id stringlengths 7 14 | test_class dict | test_case dict | focal_class dict | focal_method dict | repository dict |
|---|---|---|---|---|---|
52478731_55 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( DatasetCombinerTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( DatasetCombinerTest.class.getName() );",
"type": "Log",
"var_name": "log"
},
... | {
"body": "@Test\n public void testFindGSE267() {\n Collection<String> result = DatasetCombiner.findGDSforGSE( \"GSE267\" );\n assertEquals( 0, result.size() );\n }",
"class_method_signature": "DatasetCombinerTest.testFindGSE267()",
"constructor": false,
"full_signature": "@Test public void ... | {
"fields": [
{
"declarator": "factory = DocumentBuilderFactory.newInstance()",
"modifier": "static final",
"original_string": "static final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();",
"type": "DocumentBuilderFactory",
"var_name": "factory"
},
{
... | {
"body": "public static Collection<String> findGDSforGSE( Collection<String> seriesAccessions ) {\n /*\n * go from GSE to GDS, using screen scraping.\n */\n // http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds&term=GSE674[Accession]&cmd=search\n // grep on \"GDS[[digits]] reco... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_43 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testPixels() {\n String a = \"B Pixels\";\n String b = \"number of background pixels\";\n PrimitiveType s = QuantitationTypeParameterGuesser.guessPrimitiveType( a.toLowerCase(), b.toLowerCase(), null );\n assertEquals( \"got \" + s, PrimitiveType.INT, s );... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static PrimitiveType guessPrimitiveType( String name, String description, Object exampleValue ) {\n\n String exampleString = null;\n boolean couldBeDouble = true;\n boolean couldBeInt = true;\n if ( exampleValue != null ) {\n if ( exampleValue instanceof Dou... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_14 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLParserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedXMLParserTest.class.getName() );",
"type": "Log",
"var_name": "log"
},
... | {
"body": "@Test\n public void testParseMulti() throws Exception {\n try {\n testStream = new GZIPInputStream(\n PubMedXMLParserTest.class.getResourceAsStream( \"/data/loader/medline.multi.xml.gz\" ) );\n Collection<BibliographicReference> brl = testParser.parse( tes... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLParser.class )",
"modifier": "protected static final",
"original_string": "protected static final Log log = LogFactory.getLog( PubMedXMLParser.class );",
"type": "Log",
"var_name": "log"
},
{
"declarator":... | {
"body": "public Collection<BibliographicReference> parse( InputStream is ) {\n\n try {\n // if ( is.available() == 0 ) {\n // throw new IOException( \"XML stream contains no data.\" );\n // }\n\n DocumentBuilderFactory factory =... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_80 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/analysis/expression/coexpression/links/SpearmanMetricsTest.java",
"identifier": "SpearmanMetricsTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testCorrelFromRanks() {\n\n double[] a = new double[] { 4.0, 3.0, 6.0, 1.5, 1.5, 9.0, 7.0, 8.0, 10.0, 11.0, 5.0 };\n double[] b = new double[] { 4.0, 3.0, 6.0, 2, 1, 9, 7, 8, 10, 11, 5 };\n\n boolean[] usedA = new boolean[] { true, true, true, true, true, true, t... | {
"fields": [
{
"declarator": "rankTransformedData = null",
"modifier": "",
"original_string": "double[][] rankTransformedData = null;",
"type": "double[][]",
"var_name": "rankTransformedData"
}
],
"file": "gemma-core/src/main/java/ubic/gemma/core/analysis/expression/coexpres... | {
"body": "protected double spearman( double[] vectorA, double[] vectorB, boolean[] usedA, boolean[] usedB, int i, int j ) {\n\n /* because we assume there might be ties, we compute the correlation of the ranks. */\n\n /*\n * Note that if there are missing values, the precomputed ranks will be w... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_38 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testgcrma() {\n ScaleType s = QuantitationTypeParameterGuesser.guessScaleType( \"VALUE\", \"gcRMA-calculated Signal intensity\" );\n assertEquals( \"got \" + s, ScaleType.LOG2, s );\n }",
"class_method_signature": "QuantitationTypeParameterGuesserTest.testgcrma()",... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static ScaleType guessScaleType( String name, String description ) {\n for ( ScaleType type : QuantitationTypeParameterGuesser.scaleDescPatterns.keySet() ) {\n for ( String patt : QuantitationTypeParameterGuesser.scaleNamePatterns.get( type ) ) {\n if ( name.match... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_79 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/analysis/expression/coexpression/links/SpearmanMetricsTest.java",
"identifier": "SpearmanMetricsTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testCorrelB() {\n boolean[] usedA = new boolean[] { true, true, true, true, true, true, true, true, true };\n boolean[] usedB = new boolean[] { true, true, true, true, true, true, true, true, true };\n double[] a = new double[] { 400, 310, 20, 20, 688, 498, 533, ... | {
"fields": [
{
"declarator": "rankTransformedData = null",
"modifier": "",
"original_string": "double[][] rankTransformedData = null;",
"type": "double[][]",
"var_name": "rankTransformedData"
}
],
"file": "gemma-core/src/main/java/ubic/gemma/core/analysis/expression/coexpres... | {
"body": "protected double spearman( double[] vectorA, double[] vectorB, boolean[] usedA, boolean[] usedB, int i, int j ) {\n\n /* because we assume there might be ties, we compute the correlation of the ranks. */\n\n /*\n * Note that if there are missing values, the precomputed ranks will be w... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_78 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/analysis/expression/coexpression/links/SpearmanMetricsTest.java",
"identifier": "SpearmanMetricsTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testCorrel() {\n\n // note the nominal tie in one (20)\n double[] a = new double[] { 49.0, 43.0, 310.0, 20.0, 20.0, 688.0, 498.0, 533.0, 723.0, 1409.0, 279.0 };\n double[] b = new double[] { 1545.0, 1287.0, 2072.0, 1113.0, 676.0, 2648.0, 2478.0, 2574.0, 3554.0, 5... | {
"fields": [
{
"declarator": "rankTransformedData = null",
"modifier": "",
"original_string": "double[][] rankTransformedData = null;",
"type": "double[][]",
"var_name": "rankTransformedData"
}
],
"file": "gemma-core/src/main/java/ubic/gemma/core/analysis/expression/coexpres... | {
"body": "protected double spearman( double[] vectorA, double[] vectorB, boolean[] usedA, boolean[] usedB, int i, int j ) {\n\n /* because we assume there might be ties, we compute the correlation of the ranks. */\n\n /*\n * Note that if there are missing values, the precomputed ranks will be w... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_39 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testrma() {\n ScaleType s = QuantitationTypeParameterGuesser.guessScaleType( \"VALUE\", \"Signals calculated by RMA\" );\n assertEquals( \"got \" + s, ScaleType.LOG2, s );\n }",
"class_method_signature": "QuantitationTypeParameterGuesserTest.testrma()",
"construc... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static ScaleType guessScaleType( String name, String description ) {\n for ( ScaleType type : QuantitationTypeParameterGuesser.scaleDescPatterns.keySet() ) {\n for ( String patt : QuantitationTypeParameterGuesser.scaleNamePatterns.get( type ) ) {\n if ( name.match... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_81 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/analysis/expression/coexpression/links/SpearmanMetricsTest.java",
"identifier": "SpearmanMetricsTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testCorrelWithMissing() {\n\n // note the nominal tie in one (20)\n double[] a = new double[] { 400, 43, 310, 20, 20, 688, 498, 533, 723, 1409, 1500 };\n double[] b = new double[] { 1545, 1287, 2072, 1113, 676, 2648, 2478, 2574, 3554, 5155, 1624 };\n boole... | {
"fields": [
{
"declarator": "rankTransformedData = null",
"modifier": "",
"original_string": "double[][] rankTransformedData = null;",
"type": "double[][]",
"var_name": "rankTransformedData"
}
],
"file": "gemma-core/src/main/java/ubic/gemma/core/analysis/expression/coexpres... | {
"body": "protected double spearman( double[] vectorA, double[] vectorB, boolean[] usedA, boolean[] usedB, int i, int j ) {\n\n /* because we assume there might be ties, we compute the correlation of the ranks. */\n\n /*\n * Note that if there are missing values, the precomputed ranks will be w... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_15 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLParserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedXMLParserTest.class.getName() );",
"type": "Log",
"var_name": "log"
},
... | {
"body": "@Test\n public void testParseMultipartAbstract() {\n try {\n testStream = PubMedXMLParserTest.class.getResourceAsStream( \"/data/pubmed-mpabs.xml\" );\n\n Collection<BibliographicReference> brl = testParser.parse( testStream );\n BibliographicReference br = brl.it... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLParser.class )",
"modifier": "protected static final",
"original_string": "protected static final Log log = LogFactory.getLog( PubMedXMLParser.class );",
"type": "Log",
"var_name": "log"
},
{
"declarator":... | {
"body": "public Collection<BibliographicReference> parse( InputStream is ) {\n\n try {\n // if ( is.available() == 0 ) {\n // throw new IOException( \"XML stream contains no data.\" );\n // }\n\n DocumentBuilderFactory factory =... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_42 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testPercent() {\n String a = \"%_>_B532+1SD\";\n String b = \"percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm, Cy3)\";\n\n ScaleType s = QuantitationTypeParameterGuesser... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static ScaleType guessScaleType( String name, String description ) {\n for ( ScaleType type : QuantitationTypeParameterGuesser.scaleDescPatterns.keySet() ) {\n for ( String patt : QuantitationTypeParameterGuesser.scaleNamePatterns.get( type ) ) {\n if ( name.match... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_54 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( DatasetCombinerTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( DatasetCombinerTest.class.getName() );",
"type": "Log",
"var_name": "log"
},
... | {
"body": "@Test\n public void testFindGSE13() throws Exception {\n GeoFamilyParser parser = new GeoFamilyParser();\n\n try (InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSE13Short/GDS44.soft.gz\" ) )) {\n parser.... | {
"fields": [
{
"declarator": "factory = DocumentBuilderFactory.newInstance()",
"modifier": "static final",
"original_string": "static final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();",
"type": "DocumentBuilderFactory",
"var_name": "factory"
},
{
... | {
"body": "public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) {\n\n if ( dataSets == null )\n return null;\n if ( dataSets.size() == 0 ) {\n throw new IllegalArgumentException( \"No datasets!\" );\n }\n\n this.checkPlatformsMatchSe... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_74 | {
"fields": [
{
"declarator": "gene2GOAssLoader = null",
"modifier": "private",
"original_string": "private NCBIGene2GOAssociationLoader gene2GOAssLoader = null;",
"type": "NCBIGene2GOAssociationLoader",
"var_name": "gene2GOAssLoader"
},
{
"declarator": "gene2GOAssociat... | {
"body": "@Test\n public void testParseAndLoad() throws Exception {\n\n try (InputStream is = this.getClass().getResourceAsStream( \"/data/loader/association/gene2go.gz\" );\n InputStream gZipIs = new GZIPInputStream( is )) {\n gene2GOAssLoader.load( gZipIs );\n\n gZipI... | {
"fields": [
{
"declarator": "COMMENT_INDICATOR = \"#\"",
"modifier": "private static final",
"original_string": "private static final String COMMENT_INDICATOR = \"#\";",
"type": "String",
"var_name": "COMMENT_INDICATOR"
},
{
"declarator": "ignoredEvidenceCodes = new H... | {
"body": "public int getCount() {\n return count;\n }",
"class_method_signature": "NCBIGene2GOAssociationParser.getCount()",
"constructor": false,
"full_signature": "public int getCount()",
"identifier": "getCount",
"invocations": [],
"modifiers": "public",
"parameters": "()",
"return": "in... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_23 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedSearchTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedSearchTest.class.getName() );",
"type": "Log",
"var_name": "log"
}
],
"... | {
"body": "@Test\n public void testSearchAndRetrieveIdByHTTPBookshelf() throws Exception {\n try {\n PubMedSearch pms = new PubMedSearch();\n Collection<String> searchTerms = new HashSet<>();\n searchTerms.add( \"23865096\" );\n Collection<BibliographicReference> ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedSearch.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedSearch.class );",
"type": "Log",
"var_name": "log"
},
{
"declarator": "CHUNK_SI... | {
"body": "public Collection<BibliographicReference> searchAndRetrieveIdByHTTP( Collection<String> searchTerms )\n throws IOException {\n\n Collection<BibliographicReference> results;\n\n results = fetchById( searchTerms );\n\n log.info( \"Fetched \" + results.size() + \" references\" ... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_35 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testAbsCall() {\n String a = \"ABS CALL\";\n String b = \"the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or reverse present (RP)\";\n StandardQuantitationType s = QuantitationTypeParameterGuesser.guess... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static StandardQuantitationType guessType( String name, String description ) {\n for ( StandardQuantitationType type : QuantitationTypeParameterGuesser.typeDescPatterns.keySet() ) {\n\n boolean isQuant = type == StandardQuantitationType.AMOUNT || type == StandardQuantitationType... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_62 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( DatasetCombinerTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( DatasetCombinerTest.class.getName() );",
"type": "Log",
"var_name": "log"
},
... | {
"body": "@Test\n public void testFindGSECorrespondence() throws Exception {\n GeoFamilyParser parser = new GeoFamilyParser();\n try (InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/twoDatasets/GDS472.soft.gz\" ) )) {\n ... | {
"fields": [
{
"declarator": "factory = DocumentBuilderFactory.newInstance()",
"modifier": "static final",
"original_string": "static final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();",
"type": "DocumentBuilderFactory",
"var_name": "factory"
},
{
... | {
"body": "public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) {\n\n if ( dataSets == null )\n return null;\n if ( dataSets.size() == 0 ) {\n throw new IllegalArgumentException( \"No datasets!\" );\n }\n\n this.checkPlatformsMatchSe... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
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} |
52478731_19 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLFetcherTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedXMLFetcherTest.class.getName() );",
"type": "Log",
"var_name": "log"
},... | {
"body": "@Test\n public final void testRetrieveByHTTPBookshelf() {\n try {\n BibliographicReference br = pmf.retrieveByHTTP( 23865096 );\n\n assertNotNull( br );\n\n assertEquals( \"Tatton-Brown, Katrina; Rahman, Nazneen\", br.getAuthorList() );\n\n assertEquals... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLFetcher.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedXMLFetcher.class );",
"type": "Log",
"var_name": "log"
},
{
"declarator": "... | {
"body": "public Collection<BibliographicReference> retrieveByHTTP( Collection<Integer> pubMedIds ) throws IOException {\n StringBuilder buf = new StringBuilder();\n for ( Integer integer : pubMedIds ) {\n buf.append( integer ).append( \",\" );\n }\n URL toBeGotten = new URL( u... | {
"created": null,
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"stars": null,
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"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_3 | {
"fields": [
{
"declarator": "eeController",
"modifier": "@Autowired\n private",
"original_string": "@Autowired\n private ExpressionExperimentController eeController;",
"type": "ExpressionExperimentController",
"var_name": "eeController"
}
],
"file": "gemma-web/src/tes... | {
"body": "@Test\n public void testLoadStatusSummariesLimit() {\n List<Long> ids = new ArrayList<>();\n int limit;\n\n // Default ordering is by date last updated\n ExpressionExperiment lastUpdated = null;\n for ( int i = 0; i < 2; i++ ) {\n ExpressionExperiment ee = t... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( ExpressionExperimentController.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( ExpressionExperimentController.class.getName() );",
"type": "Log",
"var... | {
"body": "public Collection<ExpressionExperimentDetailsValueObject> loadStatusSummaries( Long taxonId, List<Long> ids,\n Integer limit, Integer filter, Boolean showPublic ) {\n StopWatch timer = new StopWatch();\n timer.start();\n\n Collection<ExpressionExperimentDetailsValueObject> v... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_58 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( DatasetCombinerTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( DatasetCombinerTest.class.getName() );",
"type": "Log",
"var_name": "log"
},
... | {
"body": "@Test\n public void testFindGSE493() throws Exception {\n GeoFamilyParser parser = new GeoFamilyParser();\n\n try (InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSE493Short/GDS215.soft.gz\" ) )) {\n pars... | {
"fields": [
{
"declarator": "factory = DocumentBuilderFactory.newInstance()",
"modifier": "static final",
"original_string": "static final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();",
"type": "DocumentBuilderFactory",
"var_name": "factory"
},
{
... | {
"body": "public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) {\n\n if ( dataSets == null )\n return null;\n if ( dataSets.size() == 0 ) {\n throw new IllegalArgumentException( \"No datasets!\" );\n }\n\n this.checkPlatformsMatchSe... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_53 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( DatasetCombinerTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( DatasetCombinerTest.class.getName() );",
"type": "Log",
"var_name": "log"
},
... | {
"body": "@Test\n public void testFindGDSGrouping() {\n try {\n Collection<String> result = DatasetCombiner.findGDSforGSE( \"GSE674\" );\n assertEquals( 2, result.size() );\n assertTrue( result.contains( \"GDS472\" ) && result.contains( \"GDS473\" ) );\n } catch ( Ru... | {
"fields": [
{
"declarator": "factory = DocumentBuilderFactory.newInstance()",
"modifier": "static final",
"original_string": "static final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();",
"type": "DocumentBuilderFactory",
"var_name": "factory"
},
{
... | {
"body": "public static Collection<String> findGDSforGSE( Collection<String> seriesAccessions ) {\n /*\n * go from GSE to GDS, using screen scraping.\n */\n // http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds&term=GSE674[Accession]&cmd=search\n // grep on \"GDS[[digits]] reco... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_45 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testMas6() {\n String a = \"MAS 6.1 signal intensity\";\n ScaleType guessScaleType = QuantitationTypeParameterGuesser.guessScaleType( \"VALUE\", a.toLowerCase() );\n assertEquals( ScaleType.LOG2, guessScaleType );\n }",
"class_method_signature": "Quantitatio... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static ScaleType guessScaleType( String name, String description ) {\n for ( ScaleType type : QuantitationTypeParameterGuesser.scaleDescPatterns.keySet() ) {\n for ( String patt : QuantitationTypeParameterGuesser.scaleNamePatterns.get( type ) ) {\n if ( name.match... | {
"created": null,
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"is_fork": false,
"language": "Java",
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"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
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"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_8 | {
"fields": [
{
"declarator": "userService = new UserServiceImpl()",
"modifier": "private final",
"original_string": "private final UserServiceImpl userService = new UserServiceImpl();",
"type": "UserServiceImpl",
"var_name": "userService"
},
{
"declarator": "testUser =... | {
"body": "@Test\n public void testHandleGetUser() {\n userDaoMock.findByUserName( \"foobar\" );\n expectLastCall().andReturn( testUser );\n replay( userDaoMock );\n userService.findByUserName( \"foobar\" );\n verify( userDaoMock );\n }",
"class_method_signature": "UserServi... | {
"fields": [
{
"declarator": "userDao",
"modifier": "@Autowired",
"original_string": "@Autowired\n UserDao userDao;",
"type": "UserDao",
"var_name": "userDao"
},
{
"declarator": "userGroupDao",
"modifier": "@Autowired",
"original_string": "@Autowired\n ... | {
"body": "@Override\n public User findByUserName( final String userName ) {\n return this.userDao.findByUserName( userName );\n }",
"class_method_signature": "UserServiceImpl.findByUserName( final String userName )",
"constructor": false,
"full_signature": "@Override public User findByUserName( fi... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_12 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLParserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedXMLParserTest.class.getName() );",
"type": "Log",
"var_name": "log"
},
... | {
"body": "@Test\n public void testParseBookArticle() {\n try {\n testStream = PubMedXMLParserTest.class.getResourceAsStream( \"/data/pubmed-bookarticle.xml\" );\n Collection<BibliographicReference> brl = testParser.parse( testStream );\n BibliographicReference br = brl.iter... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLParser.class )",
"modifier": "protected static final",
"original_string": "protected static final Log log = LogFactory.getLog( PubMedXMLParser.class );",
"type": "Log",
"var_name": "log"
},
{
"declarator":... | {
"body": "public Collection<BibliographicReference> parse( InputStream is ) {\n\n try {\n // if ( is.available() == 0 ) {\n // throw new IOException( \"XML stream contains no data.\" );\n // }\n\n DocumentBuilderFactory factory =... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
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"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_86 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/analysis/preprocess/batcheffects/AffyScanDateExtractorTest.java",
"identifier": "AffyScanDateExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractInputStreamV4() throws Exception {\n InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSM306831.part.CEL.gz\" ) );\n AffyScanDateExtractor extractor = new AffyScanDateExtractor();\n\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( AffyScanDateExtractor.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( AffyScanDateExtractor.class );",
"type": "Log",
"var_name": "log"
}
],
"file": "ge... | {
"body": "@Override\n public Date extract( InputStream is ) {\n\n try (DataInputStream str = new DataInputStream( is )) {\n\n BufferedReader reader;\n Date date = null;\n\n int magic = this.readByte( str );\n switch ( magic ) {\n case 64: {\n\n ... | {
"created": null,
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"is_fork": false,
"language": "Java",
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"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_69 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/loader/expression/arrayDesign/AffyChipTypeExtractorTest.java",
"identifier": "AffyChipTypeExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractInputStreamVx() throws Exception {\n InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSM239803.CEL.gz\" ) );\n AffyChipTypeExtractor extractor = new AffyChipTypeExtractor();\n\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( AffyChipTypeExtractor.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( AffyChipTypeExtractor.class );",
"type": "Log",
"var_name": "log"
},
{
"decl... | {
"body": "public static String extract( InputStream is ) {\n\n String chipType = null;\n try (DataInputStream str = new DataInputStream( is )) {\n\n BufferedReader reader;\n\n int magic = readByte( str );\n switch ( magic ) {\n case 64: {\n\n ... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_28 | {
"fields": [
{
"declarator": "TESTBLASTDB = \"testblastdb\"",
"modifier": "private static final",
"original_string": "private static final String TESTBLASTDB = \"testblastdb\";",
"type": "String",
"var_name": "TESTBLASTDB"
},
{
"declarator": "testBlastDbPath",
"m... | {
"body": "@Test\n public void testGetMultipleAcc() {\n if ( this.fastaCmdExecutableNotExists() ) {\n return;\n }\n SimpleFastaCmd fastaCmd = new SimpleFastaCmd();\n\n Collection<String> input = new ArrayList<>();\n input.add( \"AA000002.1\" );\n input.add( \"AA... | {
"fields": [
{
"declarator": "FASTA_CMD_ENV_VAR = \"fastaCmd.exe\"",
"modifier": "public static final",
"original_string": "public static final String FASTA_CMD_ENV_VAR = \"fastaCmd.exe\";",
"type": "String",
"var_name": "FASTA_CMD_ENV_VAR"
},
{
"declarator": "log = Lo... | {
"body": "@Override\n public Collection<BioSequence> getBatchAccessions( Collection<String> accessions, String database ) {\n return this.getBatchAccessions( accessions, database, SimpleFastaCmd.blastDbHome );\n }",
"class_method_signature": "SimpleFastaCmd.getBatchAccessions( Collection<String> acces... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
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"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_90 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/analysis/preprocess/batcheffects/AgilentScanDateExtractorTest.java",
"identifier": "AgilentScanDateExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractAgilent2() throws Exception {\n try (InputStream is = this.getClass()\n .getResourceAsStream( \"/data/loader/expression/rawdata/GSM1662306.agilent2.txt\" )) {\n AgilentScanDateExtractor extractor = new AgilentScanDateExtractor();\n\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( AgilentScanDateExtractor.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( AgilentScanDateExtractor.class );",
"type": "Log",
"var_name": "log"
}
],
"file... | {
"body": "@Override\n public Date extract( InputStream is ) {\n BufferedReader reader = null;\n try {\n /*\n * Read the first three characters. IF they are ATF, it's a Axon file. If it's TYPE then it's probably an\n * agilent file.\n */\n rea... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_4 | {
"fields": [
{
"declarator": "auditController",
"modifier": "@Autowired\n private",
"original_string": "@Autowired\n private AuditController auditController;",
"type": "AuditController",
"var_name": "auditController"
},
{
"declarator": "expressionExperimentServic... | {
"body": "@Test\n public void testAddUpdateEvent() {\n ExpressionExperiment e = this.getTestPersistentExpressionExperiment();\n\n EntityDelegator ed = new EntityDelegator( e );\n\n assertEquals( \"ubic.gemma.model.expression.experiment.ExpressionExperiment\", ed.getClassDelegatingFor() );\n\n... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( AuditController.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( AuditController.class.getName() );",
"type": "Log",
"var_name": "log"
},
{
... | {
"body": "@SuppressWarnings(\"unchecked\")\n public void addAuditEvent( EntityDelegator e, String auditEventType, String comment, String detail ) {\n AbstractAuditable entity = this.getAuditable( e );\n if ( entity == null ) {\n AuditController.log.warn( \"Couldn't find Auditable represen... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_49 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testPrimitiveTypeIntegerWrong() {\n String a = \"B Pixels\";\n String b = \"number of background pixels\";\n PrimitiveType s = QuantitationTypeParameterGuesser\n .guessPrimitiveType( a.toLowerCase(), b.toLowerCase(), 12232.00 );\n assertTrue... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static PrimitiveType guessPrimitiveType( String name, String description, Object exampleValue ) {\n\n String exampleString = null;\n boolean couldBeDouble = true;\n boolean couldBeInt = true;\n if ( exampleValue != null ) {\n if ( exampleValue instanceof Dou... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_65 | {
"fields": [
{
"declarator": "is",
"modifier": "private",
"original_string": "private InputStream is;",
"type": "InputStream",
"var_name": "is"
},
{
"declarator": "parser",
"modifier": "private",
"original_string": "private GeoFamilyParser parser;",
"... | {
"body": "@Test\n public void testParseGse432() throws Exception {\n is = new GZIPInputStream( this.getClass()\n .getResourceAsStream( \"/data/loader/expression/geo/gse432Short/GSE432_family.soft.gz\" ) );\n parser.parse( is );\n }",
"class_method_signature": "GeoFamilyParserTest... | {
"fields": [
{
"declarator": "FIELD_DELIM = '\\t'",
"modifier": "private static final",
"original_string": "private static final char FIELD_DELIM = '\\t';",
"type": "char",
"var_name": "FIELD_DELIM"
},
{
"declarator": "MAX_WARNINGS = 100",
"modifier": "private st... | {
"body": "@Override\n public void parse( File f ) throws IOException {\n try (InputStream a = new FileInputStream( f )) {\n this.parse( a );\n }\n }",
"class_method_signature": "GeoFamilyParser.parse( File f )",
"constructor": false,
"full_signature": "@Override public void parse... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_32 | {
"fields": [
{
"declarator": "TESTBLASTDB = \"testblastdb\"",
"modifier": "private static final",
"original_string": "private static final String TESTBLASTDB = \"testblastdb\";",
"type": "String",
"var_name": "TESTBLASTDB"
},
{
"declarator": "testBlastDbPath",
"m... | {
"body": "@Test\n public void testGetSingleAccNotFound() {\n if ( this.fastaCmdExecutableNotExists() ) {\n return;\n }\n SimpleFastaCmd fastaCmd = new SimpleFastaCmd();\n\n BioSequence bs = fastaCmd.getByAccession( \"FAKE.1\", SimpleFastaCmdTest.TESTBLASTDB, testBlastDbPath ... | {
"fields": [
{
"declarator": "FASTA_CMD_ENV_VAR = \"fastaCmd.exe\"",
"modifier": "public static final",
"original_string": "public static final String FASTA_CMD_ENV_VAR = \"fastaCmd.exe\";",
"type": "String",
"var_name": "FASTA_CMD_ENV_VAR"
},
{
"declarator": "log = Lo... | {
"body": "@Override\n public BioSequence getByAccession( String accession, String database ) {\n return this.getByAccession( accession, database, SimpleFastaCmd.blastDbHome );\n }",
"class_method_signature": "SimpleFastaCmd.getByAccession( String accession, String database )",
"constructor": false,
... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_24 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedSearchTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedSearchTest.class.getName() );",
"type": "Log",
"var_name": "log"
}
],
"... | {
"body": "@Test\n public void testSearchAndRetrievIdsByHTTP() throws Exception {\n try {\n PubMedSearch pms = new PubMedSearch();\n Collection<String> searchTerms = new HashSet<>();\n searchTerms.add( \"brain\" );\n searchTerms.add( \"hippocampus\" );\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedSearch.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedSearch.class );",
"type": "Log",
"var_name": "log"
},
{
"declarator": "CHUNK_SI... | {
"body": "public Collection<String> searchAndRetrieveIdsByHTTP( Collection<String> searchTerms )\n throws IOException, SAXException, ParserConfigurationException {\n StringBuilder builder = new StringBuilder();\n for ( String word : searchTerms ) {\n // space them out, then let th... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
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52478731_73 | {
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{
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"type": "GeoService",
"var_name": "geoService"
},
{
"declarator": "dataUpdater",
"modifier": "@Autowired\n pr... | {
"body": "@Test\n public void testLoadRNASeqDataWithMissingSamples() throws Exception {\n\n geoService.setGeoDomainObjectGenerator( new GeoDomainObjectGenerator() );\n ExpressionExperiment ee = experimentService.findByShortName( \"GSE29006\" );\n if ( ee != null ) {\n experimentSer... | {
"fields": [
{
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"type": "Log",
"var_name": "log"
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{
"declarator": "arrayDesig... | {
"body": "public void addCountData( ExpressionExperiment ee, ArrayDesign targetArrayDesign,\n DoubleMatrix<String, String> countMatrix, DoubleMatrix<String, String> rpkmMatrix, Integer readLength,\n Boolean isPairedReads, boolean allowMissingSamples ) {\n\n if ( countMatrix == null )\n ... | {
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52478731_72 | {
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{
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"type": "GeoService",
"var_name": "geoService"
},
{
"declarator": "dataUpdater",
"modifier": "@Autowired\n pr... | {
"body": "@Test\n public void testLoadRNASeqData() throws Exception {\n\n geoService.setGeoDomainObjectGenerator( new GeoDomainObjectGenerator() );\n ExpressionExperiment ee;\n\n // These tests were failing due to too many requests being made to geo, this is a workaround\n try {\n ... | {
"fields": [
{
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"type": "Log",
"var_name": "log"
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{
"declarator": "arrayDesig... | {
"body": "public void addCountData( ExpressionExperiment ee, ArrayDesign targetArrayDesign,\n DoubleMatrix<String, String> countMatrix, DoubleMatrix<String, String> rpkmMatrix, Integer readLength,\n Boolean isPairedReads, boolean allowMissingSamples ) {\n\n if ( countMatrix == null )\n ... | {
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52478731_25 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( ExpressionExperimentBibRefFinderTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( ExpressionExperimentBibRefFinderTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testLocatePrimaryReference() throws Exception {\n ExpressionExperimentBibRefFinder finder = new ExpressionExperimentBibRefFinder();\n ExpressionExperiment ee = ExpressionExperiment.Factory.newInstance();\n DatabaseEntry de = DatabaseEntry.Factory.newInstance();\n... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( ExpressionExperimentBibRefFinder.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( ExpressionExperimentBibRefFinder.class.getName() );",
"type": "Log",
... | {
"body": "public BibliographicReference locatePrimaryReference( ExpressionExperiment ee ) {\n\n if ( ee.getPrimaryPublication() != null )\n return ee.getPrimaryPublication();\n\n DatabaseEntry accession = ee.getAccession();\n\n ExternalDatabase ed = accession.getExternalDatabase();\n\... | {
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52478731_33 | {
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"file": "gemma-core/src/test/java/ubic/gemma/core/loader/genome/gene/ncbi/NCBIGeneHistoryParserTest.java",
"identifier": "NCBIGeneHistoryParserTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testParseA() throws Exception {\n\n NcbiGeneHistoryParser parser = new NcbiGeneHistoryParser();\n parser.parse( NCBIGeneHistoryParserTest.class.getResourceAsStream( \"/data/loader/genome/gene/gene_history.human.sample\" ) );\n\n String r = parser.discontinuedIdFo... | {
"fields": [
{
"declarator": "GENE_HISTORY_FILE_NUM_FIELDS = 5",
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"type": "int",
"var_name": "GENE_HISTORY_FILE_NUM_FIELDS"
},
{
"declarator": "id2histor... | {
"body": "public String discontinuedIdForSymbol( String geneSymbol, Integer taxonId ) {\n if ( !discontinuedGenes.containsKey( taxonId ) )\n return null;\n return discontinuedGenes.get( taxonId ).get( geneSymbol );\n }",
"class_method_signature": "NcbiGeneHistoryParser.discontinuedIdFor... | {
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} |
52478731_64 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( DatasetCombinerTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( DatasetCombinerTest.class.getName() );",
"type": "Log",
"var_name": "log"
},
... | {
"body": "@Test\n public void testGSE465() throws Exception {\n GeoFamilyParser parser = new GeoFamilyParser();\n\n try (InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSE465Short/GDS214.soft.gz\" ) )) {\n parser.p... | {
"fields": [
{
"declarator": "factory = DocumentBuilderFactory.newInstance()",
"modifier": "static final",
"original_string": "static final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();",
"type": "DocumentBuilderFactory",
"var_name": "factory"
},
{
... | {
"body": "public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) {\n\n if ( dataSets == null )\n return null;\n if ( dataSets.size() == 0 ) {\n throw new IllegalArgumentException( \"No datasets!\" );\n }\n\n this.checkPlatformsMatchSe... | {
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52478731_48 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testPrimitiveTypeInteger() {\n String a = \"B Pixels\";\n String b = \"number of background pixels\";\n PrimitiveType s = QuantitationTypeParameterGuesser\n .guessPrimitiveType( a.toLowerCase(), b.toLowerCase(), 12232 );\n assertTrue( \"got ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static PrimitiveType guessPrimitiveType( String name, String description, Object exampleValue ) {\n\n String exampleString = null;\n boolean couldBeDouble = true;\n boolean couldBeInt = true;\n if ( exampleValue != null ) {\n if ( exampleValue instanceof Dou... | {
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52478731_5 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/model/analysis/expression/coexpression/SupportDetailsTest.java",
"identifier": "SupportDetailsTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void test() {\n Gene g1 = Gene.Factory.newInstance();\n g1.setId( 3L );\n\n Gene g2 = Gene.Factory.newInstance();\n g2.setId( 4L );\n\n SupportDetails sd1 = new MouseCoexpressionSupportDetailsImpl( g1, g2, true );\n SupportDetails sd2 = new MouseC... | {
"fields": [
{
"declarator": "serialVersionUID = -8148641748805015611L",
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"original_string": "private static final long serialVersionUID = -8148641748805015611L;",
"type": "long",
"var_name": "serialVersionUID"
},
{
"declarator": "id"... | {
"body": "@SuppressWarnings({ \"unused\", \"WeakerAccess\" }) // Possible external use\n public void setId( Long id ) {\n this.id = id;\n }",
"class_method_signature": "SupportDetails.setId( Long id )",
"constructor": false,
"full_signature": "@SuppressWarnings({ \"unused\", \"WeakerAccess\" }) //... | {
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52478731_91 | {
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"identifier": "GenericScanFileDateExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractGeneSpring() throws Exception {\n try (InputStream is = this.getClass()\n .getResourceAsStream( \"/data/loader/expression/geo/GSM522322.part.genespring.txt\" )) {\n GenericScanFileDateExtractor extractor = new GenericScanFileDateExtractor()... | {
"fields": [
{
"declarator": "MAX_HEADER_LINES = 100",
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"type": "int",
"var_name": "MAX_HEADER_LINES"
}
],
"file": "gemma-core/src/main/java/ubic/gemma/core/analysis/pre... | {
"body": "@Override\n public Date extract( InputStream is ) throws IOException {\n Date date = null;\n try (BufferedReader reader = new BufferedReader( new InputStreamReader( is ) )) {\n String line;\n int count = 0;\n while ( ( line = reader.readLine() ) != null ) {... | {
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52478731_29 | {
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{
"declarator": "TESTBLASTDB = \"testblastdb\"",
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"type": "String",
"var_name": "TESTBLASTDB"
},
{
"declarator": "testBlastDbPath",
"m... | {
"body": "@Test\n public void testGetMultipleAccSomeNotFound() {\n if ( this.fastaCmdExecutableNotExists() ) {\n return;\n }\n SimpleFastaCmd fastaCmd = new SimpleFastaCmd();\n\n Collection<String> input = new ArrayList<>();\n input.add( \"FAKE.2\" );\n input.a... | {
"fields": [
{
"declarator": "FASTA_CMD_ENV_VAR = \"fastaCmd.exe\"",
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"type": "String",
"var_name": "FASTA_CMD_ENV_VAR"
},
{
"declarator": "log = Lo... | {
"body": "@Override\n public Collection<BioSequence> getBatchAccessions( Collection<String> accessions, String database ) {\n return this.getBatchAccessions( accessions, database, SimpleFastaCmd.blastDbHome );\n }",
"class_method_signature": "SimpleFastaCmd.getBatchAccessions( Collection<String> acces... | {
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52478731_87 | {
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"identifier": "AffyScanDateExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractInputStreamVx() throws Exception {\n InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSM239803.CEL.gz\" ) );\n AffyScanDateExtractor extractor = new AffyScanDateExtractor();\n\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( AffyScanDateExtractor.class )",
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"original_string": "private static final Log log = LogFactory.getLog( AffyScanDateExtractor.class );",
"type": "Log",
"var_name": "log"
}
],
"file": "ge... | {
"body": "@Override\n public Date extract( InputStream is ) {\n\n try (DataInputStream str = new DataInputStream( is )) {\n\n BufferedReader reader;\n Date date = null;\n\n int magic = this.readByte( str );\n switch ( magic ) {\n case 64: {\n\n ... | {
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52478731_68 | {
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"identifier": "AffyChipTypeExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractInputStreamV4() throws Exception {\n InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSM306831.part.CEL.gz\" ) );\n AffyChipTypeExtractor extractor = new AffyChipTypeExtractor();\n\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( AffyChipTypeExtractor.class )",
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"original_string": "private static final Log log = LogFactory.getLog( AffyChipTypeExtractor.class );",
"type": "Log",
"var_name": "log"
},
{
"decl... | {
"body": "public static String extract( InputStream is ) {\n\n String chipType = null;\n try (DataInputStream str = new DataInputStream( is )) {\n\n BufferedReader reader;\n\n int magic = readByte( str );\n switch ( magic ) {\n case 64: {\n\n ... | {
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} |
52478731_13 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLParserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedXMLParserTest.class.getName() );",
"type": "Log",
"var_name": "log"
},
... | {
"body": "@Test\n public void testParseMesh() {\n try {\n testStream = PubMedXMLParserTest.class.getResourceAsStream( \"/data/pubmed-mesh-test.xml\" );\n Collection<BibliographicReference> brl = testParser.parse( testStream );\n BibliographicReference br = brl.iterator().ne... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLParser.class )",
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"original_string": "protected static final Log log = LogFactory.getLog( PubMedXMLParser.class );",
"type": "Log",
"var_name": "log"
},
{
"declarator":... | {
"body": "public Collection<BibliographicReference> parse( InputStream is ) {\n\n try {\n // if ( is.available() == 0 ) {\n // throw new IOException( \"XML stream contains no data.\" );\n // }\n\n DocumentBuilderFactory factory =... | {
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52478731_9 | {
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{
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"type": "UserServiceImpl",
"var_name": "userService"
},
{
"declarator": "testUser =... | {
"body": "@Test\n public void testHandleRemoveUser() {\n\n userDaoMock.loadGroups( testUser );\n expectLastCall().andReturn( userGroups );\n userDaoMock.remove( testUser );\n expectLastCall().once();\n replay( userDaoMock );\n userService.delete( testUser );\n veri... | {
"fields": [
{
"declarator": "userDao",
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"var_name": "userDao"
},
{
"declarator": "userGroupDao",
"modifier": "@Autowired",
"original_string": "@Autowired\n ... | {
"body": "@Override\n public void delete( User user ) {\n for ( UserGroup group : this.userDao.loadGroups( ( ubic.gemma.model.common.auditAndSecurity.User ) user ) ) {\n group.getGroupMembers().remove( user );\n this.userGroupDao.update( ( ubic.gemma.model.common.auditAndSecurity.User... | {
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} |
52478731_44 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testMas5() {\n String a = \"MAS5.0 signal intensity\";\n ScaleType guessScaleType = QuantitationTypeParameterGuesser.guessScaleType( \"VALUE\", a.toLowerCase() );\n assertEquals( ScaleType.LOG2, guessScaleType );\n\n a = \"MAS 5.0 signal intensity\";\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static ScaleType guessScaleType( String name, String description ) {\n for ( ScaleType type : QuantitationTypeParameterGuesser.scaleDescPatterns.keySet() ) {\n for ( String patt : QuantitationTypeParameterGuesser.scaleNamePatterns.get( type ) ) {\n if ( name.match... | {
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52478731_52 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testTortureQuantitationTypes() throws Exception {\n Collection<String> failed = new ArrayList<>();\n Collection<String> passed = new ArrayList<>();\n try (InputStream is = new FileInputStream(\n FileTools.resourceToPath( \"/data/loader/expression/q... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "public static void guessQuantitationTypeParameters( QuantitationType qt, String name, String description ) {\n QuantitationTypeParameterGuesser.guessQuantitationTypeParameters( qt, name, description, null );\n }",
"class_method_signature": "QuantitationTypeParameterGuesser.guessQuantitationType... | {
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} |
52478731_92 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/analysis/preprocess/batcheffects/GenericScanFileDateExtractorTest.java",
"identifier": "GenericScanFileDateExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractGpr() throws Exception {\n InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/rawdata/GSM489680.short.gpr.gz\" ) );\n GenericScanFileDateExtractor extractor = new GenericScanFileDateExtractor(... | {
"fields": [
{
"declarator": "MAX_HEADER_LINES = 100",
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"var_name": "MAX_HEADER_LINES"
}
],
"file": "gemma-core/src/main/java/ubic/gemma/core/analysis/pre... | {
"body": "@Override\n public Date extract( InputStream is ) throws IOException {\n Date date = null;\n try (BufferedReader reader = new BufferedReader( new InputStreamReader( is ) )) {\n String line;\n int count = 0;\n while ( ( line = reader.readLine() ) != null ) {... | {
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52478731_84 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/analysis/preprocess/batcheffects/AffyScanDateExtractorTest.java",
"identifier": "AffyScanDateExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractInputStreamGCOS() throws Exception {\n InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSM506974.part.CEL.gz\" ) );\n AffyScanDateExtractor extractor = new AffyScanDateExtractor();\n\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( AffyScanDateExtractor.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( AffyScanDateExtractor.class );",
"type": "Log",
"var_name": "log"
}
],
"file": "ge... | {
"body": "@Override\n public Date extract( InputStream is ) {\n\n try (DataInputStream str = new DataInputStream( is )) {\n\n BufferedReader reader;\n Date date = null;\n\n int magic = this.readByte( str );\n switch ( magic ) {\n case 64: {\n\n ... | {
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"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_10 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLParserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedXMLParserTest.class.getName() );",
"type": "Log",
"var_name": "log"
},
... | {
"body": "@Test\n public void testParse() {\n try {\n testStream = PubMedXMLParserTest.class.getResourceAsStream( \"/data/pubmed-test.xml\" );\n\n Collection<BibliographicReference> brl = testParser.parse( testStream );\n BibliographicReference br = brl.iterator().next();\n... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLParser.class )",
"modifier": "protected static final",
"original_string": "protected static final Log log = LogFactory.getLog( PubMedXMLParser.class );",
"type": "Log",
"var_name": "log"
},
{
"declarator":... | {
"body": "public Collection<BibliographicReference> parse( InputStream is ) {\n\n try {\n // if ( is.available() == 0 ) {\n // throw new IOException( \"XML stream contains no data.\" );\n // }\n\n DocumentBuilderFactory factory =... | {
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"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_47 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testPrimitiveTypeDoubleWrong() {\n String a = \"VALUE\";\n String b = \"green_processed_Signal; the signal left after all the Feature extraction processing steps have been completed (e.g. background substraction)\";\n PrimitiveType s = QuantitationTypeParameterGu... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static PrimitiveType guessPrimitiveType( String name, String description, Object exampleValue ) {\n\n String exampleString = null;\n boolean couldBeDouble = true;\n boolean couldBeInt = true;\n if ( exampleValue != null ) {\n if ( exampleValue instanceof Dou... | {
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"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_51 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testBadRatio() {\n String a = \"VALUE\";\n String b = \"Log2 ratio (CH_1 Median-CH1_B/CH2_Median-CH2_B)\";\n PrimitiveType s = QuantitationTypeParameterGuesser\n .guessPrimitiveType( a.toLowerCase(), b.toLowerCase(), \"null\" );\n assertEqua... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static PrimitiveType guessPrimitiveType( String name, String description, Object exampleValue ) {\n\n String exampleString = null;\n boolean couldBeDouble = true;\n boolean couldBeInt = true;\n if ( exampleValue != null ) {\n if ( exampleValue instanceof Dou... | {
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"language": "Java",
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"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
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"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_71 | {
"fields": [
{
"declarator": "geoService",
"modifier": "@Autowired\n private",
"original_string": "@Autowired\n private GeoService geoService;",
"type": "GeoService",
"var_name": "geoService"
},
{
"declarator": "dataUpdater",
"modifier": "@Autowired\n pr... | {
"body": "@Test\n public void testAddData() throws Exception {\n\n /*\n * Load a regular data set that has no data. Platform is (basically) irrelevant.\n */\n geoService.setGeoDomainObjectGenerator( new GeoDomainObjectGeneratorLocal( this.getTestFileBasePath() ) );\n Expressio... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( DataUpdater.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( DataUpdater.class );",
"type": "Log",
"var_name": "log"
},
{
"declarator": "arrayDesig... | {
"body": "ExpressionExperiment addData( ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data ) {\n\n if ( data.rows() == 0 ) {\n throw new IllegalArgumentException( \"Data had no rows\" );\n }\n\n Collection<QuantitationType> qts = data.getQuantitationT... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_26 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( ExpressionExperimentBibRefFinderTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( ExpressionExperimentBibRefFinderTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testLocatePrimaryReferenceInvalidGSE() throws Exception {\n ExpressionExperimentBibRefFinder finder = new ExpressionExperimentBibRefFinder();\n ExpressionExperiment ee = ExpressionExperiment.Factory.newInstance();\n DatabaseEntry de = DatabaseEntry.Factory.newIns... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( ExpressionExperimentBibRefFinder.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( ExpressionExperimentBibRefFinder.class.getName() );",
"type": "Log",
... | {
"body": "public BibliographicReference locatePrimaryReference( ExpressionExperiment ee ) {\n\n if ( ee.getPrimaryPublication() != null )\n return ee.getPrimaryPublication();\n\n DatabaseEntry accession = ee.getAccession();\n\n ExternalDatabase ed = accession.getExternalDatabase();\n\... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_30 | {
"fields": [
{
"declarator": "TESTBLASTDB = \"testblastdb\"",
"modifier": "private static final",
"original_string": "private static final String TESTBLASTDB = \"testblastdb\";",
"type": "String",
"var_name": "TESTBLASTDB"
},
{
"declarator": "testBlastDbPath",
"m... | {
"body": "@Test\n public void testGetSingle() {\n if ( this.fastaCmdExecutableNotExists() ) {\n return;\n }\n\n SimpleFastaCmd fastaCmd = new SimpleFastaCmd();\n BioSequence bs = fastaCmd.getByIdentifier( 1435867, SimpleFastaCmdTest.TESTBLASTDB, testBlastDbPath );\n a... | {
"fields": [
{
"declarator": "FASTA_CMD_ENV_VAR = \"fastaCmd.exe\"",
"modifier": "public static final",
"original_string": "public static final String FASTA_CMD_ENV_VAR = \"fastaCmd.exe\";",
"type": "String",
"var_name": "FASTA_CMD_ENV_VAR"
},
{
"declarator": "log = Lo... | {
"body": "private BioSequence getSingle( Object key, String database, String blastHome ) throws IOException {\n if ( blastHome == null ) {\n blastHome = SimpleFastaCmd.blastDbHome;\n }\n String[] opts = new String[] { \"BLASTDB=\" + blastHome };\n String command = SimpleFastaCm... | {
"created": null,
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"is_fork": false,
"language": "Java",
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"repo_id": 52478731,
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"stargazer_count": 6,
"stars": null,
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"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_67 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/loader/expression/arrayDesign/AffyChipTypeExtractorTest.java",
"identifier": "AffyChipTypeExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractInputStreamV3() throws Exception {\n InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSM3448.part.CEL.txt.gz\" ) );\n AffyChipTypeExtractor extractor = new AffyChipTypeExtractor();\n\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( AffyChipTypeExtractor.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( AffyChipTypeExtractor.class );",
"type": "Log",
"var_name": "log"
},
{
"decl... | {
"body": "public static String extract( InputStream is ) {\n\n String chipType = null;\n try (DataInputStream str = new DataInputStream( is )) {\n\n BufferedReader reader;\n\n int magic = readByte( str );\n switch ( magic ) {\n case 64: {\n\n ... | {
"created": null,
"fork": null,
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"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
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"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_88 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/analysis/preprocess/batcheffects/AgilentScanDateExtractorTest.java",
"identifier": "AgilentScanDateExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractGPR() throws Exception {\n try (InputStream is = this.getClass()\n .getResourceAsStream( \"/data/loader/expression/rawdata/GSM393974.gpr.txt\" )) {\n AgilentScanDateExtractor extractor = new AgilentScanDateExtractor();\n\n Date a... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( AgilentScanDateExtractor.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( AgilentScanDateExtractor.class );",
"type": "Log",
"var_name": "log"
}
],
"file... | {
"body": "@Override\n public Date extract( InputStream is ) {\n BufferedReader reader = null;\n try {\n /*\n * Read the first three characters. IF they are ATF, it's a Axon file. If it's TYPE then it's probably an\n * agilent file.\n */\n rea... | {
"created": null,
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"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_6 | {
"fields": [
{
"declarator": "TEST_PHENOTYPE_URI = \"http://purl.obolibrary.org/obo/DOID_162\"",
"modifier": "private static final",
"original_string": "private static final String TEST_PHENOTYPE_URI = \"http://purl.obolibrary.org/obo/DOID_162\";",
"type": "String",
"var_name": "TES... | {
"body": "@Test\n public void testLoadUpdateDeleteEvidence() {\n // 1- findEvidenceByGeneNCBI\n Collection<EvidenceValueObject<? extends PhenotypeAssociation>> evidences = this.phenotypeAssociationManagerService\n .findEvidenceByGeneNCBI( this.geneNCBI );\n assertNotNull( evide... | {
"fields": [
{
"declarator": "serialVersionUID = -1734685902449428500L",
"modifier": "private static final",
"original_string": "private static final long serialVersionUID = -1734685902449428500L;",
"type": "long",
"var_name": "serialVersionUID"
},
{
"declarator": "evi... | {
"body": "public Collection<Characteristic> getPhenotypes() {\n return this.phenotypes;\n }",
"class_method_signature": "PhenotypeAssociation.getPhenotypes()",
"constructor": false,
"full_signature": "public Collection<Characteristic> getPhenotypes()",
"identifier": "getPhenotypes",
"invocations"... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_7 | {
"fields": [
{
"declarator": "svc = null",
"modifier": "private",
"original_string": "private BibliographicReferenceServiceImpl svc = null;",
"type": "BibliographicReferenceServiceImpl",
"var_name": "svc"
},
{
"declarator": "brdao = null",
"modifier": "private",
... | {
"body": "@Test\n public final void testFindByExternalId() {\n\n BibliographicReference mockBR = BibliographicReference.Factory.newInstance();\n mockBR.setPubAccession( de );\n mockBR.setTitle( \"My Title\" );\n brdao.findByExternalId( \"12345\", \"PUBMED\" );\n expectLastCall()... | {
"fields": [
{
"declarator": "PUB_MED_DATABASE_NAME = \"PubMed\"",
"modifier": "private static final",
"original_string": "private static final String PUB_MED_DATABASE_NAME = \"PubMed\";",
"type": "String",
"var_name": "PUB_MED_DATABASE_NAME"
},
{
"declarator": "pubMed... | {
"body": "@Override\n @Transactional(readOnly = true)\n public BibliographicReference findByExternalId( DatabaseEntry accession ) {\n return this.bibliographicReferenceDao.findByExternalId( accession );\n }",
"class_method_signature": "BibliographicReferenceServiceImpl.findByExternalId( DatabaseEnt... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
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"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
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"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_66 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/loader/expression/arrayDesign/AffyChipTypeExtractorTest.java",
"identifier": "AffyChipTypeExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractInputStreamGCOS() throws Exception {\n InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSM506974.part.CEL.gz\" ) );\n AffyChipTypeExtractor extractor = new AffyChipTypeExtractor();\n\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( AffyChipTypeExtractor.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( AffyChipTypeExtractor.class );",
"type": "Log",
"var_name": "log"
},
{
"decl... | {
"body": "public static String extract( InputStream is ) {\n\n String chipType = null;\n try (DataInputStream str = new DataInputStream( is )) {\n\n BufferedReader reader;\n\n int magic = readByte( str );\n switch ( magic ) {\n case 64: {\n\n ... | {
"created": null,
"fork": null,
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"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_89 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/analysis/preprocess/batcheffects/AgilentScanDateExtractorTest.java",
"identifier": "AgilentScanDateExtractorTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractAgilent() throws Exception {\n try (InputStream is = this.getClass()\n .getResourceAsStream( \"/data/loader/expression/rawdata/GSM361301.agilent.txt\" )) {\n AgilentScanDateExtractor extractor = new AgilentScanDateExtractor();\n\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( AgilentScanDateExtractor.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( AgilentScanDateExtractor.class );",
"type": "Log",
"var_name": "log"
}
],
"file... | {
"body": "@Override\n public Date extract( InputStream is ) {\n BufferedReader reader = null;\n try {\n /*\n * Read the first three characters. IF they are ATF, it's a Axon file. If it's TYPE then it's probably an\n * agilent file.\n */\n rea... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_31 | {
"fields": [
{
"declarator": "TESTBLASTDB = \"testblastdb\"",
"modifier": "private static final",
"original_string": "private static final String TESTBLASTDB = \"testblastdb\";",
"type": "String",
"var_name": "TESTBLASTDB"
},
{
"declarator": "testBlastDbPath",
"m... | {
"body": "@Test\n public void testGetSingleAcc() {\n if ( this.fastaCmdExecutableNotExists() ) {\n return;\n }\n SimpleFastaCmd fastaCmd = new SimpleFastaCmd();\n String accession = \"AA000002\";\n\n BioSequence bs = fastaCmd.getByAccession( accession, SimpleFastaCmdT... | {
"fields": [
{
"declarator": "FASTA_CMD_ENV_VAR = \"fastaCmd.exe\"",
"modifier": "public static final",
"original_string": "public static final String FASTA_CMD_ENV_VAR = \"fastaCmd.exe\";",
"type": "String",
"var_name": "FASTA_CMD_ENV_VAR"
},
{
"declarator": "log = Lo... | {
"body": "@Override\n public BioSequence getByAccession( String accession, String database ) {\n return this.getByAccession( accession, database, SimpleFastaCmd.blastDbHome );\n }",
"class_method_signature": "SimpleFastaCmd.getByAccession( String accession, String database )",
"constructor": false,
... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_27 | {
"fields": [
{
"declarator": "TESTBLASTDB = \"testblastdb\"",
"modifier": "private static final",
"original_string": "private static final String TESTBLASTDB = \"testblastdb\";",
"type": "String",
"var_name": "TESTBLASTDB"
},
{
"declarator": "testBlastDbPath",
"m... | {
"body": "@Test\n public void testGetMultiple() {\n if ( this.fastaCmdExecutableNotExists() ) {\n return;\n }\n SimpleFastaCmd fastaCmd = new SimpleFastaCmd();\n\n Collection<Integer> input = new ArrayList<>();\n input.add( 1435867 );\n input.add( 1435868 );\n\... | {
"fields": [
{
"declarator": "FASTA_CMD_ENV_VAR = \"fastaCmd.exe\"",
"modifier": "public static final",
"original_string": "public static final String FASTA_CMD_ENV_VAR = \"fastaCmd.exe\";",
"type": "String",
"var_name": "FASTA_CMD_ENV_VAR"
},
{
"declarator": "log = Lo... | {
"body": "private Collection<BioSequence> getMultiple( Collection<?> keys, String database, String blastHome )\n throws IOException {\n\n if ( StringUtils.isBlank( SimpleFastaCmd.fastaCmdExecutable ) )\n throw new IllegalStateException( \"No fastacmd executable: You must set \" + SimpleF... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_70 | {
"fields": [],
"file": "gemma-core/src/test/java/ubic/gemma/core/loader/expression/AffyPowerToolsProbesetSummarizeTest.java",
"identifier": "AffyPowerToolsProbesetSummarizeTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testLoadMPSNames() {\n AffyPowerToolsProbesetSummarize t = new AffyPowerToolsProbesetSummarize();\n Map<String, Map<String, String>> mpsnames = t.loadMpsNames();\n\n assertEquals( \"MoGene-2_1-st.mps\", mpsnames.get( \"GPL17400\" ).get( \"mps\" ) );\n asse... | {
"fields": [
{
"declarator": "GEO_CEL_FILE_NAME_REGEX = \"^(GSM[0-9]+).*\\\\.(?i)CEL(\\\\.gz)?\"",
"modifier": "protected static final",
"original_string": "protected static final String GEO_CEL_FILE_NAME_REGEX = \"^(GSM[0-9]+).*\\\\.(?i)CEL(\\\\.gz)?\";",
"type": "String",
"var_nam... | {
"body": "protected Map<String, Map<String, String>> loadMpsNames() {\n try {\n PropertiesConfiguration pc = ConfigUtils\n .loadClasspathConfig( AffyPowerToolsProbesetSummarize.AFFY_MPS_PROPERTIES_FILE_NAME );\n Map<String, Map<String, String>> result = new HashMap<>()... | {
"created": null,
"fork": null,
"fork_count": 1,
"is_fork": false,
"language": "Java",
"license": "licensed",
"repo_id": 52478731,
"size": 460145,
"stargazer_count": 6,
"stars": null,
"updates": null,
"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_50 | {
"fields": [
{
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"body": "@Test\n public void testRatio() {\n String a = \"RAT1_MEAN\";\n String b = \"ratio of CH1D_MEAN to CH2D_MEAN\";\n StandardQuantitationType s = QuantitationTypeParameterGuesser.guessType( a.toLowerCase(), b.toLowerCase() );\n assertEquals( \"got \" + s, StandardQuantitationTyp... | {
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... | {
"body": "protected static StandardQuantitationType guessType( String name, String description ) {\n for ( StandardQuantitationType type : QuantitationTypeParameterGuesser.typeDescPatterns.keySet() ) {\n\n boolean isQuant = type == StandardQuantitationType.AMOUNT || type == StandardQuantitationType... | {
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52478731_46 | {
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"body": "@Test\n public void testPrimitiveType() {\n String a = \"VALUE\";\n String b = \"green_processed_Signal; the signal left after all the Feature extraction processing steps have been completed (e.g. background substraction)\";\n PrimitiveType s = QuantitationTypeParameterGuesser.guess... | {
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"type": "Log",
... | {
"body": "protected static PrimitiveType guessPrimitiveType( String name, String description, Object exampleValue ) {\n\n String exampleString = null;\n boolean couldBeDouble = true;\n boolean couldBeInt = true;\n if ( exampleValue != null ) {\n if ( exampleValue instanceof Dou... | {
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52478731_11 | {
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... | {
"body": "@Test\n public void testParseBook() {\n try {\n testStream = PubMedXMLParserTest.class.getResourceAsStream( \"/data/pubmed-fullbook.xml\" );\n Collection<BibliographicReference> brl = testParser.parse( testStream );\n BibliographicReference br = brl.iterator().nex... | {
"fields": [
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"declarator":... | {
"body": "public Collection<BibliographicReference> parse( InputStream is ) {\n\n try {\n // if ( is.available() == 0 ) {\n // throw new IOException( \"XML stream contains no data.\" );\n // }\n\n DocumentBuilderFactory factory =... | {
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52478731_85 | {
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"superclass": ""
} | {
"body": "@Test\n public void testExtractInputStreamV3() throws Exception {\n InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSM3448.part.CEL.txt.gz\" ) );\n AffyScanDateExtractor extractor = new AffyScanDateExtractor();\n\n ... | {
"fields": [
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],
"file": "ge... | {
"body": "@Override\n public Date extract( InputStream is ) {\n\n try (DataInputStream str = new DataInputStream( is )) {\n\n BufferedReader reader;\n Date date = null;\n\n int magic = this.readByte( str );\n switch ( magic ) {\n case 64: {\n\n ... | {
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52478731_93 | {
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"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testExtractImagene() throws Exception {\n try (InputStream is = this.getClass()\n .getResourceAsStream( \"/data/loader/expression/geo/GSM542196.imagene.part.txt\" )) {\n GenericScanFileDateExtractor extractor = new GenericScanFileDateExtractor();\n\n ... | {
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],
"file": "gemma-core/src/main/java/ubic/gemma/core/analysis/pre... | {
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52478731_77 | {
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} | {
"body": "@Test\n public void testScoreResults() {\n\n // there's only one gene product that is aligned to two different regions\n GeneProduct geneProduct = this.createGeneProduct();\n\n BlatResult blatResult_1 = this.createBlatResult( \"6_cox_hap2\" );\n BlatResult blatResult_2 = this... | {
"fields": [
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... | {
"body": "public static BlatAssociation scoreResults( Collection<BlatAssociation> blatAssociations ) {\n\n Map<GeneProduct, Collection<BlatAssociation>> geneProducts2Associations = BlatAssociationScorer\n .organizeBlatAssociationsByGeneProductAndInitializeScores( blatAssociations );\n\n ... | {
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52478731_20 | {
"fields": [
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"body": "@Test\n public final void testRetrieveByHTTPNotFound() {\n try {\n BibliographicReference br = pmf.retrieveByHTTP( 1517311444 );\n assertNull( br );\n } catch ( RuntimeException e ) {\n this.checkCause( e );\n }\n }",
"class_method_signature": "... | {
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{
"declarator": "... | {
"body": "public Collection<BibliographicReference> retrieveByHTTP( Collection<Integer> pubMedIds ) throws IOException {\n StringBuilder buf = new StringBuilder();\n for ( Integer integer : pubMedIds ) {\n buf.append( integer ).append( \",\" );\n }\n URL toBeGotten = new URL( u... | {
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52478731_36 | {
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"type": "Log"... | {
"body": "@Test\n public void testareaCall() {\n String a = \"AREA\";\n String b = \"Number of pixels used to calculate a feature's intensity\";\n StandardQuantitationType s = QuantitationTypeParameterGuesser.guessType( a.toLowerCase(), b.toLowerCase() );\n assertEquals( \"got \" + s, ... | {
"fields": [
{
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... | {
"body": "protected static StandardQuantitationType guessType( String name, String description ) {\n for ( StandardQuantitationType type : QuantitationTypeParameterGuesser.typeDescPatterns.keySet() ) {\n\n boolean isQuant = type == StandardQuantitationType.AMOUNT || type == StandardQuantitationType... | {
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52478731_61 | {
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... | {
"body": "@Test\n public void testFindGSE91() throws Exception {\n GeoFamilyParser parser = new GeoFamilyParser();\n\n try (InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSE91Short/GDS168.soft.gz\" ) )) {\n parser... | {
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... | {
"body": "public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) {\n\n if ( dataSets == null )\n return null;\n if ( dataSets.size() == 0 ) {\n throw new IllegalArgumentException( \"No datasets!\" );\n }\n\n this.checkPlatformsMatchSe... | {
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52478731_0 | {
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} | {
"body": "@Test\n public void testCopyUploadedFileStreamClosed() throws FileNotFoundException, IOException {\n\n MockMultipartHttpServletRequest request = new MockMultipartHttpServletRequest();\n request.setMethod( \"POST\" );\n\n String text_contents = \"test\";\n String key = \"file1... | {
"fields": [
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{
"declarator": "log = LogFactory.getLog( FileUploadUtil.class.getName() )",
... | {
"body": "public static File copyUploadedFile( HttpServletRequest request, String key ) throws IOException {\n MultipartHttpServletRequest multipartRequest = ( MultipartHttpServletRequest ) request;\n MultipartFile file = multipartRequest.getFile( key );\n\n if ( file == null ) {\n th... | {
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52478731_94 | {
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{
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"body": "@Test\n public final void test3() throws Exception {\n DoubleMatrixReader f = new DoubleMatrixReader();\n DoubleMatrix<String, String> testMatrix = f.read( this.getClass()\n .getResourceAsStream( \"/data/analysis/preprocess/batcheffects/comat.test.data.txt\" ) );\n St... | {
"fields": [
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"declarator": "log = LogFactory.get... | {
"body": "public DoubleMatrix2D run() throws ComBatException {\n return this.run( true );\n }",
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52478731_82 | {
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{
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"var_name": "... | {
"body": "@Test\n public void testsvd() throws Exception {\n\n geoService.setGeoDomainObjectGenerator(\n new GeoDomainObjectGeneratorLocal( this.getTestFileBasePath( \"shortTest\" ) ) );\n // also used in the GeoDatasetServiceIntegrationTest.\n try {\n Collection<?> ... | {
"fields": [
{
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... | {
"body": "@Override\n public SVDValueObject svd( Long eeId ) {\n\n ExpressionExperiment ee = expressionExperimentService.load( eeId );\n\n return svdServiceHelper.svd( ee );\n }",
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52478731_16 | {
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... | {
"body": "@Test\n public void testParseRetracted() {\n try {\n testStream = PubMedXMLParserTest.class.getResourceAsStream( \"/data/pubmed-retracted.xml\" );\n\n Collection<BibliographicReference> brl = testParser.parse( testStream );\n BibliographicReference br = brl.iterat... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLParser.class )",
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"type": "Log",
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{
"declarator":... | {
"body": "public Collection<BibliographicReference> parse( InputStream is ) {\n\n try {\n // if ( is.available() == 0 ) {\n // throw new IOException( \"XML stream contains no data.\" );\n // }\n\n DocumentBuilderFactory factory =... | {
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52478731_41 | {
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{
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"type": "Log"... | {
"body": "@Test\n public void testGuessQuantitationTypeParameters() {\n String name = \"CH1_MEAN\";\n String description = \"CH1 Mean Intensity\";\n qt.setName( name );\n QuantitationTypeParameterGuesser.guessQuantitationTypeParameters( qt, name, description );\n\n assertEquals(... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
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"type": "Log",
... | {
"body": "public static void guessQuantitationTypeParameters( QuantitationType qt, String name, String description ) {\n QuantitationTypeParameterGuesser.guessQuantitationTypeParameters( qt, name, description, null );\n }",
"class_method_signature": "QuantitationTypeParameterGuesser.guessQuantitationType... | {
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52478731_57 | {
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{
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"type": "Log",
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},
... | {
"body": "@Test\n public void testFindGSE469() throws Exception {\n GeoFamilyParser parser = new GeoFamilyParser();\n try (InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSE469Short/GDS233.soft.gz\" ) )) {\n parser... | {
"fields": [
{
"declarator": "factory = DocumentBuilderFactory.newInstance()",
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{
... | {
"body": "public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) {\n\n if ( dataSets == null )\n return null;\n if ( dataSets.size() == 0 ) {\n throw new IllegalArgumentException( \"No datasets!\" );\n }\n\n this.checkPlatformsMatchSe... | {
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52478731_56 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( DatasetCombinerTest.class.getName() )",
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"original_string": "private static final Log log = LogFactory.getLog( DatasetCombinerTest.class.getName() );",
"type": "Log",
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},
... | {
"body": "@Test\n public void testFindGSE3193() throws Exception {\n\n GeoFamilyParser parser = new GeoFamilyParser();\n\n try (InputStream is = new GZIPInputStream( this.getClass()\n .getResourceAsStream( \"/data/loader/expression/geo/GSE3193Short/GSE3193_family.soft.gz\" ) )) {\n ... | {
"fields": [
{
"declarator": "factory = DocumentBuilderFactory.newInstance()",
"modifier": "static final",
"original_string": "static final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();",
"type": "DocumentBuilderFactory",
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},
{
... | {
"body": "public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) {\n\n if ( dataSets == null )\n return null;\n if ( dataSets.size() == 0 ) {\n throw new IllegalArgumentException( \"No datasets!\" );\n }\n\n this.checkPlatformsMatchSe... | {
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52478731_40 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testbkdst() {\n String a = \"CH2_BKD_ SD\";\n String b = \"NChannel 2 background standard deviation\";\n StandardQuantitationType s = QuantitationTypeParameterGuesser.guessType( a.toLowerCase(), b.toLowerCase() );\n assertEquals( \"got \" + s, StandardQuan... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static StandardQuantitationType guessType( String name, String description ) {\n for ( StandardQuantitationType type : QuantitationTypeParameterGuesser.typeDescPatterns.keySet() ) {\n\n boolean isQuant = type == StandardQuantitationType.AMOUNT || type == StandardQuantitationType... | {
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52478731_17 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLFetcherTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedXMLFetcherTest.class.getName() );",
"type": "Log",
"var_name": "log"
},... | {
"body": "@Test\n public final void testRetrieveByHTTP() {\n try {\n BibliographicReference br = pmf.retrieveByHTTP( 15173114 );\n\n assertNotNull( br );\n\n assertEquals( \"Lee, Homin K; Hsu, Amy K; Sajdak, Jon; Qin, Jie; Pavlidis, Paul\", br.getAuthorList() );\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedXMLFetcher.class )",
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"type": "Log",
"var_name": "log"
},
{
"declarator": "... | {
"body": "public Collection<BibliographicReference> retrieveByHTTP( Collection<Integer> pubMedIds ) throws IOException {\n StringBuilder buf = new StringBuilder();\n for ( Integer integer : pubMedIds ) {\n buf.append( integer ).append( \",\" );\n }\n URL toBeGotten = new URL( u... | {
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52478731_83 | {
"fields": [
{
"declarator": "processedExpressionDataVectorService = null",
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"original_string": "@Autowired\n ProcessedExpressionDataVectorService processedExpressionDataVectorService = null;",
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"var_name": "... | {
"body": "@Test\n public void testsvdGapped() throws Exception {\n\n geoService.setGeoDomainObjectGenerator(\n new GeoDomainObjectGeneratorLocal( this.getTestFileBasePath( \"gse482short\" ) ) );\n // also used in the GeoDatasetServiceIntegrationTest.\n try {\n Collec... | {
"fields": [
{
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"type": "ExpressionExperimentService",
"var_name": "expressionExperimentService"
... | {
"body": "@Override\n public SVDValueObject svd( Long eeId ) {\n\n ExpressionExperiment ee = expressionExperimentService.load( eeId );\n\n return svdServiceHelper.svd( ee );\n }",
"class_method_signature": "SVDServiceImpl.svd( Long eeId )",
"constructor": false,
"full_signature": "@Override... | {
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52478731_95 | {
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"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public final void testGenerateTaskId() {\n Collection<String> seen = new HashSet<>();\n\n for ( int i = 0; i < 1000; i++ ) {\n String id = TaskUtils.generateTaskId();\n assertTrue( StringUtils.isNotBlank( id ) );\n assertTrue( !seen.contains( id ) )... | {
"fields": [
{
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{
"declarator": "MAX_ATTEMPTS = 1000",
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"body": "public static String generateTaskId() {\n /*\n * Ensure we have a unique id.\n */\n int keepTrying = 0;\n while ( ++keepTrying < TaskUtils.MAX_ATTEMPTS ) {\n String id = RandomStringUtils.randomAlphanumeric( TaskUtils.KEY_LENGTH ).toUpperCase();\n ... | {
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52478731_1 | {
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{
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"var_name": "whatsNewService"
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{
"declarator": "rssFeedController",
... | {
"body": "@Test\n public void testGetLatestExperiments() {\n ModelAndView mav = rssFeedController.getLatestExperiments( null, null );\n assertNotNull( mav );\n\n Map<String, Object> model = mav.getModel();\n assertNotNull( model );\n\n @SuppressWarnings(\"unchecked\") Map<Expres... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( RssFeedController.class.getName() )",
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{
"decl... | {
"body": "@RequestMapping(value = { \"/rssfeed\" }, method = RequestMethod.GET)\n public ModelAndView getLatestExperiments( HttpServletRequest request, HttpServletResponse response ) {\n\n WhatsNew wn = whatsNewService.retrieveReport();\n if ( wn == null ) {\n wn = whatsNewService.getRepo... | {
"created": null,
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52478731_60 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( DatasetCombinerTest.class.getName() )",
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"original_string": "private static final Log log = LogFactory.getLog( DatasetCombinerTest.class.getName() );",
"type": "Log",
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... | {
"body": "@Test\n public void testFindGSE88() throws Exception {\n GeoFamilyParser parser = new GeoFamilyParser();\n\n try (InputStream is = new GZIPInputStream(\n this.getClass().getResourceAsStream( \"/data/loader/expression/geo/GSE88Short/GDS184.soft.gz\" ) )) {\n parser... | {
"fields": [
{
"declarator": "factory = DocumentBuilderFactory.newInstance()",
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},
{
... | {
"body": "public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) {\n\n if ( dataSets == null )\n return null;\n if ( dataSets.size() == 0 ) {\n throw new IllegalArgumentException( \"No datasets!\" );\n }\n\n this.checkPlatformsMatchSe... | {
"created": null,
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"repo_id": 52478731,
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"stars": null,
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"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_37 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesserTest.class.getName() );",
"type": "Log"... | {
"body": "@Test\n public void testbackground() {\n String a = \"B635_MEDIAN\";\n String b = \"median Cy5 feature background intensity\";\n Boolean s = QuantitationTypeParameterGuesser.guessIsBackground( a.toLowerCase(), b.toLowerCase() );\n assertEquals( \"got \" + s, Boolean.TRUE, s )... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( QuantitationTypeParameterGuesser.class.getName() );",
"type": "Log",
... | {
"body": "protected static Boolean guessIsBackground( String name, String description ) {\n for ( Boolean type : QuantitationTypeParameterGuesser.isBackgroundDescPatterns.keySet() ) {\n for ( String patt : QuantitationTypeParameterGuesser.isBackgroundDescPatterns.get( type ) ) {\n if... | {
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} |
52478731_21 | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedSearchTest.class.getName() )",
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"original_string": "private static final Log log = LogFactory.getLog( PubMedSearchTest.class.getName() );",
"type": "Log",
"var_name": "log"
}
],
"... | {
"body": "@Test\n public void testSearchAndRetrieveByHTTP() throws Exception {\n try {\n PubMedSearch pms = new PubMedSearch();\n Collection<String> searchTerms = new HashSet<>();\n searchTerms.add( \"brain\" );\n searchTerms.add( \"hippocampus\" );\n ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( PubMedSearch.class )",
"modifier": "private static final",
"original_string": "private static final Log log = LogFactory.getLog( PubMedSearch.class );",
"type": "Log",
"var_name": "log"
},
{
"declarator": "CHUNK_SI... | {
"body": "public Collection<BibliographicReference> searchAndRetrieveByHTTP( Collection<String> searchTerms )\n throws IOException, SAXException, ParserConfigurationException {\n StringBuilder builder = new StringBuilder();\n builder.append( uri );\n builder.append( \"&term=\" );\n ... | {
"created": null,
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"stars": null,
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"url": "https://github.com/PavlidisLab/Gemma"
} |
52478731_76 | {
"fields": [
{
"declarator": "shortName = \"GSE1611\"",
"modifier": "private final",
"original_string": "private final String shortName = \"GSE1611\";",
"type": "String",
"var_name": "shortName"
},
{
"declarator": "ee = null",
"modifier": "private",
"origin... | {
"body": "@Test\n public void testWrite() throws Exception {\n if ( ee == null ) {\n log.error( \"Could not find experiment \" + shortName + \". Skipping test ...\" );\n return;\n }\n\n ExperimentalDesignWriter edWriter = new ExperimentalDesignWriter();\n\n File ... | {
"fields": [
{
"declarator": "log = LogFactory.getLog( this.getClass() )",
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"original_string": "private final Log log = LogFactory.getLog( this.getClass() );",
"type": "Log",
"var_name": "log"
}
],
"file": "gemma-core/src/main/java/ubic/gemma/core... | {
"body": "public void write( Writer writer, ExpressionExperiment ee, boolean writeHeader ) throws IOException {\n\n Collection<BioAssay> bioAssays = ee.getBioAssays();\n this.write( writer, ee, bioAssays, writeHeader, writeHeader );\n }",
"class_method_signature": "ExperimentalDesignWriter.write( ... | {
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"url": "https://github.com/PavlidisLab/Gemma"
} |
10230369_112 | {
"fields": [
{
"declarator": "compilation = new CompilationRule()",
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"original_string": "@Rule public final CompilationRule compilation = new CompilationRule();",
"type": "CompilationRule",
"var_name": "compilation"
},
{
"declarator": "... | {
"body": "@Test\n public void getByte() {\n AnnotationValue value = AnnotationMirrors.getAnnotationValue(annotationMirror, \"byteValue\");\n assertThat(AnnotationValues.getByte(value)).isEqualTo((byte) 7);\n }",
"class_method_signature": "AnnotationValuesTest.getByte()",
"constructor": false,
"full_sig... | {
"fields": [
{
"declarator": "ANNOTATION_VALUE_EQUIVALENCE =\n new Equivalence<AnnotationValue>() {\n @Override protected boolean doEquivalent(AnnotationValue left, AnnotationValue right) {\n return left.accept(new SimpleAnnotationValueVisitor8<Boolean, AnnotationValue>() {\n ... | {
"body": "public static byte getByte(AnnotationValue value) {\n return valueOfType(value, Byte.class);\n }",
"class_method_signature": "AnnotationValues.getByte(AnnotationValue value)",
"constructor": false,
"full_signature": "public static byte getByte(AnnotationValue value)",
"identifier": "getByte",
... | {
"created": "5/22/2013 9:41:56 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 10230369,
"size": null,
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"stars": 8408,
"updates": "2020-01-27T16:25:00+00:00",
"url": "https://github.com/google/auto"
} |
10230369_104 | {
"fields": [
{
"declarator": "compilation = new CompilationRule()",
"modifier": "@Rule public final",
"original_string": "@Rule public final CompilationRule compilation = new CompilationRule();",
"type": "CompilationRule",
"var_name": "compilation"
},
{
"declarator": "... | {
"body": "@Test\n public void getStrings() {\n AnnotationValue value = AnnotationMirrors.getAnnotationValue(annotationMirror, \"stringValues\");\n assertThat(AnnotationValues.getStrings(value)).containsExactly(\"it's\", \"me\").inOrder();\n }",
"class_method_signature": "AnnotationValuesTest.getStrings()",... | {
"fields": [
{
"declarator": "ANNOTATION_VALUE_EQUIVALENCE =\n new Equivalence<AnnotationValue>() {\n @Override protected boolean doEquivalent(AnnotationValue left, AnnotationValue right) {\n return left.accept(new SimpleAnnotationValueVisitor8<Boolean, AnnotationValue>() {\n ... | {
"body": "public static ImmutableList<String> getStrings(AnnotationValue value) {\n return STRINGS_VISITOR.visit(value);\n }",
"class_method_signature": "AnnotationValues.getStrings(AnnotationValue value)",
"constructor": false,
"full_signature": "public static ImmutableList<String> getStrings(AnnotationVa... | {
"created": "5/22/2013 9:41:56 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 10230369,
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"stars": 8408,
"updates": "2020-01-27T16:25:00+00:00",
"url": "https://github.com/google/auto"
} |
10230369_49 | {
"fields": [
{
"declarator": "compilationRule = new CompilationRule()",
"modifier": "@Rule public final",
"original_string": "@Rule public final CompilationRule compilationRule = new CompilationRule();",
"type": "CompilationRule",
"var_name": "compilationRule"
},
{
"de... | {
"body": "@Test\n public void testIsCastingUnchecked() {\n TypeElement erasureClass = typeElementOf(Erasure.class);\n List<VariableElement> fields = ElementFilter.fieldsIn(erasureClass.getEnclosedElements());\n assertThat(fields).isNotEmpty();\n for (VariableElement field : fields) {\n String field... | {
"fields": [
{
"declarator": "imports",
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"type": "Map<String, Spelling>",
"var_name": "imports"
},
{
"declarator": "CASTING_UNCHECKED_VISITOR =\n new SimpleTypeVisitor8<... | {
"body": "static boolean isCastingUnchecked(TypeMirror type) {\n return CASTING_UNCHECKED_VISITOR.visit(type, null);\n }",
"class_method_signature": "TypeSimplifier.isCastingUnchecked(TypeMirror type)",
"constructor": false,
"full_signature": "static boolean isCastingUnchecked(TypeMirror type)",
"identif... | {
"created": "5/22/2013 9:41:56 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 10230369,
"size": null,
"stargazer_count": null,
"stars": 8408,
"updates": "2020-01-27T16:25:00+00:00",
"url": "https://github.com/google/auto"
} |
10230369_32 | {
"fields": [],
"file": "value/src/test/java/com/google/auto/value/processor/SimpleServiceLoaderTest.java",
"identifier": "SimpleServiceLoaderTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void classNotFound() throws Exception {\n ClassLoader loader =\n loaderForJarWithEntries(CharSequence.class.getName(), \"this.is.not.a.Class\");\n\n try {\n SimpleServiceLoader.load(CharSequence.class, loader);\n fail();\n } catch (ServiceConfigurationError expecte... | {
"fields": [],
"file": "value/src/main/java/com/google/auto/value/processor/SimpleServiceLoader.java",
"identifier": "SimpleServiceLoader",
"interfaces": "",
"methods": [
{
"class_method_signature": "SimpleServiceLoader.SimpleServiceLoader()",
"constructor": true,
"full_signature": "pri... | {
"body": "public static <T> ImmutableList<T> load(Class<? extends T> service, ClassLoader loader) {\n String resourceName = \"META-INF/services/\" + service.getName();\n List<URL> resourceUrls;\n try {\n resourceUrls = Collections.list(loader.getResources(resourceName));\n } catch (IOException e) {\... | {
"created": "5/22/2013 9:41:56 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 10230369,
"size": null,
"stargazer_count": null,
"stars": 8408,
"updates": "2020-01-27T16:25:00+00:00",
"url": "https://github.com/google/auto"
} |
10230369_65 | {
"fields": [
{
"declarator": "compilation = new CompilationRule()",
"modifier": "@Rule public",
"original_string": "@Rule public CompilationRule compilation = new CompilationRule();",
"type": "CompilationRule",
"var_name": "compilation"
},
{
"declarator": "expect = Exp... | {
"body": "@Test\n public void asPackage() {\n assertThat(MoreElements.asPackage(javaLangPackageElement))\n .isEqualTo(javaLangPackageElement);\n }",
"class_method_signature": "MoreElementsTest.asPackage()",
"constructor": false,
"full_signature": "@Test public void asPackage()",
"identifier": "as... | {
"fields": [],
"file": "common/src/main/java/com/google/auto/common/MoreElements.java",
"identifier": "MoreElements",
"interfaces": "",
"methods": [
{
"class_method_signature": "MoreElements.getPackage(Element element)",
"constructor": false,
"full_signature": "public static PackageElem... | {
"body": "public static PackageElement asPackage(Element element) {\n return element.accept(PackageElementVisitor.INSTANCE, null);\n }",
"class_method_signature": "MoreElements.asPackage(Element element)",
"constructor": false,
"full_signature": "public static PackageElement asPackage(Element element)",
... | {
"created": "5/22/2013 9:41:56 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 10230369,
"size": null,
"stargazer_count": null,
"stars": 8408,
"updates": "2020-01-27T16:25:00+00:00",
"url": "https://github.com/google/auto"
} |
10230369_73 | {
"fields": [
{
"declarator": "compilation = new CompilationRule()",
"modifier": "@Rule public",
"original_string": "@Rule public CompilationRule compilation = new CompilationRule();",
"type": "CompilationRule",
"var_name": "compilation"
},
{
"declarator": "expect = Exp... | {
"body": "@Test\n public void asExecutable_illegalArgument() {\n try {\n MoreElements.asExecutable(javaLangPackageElement);\n fail();\n } catch (IllegalArgumentException expected) {}\n }",
"class_method_signature": "MoreElementsTest.asExecutable_illegalArgument()",
"constructor": false,
"full... | {
"fields": [],
"file": "common/src/main/java/com/google/auto/common/MoreElements.java",
"identifier": "MoreElements",
"interfaces": "",
"methods": [
{
"class_method_signature": "MoreElements.getPackage(Element element)",
"constructor": false,
"full_signature": "public static PackageElem... | {
"body": "public static ExecutableElement asExecutable(Element element) {\n return element.accept(ExecutableElementVisitor.INSTANCE, null);\n }",
"class_method_signature": "MoreElements.asExecutable(Element element)",
"constructor": false,
"full_signature": "public static ExecutableElement asExecutable(Ele... | {
"created": "5/22/2013 9:41:56 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 10230369,
"size": null,
"stargazer_count": null,
"stars": 8408,
"updates": "2020-01-27T16:25:00+00:00",
"url": "https://github.com/google/auto"
} |
10230369_24 | {
"fields": [],
"file": "value/src/test/java/com/google/auto/value/processor/ReformatterTest.java",
"identifier": "ReformatterTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void testSimple() {\n String input =\n \"\\n\"\n + \"package com.latin.declension; \\n\"\n + \"\\n\"\n + \"\\n\"\n + \"public class Idem { \\n\"\n + \" \\n\"\n + \" Eadem idem ; \\n\"\n + \"\\n... | {
"fields": [],
"file": "value/src/main/java/com/google/auto/value/processor/Reformatter.java",
"identifier": "Reformatter",
"interfaces": "",
"methods": [
{
"class_method_signature": "Reformatter.fixup(String s)",
"constructor": false,
"full_signature": "static String fixup(String s)",
... | {
"body": "static String fixup(String s) {\n StringBuilder out = new StringBuilder();\n JavaScanner scanner = new JavaScanner(s);\n s = scanner.string();\n int len = s.length();\n for (int start = 0, previous = 0, braces = 0, parens = 0, end = 0;\n start < len;\n previous = start, start =... | {
"created": "5/22/2013 9:41:56 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 10230369,
"size": null,
"stargazer_count": null,
"stars": 8408,
"updates": "2020-01-27T16:25:00+00:00",
"url": "https://github.com/google/auto"
} |
10230369_53 | {
"fields": [],
"file": "common/src/test/java/com/google/auto/common/SuperficialValidationTest.java",
"identifier": "SuperficialValidationTest",
"interfaces": "",
"superclass": ""
} | {
"body": "@Test\n public void missingGenericReturnType() {\n JavaFileObject javaFileObject = JavaFileObjects.forSourceLines(\n \"test.TestClass\",\n \"package test;\",\n \"\",\n \"abstract class TestClass {\",\n \" abstract MissingType<?> blah();\",\n \"}\");\n asser... | {
"fields": [
{
"declarator": "ELEMENT_VALIDATING_VISITOR =\n new AbstractElementVisitor8<Boolean, Void>() {\n @Override public Boolean visitPackage(PackageElement e, Void p) {\n // don't validate enclosed elements because it will return types in the package\n return validateAn... | {
"body": "public static boolean validateElement(Element element) {\n return element.accept(ELEMENT_VALIDATING_VISITOR, null);\n }",
"class_method_signature": "SuperficialValidation.validateElement(Element element)",
"constructor": false,
"full_signature": "public static boolean validateElement(Element elem... | {
"created": "5/22/2013 9:41:56 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 10230369,
"size": null,
"stargazer_count": null,
"stars": 8408,
"updates": "2020-01-27T16:25:00+00:00",
"url": "https://github.com/google/auto"
} |
10230369_12 | {
"fields": [],
"file": "value/src/test/java/com/google/auto/value/extension/serializable/serializer/impl/SerializerFactoryImplTest.java",
"identifier": "SerializerFactoryImplTest",
"interfaces": "",
"superclass": "extends CompilationAbstractTest"
} | {
"body": "@Test\n public void getSerializer_emptyFactories_identitySerializerReturned() throws Exception {\n SerializerFactoryImpl factory =\n new SerializerFactoryImpl(ImmutableList.of(), mockProcessingEnvironment);\n\n Serializer actualSerializer = factory.getSerializer(typeMirrorOf(String.class));\n... | {
"fields": [
{
"declarator": "extensions",
"modifier": "private final",
"original_string": "private final ImmutableList<SerializerExtension> extensions;",
"type": "ImmutableList<SerializerExtension>",
"var_name": "extensions"
},
{
"declarator": "env",
"modifier":... | {
"body": "@Override\n public Serializer getSerializer(TypeMirror typeMirror) {\n for (SerializerExtension extension : extensions) {\n Optional<Serializer> serializer = extension.getSerializer(typeMirror, this, env);\n if (serializer.isPresent()) {\n return serializer.get();\n }\n }\n ... | {
"created": "5/22/2013 9:41:56 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 10230369,
"size": null,
"stargazer_count": null,
"stars": 8408,
"updates": "2020-01-27T16:25:00+00:00",
"url": "https://github.com/google/auto"
} |
10230369_108 | {
"fields": [
{
"declarator": "compilation = new CompilationRule()",
"modifier": "@Rule public final",
"original_string": "@Rule public final CompilationRule compilation = new CompilationRule();",
"type": "CompilationRule",
"var_name": "compilation"
},
{
"declarator": "... | {
"body": "@Test\n public void getInt() {\n AnnotationValue value = AnnotationMirrors.getAnnotationValue(annotationMirror, \"intValue\");\n assertThat(AnnotationValues.getInt(value)).isEqualTo(5);\n }",
"class_method_signature": "AnnotationValuesTest.getInt()",
"constructor": false,
"full_signature": "@... | {
"fields": [
{
"declarator": "ANNOTATION_VALUE_EQUIVALENCE =\n new Equivalence<AnnotationValue>() {\n @Override protected boolean doEquivalent(AnnotationValue left, AnnotationValue right) {\n return left.accept(new SimpleAnnotationValueVisitor8<Boolean, AnnotationValue>() {\n ... | {
"body": "public static int getInt(AnnotationValue value) {\n return valueOfType(value, Integer.class);\n }",
"class_method_signature": "AnnotationValues.getInt(AnnotationValue value)",
"constructor": false,
"full_signature": "public static int getInt(AnnotationValue value)",
"identifier": "getInt",
"i... | {
"created": "5/22/2013 9:41:56 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 10230369,
"size": null,
"stargazer_count": null,
"stars": 8408,
"updates": "2020-01-27T16:25:00+00:00",
"url": "https://github.com/google/auto"
} |
10230369_45 | {
"fields": [
{
"declarator": "expect = Expect.create()",
"modifier": "@Rule public",
"original_string": "@Rule public Expect expect = Expect.create();",
"type": "Expect",
"var_name": "expect"
},
{
"declarator": "NORMAL_CASES =\n ImmutableMap.<String, String>builde... | {
"body": "@Test\n public void decapitalizeLikeJavaBeans() {\n NORMAL_CASES\n .forEach(\n (input, output) -> {\n expect.that(PropertyNames.decapitalizeLikeJavaBeans(input)).isEqualTo(output);\n });\n expect.that(PropertyNames.decapitalizeLikeJavaBeans(null)).isNull();\... | {
"fields": [],
"file": "value/src/main/java/com/google/auto/value/processor/PropertyNames.java",
"identifier": "PropertyNames",
"interfaces": "",
"methods": [
{
"class_method_signature": "PropertyNames.decapitalizeLikeJavaBeans(String propertyName)",
"constructor": false,
"full_signatur... | {
"body": "static String decapitalizeLikeJavaBeans(String propertyName) {\n if (propertyName != null\n && propertyName.length() >= 2\n && Character.isUpperCase(propertyName.charAt(0))\n && Character.isUpperCase(propertyName.charAt(1))) {\n return propertyName;\n }\n return decapital... | {
"created": "5/22/2013 9:41:56 PM +00:00",
"fork": "False",
"fork_count": null,
"is_fork": null,
"language": null,
"license": "licensed",
"repo_id": 10230369,
"size": null,
"stargazer_count": null,
"stars": 8408,
"updates": "2020-01-27T16:25:00+00:00",
"url": "https://github.com/google/auto"
} |
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