TASK-4389 - OpenCGA Catalog - Organizations

checkstyle.xml

@@ -21,7 +21,7 @@
 
 <module name="Checker">
     <module name="FileLength">
-        <property name="max" value="4100"/>
+        <property name="max" value="4500"/>
     </module>
     <module name="FileTabCharacter"/>
     <module name="NewlineAtEndOfFile"/>

opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisUtils.java

@@ -1,6 +1,5 @@
 package org.opencb.opencga.analysis;
 
-import org.opencb.biodata.models.clinical.qc.RelatednessScore;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.catalog.db.api.FileDBAdaptor;
@@ -17,8 +16,6 @@
 import java.nio.file.Path;
 import java.util.*;
 
-import static org.opencb.opencga.core.api.ParamConstants.SAMTOOLS_COMMANDS_SUPPORTED;
-
 public class AnalysisUtils {
 
     public static boolean isSupportedCommand(String commands) {

opencga-analysis/src/main/java/org/opencb/opencga/analysis/ResourceUtils.java

@@ -24,6 +24,8 @@
 import org.opencb.opencga.catalog.db.api.ProjectDBAdaptor;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.project.Project;
 import org.opencb.opencga.core.response.OpenCGAResult;
 
@@ -116,7 +118,12 @@ public static DownloadedRefGenome downloadRefGenome(String assembly, Path outDir
     public static String getAssembly(CatalogManager catalogManager, String studyId, String sessionId) throws CatalogException {
         String assembly = "";
         OpenCGAResult<Project> projectQueryResult;
-        projectQueryResult = catalogManager.getProjectManager().search(new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), studyId),
+
+        JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(sessionId);
+        CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyId, jwtPayload);
+        String organizationId = studyFqn.getOrganizationId();
+
+        projectQueryResult = catalogManager.getProjectManager().search(organizationId, new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), studyId),
                 new QueryOptions(QueryOptions.INCLUDE, ProjectDBAdaptor.QueryParams.ORGANISM.key()), sessionId);
         if (CollectionUtils.isNotEmpty(projectQueryResult.getResults())
                 && projectQueryResult.first().getOrganism() != null

opencga-analysis/src/main/java/org/opencb/opencga/analysis/StorageManager.java

@@ -24,8 +24,10 @@
 import org.opencb.opencga.catalog.db.api.ProjectDBAdaptor;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
 import org.opencb.opencga.core.config.Configuration;
 import org.opencb.opencga.core.config.storage.StorageConfiguration;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.file.File;
 import org.opencb.opencga.core.models.project.DataStore;
 import org.opencb.opencga.core.models.project.Project;
@@ -73,19 +75,6 @@ protected StorageManager(CatalogManager catalogManager, CacheManager cacheManage
         logger = LoggerFactory.getLogger(getClass());
     }
 
-
-    public void clearCache(String sessionId) throws CatalogException {
-        String userId = catalogManager.getUserManager().getUserId(sessionId);
-
-    }
-
-
-    public void clearCache(String studyId, String sessionId) throws CatalogException {
-        String userId = catalogManager.getUserManager().getUserId(sessionId);
-
-    }
-
-
     public abstract void testConnection() throws StorageEngineException;
 
     @Deprecated
@@ -95,18 +84,20 @@ protected StudyInfo getStudyInfo(@Nullable String studyIdStr, String fileIdStr,
     }
 
     @Deprecated
-    protected StudyInfo getStudyInfo(@Nullable String studyIdStr, List<String> fileIdStrs, String sessionId)
-            throws CatalogException {
-        StudyInfo studyInfo = new StudyInfo().setSessionId(sessionId);
+    protected StudyInfo getStudyInfo(@Nullable String studyIdStr, List<String> fileIdStrs, String token) throws CatalogException {
+        StudyInfo studyInfo = new StudyInfo().setSessionId(token);
+
+        JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(token);
+        CatalogFqn catalogFqn = CatalogFqn.extractFqnFromStudy(studyIdStr, jwtPayload);
+        String organizationId = catalogFqn.getOrganizationId();
 
-        String userId = catalogManager.getUserManager().getUserId(sessionId);
-        Study study = catalogManager.getStudyManager().get(studyIdStr, QueryOptions.empty(), sessionId).first();
+        Study study = catalogManager.getStudyManager().get(studyIdStr, QueryOptions.empty(), token).first();
 
         List<File> files;
         if (fileIdStrs.isEmpty()) {
             files = Collections.emptyList();
         } else {
-            DataResult<File> queryResult = catalogManager.getFileManager().get(studyIdStr, fileIdStrs, null, sessionId);
+            DataResult<File> queryResult = catalogManager.getFileManager().get(studyIdStr, fileIdStrs, null, token);
             files = queryResult.getResults();
         }
         List<FileInfo> fileInfos = new ArrayList<>(fileIdStrs.size());
@@ -130,17 +121,15 @@ protected StudyInfo getStudyInfo(@Nullable String studyIdStr, List<String> fileI
 
         studyInfo.setStudy(study);
         String projectFqn = catalogManager.getStudyManager().getProjectFqn(study.getFqn());
-        Project project = catalogManager.getProjectManager().search(new Query(ProjectDBAdaptor.QueryParams.FQN.key(), projectFqn),
-                new QueryOptions(), sessionId).first();
+        Project project = catalogManager.getProjectManager().search(organizationId, new Query(ProjectDBAdaptor.QueryParams.FQN.key(), projectFqn),
+                new QueryOptions(), token).first();
         studyInfo.setProjectUid(project.getUid());
         studyInfo.setProjectId(project.getId());
         studyInfo.setOrganism(project.getOrganism());
-        String user = catalogManager.getProjectManager().getOwner(project.getUid());
-        studyInfo.setUserId(user);
 
         Map<File.Bioformat, DataStore> dataStores = new HashMap<>();
-        dataStores.put(File.Bioformat.VARIANT, getDataStore(catalogManager, study.getFqn(), File.Bioformat.VARIANT, sessionId));
-        dataStores.put(File.Bioformat.ALIGNMENT, getDataStore(catalogManager, study.getFqn(), File.Bioformat.ALIGNMENT, sessionId));
+        dataStores.put(File.Bioformat.VARIANT, getDataStore(catalogManager, study.getFqn(), File.Bioformat.VARIANT, token));
+        dataStores.put(File.Bioformat.ALIGNMENT, getDataStore(catalogManager, study.getFqn(), File.Bioformat.ALIGNMENT, token));
         studyInfo.setDataStores(dataStores);
 
         return studyInfo;

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

@@ -30,16 +30,17 @@
 import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
-import org.opencb.commons.utils.FileUtils;
 import org.opencb.opencga.analysis.StorageManager;
 import org.opencb.opencga.analysis.models.FileInfo;
 import org.opencb.opencga.analysis.models.StudyInfo;
 import org.opencb.opencga.catalog.db.api.FileDBAdaptor;
 import org.opencb.opencga.catalog.db.api.ProjectDBAdaptor;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
 import org.opencb.opencga.catalog.utils.ParamUtils;
 import org.opencb.opencga.core.exceptions.ToolException;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.file.File;
 import org.opencb.opencga.core.models.project.Project;
 import org.opencb.opencga.core.models.study.Study;
@@ -219,9 +220,13 @@ public OpenCGAResult<GeneCoverageStats> coverageStats(String studyIdStr, String
         File file = extractAlignmentOrCoverageFile(studyIdStr, fileIdStr, token);
 //        System.out.println("file = " + file.getUri());
 
+        JwtPayload jwtPayload = new JwtPayload(token);
+        CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyIdStr, jwtPayload);
+        String organizationId = studyFqn.getOrganizationId();
+
         // Get species and assembly from catalog
         OpenCGAResult<Project> projectQueryResult = catalogManager.getProjectManager().search(
-                new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), studyIdStr),
+                organizationId, new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), studyIdStr),
                 new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(ProjectDBAdaptor.QueryParams.ORGANISM.key(),
                         ProjectDBAdaptor.QueryParams.CELLBASE.key())), token);
         if (projectQueryResult.getNumResults() != 1) {
@@ -437,9 +442,12 @@ public List<Region> mergeRegions(List<Region> regions, List<String> genes, boole
             }
         }
 
+        JwtPayload jwtPayload = new JwtPayload(token);
+        CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(study, jwtPayload);
+        String organizationId = studyFqn.getOrganizationId();
         // Get species and assembly from catalog
         OpenCGAResult<Project> projectQueryResult = catalogManager.getProjectManager().search(
-                new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), study),
+                organizationId, new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), study),
                 new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(
                         ProjectDBAdaptor.QueryParams.ORGANISM.key(),
                         ProjectDBAdaptor.QueryParams.CELLBASE.key())), token);
@@ -562,23 +570,6 @@ private void checkAlignmentBioformat(List<FileInfo> fileInfo) throws CatalogExce
     public void testConnection() throws StorageEngineException {
     }
 
-    @Deprecated
-    private Path getFilePath(long fileId, String sessionId) throws CatalogException, IOException {
-        QueryOptions fileOptions = new QueryOptions(QueryOptions.INCLUDE,
-                Arrays.asList(FileDBAdaptor.QueryParams.URI.key(), FileDBAdaptor.QueryParams.NAME.key()));
-        OpenCGAResult<File> fileResult = catalogManager.getFileManager().get(fileId, fileOptions, sessionId);
-
-        if (fileResult.getNumResults() != 1) {
-            logger.error("Critical error: File {} not found in catalog.", fileId);
-            throw new CatalogException("Critical error: File " + fileId + " not found in catalog");
-        }
-
-        Path path = Paths.get(fileResult.first().getUri().getRawPath());
-        FileUtils.checkFile(path);
-
-        return path;
-    }
-
     @Deprecated
     private Path getWorkspace(long studyId, String sessionId) throws CatalogException, IOException {
         // Obtain the study uri

opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentFastQcMetricsAnalysis.java

@@ -17,7 +17,6 @@
 package org.opencb.opencga.analysis.alignment.qc;
 
 import org.apache.commons.lang3.StringUtils;
-import org.opencb.biodata.formats.alignment.samtools.SamtoolsFlagstats;
 import org.opencb.biodata.formats.sequence.fastqc.FastQcMetrics;
 import org.opencb.biodata.formats.sequence.fastqc.io.FastQcParser;
 import org.opencb.commons.datastore.core.Query;
@@ -29,8 +28,6 @@
 import org.opencb.opencga.core.models.alignment.AlignmentFastQcMetricsParams;
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.models.file.File;
-import org.opencb.opencga.core.models.file.FileQualityControl;
-import org.opencb.opencga.core.models.file.FileUpdateParams;
 import org.opencb.opencga.core.response.OpenCGAResult;
 import org.opencb.opencga.core.tools.annotations.Tool;
 import org.opencb.opencga.core.tools.annotations.ToolParams;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentFlagStatsAnalysis.java

@@ -30,8 +30,6 @@
 import org.opencb.opencga.core.models.alignment.AlignmentFlagStatsParams;
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.models.file.File;
-import org.opencb.opencga.core.models.file.FileQualityControl;
-import org.opencb.opencga.core.models.file.FileUpdateParams;
 import org.opencb.opencga.core.response.OpenCGAResult;
 import org.opencb.opencga.core.tools.annotations.Tool;
 import org.opencb.opencga.core.tools.annotations.ToolParams;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentQcAnalysis.java

@@ -17,7 +17,6 @@
 package org.opencb.opencga.analysis.alignment.qc;
 
 import org.apache.commons.lang3.StringUtils;
-import org.opencb.biodata.formats.alignment.picard.HsMetrics;
 import org.opencb.biodata.formats.alignment.samtools.SamtoolsFlagstats;
 import org.opencb.biodata.formats.alignment.samtools.SamtoolsStats;
 import org.opencb.biodata.formats.sequence.fastqc.FastQcMetrics;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentStatsAnalysis.java

@@ -18,9 +18,7 @@
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.opencb.biodata.formats.alignment.samtools.SamtoolsFlagstats;
 import org.opencb.biodata.formats.alignment.samtools.SamtoolsStats;
-import org.opencb.biodata.formats.alignment.samtools.io.SamtoolsFlagstatsParser;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.analysis.tools.OpenCgaToolScopeStudy;
@@ -32,8 +30,6 @@
 import org.opencb.opencga.core.models.alignment.AlignmentStatsParams;
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.models.file.File;
-import org.opencb.opencga.core.models.file.FileQualityControl;
-import org.opencb.opencga.core.models.file.FileUpdateParams;
 import org.opencb.opencga.core.response.OpenCGAResult;
 import org.opencb.opencga.core.tools.annotations.Tool;
 import org.opencb.opencga.core.tools.annotations.ToolParams;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/annotations/TsvAnnotationLoader.java

@@ -26,9 +26,11 @@
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.FileManager;
 import org.opencb.opencga.catalog.utils.AnnotationUtils;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
 import org.opencb.opencga.catalog.utils.Constants;
 import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.exceptions.ToolException;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.common.AnnotationSet;
 import org.opencb.opencga.core.models.file.File;
 import org.opencb.opencga.core.models.sample.SamplePermissions;
@@ -71,7 +73,9 @@ public void setStudy(String study) {
 
     @Override
     protected void check() throws Exception {
-        String userId = catalogManager.getUserManager().getUserId(token);
+        JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(token);
+        CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(study, jwtPayload);
+        String userId = jwtPayload.getUserId(studyFqn.getOrganizationId());
 
         OpenCGAResult<File> fileResult = catalogManager.getFileManager().get(study, path, FileManager.INCLUDE_FILE_URI_PATH, token);
         if (fileResult.getNumResults() == 0) {