.setId(individual.getId()) .setSource(pedFile.getName()) .setDescription("Sample loaded from the pedigree File = {path: " + pedFile.getPath() + ", name: \"" + pedFile.getName() + "\" }"), QueryOptions.empty(), sessionId);
ParamUtils.checkAlias(sample.getId(), "name"); sample.setSource(ParamUtils.defaultString(sample.getSource(), "")); sample.setDescription(ParamUtils.defaultString(sample.getDescription(), "")); sample.setType(ParamUtils.defaultString(sample.getType(), "")); sample.setPhenotypes(ParamUtils.defaultObject(sample.getPhenotypes(), Collections.emptyList()));
@Test public void updateCollectionField() throws CatalogException { catalogManager.getSampleManager().create(studyFqn, new Sample().setId("testSample").setDescription("description"), null, sessionIdUser); SampleCollection collection = new SampleCollection("tissue", "organ", "quantity", "method", "date", Collections.emptyMap()); ObjectMap params = new ObjectMap(SampleDBAdaptor.UpdateParams.COLLECTION.key(), collection); catalogManager.getSampleManager().update(studyFqn, "testSample", params, new QueryOptions(Constants.INCREMENT_VERSION, true), sessionIdUser); QueryResult<Sample> testSample = catalogManager.getSampleManager().get(studyFqn, "testSample", new QueryOptions(), sessionIdUser); assertEquals("tissue", testSample.first().getCollection().getTissue()); assertEquals("organ", testSample.first().getCollection().getOrgan()); assertEquals("quantity", testSample.first().getCollection().getQuantity()); assertEquals("method", testSample.first().getCollection().getMethod()); assertEquals("date", testSample.first().getCollection().getDate()); assertTrue(testSample.first().getCollection().getAttributes().isEmpty()); }
@Test public void updateProcessingField() throws CatalogException { catalogManager.getSampleManager().create(studyFqn, new Sample().setId("testSample").setDescription("description"), null, sessionIdUser); SampleProcessing processing = new SampleProcessing("product", "preparationMethod", "extractionMethod", "labSampleId", "quantity", "date", Collections.emptyMap()); ObjectMap params = new ObjectMap(SampleDBAdaptor.UpdateParams.PROCESSING.key(), processing); catalogManager.getSampleManager().update(studyFqn, "testSample", params, new QueryOptions(Constants.INCREMENT_VERSION, true), sessionIdUser); QueryResult<Sample> testSample = catalogManager.getSampleManager().get(studyFqn, "testSample", new QueryOptions(), sessionIdUser); assertEquals("product", testSample.first().getProcessing().getProduct()); assertEquals("preparationMethod", testSample.first().getProcessing().getPreparationMethod()); assertEquals("extractionMethod", testSample.first().getProcessing().getExtractionMethod()); assertEquals("labSampleId", testSample.first().getProcessing().getLabSampleId()); assertEquals("quantity", testSample.first().getProcessing().getQuantity()); assertEquals("date", testSample.first().getProcessing().getDate()); assertTrue(testSample.first().getProcessing().getAttributes().isEmpty()); }
new Sample().setId("testSample").setDescription("description"), null, sessionIdUser); catalogManager.getSampleManager().update(studyFqn, "testSample", new ObjectMap(), new QueryOptions(Constants.INCREMENT_VERSION, true), sessionIdUser);