@Override protected List<String> validate(String defaultStudyStr, List<String> values, Integer release, VariantQueryParam param, String sessionId) throws CatalogException { if (release == null) { AbstractManager.MyResources<Sample> uids = catalogManager.getSampleManager().getUids(values, defaultStudyStr, sessionId); return uids.getResourceList().stream().map(Sample::getId).collect(Collectors.toList()); } else { return validate(defaultStudyStr, values, release, param, catalogManager.getSampleManager(), Sample::getId, Sample::getRelease, null, sessionId); } } }
private void fixQueryObject(Study study, Query query, String sessionId) throws CatalogException { if (query.containsKey(CohortDBAdaptor.QueryParams.SAMPLES.key())) { // First look for the sample ids. MyResources<Sample> samples = catalogManager.getSampleManager() .getUids(query.getAsStringList(CohortDBAdaptor.QueryParams.SAMPLES.key()), study.getFqn(), sessionId); query.remove(CohortDBAdaptor.QueryParams.SAMPLES.key()); query.append(CohortDBAdaptor.QueryParams.SAMPLE_UIDS.key(), samples.getResourceList().stream().map(Sample::getUid) .collect(Collectors.toList())); } }
void fixQueryObject(Study study, Query query, String sessionId) throws CatalogException { if (StringUtils.isNotEmpty(query.getString(FileDBAdaptor.QueryParams.ID.key()))) { MyResources<File> uids = getUids(query.getAsStringList(FileDBAdaptor.QueryParams.ID.key()), study.getFqn(), sessionId); query.remove(FileDBAdaptor.QueryParams.ID.key()); query.put(FileDBAdaptor.QueryParams.UID.key(), uids.getResourceList().stream().map(File::getUid).collect(Collectors.toList())); } // The samples introduced could be either ids or names. As so, we should use the smart resolutor to do this. if (StringUtils.isNotEmpty(query.getString(FileDBAdaptor.QueryParams.SAMPLES.key()))) { MyResources<Sample> resource = catalogManager.getSampleManager().getUids( query.getAsStringList(FileDBAdaptor.QueryParams.SAMPLES.key()), study.getFqn(), sessionId); query.put(FileDBAdaptor.QueryParams.SAMPLE_UIDS.key(), resource.getResourceList().stream().map(Sample::getUid) .collect(Collectors.toList())); query.remove(FileDBAdaptor.QueryParams.SAMPLES.key()); } }
MyResources<Sample> resource = catalogManager.getSampleManager().getUids( Arrays.asList(StringUtils.split(fileAclParams.getSample(), ",")), studyStr, sessionId);
MyResources<Sample> resource = getUids(sampleList, studyStr, sessionId); authorizationManager.checkCanAssignOrSeePermissions(resource.getStudy().getUid(), resource.getUser());
private void fixQuery(Study study, Query query, String sessionId) throws CatalogException { if (StringUtils.isNotEmpty(query.getString(IndividualDBAdaptor.QueryParams.FATHER.key()))) { MyResource resource = getUid(query.getString(IndividualDBAdaptor.QueryParams.FATHER.key()), study.getFqn(), sessionId); query.remove(IndividualDBAdaptor.QueryParams.FATHER.key()); query.append(IndividualDBAdaptor.QueryParams.FATHER_UID.key(), resource.getResource().getUid()); } if (StringUtils.isNotEmpty(query.getString(IndividualDBAdaptor.QueryParams.MOTHER.key()))) { MyResource resource = getUid(query.getString(IndividualDBAdaptor.QueryParams.MOTHER.key()), study.getFqn(), sessionId); query.remove(IndividualDBAdaptor.QueryParams.MOTHER.key()); query.append(IndividualDBAdaptor.QueryParams.MOTHER_UID.key(), resource.getResource().getUid()); } if (StringUtils.isNotEmpty(query.getString(IndividualDBAdaptor.QueryParams.SAMPLES.key()))) { MyResources<Sample> resource = catalogManager.getSampleManager().getUids( query.getString(IndividualDBAdaptor.QueryParams.SAMPLES.key()), study.getFqn(), sessionId); query.remove(IndividualDBAdaptor.QueryParams.SAMPLES.key()); query.append(IndividualDBAdaptor.QueryParams.SAMPLE_UIDS.key(), resource.getResourceList().stream().map(Sample::getUid) .collect(Collectors.toList())); } }
List<String> sampleIdStr = parameters.getAsStringList(FileDBAdaptor.QueryParams.SAMPLES.key()); MyResources<Sample> sampleResource = catalogManager.getSampleManager().getUids(sampleIdStr, studyStr, sessionId);
MyResources<Sample> sampleResource = catalogManager.getSampleManager().getUids(samples, studyStr, sessionId); Map<Long, Integer> existingSamplesInIndividual = checkSamplesNotInUseInOtherIndividual( sampleResource.getResourceList().stream().map(Sample::getUid).collect(Collectors.toSet()), studyId, individualId);