TASK-7097 - Port Patch 3.3.0 -> 4.0.0 Xetabase 2.3.0 -> 3.0.0

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomUsersCommandExecutor.java

@@ -77,7 +77,7 @@ public RestResponse<AuthenticationResponse> login(CustomUsersCommandOptions.Logi
                 String token = session.getSession().getToken();
                 String errorMsg = "Missing password. ";
                 if (StringUtils.isNotEmpty(token)) {
-                    errorMsg += "Active token detected ";
+                    errorMsg += "Active token detected. Please logout first.";
                 }
                 CommandLineUtils.error(errorMsg);
             }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/processors/CommandProcessor.java

@@ -136,9 +136,13 @@ private boolean checkAutoRefresh(OpencgaCommandExecutor commandExecutor) {
 
     public void loadSessionStudies(OpencgaCommandExecutor commandExecutor) {
         Session session = commandExecutor.getSessionManager().getSession();
-        logger.debug("Loading session studies using token: "
-                + session.getToken());
         OpenCGAClient openCGAClient = commandExecutor.getOpenCGAClient();
+        logger.debug("openCGAClient Token: " + openCGAClient.getToken());
+        if(StringUtils.isEmpty(openCGAClient.getToken())) {
+            openCGAClient.setToken(session.getToken());
+        }
+        logger.debug("Loading session studies using token: "
+                + openCGAClient.getToken());
         try {
             // Query the server to retrieve the studies of user projects
             RestResponse<Project> res = openCGAClient.getProjectClient().search(new ObjectMap());

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_5/storage/DetectIllegalConcurrentFileLoadingsMigration.java

@@ -1,5 +1,6 @@
 package org.opencb.opencga.app.migrations.v2.v2_12_5.storage;
 
+import org.apache.commons.lang3.tuple.Pair;
 import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
@@ -67,6 +68,8 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag
         if (fileSets.isEmpty()) {
             logger.info("No concurrent file loadings found in study '{}'", study);
             return;
+        } else {
+            logger.info("Found {} sets of files with shared samples in study '{}'", fileSets.size(), study);
         }
 
         Map<Integer, TaskMetadata> fileTasks = new HashMap<>();
@@ -85,10 +88,12 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag
             }
         }
 
-        Set<Set<Integer>> fileSetsToInvalidate = new HashSet<>();
-        Set<Integer> affectedFiles = new HashSet<>();
-        Set<Integer> affectedSamples = new HashSet<>();
         for (Set<Integer> fileSet : fileSets) {
+            Set<Integer> affectedFiles = new HashSet<>();
+            Set<Integer> affectedSamples = new HashSet<>();
+            Set<Integer> invalidFiles = new HashSet<>();
+            Set<Integer> invalidSampleIndexes = new HashSet<>();
+
             // Check if any task from this file set overlaps in time
             List<TaskMetadata> tasks = new ArrayList<>();
             for (Integer fileId : fileSet) {
@@ -97,8 +102,11 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag
                     tasks.add(task);
                 }
             }
-            if (tasks.size() > 1) {
-                logger.info("Found {} tasks loading files {}", tasks.size(), fileSet);
+            if (tasks.size() <= 1) {
+                continue;
+            } else {
+                logger.info("--------------------");
+                logger.info("Found {} tasks loading files {} in study {}", tasks.size(), fileSet, study);
                 for (int i = 0; i < tasks.size(); i++) {
                     TaskMetadata task1 = tasks.get(i);
                     Date task1start = task1.getStatus().firstKey();
@@ -108,8 +116,7 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag
                         Date task2start = task2.getStatus().firstKey();
                         Date task2end = task2.getStatus().lastKey();
                         if (task1start.before(task2end) && task1end.after(task2start)) {
-                            fileSetsToInvalidate.add(fileSet);
-                            affectedFiles.addAll(task1.getFileIds());
+                            affectedFiles.addAll(fileSet);
 
                             List<String> task1Files = task1.getFileIds().stream().map(fileId -> "'" + metadataManager.getFileName(studyId, fileId) + "'(" + fileId + ")").collect(Collectors.toList());
                             List<String> task2Files = task2.getFileIds().stream().map(fileId -> "'" + metadataManager.getFileName(studyId, fileId) + "'(" + fileId + ")").collect(Collectors.toList());
@@ -131,8 +138,6 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag
                 }
             }
 
-            Set<Integer> invalidFiles = new HashSet<>();
-            List<Integer> invalidSampleIndexes = new ArrayList<>();
             for (Integer sampleId : affectedSamples) {
                 String sampleName = metadataManager.getSampleName(studyId, sampleId);
                 SampleMetadata sampleMetadata = metadataManager.getSampleMetadata(studyId, sampleId);
@@ -145,7 +150,7 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag
                                     metadataManager.getFileName(studyId, file), file);
                         }
                     }
-                } else if (sampleMetadata.getSampleIndexStatus(Optional.of(sampleMetadata.getSampleIndexVersion()).orElse(-1)) == TaskMetadata.Status.READY) {
+                } else if (sampleMetadata.getSampleIndexStatus(Optional.ofNullable(sampleMetadata.getSampleIndexVersion()).orElse(-1)) == TaskMetadata.Status.READY) {
                     for (Integer fileId : sampleMetadata.getFiles()) {
                         if (affectedFiles.contains(fileId)) {
                             FileMetadata fileMetadata = metadataManager.getFileMetadata(studyId, fileId);
@@ -195,6 +200,8 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag
                         }
                     }
                 } else {
+                    logger.info("Sample '{}'({}) sample index is not in READY status. Invalidate to ensure rebuild", sampleName, sampleId);
+                    logger.info(" - Invalidating sample index for sample '{}'({})", sampleName, sampleId);
                     invalidSampleIndexes.add(sampleId);
                 }
             }
@@ -210,9 +217,19 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag
                         invalidSamples.addAll(metadataManager.getSampleIdsFromFileId(studyId, fileId));
                     }
 
-                    logger.info("Affected files: {}", invalidFiles);
-                    logger.info("Affected samples: {}", invalidSamples);
-                    logger.info("Affected sample indexes: {}", invalidSampleIndexes);
+                    logger.info("Study '{}'", study);
+                    List<Pair<String, Integer>> invalidFilesPairs = invalidFiles.stream()
+                            .map(fileId -> Pair.of(metadataManager.getFileName(studyId, fileId), fileId))
+                            .collect(Collectors.toList());
+                    logger.info("Affected files: {}", invalidFilesPairs);
+                    List<Pair<String, Integer>> invalidSamplesPairs = invalidSamples.stream()
+                            .map(sampleId -> Pair.of(metadataManager.getSampleName(studyId, sampleId), sampleId))
+                            .collect(Collectors.toList());
+                    logger.info("Affected samples: {}", invalidSamplesPairs);
+                    List<Pair<String, Integer>> invalidSampleIndexesPairs = invalidSampleIndexes.stream()
+                            .map(sampleId -> Pair.of(metadataManager.getSampleName(studyId, sampleId), sampleId))
+                            .collect(Collectors.toList());
+                    logger.info("Affected sample indexes: {}", invalidSampleIndexesPairs);
                 }
             } else {
                 ObjectMap event = new ObjectMap()

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_6/SyncCohortsAndSamplesMigration.java

@@ -9,20 +9,24 @@
 import org.bson.conversions.Bson;
 import org.opencb.opencga.catalog.db.api.CohortDBAdaptor;
 import org.opencb.opencga.catalog.db.api.SampleDBAdaptor;
+import org.opencb.opencga.catalog.db.api.StudyDBAdaptor;
 import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor;
 import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory;
 import org.opencb.opencga.catalog.migration.Migration;
 import org.opencb.opencga.catalog.migration.MigrationTool;
 
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.stream.Collectors;
 
 @Migration(id = "syncCohortsAndSamplesMigration" ,
-        description = "Sync array of samples from cohort with array of cohortIds from Sample",
+        description = "Sync array of samples from cohort with array of cohortIds from Sample.",
         version = "2.12.6",
         domain = Migration.MigrationDomain.CATALOG,
         language = Migration.MigrationLanguage.JAVA,
-        date = 20240621
+        date = 20240621,
+        patch = 2 // TASK-6998
 )
 public class SyncCohortsAndSamplesMigration extends MigrationTool {
 
@@ -31,8 +35,18 @@ protected void run() throws Exception {
         MongoCollection<Document> sampleCollection = getMongoCollection(OrganizationMongoDBAdaptorFactory.SAMPLE_COLLECTION);
         MongoCollection<Document> sampleArchiveCollection = getMongoCollection(OrganizationMongoDBAdaptorFactory.SAMPLE_ARCHIVE_COLLECTION);
 
+        // Fill map study uid - fqn
+        Map<Long, String> uidFqnMap = new HashMap<>();
+        Bson studyProjection = Projections.include(StudyDBAdaptor.QueryParams.UID.key(), StudyDBAdaptor.QueryParams.FQN.key());
+        queryMongo(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION, new Document(), studyProjection, study -> {
+            long studyUid = study.get(StudyDBAdaptor.QueryParams.UID.key(), Number.class).longValue();
+            String studyFqn = study.getString(StudyDBAdaptor.QueryParams.FQN.key());
+            uidFqnMap.put(studyUid, studyFqn);
+        });
+
         queryMongo(OrganizationMongoDBAdaptorFactory.COHORT_COLLECTION, new Document(),
-                Projections.include(CohortDBAdaptor.QueryParams.ID.key(), CohortDBAdaptor.QueryParams.SAMPLES.key()),
+                Projections.include(CohortDBAdaptor.QueryParams.ID.key(), CohortDBAdaptor.QueryParams.SAMPLES.key(),
+                        CohortDBAdaptor.QueryParams.STUDY_UID.key()),
                 cohortDoc -> {
                     String cohortId = cohortDoc.getString(CohortDBAdaptor.QueryParams.ID.key());
                     List<Document> samples = cohortDoc.getList(CohortDBAdaptor.QueryParams.SAMPLES.key(), Document.class);
@@ -50,8 +64,11 @@ protected void run() throws Exception {
                         long addedMissingCohort = sampleCollection.updateMany(query, update).getModifiedCount();
                         sampleArchiveCollection.updateMany(query, update);
 
+                        long studyUid = cohortDoc.get(CohortDBAdaptor.QueryParams.STUDY_UID.key(), Number.class).longValue();
+
                         // Ensure there aren't any samples pointing to this cohort that are not in the samples array
                         query = Filters.and(
+                                Filters.eq(SampleDBAdaptor.QueryParams.STUDY_UID.key(), studyUid),
                                 Filters.nin(SampleDBAdaptor.QueryParams.UID.key(), sampleUids),
                                 Filters.eq(SampleDBAdaptor.QueryParams.COHORT_IDS.key(), cohortId),
                                 Filters.eq(MongoDBAdaptor.LAST_OF_VERSION, true)
@@ -61,10 +78,10 @@ protected void run() throws Exception {
                         sampleArchiveCollection.updateMany(query, update);
 
                         if (addedMissingCohort > 0 || removedNonAssociatedCohort > 0) {
-                            logger.info("Fixed cohort '{}' references. "
+                            logger.info("Fixed cohort '{}' references from study '{}'. "
                                             + "Added missing reference to {} samples. "
                                             + "Removed non-associated reference from {} samples.",
-                                    cohortId, addedMissingCohort, removedNonAssociatedCohort);
+                                    cohortId, uidFqnMap.get(studyUid), addedMissingCohort, removedNonAssociatedCohort);
                         }
                     }
                 });

opencga-core/src/main/resources/configuration.yml

@@ -9,7 +9,7 @@ jobDir: ${OPENCGA.USER.WORKSPACE}/jobs
 # Maximum number of login attempts before banning a user account
 account:
   maxLoginAttempts: ${OPENCGA.ACCOUNT.MAX_LOGIN_ATTEMPTS}
-  passwordExpirationDays: 0
+  passwordExpirationDays: 90
 
 panel:
   host: "http://resources.opencb.org/opencb/opencga/disease-panels"

opencga-server/src/main/java/org/opencb/opencga/server/rest/OpenCGAWSServer.java

@@ -882,7 +882,12 @@ protected DataResult<Job> submitJobRaw(String toolId, String project, String stu
                                            String jobDescription, String jobDependsOnStr, String jobTagsStr, String jobScheduledStartTime,
                                            String jobPriority, Boolean dryRun)
             throws CatalogException {
-        Map<String, Object> paramsMap = bodyParams.toParams();
+        Map<String, Object> paramsMap;
+        if (bodyParams != null) {
+            paramsMap = bodyParams.toParams();
+        } else {
+            paramsMap = new HashMap<>();
+        }
         if (StringUtils.isNotEmpty(study)) {
             paramsMap.putIfAbsent(ParamConstants.STUDY_PARAM, study);
         }

opencga-server/src/main/java/org/opencb/opencga/server/rest/operations/VariantOperationWebService.java

@@ -593,7 +593,12 @@ public Response submitOperationToProject(String toolId, String project, ToolPara
     public Response submitOperation(String toolId, String project, String study, ToolParams params, String jobName, String jobDescription,
                                     String jobDependsOn, String jobTags, String jobScheduledStartTime, String jobPriority, Boolean dryRun) {
         try {
-            Map<String, Object> paramsMap = params.toParams();
+            Map<String, Object> paramsMap;
+            if (params != null) {
+                paramsMap = params.toParams();
+            } else {
+                paramsMap = new HashMap<>();
+            }
             if (StringUtils.isNotEmpty(study)) {
                 paramsMap.put(ParamConstants.STUDY_PARAM, study);
             }

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageOptions.java

@@ -81,6 +81,10 @@ public enum VariantStorageOptions implements ConfigurationOption {
     ANNOTATOR_CELLBASE_VARIANT_LENGTH_THRESHOLD("annotator.cellbase.variantLengthThreshold", Integer.MAX_VALUE),
     ANNOTATOR_CELLBASE_IMPRECISE_VARIANTS("annotator.cellbase.impreciseVariants", true),
     ANNOTATOR_CELLBASE_STAR_ALTERNATE("annotator.cellbase.starAlternate", false),
+    ANNOTATOR_EXTENSION_PREFIX("annotator.extension."),
+    ANNOTATOR_EXTENSION_LIST("annotator.extension.list"),
+    ANNOTATOR_EXTENSION_COSMIC_FILE("annotator.extension.cosmic.file"),
+    ANNOTATOR_EXTENSION_COSMIC_VERSION("annotator.extension.cosmic.version"),
 
     INDEX_SEARCH("indexSearch", false), // Build secondary indexes using search engine.
 

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/DefaultVariantAnnotationManager.java

@@ -52,6 +52,8 @@
 import org.opencb.opencga.storage.core.variant.adaptors.VariantField;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;
 import org.opencb.opencga.storage.core.variant.annotation.annotators.VariantAnnotator;
+import org.opencb.opencga.storage.core.variant.annotation.annotators.extensions.VariantAnnotatorExtensionTask;
+import org.opencb.opencga.storage.core.variant.annotation.annotators.extensions.VariantAnnotatorExtensionsFactory;
 import org.opencb.opencga.storage.core.variant.io.VariantReaderUtils;
 import org.opencb.opencga.storage.core.variant.io.db.VariantAnnotationDBWriter;
 import org.opencb.opencga.storage.core.variant.io.db.VariantDBReader;
@@ -265,6 +267,13 @@ public URI createAnnotation(URI outDir, String fileName, Query query, ObjectMap
                 return variantAnnotationList;
             };
 
+            List<VariantAnnotatorExtensionTask> extensions = new VariantAnnotatorExtensionsFactory().getVariantAnnotatorExtensions(params);
+            for (VariantAnnotatorExtensionTask extension : extensions) {
+                extension.setup(outDir);
+                extension.checkAvailable();
+                annotationTask = annotationTask.then(extension);
+            }
+
             final DataWriter<VariantAnnotation> variantAnnotationDataWriter;
             if (avro) {
                 //FIXME
@@ -286,7 +295,7 @@ public URI createAnnotation(URI outDir, String fileName, Query query, ObjectMap
             ParallelTaskRunner<Variant, VariantAnnotation> parallelTaskRunner =
                     new ParallelTaskRunner<>(variantDataReader, annotationTask, variantAnnotationDataWriter, config);
             parallelTaskRunner.run();
-        } catch (ExecutionException e) {
+        } catch (Exception e) {
             throw new VariantAnnotatorException("Error creating annotations", e);
         }
 

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/extensions/VariantAnnotatorExtensionTask.java

@@ -0,0 +1,59 @@
+package org.opencb.opencga.storage.core.variant.annotation.annotators.extensions;
+
+import org.opencb.biodata.models.variant.avro.VariantAnnotation;
+import org.opencb.commons.datastore.core.ObjectMap;
+import org.opencb.commons.run.Task;
+
+import java.net.URI;
+import java.util.List;
+
+public interface VariantAnnotatorExtensionTask extends Task<VariantAnnotation, VariantAnnotation> {
+
+    /**
+     * Set up the annotator extension.
+     * This method will be called before any other method. It might generate extra files or data needed for the annotation.
+     *
+     * @param output  Output directory where the annotator extension should write the files
+     * @return List of URIs of generated files (if any)
+     * @throws Exception if the annotator extension set up fails
+     */
+    List<URI> setup(URI output) throws Exception;
+
+    /**
+     * Check if the annotator extension is available for the given options.
+     * @throws IllegalArgumentException if the annotator extension is not available
+     */
+    void checkAvailable() throws IllegalArgumentException;
+
+    /**
+     * Check if the annotator extension is available for the given options. Do not throw any exception if the extension is not available.
+     * @return true if the annotator extension is available
+     */
+    default boolean isAvailable() {
+        try {
+            checkAvailable();
+            return true;
+        } catch (IllegalArgumentException e) {
+            return false;
+        }
+    }
+
+    @Override
+    default void pre() throws Exception {
+        Task.super.pre();
+        checkAvailable();
+    }
+
+    /**
+     * Get the options for the annotator extension.
+     * @return Options for the annotator extension
+     */
+    ObjectMap getOptions();
+
+    /**
+     * Get the metadata for the annotator extension.
+     * @return Metadata for the annotator extension
+     */
+    ObjectMap getMetadata();
+
+}