catalog: add aggregation stats (facets) for cohorts, clinical analyse…

…s, families, individuals, interpretations, jobs and panels, #TASK-7152, #TASK-7134
opencb · Oct 28, 2024 · 7bbfea6 · 7bbfea6
1 parent d43005e
commit 7bbfea6
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Showing 17 changed files with 103 additions and 34 deletions.
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java
@@ -152,7 +152,7 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--annotation"}, description = "Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0", required = false, arity = 1)
         public String annotation; 
 
-        @Parameter(names = {"--field"}, description = "List of fields to aggregate separated by semicolons, e.g.: max(version);release", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons, e.g.: studies;type;numSamples[0..10]:1", required = false, arity = 1)
         public String field; 
 
     }

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AbstractManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AbstractManager.java
@@ -28,10 +28,13 @@
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.exceptions.CatalogParameterException;
 import org.opencb.opencga.catalog.models.InternalGetDataResult;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
 import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.config.Configuration;
 import org.opencb.opencga.core.models.IPrivateStudyUid;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.study.Group;
+import org.opencb.opencga.core.models.study.Study;
 import org.opencb.opencga.core.response.OpenCGAResult;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -62,6 +65,11 @@ public abstract class AbstractManager {
 
     protected static final String INTERNAL_DELIMITER = "__";
 
+    protected JwtPayload tokenPayload;
+    protected String organizationId;
+    protected String userId;
+    protected Study study;
+
     AbstractManager(AuthorizationManager authorizationManager, AuditManager auditManager, CatalogManager catalogManager,
                     DBAdaptorFactory catalogDBAdaptorFactory, Configuration configuration) {
         this.authorizationManager = authorizationManager;
@@ -73,6 +81,15 @@ public abstract class AbstractManager {
         logger = LoggerFactory.getLogger(this.getClass());
     }
 
+    protected void setInternalVariables(String studyStr, String token) throws CatalogException {
+        tokenPayload = catalogManager.getUserManager().validateToken(token);
+        CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyStr, tokenPayload);
+        organizationId = studyFqn.getOrganizationId();
+        userId = tokenPayload.getUserId(organizationId);
+
+        study = catalogManager.getStudyManager().resolveId(studyFqn, StudyManager.INCLUDE_VARIABLE_SET, tokenPayload);
+    }
+
     protected DBAdaptorFactory getCatalogDBAdaptorFactory() {
         return catalogDBAdaptorFactory;
     }

diff --git a/...ga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManager.java b/...ga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManager.java
@@ -233,7 +233,15 @@ public DBIterator<ClinicalAnalysis> iterator(String studyStr, Query query, Query
 
     @Override
     public OpenCGAResult<FacetField> facet(String studyStr, Query query, String facet, String token) throws CatalogException {
-        return null;
+        query = ParamUtils.defaultObject(query, Query::new);
+
+        // Set internal variables: tokenPayload, study, organizationId, userId
+        setInternalVariables(studyStr, token);
+
+        fixQueryObject(organizationId, study, query, userId, token);
+        query.append(ClinicalAnalysisDBAdaptor.QueryParams.STUDY_UID.key(), study.getUid());
+
+        return getClinicalAnalysisDBAdaptor(organizationId).facet(study.getUid(), query, facet, userId);
     }
 
     @Override

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/CohortManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/CohortManager.java
@@ -471,7 +471,16 @@ public DBIterator<Cohort> iterator(String studyStr, Query query, QueryOptions op
 
     @Override
     public OpenCGAResult<FacetField> facet(String studyStr, Query query, String facet, String token) throws CatalogException {
-        return null;
+        query = ParamUtils.defaultObject(query, Query::new);
+
+        // Set internal variables: tokenPayload, study, organizationId, userId
+        setInternalVariables(studyStr, token);
+
+        Query finalQuery = new Query(query);
+        fixQueryObject(organizationId, study, finalQuery, userId);
+        finalQuery.append(CohortDBAdaptor.QueryParams.STUDY_UID.key(), study.getUid());
+
+        return getCohortDBAdaptor(organizationId).facet(study.getUid(), finalQuery, facet, userId);
     }
 
     @Override

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/FamilyManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/FamilyManager.java
@@ -222,7 +222,16 @@ public DBIterator<Family> iterator(String studyStr, Query query, QueryOptions op
 
     @Override
     public OpenCGAResult<FacetField> facet(String studyStr, Query query, String facet, String token) throws CatalogException {
-        return null;
+        query = ParamUtils.defaultObject(query, Query::new);
+
+        // Set internal variables: tokenPayload, study, organizationId, userId
+        setInternalVariables(studyStr, token);
+
+        Query finalQuery = new Query(query);
+        fixQueryObject(organizationId, study, query, tokenPayload);
+        query.append(FamilyDBAdaptor.QueryParams.STUDY_UID.key(), study.getUid());
+
+        return getFamilyDBAdaptor(organizationId).facet(study.getUid(), query, facet, userId);
     }
 
     @Override

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/FileManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/FileManager.java
@@ -1422,15 +1422,10 @@ public DBIterator<File> iterator(String studyStr, Query query, QueryOptions opti
     public OpenCGAResult facet(String studyStr, Query query, String facet, String token) throws CatalogException {
         query = ParamUtils.defaultObject(query, Query::new);
 
-        JwtPayload tokenPayload = catalogManager.getUserManager().validateToken(token);
-        CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyStr, tokenPayload);
-        String organizationId = studyFqn.getOrganizationId();
-        String userId = tokenPayload.getUserId(organizationId);
-
-        Study study = catalogManager.getStudyManager().resolveId(studyFqn, StudyManager.INCLUDE_VARIABLE_SET, tokenPayload);
+        // Set internal variables: tokenPayload, study, organizationId, userId
+        setInternalVariables(studyStr, token);
 
         fixQueryObject(study, query, userId);
-
         query.append(FileDBAdaptor.QueryParams.STUDY_UID.key(), study.getUid());
 
         return getFileDBAdaptor(organizationId).facet(study.getUid(), query, facet, userId);

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/IndividualManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/IndividualManager.java
@@ -404,7 +404,16 @@ public DBIterator<Individual> iterator(String studyStr, Query query, QueryOption
 
     @Override
     public OpenCGAResult<FacetField> facet(String studyStr, Query query, String facet, String token) throws CatalogException {
-        return null;
+        query = ParamUtils.defaultObject(query, Query::new);
+
+        // Set internal variables: tokenPayload, study, organizationId, userId
+        setInternalVariables(studyStr, token);
+
+        Query finalQuery = new Query(query);
+        fixQuery(organizationId, study, finalQuery, userId);
+        finalQuery.append(IndividualDBAdaptor.QueryParams.STUDY_UID.key(), study.getUid());
+
+        return getIndividualDBAdaptor(organizationId).facet(study.getUid(), finalQuery, facet, userId);
     }
 
     @Override

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/InterpretationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/InterpretationManager.java
@@ -1267,7 +1267,15 @@ public DBIterator<Interpretation> iterator(String studyStr, Query query, QueryOp
 
     @Override
     public OpenCGAResult<FacetField> facet(String studyStr, Query query, String facet, String token) throws CatalogException {
-        return null;
+        query = ParamUtils.defaultObject(query, Query::new);
+
+        // Set internal variables: tokenPayload, study, organizationId, userId
+        setInternalVariables(studyStr, token);
+
+        fixQueryObject(organizationId, study, query, userId);
+        query.append(InterpretationDBAdaptor.QueryParams.STUDY_UID.key(), study.getUid());
+
+        return getInterpretationDBAdaptor(organizationId).facet(study.getUid(), query, facet, userId);
     }
 
     @Override

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/JobManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/JobManager.java
@@ -812,7 +812,15 @@ public DBIterator<Job> iterator(String studyId, Query query, QueryOptions option
 
     @Override
     public OpenCGAResult<FacetField> facet(String studyStr, Query query, String facet, String token) throws CatalogException {
-        return null;
+        query = ParamUtils.defaultObject(query, Query::new);
+
+        // Set internal variables: tokenPayload, study, organizationId, userId
+        setInternalVariables(studyStr, token);
+
+        fixQueryObject(organizationId, study, query, userId);
+        query.append(JobDBAdaptor.QueryParams.STUDY_UID.key(), study.getUid());
+
+        return getJobDBAdaptor(organizationId).facet(study.getUid(), query, facet, userId);
     }
 
     public OpenCGAResult countInOrganization(String organizationId, Query query, String token) throws CatalogException {

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/PanelManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/PanelManager.java
@@ -25,10 +25,7 @@
 import org.opencb.commons.utils.ListUtils;
 import org.opencb.opencga.catalog.auth.authorization.AuthorizationManager;
 import org.opencb.opencga.catalog.db.DBAdaptorFactory;
-import org.opencb.opencga.catalog.db.api.DBIterator;
-import org.opencb.opencga.catalog.db.api.FamilyDBAdaptor;
-import org.opencb.opencga.catalog.db.api.PanelDBAdaptor;
-import org.opencb.opencga.catalog.db.api.StudyDBAdaptor;
+import org.opencb.opencga.catalog.db.api.*;
 import org.opencb.opencga.catalog.exceptions.CatalogAuthorizationException;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.exceptions.CatalogParameterException;
@@ -596,7 +593,15 @@ public DBIterator<Panel> iterator(String studyStr, Query query, QueryOptions opt
 
     @Override
     public OpenCGAResult<FacetField> facet(String studyStr, Query query, String facet, String token) throws CatalogException {
-        return null;
+        query = ParamUtils.defaultObject(query, Query::new);
+
+        // Set internal variables: tokenPayload, study, organizationId, userId
+        setInternalVariables(studyStr, token);
+
+        fixQueryObject(query);
+        query.append(PanelDBAdaptor.QueryParams.STUDY_UID.key(), study.getUid());
+
+        return getPanelDBAdaptor(organizationId).facet(study.getUid(), query, facet, userId);
     }
 
     @Override

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/SampleManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/SampleManager.java
@@ -89,6 +89,12 @@ public class SampleManager extends AnnotationSetManager<Sample> {
         studyManager = catalogManager.getStudyManager();
     }
 
+    protected void test(Query query) throws CatalogException {
+        fixQueryObject(organizationId, study, query, userId);
+
+        query.append(SampleDBAdaptor.QueryParams.STUDY_UID.key(), study.getUid());
+    }
+
     @Override
     Enums.Resource getEntity() {
         return Enums.Resource.SAMPLE;
@@ -288,15 +294,10 @@ public DBIterator<Sample> iterator(String studyStr, Query query, QueryOptions op
     public OpenCGAResult facet(String studyStr, Query query, String facet, String token) throws CatalogException {
         query = ParamUtils.defaultObject(query, Query::new);
 
-        JwtPayload tokenPayload = catalogManager.getUserManager().validateToken(token);
-        CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyStr, tokenPayload);
-        String organizationId = studyFqn.getOrganizationId();
-        String userId = tokenPayload.getUserId(organizationId);
-
-        Study study = catalogManager.getStudyManager().resolveId(studyFqn, StudyManager.INCLUDE_VARIABLE_SET, tokenPayload);
+        // Set internal variables: tokenPayload, study, organizationId, userId
+        setInternalVariables(studyStr, token);
 
         fixQueryObject(organizationId, study, query, userId);
-
         query.append(SampleDBAdaptor.QueryParams.STUDY_UID.key(), study.getUid());
 
         return getSampleDBAdaptor(organizationId).facet(study.getUid(), query, facet, userId);

diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R
@@ -66,7 +66,7 @@ setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, members,
         #' @param version Version.
         #' @param somatic Somatic.
         #' @param annotation Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-        #' @param field List of fields to aggregate separated by semicolons, e.g.: max(version);release.
+        #' @param field List of fields separated by semicolons, e.g.: studies;type;numSamples[0..10]:1.
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="samples", categoryId=NULL, subcategory=NULL,
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),

diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java
@@ -88,7 +88,7 @@ public RestResponse<SampleAclEntryList> updateAcl(String members, String action,
      *       somatic: Somatic.
      *       annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit
      *            http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-     *       field: List of fields to aggregate separated by semicolons, e.g.: max(version);release.
+     *       field: List of fields separated by semicolons, e.g.: studies;type;numSamples[0..10]:1.
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.
      */

diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js
@@ -63,7 +63,7 @@ export default class Sample extends OpenCGAParentClass {
     * @param {Boolean} [params.somatic] - Somatic.
     * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit
     *     http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-    * @param {String} [params.field] - List of fields to aggregate separated by semicolons, e.g.: max(version);release.
+    * @param {String} [params.field] - List of fields separated by semicolons, e.g.: studies;type;numSamples[0..10]:1.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     aggregationStats(params) {

diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py
@@ -61,8 +61,8 @@ def aggregation_stats(self, **options):
         :param str annotation: Annotation filters. Example:
             age>30;gender=FEMALE. For more information, please visit
             http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-        :param str field: List of fields to aggregate separated by semicolons,
-            e.g.: max(version);release.
+        :param str field: List of fields separated by semicolons, e.g.:
+            studies;type;numSamples[0..10]:1.
         """
 
         return self._get(category='samples', resource='aggregationStats', **options)

diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/FileWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/FileWSServer.java
@@ -1051,7 +1051,7 @@ public Response getAggregationStats(
         return run(() -> {
             query.remove(ParamConstants.STUDY_PARAM);
             query.remove("field");
-            return catalogManager.getFileManager().facet(studyStr, query, facet, token);
+            return catalogManager.getSampleManager().facet(studyStr, query, facet, token);
         });
     }
 }
diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/SampleWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/SampleWSServer.java
@@ -462,11 +462,11 @@ public Response getAggregationStats(
             @ApiParam(value = "Version") @QueryParam("version") String version,
             @ApiParam(value = "Somatic") @QueryParam("somatic") Boolean somatic,
             @ApiParam(value = ParamConstants.ANNOTATION_DESCRIPTION) @QueryParam("annotation") String annotation,
-            @ApiParam(value = "List of fields to aggregate separated by semicolons, e.g.: max(version);release") @QueryParam("field") String field) {
+            @ApiParam(value = "List of fields separated by semicolons, e.g.: studies;type;numSamples[0..10]:1") @QueryParam("field") String facet) {
         return run(() -> {
             query.remove(ParamConstants.STUDY_PARAM);
             query.remove("field");
-            return catalogManager.getSampleManager().facet(studyStr, query, field, token);
+            return catalogManager.getSampleManager().facet(studyStr, query, facet, token);
         });
     }
 }