils;
<<<<<<<
import org.opencb.opencga.storage.mongodb.a... |
<<<<<<<
long projectId = catalogManager.getStudyManager().getProjectId(study.getUid());
dataStore = getDataStoreByProjectId(catalogManager, projectId, bioformat, sessionId);
=======
long projectId = catalogManager.getStudyManager().getProjectId(study.getId());
dataStore... |
<<<<<<<
OpenCGAResult<Individual> individualDataResult = individualDBAdaptor.get(queryCopy, queryOptions, user);
if (individualDataResult.getNumResults() == 0) {
individualDataResult = individualDBAdaptor.get(queryCopy, queryOptions);
if (individualDataResult.getNumResults() == 0... |
<<<<<<<
Job job = new Job(name, userId, toolName, description, commandLine, outDir, inputFiles);
=======
Job job = new Job(name, userId, toolName, description, commandLine, outDir.getId(), inputFiles,
catalogManager.getStudyManager().getCurrentRelease(studyId));
>>>>>>>
Job jo... |
<<<<<<<
import org.opencb.commons.datastore.core.ObjectMap;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.commons.datastore.core.QueryResult;
=======
import org.opencb.biodata.tools.variant.stats.VariantAggregatedStatsCalculator;
>>>>>>>
impo... |
<<<<<<<
.enableDefaultTyping(NoCheckSubTypeValidator.instance,
DefaultTyping.NON_FINAL)
=======
.activateDefaultTyping(NoCheckSubTypeValidator.instance,
ObjectMapper.DefaultTyping.NON_FINAL)
>>>>>>>
.activateDefaultTyping(NoCheckSubTypeValid... |
<<<<<<<
import java.io.IOException;
import java.net.URI;
import java.util.ArrayList;
=======
import java.net.URI;
import java.nio.file.Path;
>>>>>>>
import java.io.IOException;
import java.net.URI;
import java.nio.file.Path;
import java.util.ArrayList;
<<<<<<<
public void loadVariantAnnotation(URI uri, ObjectMa... |
<<<<<<<
// This separator is not valid at Bytes.toStringBinary
private static final String REGION_SEPARATOR = "\\\\";
=======
public static final String DELETE_HBASE_COLUMN_MAPPER_CLASS = "delete.hbase.column.mapper.class";
private String table;
private List<String> columns;
@Override
pub... |
<<<<<<<
for (VariantAnnotation annotation : variantStorageEngine.getAnnotation("v2", null, new QueryOptions(QueryOptions.EXCLUDE, consequenceTypes)).getResult()) {
assertThat(annotation.getConsequenceTypes(), VariantMatchers.isEmpty());
=======
for (VariantAnnotation annotation : variantSt... |
<<<<<<<
Cohort cohort = new Cohort(name, type, TimeUtils.getTime(), description, samples, annotationSetList, attributes);
=======
Cohort cohort = new Cohort(name, type, TimeUtils.getTime(), description, sampleIds, annotationSetList,
catalogManager.getStudyManager().getCurrentRelease(st... |
<<<<<<<
individualDataResult = individualDBAdaptor.nativeGet(query, queryOptions, user);
=======
individualQueryResult = individualDBAdaptor.nativeGet(studyUid, query, queryOptions, user);
>>>>>>>
individualDataResult = individualDBAdaptor.nativeGet(studyUi... |
<<<<<<<
=======
import static org.opencb.opencga.storage.core.variant.VariantStorageEngine.Options.RELEASE;
import static org.opencb.opencga.storage.core.variant.VariantStorageEngine.Options.SEARCH_INDEX_LAST_TIMESTAMP;
>>>>>>>
import static org.opencb.opencga.storage.core.variant.VariantStorageEngine.Options.SEARCH... |
<<<<<<<
import org.apache.commons.collections4.CollectionUtils;
=======
import org.apache.commons.collections.CollectionUtils;
import org.apache.hadoop.hbase.Cell;
>>>>>>>
import org.apache.commons.collections4.CollectionUtils;
import org.apache.hadoop.hbase.Cell; |
<<<<<<<
User user = parseUser(result);
return endQuery("get user", startTime, Arrays.asList(user));
=======
User user;
List<User> users = new LinkedList<>();
try {
if (result.getNumResults() != 0) {
user = jsonUserReader.readValue(result.getResult().... |
<<<<<<<
OpenCGAResult<Sample> sampleDataResult = sampleDBAdaptor.get(queryCopy, queryOptions, user);
if (sampleDataResult.getNumResults() == 0) {
sampleDataResult = sampleDBAdaptor.get(queryCopy, queryOptions);
if (sampleDataResult.getNumResults() == 0) {
=======
QueryR... |
<<<<<<<
return new Enums.ExecutionStatus(Enums.ExecutionStatus.ERROR, "File '" + resultJson + "' seems corrupted.");
=======
if (Files.exists(resultJson)) {
logger.warn("File '" + resultJson + "' seems corrupted.");
} else {
logge... |
<<<<<<<
* Panel search.
* @param params Map containing any additional optional parameters.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse<Panel> search(ObjectMap params) throws ClientException {
params ... |
<<<<<<<
OpenCGAResult<Panel> panelDataResult = panelDBAdaptor.get(queryCopy, queryOptions, user);
if (panelDataResult.getNumResults() == 0) {
panelDataResult = panelDBAdaptor.get(queryCopy, queryOptions);
if (panelDataResult.getNumResults() == 0) {
=======
QueryResult<P... |
<<<<<<<
import org.apache.commons.lang3.StringUtils;
import org.opencb.biodata.models.commons.Software;
=======
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
>>>>>>>
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.... |
<<<<<<<
public final SampleEligibilityCommandOptions sampleEligibilityCommandOptions;
=======
public final MutationalSignatureCommandOptions mutationalSignatureCommandOptions;
>>>>>>>
public final SampleEligibilityCommandOptions sampleEligibilityCommandOptions;
public final MutationalSignatureCommand... |
<<<<<<<
=======
import org.opencb.hpg.bigdata.analysis.exceptions.AnalysisException;
>>>>>>> |
<<<<<<<
// .append(" --study-id ").append(studyId)
.append(" --database ").append(dbName)
=======
.append(" --study-id ").append(studyId)
.append(" --database ").append(dataStore.getDbName())
>>>>>>>
// .append(" --study-id ").append(study... |
<<<<<<<
public OpenCGAResult<Long> count(final Query query, final String user, final StudyAclEntry.StudyPermissions studyPermissions)
=======
public QueryResult<Long> count(long studyUid, final Query query, final String user,
final StudyAclEntry.StudyPermissions studyPermiss... |
<<<<<<<
=======
import org.opencb.opencga.storage.core.variant.VariantStorageEngine;
>>>>>>>
<<<<<<<
for (Integer studyId : studies.keySet()) {
StudyEntry studyEntry = studies.get(studyId);
stats.getOrDefault(studyId, Collections.emptyMap()).forEach((cohortId, variantStats) -> {
... |
<<<<<<<
if (hBaseManager.act(connection, tableName, (table, admin) -> admin.tableExists(table.getName()))) {
studyConfigurationList = hBaseManager.act(connection, tableName, table -> {
=======
if (!hBaseManager.act(getConnection(), credentials.getTable(), (table, admin) -> admi... |
<<<<<<<
OUT_DIR("outDir", TEXT_ARRAY, ""),
OUT_DIR_ID("outDir.id", INTEGER, ""),
=======
RELEASE("release", INTEGER, ""),
OUT_DIR_ID("outDirId", INTEGER_ARRAY, ""),
>>>>>>>
RELEASE("release", INTEGER, ""),
OUT_DIR("outDir", TEXT_ARRAY, ""),
OUT_DIR_ID("outDir.i... |
<<<<<<<
import org.opencb.opencga.storage.core.search.SearchManager;
=======
import org.opencb.opencga.storage.core.metadata.StudyConfigurationManager;
>>>>>>>
import org.opencb.opencga.storage.core.metadata.StudyConfigurationManager;
import org.opencb.opencga.storage.core.search.SearchManager; |
<<<<<<<
taskSupplier = () -> new VariantAvroTransformTask(header, headerVersion, finalSource, finalOutputMetaFile,
statsCalculator);
=======
taskSupplier = () -> new VariantAvroTransformTask(header, headerVersion, finalSource, finalOutputMetaFile, st... |
<<<<<<<
import org.opencb.opencga.storage.core.variant.VariantStorageOptions;
import org.opencb.opencga.storage.core.variant.adaptors.*;
=======
import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptorTest;
import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;
>>>>>>>
import org.... |
<<<<<<<
import org.opencb.commons.datastore.core.DataResponse;
=======
import org.opencb.biodata.tools.alignment.stats.AlignmentGlobalStats;
>>>>>>>
<<<<<<<
private DataResponse<File> statsQuery() throws IOException {
AlignmentCommandOptions.StatsQueryAlignmentCommandOptions cliOptions = alignmentComman... |
<<<<<<<
study.setFiles(dbAdaptorFactory.getCatalogFileDBAdaptor().get(query, options, user).getResults());
=======
study.setFiles(dbAdaptorFactory.getCatalogFileDBAdaptor().get(studyId, query, options, user).getResult());
>>>>>>>
study.setFiles(dbAdaptorFactory.getCata... |
<<<<<<<
/**
* Tool methods
* ***************************
*/
@Override
public QueryResult<Tool> createTool(String userId, Tool tool) throws CatalogManagerException {
long startTime = startQuery();
if (!userExists(userId)) {
throw new CatalogManagerException("User ... |
<<<<<<<
OpenCGAResult<File> pathDataResult = fileDBAdaptor.get(queryCopy, queryOptions, user);
if (pathDataResult.getNumResults() > 1) {
=======
QueryResult<File> pathQueryResult = fileDBAdaptor.get(studyUid, queryCopy, queryOptions, user);
if (pathQueryResult.getNumResults() > 1) {
>... |
<<<<<<<
=======
query.putIfNotEmpty(IndividualDBAdaptor.QueryParams.ANNOTATION_SET_NAME.key(),
individualsCommandOptions.searchCommandOptions.annotationSetName);
query.putAll(individualsCommandOptions.searchCommandOptions.commonOptions.params);
>>>>>>>
query.putAll(individuals... |
<<<<<<<
void setToMembers(List<Long> resourceIds, List<String> members, List<String> permissions, Entity entry) throws CatalogDBException;
=======
void setToMembers(List<Long> resourceIds, List<String> members, List<String> permissions, List<String> allPermissions, String entity)
throws CatalogDBE... |
<<<<<<<
private static void printAnnotationIndexTable(VariantHadoopDBAdaptor dbAdaptor, Path outDir) throws IOException {
String tableName = dbAdaptor.getTableNameGenerator().getAnnotationIndexTableName();
if (dbAdaptor.getHBaseManager().tableExists(tableName)) {
AnnotationIndexDBAdaptor... |
<<<<<<<
import org.apache.solr.common.SolrException;
import org.opencb.biodata.models.core.Region;
=======
>>>>>>>
import org.apache.solr.common.SolrException; |
<<<<<<<
AnnotatedMethodCollector(AnnotationIntrospector intr, MixInResolver mixins)
=======
/**
* @since 2.11
*/
private final boolean _collectAnnotations;
AnnotatedMethodCollector(AnnotationIntrospector intr,
MixInResolver mixins, boolean collectAnnotations)
>>>>>>>
privat... |
<<<<<<<
import java.io.IOException;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.opencb.biodata.formats.io.FileFormatException;
=======
import org.opencb.biodata.formats.pedigree.io.PedigreePedReader;
import org.opencb.biodata.formats.pedigree.... |
<<<<<<<
.append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz");
queryResult = query(query, options);
=======
.append(VariantQueryParam.INCLUDE_FILE.key(), file12877);
queryResult = dbAdaptor.get(query, options);
>>>>>>>
... |
<<<<<<<
=======
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.core.type.TypeReference;
>>>>>>>
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.core.type.TypeReference;
<<<<<<<
=======
enum ABC {
A, B, C
}
enum AbcLC {
A,... |
<<<<<<<
StudyConfiguration studyConfiguration = studyConfigurationFactory.getStudyConfiguration(studyId, scm, new QueryOptions(), sessionId);
=======
StudyConfiguration studyConfiguration = studyConfigurationManager.getStudyConfiguration(studyId, null, scm, new QueryOptions(), sessionId);
>>>>>>>
... |
<<<<<<<
import org.opencb.commons.utils.StringUtils;
import org.opencb.opencga.catalog.managers.CatalogManagerExternalResource;
=======
>>>>>>>
import org.opencb.commons.utils.StringUtils;
<<<<<<<
=======
import org.opencb.opencga.catalog.managers.CatalogManagerExternalResource;
import org.opencb.opencga.catalog.... |
<<<<<<<
String study = String.valueOf(job.getAttributes().get(Job.OPENCGA_STUDY));
logger.info("[{}] - Registering job results from '{}'", job.getId(), outDirUri);
=======
logger.info("{} - Registering job results from '{}'", job.getId(), outDirUri);
>>>>>>>
logger.info("[{}] - Regis... |
<<<<<<<
o.putIfNotNull(FileDBAdaptor.QueryParams.STUDY.key(), filesCommandOptions.indexCommandOptions.studyId);
=======
o.putIfNotNull(VariantStorageManager.Options.RESUME.key(), filesCommandOptions.indexCommandOptions.resume);
>>>>>>>
o.putIfNotNull(FileDBAdaptor.QueryParams.STUDY.key(), fil... |
<<<<<<<
=======
import org.opencb.opencga.catalog.monitor.exceptions.ExecutionException;
import org.opencb.opencga.catalog.monitor.executors.old.ExecutorManager;
import org.opencb.opencga.catalog.managers.CatalogManager;
>>>>>>>
<<<<<<<
import org.opencb.opencga.catalog.monitor.exceptions.ExecutionException;
import... |
<<<<<<<
customAnalysisOptions, opencgaHome.toString(), token);
InterpretationResult interpretationResult = customAnalysis.execute();
=======
customAnalysisOptions, opencgaHome.toString(), sessionId);
InterpretationResult interpretationResult = customAnal... |
<<<<<<<
TimeUtils.getTime(), description, status, external, size, new Experiment().setId(experimentId), samples,
new Job().setId(jobId), Collections.emptyList(), Collections.emptyList(), null, stats, attributes);
=======
TimeUtils.getTime(), description, status, externa... |
<<<<<<<
OpenCGAResult<Cohort> cohortDataResult = cohortDBAdaptor.get(queryCopy, queryOptions, user);
if (cohortDataResult.getNumResults() == 0) {
cohortDataResult = cohortDBAdaptor.get(queryCopy, queryOptions);
if (cohortDataResult.getNumResults() == 0) {
=======
QueryR... |
<<<<<<<
if (isValidParam(query, VariantHadoopDBAdaptor.ANNOT_NAME)) {
String name = query.getString(VariantHadoopDBAdaptor.ANNOT_NAME.key());
scan.addColumn(genomeHelper.getColumnFamily(), Bytes.toBytes(VariantPhoenixHelper.getAnnotationSnapshotColumn(name)));
} e... |
<<<<<<<
import org.opencb.opencga.storage.core.variant.VariantStorageOptions;
=======
import org.opencb.opencga.storage.core.variant.VariantStorageEngine;
import org.opencb.opencga.storage.core.variant.adaptors.GenotypeClass;
>>>>>>>
import org.opencb.opencga.storage.core.variant.VariantStorageOptions;
import org.op... |
<<<<<<<
@Deprecated public static final String CONFIG_VCF_META_PROTO_FILE = "opencga.storage.hadoop.vcf.meta.proto.file";
@Deprecated public static final String CONFIG_VCF_META_PROTO_STRING = "opencga.storage.hadoop.vcf.meta.proto.string";
public static final String CONFIG_FILE_ID = "opencga.storage.hadoop... |
<<<<<<<
public OpenCGAResult<Long> count(Query query, String user, StudyAclEntry.StudyPermissions studyPermissions)
throws CatalogDBException, CatalogAuthorizationException {
return count(null, query, user, studyPermissions);
}
OpenCGAResult<Long> count(ClientSession clientSession, Quer... |
<<<<<<<
QueryResult<Study> studyQueryResult = catalogManager.getStudyManager().get(String.valueOf((Long) studyUid), QueryOptions.empty(),
token);
assertEquals(1, studyQueryResult.getNumResults());
=======
assertEquals(9, catalogManager.getSampleManager().count(String.valueOf(st... |
<<<<<<<
BeanPropertyDefinition propDef = candidate.propertyDef(0);
boolean useProps = _checkIfCreatorPropertyBased(ctxt, ctor, propDef);
=======
final BeanPropertyDefinition propDef = candidate.propertyDef(0);
final boolean useProps = preferPropsBased ||... |
<<<<<<<
=======
import org.opencb.biodata.models.variant.avro.VariantAnnotation;
import org.opencb.biodata.models.variant.avro.VariantType;
>>>>>>>
<<<<<<<
variant.getStudy(STUDY_NAME).getAttributes().remove("src");
Variant loadedVariant = dbAdaptor.get(new Query(VariantDBAdaptor.VariantQuer... |
<<<<<<<
Map missingSamples = Collections.emptyMap();
String defaultGenotype = studyConfiguration.getAttributes().getString(MongoDBVariantStorageManager.DEFAULT_GENOTYPE, "");
if (defaultGenotype.equals(DBObjectToSamplesConverter.UNKNOWN_GENOTYPE)) {
logger.debug("Do not need fill ga... |
<<<<<<<
import org.apache.phoenix.schema.types.PInteger;
=======
import org.apache.phoenix.schema.types.PhoenixArray;
>>>>>>>
import org.apache.phoenix.schema.types.PInteger;
import org.apache.phoenix.schema.types.PhoenixArray;
<<<<<<<
=======
import org.opencb.opencga.storage.hadoop.variant.converters.AbstractPh... |
<<<<<<<
public Cohort(String name, Study.Type type, String creationDate, String description, List<Sample> samples,
=======
public Cohort(String name, Study.Type type, String creationDate, String description, List<Long> samples, int release,
>>>>>>>
public Cohort(String name, Study.Type type, String creat... |
<<<<<<<
final Long fileId = fileIdStr == null ? null : catalogManager.getFileId(fileIdStr, Long.toString(studyId), sessionId);
=======
boolean resume = options.getBoolean(Options.RESUME.key(), Options.RESUME.defaultValue());
final Long fileId = fileIdStr == null ? null : catalogManager.getFile... |
<<<<<<<
import org.opencb.biodata.models.variant.Variant;
=======
import org.opencb.biodata.models.variant.VariantSource;
>>>>>>>
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.VariantSource; |
<<<<<<<
=======
// [databind#28]: ObjectMapper.copy()
public void testCopy() throws Exception
{
ObjectMapper m = new ObjectMapper();
assertTrue(m.isEnabled(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES));
m.disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES);
ass... |
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