Merge pull request #2328 from opencb/TASK-4641

TASK-4641- Update according to CellBase changes and remove and use VersionUtils from java-common-libs

opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java

@@ -230,7 +230,7 @@ public OpenCGAResult<GeneCoverageStats> coverageStats(String studyIdStr, String
         String species = projectQueryResult.first().getOrganism().getScientificName();
         String assembly = projectQueryResult.first().getOrganism().getAssembly();
         String dataRelease = projectQueryResult.first().getCellbase().getDataRelease();
-        String cellbaseToken = projectQueryResult.first().getCellbase().getToken();
+        String cellbaseToken = projectQueryResult.first().getCellbase().getApiKey();
 
         for (String geneName : geneNames) {
 
@@ -451,7 +451,7 @@ public List<Region> mergeRegions(List<Region> regions, List<String> genes, boole
         String species = projectQueryResult.first().getOrganism().getScientificName();
         String assembly = projectQueryResult.first().getOrganism().getAssembly();
         String dataRelease = projectQueryResult.first().getCellbase().getDataRelease();
-        String cellbaseToken = projectQueryResult.first().getCellbase().getToken();
+        String cellbaseToken = projectQueryResult.first().getCellbase().getApiKey();
         CellBaseClient cellBaseClient = new CellBaseClient(species, assembly, dataRelease, cellbaseToken,
                 projectQueryResult.first().getCellbase().toClientConfiguration());
         GeneClient geneClient = cellBaseClient.getGeneClient();

opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java

@@ -1021,8 +1021,9 @@ private void setCellbaseConfiguration(VariantStorageEngine engine, String projec
                 .get(project, new QueryOptions(INCLUDE, ProjectDBAdaptor.QueryParams.CELLBASE.key()), token)
                 .first().getCellbase();
         if (cellbase != null) {
-            if (StringUtils.isEmpty(cellbase.getToken()) || storageConfiguration.getCellbase() != null) {
-                cellbase.setToken(storageConfiguration.getCellbase().getToken());
+            // To ensure that we use the project API key before using the storage API key
+            if (StringUtils.isEmpty(cellbase.getApiKey()) && storageConfiguration.getCellbase() != null) {
+                cellbase.setApiKey(storageConfiguration.getCellbase().getApiKey());
             }
             engine.getConfiguration().setCellbase(cellbase);
             engine.reloadCellbaseConfiguration();

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-09-01 OpenCB
+* Copyright 2015-2023-09-08 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-09-01 OpenCB
+* Copyright 2015-2023-09-08 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java

@@ -197,7 +197,7 @@ private RestResponse<Job> configureCellbase() throws Exception {
             putNestedIfNotEmpty(beanParams, "url",commandOptions.url, true);
             putNestedIfNotEmpty(beanParams, "version",commandOptions.version, true);
             putNestedIfNotEmpty(beanParams, "dataRelease",commandOptions.dataRelease, true);
-            putNestedIfNotEmpty(beanParams, "token",commandOptions.token, true);
+            putNestedIfNotEmpty(beanParams, "apiKey",commandOptions.apiKey, true);
 
             cellBaseConfiguration = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java

@@ -123,7 +123,7 @@ private RestResponse<Project> create() throws Exception {
             putNestedIfNotEmpty(beanParams, "cellbase.url",commandOptions.cellbaseUrl, true);
             putNestedIfNotEmpty(beanParams, "cellbase.version",commandOptions.cellbaseVersion, true);
             putNestedIfNotEmpty(beanParams, "cellbase.dataRelease",commandOptions.cellbaseDataRelease, true);
-            putNestedIfNotEmpty(beanParams, "cellbase.token",commandOptions.cellbaseToken, true);
+            putNestedIfNotEmpty(beanParams, "cellbase.apiKey",commandOptions.cellbaseApiKey, true);
             putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
 
             projectCreateParams = JacksonUtils.getDefaultObjectMapper().copy()

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/OperationsVariantStorageCommandOptions.java

@@ -128,8 +128,8 @@ public class ConfigureCellbaseCommandOptions {
         @Parameter(names = {"--data-release"}, description = "CellBase data release version to be used. If empty, will use the active one", required = false, arity = 1)
         public String dataRelease;
 
-        @Parameter(names = {"--token"}, description = "CellBase token to access to the licensed/restricted data sources such as COSMIC, HGMD,...", required = false, arity = 1)
-        public String token;
+        @Parameter(names = {"--api-key"}, description = "API key to access to the licensed/restricted data sources (COSMIC, HGMD,...) and to manage quota.", required = false, arity = 1)
+        public String apiKey;
 
     }
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/ProjectsCommandOptions.java

@@ -110,8 +110,8 @@ public class CreateCommandOptions {
         @Parameter(names = {"--cellbase-data-release"}, description = "CellBase data release version to be used. If empty, will use the active one", required = false, arity = 1)
         public String cellbaseDataRelease;
 
-        @Parameter(names = {"--cellbase-token"}, description = "CellBase token to access to the licensed/restricted data sources such as COSMIC, HGMD,...", required = false, arity = 1)
-        public String cellbaseToken;
+        @Parameter(names = {"--cellbase-api-key"}, description = "API key to access to the licensed/restricted data sources (COSMIC, HGMD,...) and to manage quota.", required = false, arity = 1)
+        public String cellbaseApiKey;
 
         @DynamicParameter(names = {"--attributes"}, description = "The body web service attributes parameter. Use: --attributes key=value", required = false)
         public java.util.Map<java.lang.String,java.lang.Object> attributes = new HashMap<>(); //Dynamic parameters must be initialized;

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java

@@ -0,0 +1,50 @@
+package org.opencb.opencga.app.migrations.v2_9_0.catalog;
+
+import com.mongodb.client.model.Projections;
+import com.mongodb.client.model.UpdateOneModel;
+import com.mongodb.client.model.Updates;
+import org.bson.Document;
+import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptorFactory;
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+import java.util.List;
+
+import static com.mongodb.client.model.Filters.eq;
+
+@Migration(id = "rename_cellbase_token_2_api_key" ,
+        description = "Rename CellBase Token to ApiKey",
+        version = "2.9.0",
+        domain = Migration.MigrationDomain.CATALOG,
+        language = Migration.MigrationLanguage.JAVA,
+        date = 20230829
+)
+public class RenameCellBaseToken2ApiKey extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+
+        migrateCollection(MongoDBAdaptorFactory.USER_COLLECTION,
+                new Document("projects.id", new Document("$exists", true)),
+                Projections.include("_id", "projects"),
+                (userDocument, bulk) -> {
+                    List<Document> projects = userDocument.getList("projects", Document.class);
+                    for (int i = 0; i < projects.size(); i++) {
+                        Document project = projects.get(i);
+                        Document cellbase = project.get("cellbase", Document.class);
+                        if (cellbase != null) {
+                            String token = cellbase.getString("token");
+                            if (token != null) {
+                                bulk.add(new UpdateOneModel<>(
+                                        eq("_id", userDocument.get("_id")),
+                                        Updates.combine(
+                                                Updates.set("projects." + i + ".cellbase.apiKey", token),
+                                                Updates.unset("projects." + i + ".cellbase.token")
+                                        )));
+                            }
+                        }
+                    }
+                });
+    }
+
+}

opencga-client/src/main/R/R/Admin-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Alignment-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/AllGenerics.R

@@ -1,6 +1,6 @@
 # ##############################################################################
 ## UserClient
-setGeneric("userClient", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...)
+setGeneric("userClient", function(OpencgaR, users, user, filterId, endpointName, params=NULL, ...)
     standardGeneric("userClient"))
 
 # ##############################################################################
@@ -10,37 +10,37 @@ setGeneric("projectClient", function(OpencgaR, projects, project, endpointName,
 
 # ##############################################################################
 ## StudyClient
-setGeneric("studyClient", function(OpencgaR, variableSet, studies, members, group, study, templateId, endpointName, params=NULL, ...)
+setGeneric("studyClient", function(OpencgaR, study, group, variableSet, studies, members, templateId, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-setGeneric("fileClient", function(OpencgaR, members, folder, annotationSet, files, file, endpointName, params=NULL, ...)
+setGeneric("fileClient", function(OpencgaR, folder, annotationSet, file, members, files, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
 ## JobClient
-setGeneric("jobClient", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...)
+setGeneric("jobClient", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...)
     standardGeneric("jobClient"))
 
 # ##############################################################################
 ## SampleClient
-setGeneric("sampleClient", function(OpencgaR, annotationSet, sample, samples, members, endpointName, params=NULL, ...)
+setGeneric("sampleClient", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("sampleClient"))
 
 # ##############################################################################
 ## IndividualClient
-setGeneric("individualClient", function(OpencgaR, individual, individuals, annotationSet, members, endpointName, params=NULL, ...)
+setGeneric("individualClient", function(OpencgaR, individuals, members, individual, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("individualClient"))
 
 # ##############################################################################
 ## FamilyClient
-setGeneric("familyClient", function(OpencgaR, families, family, annotationSet, members, endpointName, params=NULL, ...)
+setGeneric("familyClient", function(OpencgaR, family, members, families, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("familyClient"))
 
 # ##############################################################################
 ## CohortClient
-setGeneric("cohortClient", function(OpencgaR, annotationSet, cohorts, members, cohort, endpointName, params=NULL, ...)
+setGeneric("cohortClient", function(OpencgaR, annotationSet, members, cohort, cohorts, endpointName, params=NULL, ...)
     standardGeneric("cohortClient"))
 
 # ##############################################################################
@@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-setGeneric("clinicalClient", function(OpencgaR, interpretation, members, interpretations, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...)
+setGeneric("clinicalClient", function(OpencgaR, clinicalAnalyses, interpretation, clinicalAnalysis, interpretations, members, endpointName, params=NULL, ...)
     standardGeneric("clinicalClient"))
 
 # ##############################################################################

opencga-client/src/main/R/R/Clinical-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -58,7 +58,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretation, members, interpretations, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) {
+setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalyses, interpretation, clinicalAnalysis, interpretations, members, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update:

opencga-client/src/main/R/R/Cohort-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohorts, members, cohort, endpointName, params=NULL, ...) {
+setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, members, cohort, cohorts, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update:

opencga-client/src/main/R/R/Family-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -38,7 +38,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("familyClient", "OpencgaR", function(OpencgaR, families, family, annotationSet, members, endpointName, params=NULL, ...) {
+setMethod("familyClient", "OpencgaR", function(OpencgaR, family, members, families, annotationSet, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/families/acl/{members}/update:

opencga-client/src/main/R/R/File-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -54,7 +54,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, annotationSet, files, file, endpointName, params=NULL, ...) {
+setMethod("fileClient", "OpencgaR", function(OpencgaR, folder, annotationSet, file, members, files, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/files/acl/{members}/update:

opencga-client/src/main/R/R/GA4GH-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Individual-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, individuals, annotationSet, members, endpointName, params=NULL, ...) {
+setMethod("individualClient", "OpencgaR", function(OpencgaR, individuals, members, individual, annotationSet, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update:

opencga-client/src/main/R/R/Job-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -40,7 +40,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("jobClient", "OpencgaR", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) {
+setMethod("jobClient", "OpencgaR", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update:

opencga-client/src/main/R/R/Meta-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Operation-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Panel-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Project-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Sample-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-09-01
+#    Autogenerated on: 2023-09-08
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, sample, samples, members, endpointName, params=NULL, ...) {
+setMethod("sampleClient", "OpencgaR", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: