catalog: add organizationId to some managers, #TASK-4389

opencb · Aug 28, 2023 · 1de04f2 · 1de04f2
1 parent 91b5aed
commit 1de04f2
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Showing 174 changed files with 3,185 additions and 3,143 deletions.
diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisUtils.java b/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) {
@@ -36,7 +33,7 @@ public static File getBamFileBySampleId(String sampleId, String studyId, FileMan
         Query query = new Query(FileDBAdaptor.QueryParams.FORMAT.key(), File.Format.BAM)
                 .append(FileDBAdaptor.QueryParams.SAMPLE_IDS.key(), sampleId);
         try {
-            fileQueryResult = fileManager.search(studyId, query, QueryOptions.empty(), token);
+            fileQueryResult = fileManager.search(organizationId, studyId, query, QueryOptions.empty(), token);
         } catch (CatalogException e) {
             throw new ToolException(e);
         }
@@ -58,7 +55,7 @@ public static File getBamFile(String filename, String sampleId, String studyId,
 
         query.put(FileDBAdaptor.QueryParams.SAMPLE_IDS.key(), sampleId);
         try {
-            fileQueryResult = fileManager.search(studyId, query, queryOptions, token);
+            fileQueryResult = fileManager.search(organizationId, studyId, query, queryOptions, token);
         } catch (CatalogException e) {
             throw new ToolException(e);
         }
@@ -84,7 +81,7 @@ public static File getCatalogFile(String file, String studyId, FileManager fileM
 
         Query query = new Query(FileDBAdaptor.QueryParams.ID.key(), file);
 
-        fileQueryResult = fileManager.search(studyId, query, QueryOptions.empty(), token);
+        fileQueryResult = fileManager.search(organizationId, studyId, query, QueryOptions.empty(), token);
 
         // Sanity check
         if (fileQueryResult.getNumResults() == 0) {
@@ -127,7 +124,7 @@ public static Map<String, Map<String, Float>> parseRelatednessThresholds(Path th
 
     public static boolean waitFor(String jobId, String study, JobManager jobManager, String token) throws ToolException, CatalogException {
         Query query = new Query("id", jobId);
-        OpenCGAResult<Job> result = jobManager.search(study, query, QueryOptions.empty(), token);
+        OpenCGAResult<Job> result = jobManager.search(organizationId, study, query, QueryOptions.empty(), token);
         Job job = result.first();
         String status = job.getInternal().getStatus().getId();
 
@@ -137,7 +134,7 @@ public static boolean waitFor(String jobId, String study, JobManager jobManager,
             try {
                 // Sleep for 30 seconds
                 Thread.sleep(30000);
-                result = jobManager.search(study, query, QueryOptions.empty(), token);
+                result = jobManager.search(organizationId, study, query, QueryOptions.empty(), token);
                 job = result.first();
             } catch (CatalogException | InterruptedException e) {
                 new ToolException("Error waiting for job '" + jobId + "': " + e.getMessage());
@@ -149,7 +146,7 @@ public static boolean waitFor(String jobId, String study, JobManager jobManager,
 
     public static Job getJob(String jobId, String study, JobManager jobManager, String token) throws ToolException, CatalogException {
         Query query = new Query("id", jobId);
-        OpenCGAResult<Job> result = jobManager.search(study, query, QueryOptions.empty(), token);
+        OpenCGAResult<Job> result = jobManager.search(organizationId, study, query, QueryOptions.empty(), token);
         Job job = result.first();
         if (job == null) {
             new ToolException("Error getting job '" + jobId + "' from study '" + study + "'.");

diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/ResourceUtils.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/ResourceUtils.java
@@ -116,7 +116,7 @@ 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),
+        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

diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/StorageManager.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/StorageManager.java
@@ -100,13 +100,13 @@ protected StudyInfo getStudyInfo(@Nullable String studyIdStr, List<String> fileI
         StudyInfo studyInfo = new StudyInfo().setSessionId(sessionId);
 
         String userId = catalogManager.getUserManager().getUserId(sessionId);
-        Study study = catalogManager.getStudyManager().get(studyIdStr, QueryOptions.empty(), sessionId).first();
+        Study study = catalogManager.getStudyManager().get(organizationId, studyIdStr, QueryOptions.empty(), sessionId).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(organizationId, studyIdStr, fileIdStrs, null, sessionId);
             files = queryResult.getResults();
         }
         List<FileInfo> fileInfos = new ArrayList<>(fileIdStrs.size());
@@ -130,12 +130,12 @@ 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),
+        Project project = catalogManager.getProjectManager().search(organizationId, new Query(ProjectDBAdaptor.QueryParams.FQN.key(), projectFqn),
                 new QueryOptions(), sessionId).first();
         studyInfo.setProjectUid(project.getUid());
         studyInfo.setProjectId(project.getId());
         studyInfo.setOrganism(project.getOrganism());
-        String user = catalogManager.getProjectManager().getOwner(project.getUid());
+        String user = catalogManager.getProjectManager().getOwner(organizationId, project.getUid());
         studyInfo.setUserId(user);
 
         Map<File.Bioformat, DataStore> dataStores = new HashMap<>();

diff --git a/...alysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentCoverageAnalysis.java b/...alysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentCoverageAnalysis.java
@@ -65,7 +65,7 @@ protected void check() throws Exception {
         OpenCGAResult<File> fileResult;
         try {
             logger.info("{}: checking file {}", ID, coverageParams.getFile());
-            fileResult = catalogManager.getFileManager().get(getStudy(), coverageParams.getFile(), QueryOptions.empty(), getToken());
+            fileResult = catalogManager.getFileManager().get(organizationId, getStudy(), coverageParams.getFile(), QueryOptions.empty(), getToken());
         } catch (CatalogException e) {
             throw new ToolException("Error accessing file '" + coverageParams.getFile() + "' of the study " + getStudy() + "'", e);
         }
@@ -143,7 +143,7 @@ protected void run() throws Exception {
             Path outputCatalogPath = Paths.get(bamCatalogFile.getPath()).getParent().resolve(outputPath.getFileName());
             OpenCGAResult<File> fileResult;
             try {
-                fileResult = catalogManager.getFileManager().get(getStudy(), outputCatalogPath.toString(), QueryOptions.empty(),
+                fileResult = catalogManager.getFileManager().get(organizationId, getStudy(), outputCatalogPath.toString(), QueryOptions.empty(),
                         getToken());
                 if (fileResult.getNumResults() <= 0) {
                     isLinked = false;

diff --git a/...analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentIndexOperation.java b/...analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentIndexOperation.java
@@ -50,7 +50,7 @@ protected void check() throws Exception {
 
         OpenCGAResult<File> fileResult;
         try {
-            fileResult = catalogManager.getFileManager().get(getStudy(), inputFile, QueryOptions.empty(), token);
+            fileResult = catalogManager.getFileManager().get(organizationId, getStudy(), inputFile, QueryOptions.empty(), token);
         } catch (CatalogException e) {
             throw new ToolException("Error accessing file '" + inputFile + "' of the study " + study + "'", e);
         }
@@ -96,7 +96,7 @@ protected void run() throws Exception {
             Path outputCatalogPath = Paths.get(inputCatalogFile.getPath()).getParent().resolve(outputPath.getFileName());
             OpenCGAResult<File> fileResult;
             try {
-                fileResult = catalogManager.getFileManager().get(getStudy(), outputCatalogPath.toString(), QueryOptions.empty(), token);
+                fileResult = catalogManager.getFileManager().get(organizationId, getStudy(), outputCatalogPath.toString(), QueryOptions.empty(), token);
                 if (fileResult.getNumResults() <= 0) {
                     isLinked = false;
                 }

diff --git a/...analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java b/...analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java
@@ -221,7 +221,7 @@ public OpenCGAResult<GeneCoverageStats> coverageStats(String studyIdStr, String
 
         // 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) {
@@ -439,7 +439,7 @@ public List<Region> mergeRegions(List<Region> regions, List<String> genes, boole
 
         // 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);
@@ -537,7 +537,7 @@ public Map<String, List<Region>> getExonRegionsPerTranscript(String geneName, Ce
     }
 
     private File extractAlignmentOrCoverageFile(String studyIdStr, String fileIdStr, String sessionId) throws CatalogException {
-        OpenCGAResult<File> fileResult = catalogManager.getFileManager().get(studyIdStr, fileIdStr, QueryOptions.empty(), sessionId);
+        OpenCGAResult<File> fileResult = catalogManager.getFileManager().get(organizationId, studyIdStr, fileIdStr, QueryOptions.empty(), sessionId);
         if (fileResult.getNumResults() == 0) {
             throw new CatalogException("File " + fileIdStr + " not found");
         }
@@ -583,7 +583,7 @@ private Path getFilePath(long fileId, String sessionId) throws CatalogException,
     private Path getWorkspace(long studyId, String sessionId) throws CatalogException, IOException {
         // Obtain the study uri
         QueryOptions studyOptions = new QueryOptions(QueryOptions.INCLUDE, FileDBAdaptor.QueryParams.URI.key());
-        OpenCGAResult<Study> studyResult = catalogManager.getStudyManager().get(String.valueOf((Long) studyId), studyOptions, sessionId);
+        OpenCGAResult<Study> studyResult = catalogManager.getStudyManager().get(organizationId, String.valueOf((Long) studyId), studyOptions, sessionId);
         if (studyResult .getNumResults() != 1) {
             logger.error("Critical error: Study {} not found in catalog.", studyId);
             throw new CatalogException("Critical error: Study " + studyId + " not found in catalog");

diff --git a/...rc/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentFastQcMetricsAnalysis.java b/...rc/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;
@@ -70,7 +67,7 @@ protected void check() throws Exception {
 
         Query query = new Query(FileDBAdaptor.QueryParams.ID.key(), analysisParams.getFile());
         query.put(FileDBAdaptor.QueryParams.FORMAT.key(), File.Format.BAM);
-        OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(getStudy(), query, QueryOptions.empty(), token);
+        OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(organizationId, getStudy(), query, QueryOptions.empty(), token);
         if (fileResult.getNumResults() != 1) {
             throw new ToolException("File " + analysisParams.getFile() + " must be a BAM file in study " + getStudy());
         }

diff --git a/...is/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentFlagStatsAnalysis.java b/...is/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;
@@ -74,7 +72,7 @@ protected void check() throws Exception {
 
         Query query = new Query(FileDBAdaptor.QueryParams.ID.key(), analysisParams.getFile());
         query.put(FileDBAdaptor.QueryParams.FORMAT.key(), File.Format.BAM);
-        OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(getStudy(), query, QueryOptions.empty(), token);
+        OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(organizationId, getStudy(), query, QueryOptions.empty(), token);
         if (fileResult.getNumResults() != 1) {
             throw new ToolException("File " + analysisParams.getFile() + " must be a BAM file in study " + getStudy());
         }

diff --git a/...-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentQcAnalysis.java b/...-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;
@@ -241,7 +240,7 @@ private boolean waitFor(String jobId) throws ToolException {
         Query query = new Query("id", jobId);
         OpenCGAResult<Job> result = null;
         try {
-            result = catalogManager.getJobManager().search(study, query, QueryOptions.empty(), token);
+            result = catalogManager.getJobManager().search(organizationId, study, query, QueryOptions.empty(), token);
         } catch (CatalogException e) {
             new ToolException("Error waiting for job '" + jobId + "': " + e.getMessage());
         }
@@ -254,7 +253,7 @@ private boolean waitFor(String jobId) throws ToolException {
             // Sleep for 1 minute
             try {
                 Thread.sleep(60000);
-                result = catalogManager.getJobManager().search(study, query, QueryOptions.empty(), token);
+                result = catalogManager.getJobManager().search(organizationId, study, query, QueryOptions.empty(), token);
                 job = result.first();
             } catch (CatalogException | InterruptedException e) {
                 new ToolException("Error waiting for job '" + jobId + "': " + e.getMessage());
@@ -269,7 +268,7 @@ private Job getJob(String jobId) {
         Job job = null;
         try {
             Query query = new Query("id", jobId);
-            OpenCGAResult<Job> result = catalogManager.getJobManager().search(study, query, QueryOptions.empty(), token);
+            OpenCGAResult<Job> result = catalogManager.getJobManager().search(organizationId, study, query, QueryOptions.empty(), token);
             job = result.first();
         } catch (CatalogException e) {
             new ToolException("Error getting job '" + jobId + "' from catalog: " + e.getMessage());

diff --git a/...alysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentStatsAnalysis.java b/...alysis/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;
@@ -77,7 +73,7 @@ protected void check() throws Exception {
 
         Query query = new Query(FileDBAdaptor.QueryParams.ID.key(), analysisParams.getFile());
         query.put(FileDBAdaptor.QueryParams.FORMAT.key(), File.Format.BAM);
-        OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(getStudy(), query, QueryOptions.empty(), token);
+        OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(organizationId, getStudy(), query, QueryOptions.empty(), token);
         if (fileResult.getNumResults() != 1) {
             throw new ToolException("File " + analysisParams.getFile() + " must be a BAM file in study " + getStudy());
         }

diff --git a/...a-analysis/src/main/java/org/opencb/opencga/analysis/annotations/TsvAnnotationLoader.java b/...a-analysis/src/main/java/org/opencb/opencga/analysis/annotations/TsvAnnotationLoader.java
@@ -73,13 +73,13 @@ public void setStudy(String study) {
     protected void check() throws Exception {
         String userId = catalogManager.getUserManager().getUserId(token);
 
-        OpenCGAResult<File> fileResult = catalogManager.getFileManager().get(study, path, FileManager.INCLUDE_FILE_URI_PATH, token);
+        OpenCGAResult<File> fileResult = catalogManager.getFileManager().get(organizationId, study, path, FileManager.INCLUDE_FILE_URI_PATH, token);
         if (fileResult.getNumResults() == 0) {
             throw new ToolException("File '" + path + "' not found");
         }
         filePath = Paths.get(fileResult.first().getUri());
 
-        OpenCGAResult<VariableSet> variableSetResult = catalogManager.getStudyManager().getVariableSet(study, variableSetId,
+        OpenCGAResult<VariableSet> variableSetResult = catalogManager.getStudyManager().getVariableSet(organizationId, study, variableSetId,
                 QueryOptions.empty(), token);
         if (variableSetResult.getNumResults() == 0) {
             throw new ToolException("Variable set '" + variableSetId + "' not found");