for (Study study : studyQueryResult.getResult()) { Map<String, Set<String>> studyAcls = SolrConverterUtil.parseInternalOpenCGAAcls((List<Map<String, Object>>) study.getAttributes().get("OPENCGA_ACL")); study.getAttributes().put("OPENCGA_ACL", studyAcls);
Study study = catalogManager.getStudyManager().get(studyId, include, sessionId).first(); Aggregation argsAggregation = options.get(VariantStorageEngine.Options.AGGREGATED_TYPE.key(), Aggregation.class, Aggregation.NONE); Object studyAggregationObj = study.getAttributes().get(VariantStorageEngine.Options.AGGREGATED_TYPE.key()); Aggregation studyAggregation = null; if (studyAggregationObj != null) {
SolrConverterUtil.parseInternalOpenCGAAcls((List<Map<String, Object>>) cohort.getAttributes().get("OPENCGA_ACL")); List<String> effectivePermissions = SolrConverterUtil.getEffectivePermissions((Map<String, Set<String>>) study.getAttributes().get("OPENCGA_ACL"), cohortAcl, "COHORT"); cohortSolrModel.setAcl(effectivePermissions);
@Test public void testAssignPermissions() throws CatalogException, IOException { catalogManager.getUserManager().create("test", "test", "test@mail.com", "test", null, 100L, "guest", null, null); catalogManager.getStudyManager().createGroup("user@1000G:phase1", "group_cancer_some_thing_else", "test", sessionIdUser); List<QueryResult<StudyAclEntry>> permissions = catalogManager.getStudyManager().updateAcl( Collections.singletonList("user@1000G:phase1"), "@group_cancer_some_thing_else", new Study.StudyAclParams("", AclParams.Action.SET, "view_only"), sessionIdUser); assertEquals("@group_cancer_some_thing_else", permissions.get(0).first().getMember()); String token = catalogManager.getUserManager().login("test", "test"); QueryResult<Study> studyQueryResult = catalogManager.getStudyManager().get("user@1000G:phase1", QueryOptions.empty(), token); assertEquals(1, studyQueryResult.getNumResults()); assertTrue(studyQueryResult.first().getAttributes().isEmpty()); studyQueryResult = catalogManager.getStudyManager().get("user@1000G:phase1", new QueryOptions(DBAdaptor.INCLUDE_ACLS, true), token); assertEquals(1, studyQueryResult.getNumResults()); assertTrue(!studyQueryResult.first().getAttributes().isEmpty()); assertTrue(studyQueryResult.first().getAttributes().containsKey("OPENCGA_ACL")); List<Map<String, Object>> acls = (List<Map<String, Object>>) studyQueryResult.first().getAttributes().get("OPENCGA_ACL"); assertEquals(1, acls.size()); assertEquals("@group_cancer_some_thing_else", acls.get(0).get("member")); assertTrue(!((List) acls.get(0).get("permissions")).isEmpty()); }
SolrConverterUtil.parseInternalOpenCGAAcls((List<Map<String, Object>>) family.getAttributes().get("OPENCGA_ACL")); List<String> effectivePermissions = SolrConverterUtil.getEffectivePermissions((Map<String, Set<String>>) study.getAttributes().get("OPENCGA_ACL"), familyAcl, "FAMILY"); familySolrModel.setAcl(effectivePermissions);
@Test public void testCalculateAggregatedStatsNonAggregatedStudy() throws Exception { beforeAggregated("variant-test-aggregated-file.vcf.gz", null); calculateAggregatedStats(new QueryOptions(VariantStorageEngine.Options.AGGREGATED_TYPE.key(), Aggregation.BASIC)); Study study = catalogManager.getStudyManager().get(studyId, null, sessionId).first(); String agg = study.getAttributes().get(VariantStorageEngine.Options.AGGREGATED_TYPE.key()).toString(); assertNotNull(agg); assertEquals(Aggregation.BASIC.toString(), agg); }
SolrConverterUtil.parseInternalOpenCGAAcls((List<Map<String, Object>>) file.getAttributes().get("OPENCGA_ACL")); List<String> effectivePermissions = SolrConverterUtil.getEffectivePermissions((Map<String, Set<String>>) study.getAttributes().get("OPENCGA_ACL"), fileAcl, "FILE"); fileSolrModel.setAcl(effectivePermissions);
SolrConverterUtil.parseInternalOpenCGAAcls((List<Map<String, Object>>) sample.getAttributes().get("OPENCGA_ACL")); List<String> effectivePermissions = SolrConverterUtil.getEffectivePermissions((Map<String, Set<String>>) study.getAttributes().get("OPENCGA_ACL"), sampleAcl, "SAMPLE"); sampleSolrModel.setAcl(effectivePermissions);
SolrConverterUtil.parseInternalOpenCGAAcls((List<Map<String, Object>>) individual.getAttributes().get("OPENCGA_ACL")); List<String> effectivePermissions = SolrConverterUtil.getEffectivePermissions((Map<String, Set<String>>) study.getAttributes().get("OPENCGA_ACL"), individualAcl, "INDIVIDUAL"); individualSolrModel.setAcl(effectivePermissions);
/** * Study methods * *************************** */ @Test public void testModifyStudy() throws Exception { Query query = new Query(StudyDBAdaptor.QueryParams.OWNER.key(), "user"); String studyId = catalogManager.getStudyManager().get(query, null, sessionIdUser).first().getId(); String newName = "Phase 1 " + StringUtils.randomString(20); String newDescription = StringUtils.randomString(500); ObjectMap parameters = new ObjectMap(); parameters.put("name", newName); parameters.put("description", newDescription); BasicDBObject attributes = new BasicDBObject("key", "value"); parameters.put("attributes", attributes); catalogManager.getStudyManager().update(studyId, parameters, null, sessionIdUser); QueryResult<Study> result = catalogManager.getStudyManager().get(studyId, null, sessionIdUser); System.out.println(result); Study study = result.first(); assertEquals(study.getName(), newName); assertEquals(study.getDescription(), newDescription); for (Map.Entry<String, Object> entry : attributes.entrySet()) { assertEquals(study.getAttributes().get(entry.getKey()), entry.getValue()); } }
SolrConverterUtil.parseInternalOpenCGAAcls((List<Map<String, Object>>) study.getAttributes().get("OPENCGA_ACL")); study.getAttributes().put("OPENCGA_ACL", studyAcls);
SolrConverterUtil.parseInternalOpenCGAAcls((List<Map<String, Object>>) study.getAttributes().get("OPENCGA_ACL")); study.getAttributes().put("OPENCGA_ACL", studyAcls);
.setAttributes(study.getAttributes()) .setCipher(study.getCipher()) .setCreationDate(study.getCreationDate())