Merge branch 'develop' into TASK-6255

Resolve conflicts by generating clients:
	opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java
	opencga-client/src/main/R/R/Clinical-methods.R

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

@@ -27,23 +27,17 @@
 import org.opencb.biodata.tools.alignment.BamUtils;
 import org.opencb.cellbase.client.rest.CellBaseClient;
 import org.opencb.cellbase.client.rest.GeneClient;
-import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.analysis.StorageManager;
 import org.opencb.opencga.analysis.models.FileInfo;
 import org.opencb.opencga.analysis.models.StudyInfo;
-import org.opencb.opencga.analysis.tools.ToolRunner;
 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.api.ParamConstants;
-import org.opencb.opencga.core.exceptions.ToolException;
-import org.opencb.opencga.core.models.alignment.AlignmentIndexParams;
-import org.opencb.opencga.core.models.alignment.CoverageIndexParams;
 import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.file.File;
 import org.opencb.opencga.core.models.project.Project;
@@ -70,6 +64,7 @@ public class AlignmentStorageManager extends StorageManager {
 
     private AlignmentStorageEngine alignmentStorageEngine;
     private String jobId;
+    private boolean dryRun;
 
     private static final Map<String, String> statsMap = new HashMap<>();
 
@@ -82,12 +77,13 @@ public AlignmentStorageManager(CatalogManager catalogManager, StorageEngineFacto
         initStatsMap();
     }
 
-    public AlignmentStorageManager(CatalogManager catalogManager, StorageEngineFactory storageEngineFactory, String jobId) {
+    public AlignmentStorageManager(CatalogManager catalogManager, StorageEngineFactory storageEngineFactory, String jobId, boolean dryRun) {
         super(catalogManager, storageEngineFactory);
 
         // TODO: Create this alignmentStorageEngine by reflection
         this.alignmentStorageEngine = new LocalAlignmentStorageEngine();
         this.jobId = jobId;
+        this.dryRun = dryRun;
 
         initStatsMap();
     }

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

@@ -120,7 +120,8 @@ protected void run() throws ToolException {
 
                     OpenCGAResult<Job> flagStatsJobResult = catalogManager.getJobManager()
                             .submit(study, AlignmentFlagStatsAnalysis.ID, Enums.Priority.MEDIUM, params, null, "Job generated by "
-                                    + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(), token);
+                                    + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(), getJobId(), null,
+                                    false, token);
                     flagStatsJobId = flagStatsJobResult.first().getId();
                     addEvent(Event.Type.INFO, "Submit job " +  flagStatsJobId + " to compute stats (" + AlignmentFlagStatsAnalysis.ID
                             + ")");
@@ -137,7 +138,8 @@ protected void run() throws ToolException {
 
                     OpenCGAResult<Job> statsJobResult = catalogManager.getJobManager()
                             .submit(study, AlignmentStatsAnalysis.ID, Enums.Priority.MEDIUM, params, null, "Job generated by "
-                                    + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(), token);
+                                    + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(), getJobId(), null,
+                                    false, token);
                     statsJobId = statsJobResult.first().getId();
                     addEvent(Event.Type.INFO, "Submit job " + statsJobId + " to compute stats (" + AlignmentStatsAnalysis.ID + ")");
                 }
@@ -154,7 +156,7 @@ protected void run() throws ToolException {
                     OpenCGAResult<Job> fastQcMetricsJobResult = catalogManager.getJobManager()
                             .submit(study, AlignmentFastQcMetricsAnalysis.ID, Enums.Priority.MEDIUM, params, null,
                                     "Job generated by " + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(),
-                                    token);
+                                    getJobId(), null, false, token);
                     fastQcMetricsJobId = fastQcMetricsJobResult.first().getId();
                     addEvent(Event.Type.INFO, "Submit job " + fastQcMetricsJobId + " to compute FastQC metrics ("
                             + AlignmentFastQcMetricsAnalysis.ID + ")");

opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/ClinicalTsvAnnotationLoader.java

@@ -32,7 +32,7 @@
 import java.util.Collections;
 
 @Tool(id = ClinicalTsvAnnotationLoader.ID, resource = Enums.Resource.CLINICAL_ANALYSIS, type = Tool.Type.OPERATION,
-        description = "Load annotations from TSV file.")
+        description = "Load annotations from TSV file.", priority = Enums.Priority.HIGH)
 public class ClinicalTsvAnnotationLoader extends TsvAnnotationLoader {
     public final static String ID = "clinical-tsv-load";
 

opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/rga/AuxiliarRgaAnalysis.java

@@ -7,7 +7,7 @@
 import org.opencb.opencga.core.tools.annotations.Tool;
 
 @Tool(id = AuxiliarRgaAnalysis.ID, resource = Enums.Resource.RGA, type = Tool.Type.OPERATION,
-        description = AuxiliarRgaAnalysis.DESCRIPTION)
+        description = AuxiliarRgaAnalysis.DESCRIPTION, priority = Enums.Priority.HIGH)
 public class AuxiliarRgaAnalysis extends OperationTool {
     public final static String ID = "rga-aux-index";
     public final static String DESCRIPTION = ParamConstants.INDEX_AUXILIAR_COLLECTION_DESCRIPTION;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/rga/RgaAnalysis.java

@@ -6,7 +6,8 @@
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.tools.annotations.Tool;
 
-@Tool(id = RgaAnalysis.ID, resource = Enums.Resource.RGA, type = Tool.Type.OPERATION, description = "Index RGA study.")
+@Tool(id = RgaAnalysis.ID, resource = Enums.Resource.RGA, type = Tool.Type.OPERATION, description = "Index RGA study.",
+        priority = Enums.Priority.HIGH)
 public class RgaAnalysis extends OperationTool {
     public final static String ID = "rga-index";
     public final static String DESCRIPTION = "Generate Recessive Gene Analysis secondary index";

opencga-analysis/src/main/java/org/opencb/opencga/analysis/cohort/CohortTsvAnnotationLoader.java

@@ -25,7 +25,7 @@
 import org.opencb.opencga.core.tools.annotations.Tool;
 
 @Tool(id = CohortTsvAnnotationLoader.ID, resource = Enums.Resource.COHORT, type = Tool.Type.OPERATION,
-        description = "Load annotations from TSV file.")
+        description = "Load annotations from TSV file.", priority = Enums.Priority.HIGH)
 public class CohortTsvAnnotationLoader extends TsvAnnotationLoader {
     public final static String ID = "cohort-tsv-load";
 

opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/FamilyTsvAnnotationLoader.java

@@ -25,7 +25,7 @@
 import org.opencb.opencga.core.tools.annotations.Tool;
 
 @Tool(id = FamilyTsvAnnotationLoader.ID, resource = Enums.Resource.FAMILY, type = Tool.Type.OPERATION,
-        description = "Load annotations from TSV file.")
+        description = "Load annotations from TSV file.", priority = Enums.Priority.HIGH)
 public class FamilyTsvAnnotationLoader extends TsvAnnotationLoader {
     public final static String ID = "family-tsv-load";
 

opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FetchAndRegisterTask.java

@@ -46,7 +46,7 @@
 import java.util.List;
 
 @Tool(id = FetchAndRegisterTask.ID, resource = Enums.Resource.FILE, type = Tool.Type.OPERATION,
-        description = "Download an external file and register it in OpenCGA.")
+        description = "Download an external file and register it in OpenCGA.", priority = Enums.Priority.HIGH)
 public class FetchAndRegisterTask extends OpenCgaToolScopeStudy {
 
     public final static String ID = "files-fetch";

opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FileDeleteTask.java

@@ -42,7 +42,8 @@
 import java.io.IOException;
 import java.util.*;
 
-@Tool(id = FileDeleteTask.ID, resource = Enums.Resource.FILE, type = Tool.Type.OPERATION, description = "Delete files.")
+@Tool(id = FileDeleteTask.ID, resource = Enums.Resource.FILE, type = Tool.Type.OPERATION, description = "Delete files.",
+        priority = Enums.Priority.HIGH)
 public class FileDeleteTask extends OpenCgaTool {
 
     public final static String ID = "files-delete";

opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FileLinkTask.java

@@ -18,7 +18,8 @@
 import java.util.List;
 import java.util.Map;
 
-@Tool(id = FileLinkTask.ID, resource = Enums.Resource.FILE, type = Tool.Type.OPERATION, description = FileLinkTask.DESCRIPTION)
+@Tool(id = FileLinkTask.ID, resource = Enums.Resource.FILE, type = Tool.Type.OPERATION, description = FileLinkTask.DESCRIPTION,
+        priority = Enums.Priority.HIGH)
 public class FileLinkTask extends OpenCgaToolScopeStudy {
 
     public static final String ID = "file-link";
@@ -69,7 +70,7 @@ protected void run() throws Exception {
             Job postLinkJob = catalogManager.getJobManager()
                     .submit(getStudy(), PostLinkSampleAssociation.ID, Enums.Priority.MEDIUM, params, null,
                             "Job generated by " + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(),
-                            getToken()).first();
+                            getJobId(), null, false, getToken()).first();
             logger.info("Submit post-link job : " + postLinkJob.getId());
         }
     }

opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FileTsvAnnotationLoader.java

@@ -32,7 +32,7 @@
 import java.util.Collections;
 
 @Tool(id = FileTsvAnnotationLoader.ID, resource = Enums.Resource.FILE, type = Tool.Type.OPERATION,
-        description = "Load annotations from TSV file.")
+        description = "Load annotations from TSV file.", priority = Enums.Priority.HIGH)
 public class FileTsvAnnotationLoader extends TsvAnnotationLoader {
     public final static String ID = "file-tsv-load";
 

opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FileUnlinkTask.java

@@ -38,7 +38,8 @@
 
 import java.util.*;
 
-@Tool(id = FileUnlinkTask.ID, resource = Enums.Resource.FILE, type = Tool.Type.OPERATION, description = "Unlink files.")
+@Tool(id = FileUnlinkTask.ID, resource = Enums.Resource.FILE, type = Tool.Type.OPERATION, description = "Unlink files.",
+        priority = Enums.Priority.HIGH)
 public class FileUnlinkTask extends OpenCgaTool {
 
     public final static String ID = "files-unlink";

opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/PostLinkSampleAssociation.java

@@ -24,7 +24,7 @@
 import java.util.*;
 
 @Tool(id = PostLinkSampleAssociation.ID, resource = Enums.Resource.FILE, type = Tool.Type.OPERATION,
-        description = PostLinkSampleAssociation.DESCRIPTION)
+        description = PostLinkSampleAssociation.DESCRIPTION, priority = Enums.Priority.HIGH)
 public class PostLinkSampleAssociation extends OpenCgaToolScopeStudy {
 
     public static final String ID = "postlink";

opencga-analysis/src/main/java/org/opencb/opencga/analysis/individual/IndividualTsvAnnotationLoader.java

@@ -25,7 +25,7 @@
 import org.opencb.opencga.core.tools.annotations.Tool;
 
 @Tool(id = IndividualTsvAnnotationLoader.ID, resource = Enums.Resource.INDIVIDUAL, type = Tool.Type.OPERATION,
-        description = "Load annotations from TSV file.")
+        description = "Load annotations from TSV file.", priority = Enums.Priority.HIGH)
 public class IndividualTsvAnnotationLoader extends TsvAnnotationLoader {
     public final static String ID = "individual-tsv-load";
 

opencga-analysis/src/main/java/org/opencb/opencga/analysis/sample/SampleTsvAnnotationLoader.java

@@ -25,7 +25,7 @@
 import org.opencb.opencga.core.tools.annotations.Tool;
 
 @Tool(id = SampleTsvAnnotationLoader.ID, resource = Enums.Resource.SAMPLE, type = Tool.Type.OPERATION,
-        description = "Load annotations from TSV file.")
+        description = "Load annotations from TSV file.", priority = Enums.Priority.HIGH)
 public class SampleTsvAnnotationLoader extends TsvAnnotationLoader {
     public final static String ID = "sample-tsv-load";
 

opencga-analysis/src/main/java/org/opencb/opencga/analysis/sample/qc/SampleQcAnalysis.java

@@ -225,7 +225,8 @@ protected void run() throws ToolException {
 
                     OpenCGAResult<Job> variantStatsJobResult = catalogManager.getJobManager()
                             .submit(study, SampleVariantStatsAnalysis.ID, Enums.Priority.MEDIUM, params, null, "Job generated by "
-                                    + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(), token);
+                                    + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(), getJobId(), null,
+                                    false, token);
                     variantStatsJobId = variantStatsJobResult.first().getId();
                     addEvent(Event.Type.INFO, "Submit job " + variantStatsJobId + " to compute stats (" + SampleVariantStatsAnalysis.ID
                             + ")");
@@ -267,7 +268,8 @@ protected void run() throws ToolException {
 
                     OpenCGAResult<Job> signatureJobResult = catalogManager.getJobManager()
                             .submit(getStudy(), MutationalSignatureAnalysis.ID, Enums.Priority.MEDIUM, params, null, "Job generated by "
-                                    + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(), token);
+                                    + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(), getJobId(), null,
+                                    false, token);
                     signatureJobId = signatureJobResult.first().getId();
                     logger.info("Submitted job {} to compute the mutational signature analysis {}", signatureJobId,
                             MutationalSignatureAnalysis.ID);
@@ -289,7 +291,7 @@ protected void run() throws ToolException {
                     OpenCGAResult<Job> genomePlotJobResult = catalogManager.getJobManager()
                             .submit(getStudy(), GenomePlotAnalysis.ID, Enums.Priority.MEDIUM, params, null,
                                     "Job generated by " + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(),
-                                    token);
+                                    getJobId(), null, false, token);
                     genomePlotJobId = genomePlotJobResult.first().getId();
                     addEvent(Event.Type.INFO, "Submit job " + genomePlotJobId + " to compute genome plot (" + GenomePlotAnalysis.ID
                             + ")");

opencga-analysis/src/main/java/org/opencb/opencga/analysis/templates/TemplateRunner.java

@@ -15,7 +15,7 @@
 import java.nio.file.Paths;
 
 @Tool(id = TemplateRunner.ID, description = TemplateRunner.DESCRIPTION, type = Tool.Type.OPERATION, resource = Enums.Resource.STUDY,
-        scope = Tool.Scope.STUDY)
+        scope = Tool.Scope.STUDY, priority = Enums.Priority.HIGH)
 public class TemplateRunner extends OperationTool {
 
     public static final String ID = "templates";

opencga-analysis/src/main/java/org/opencb/opencga/analysis/tools/OpenCgaTool.java

@@ -67,6 +67,7 @@ public abstract class OpenCgaTool {
 
     private String jobId;
     private String opencgaHome;
+    private boolean dryRun;
     protected String token;
 
     protected final ObjectMap params;
@@ -92,19 +93,20 @@ public OpenCgaTool() {
     }
 
     public final OpenCgaTool setUp(String opencgaHome, CatalogManager catalogManager, StorageEngineFactory engineFactory,
-                                   ObjectMap params, Path outDir, String jobId, String token) {
+                                   ObjectMap params, Path outDir, String jobId, boolean dryRun, String token) {
         VariantStorageManager manager = new VariantStorageManager(catalogManager, engineFactory);
-        return setUp(opencgaHome, catalogManager, manager, params, outDir, jobId, token);
+        return setUp(opencgaHome, catalogManager, manager, params, outDir, jobId, dryRun, token);
     }
 
     public final OpenCgaTool setUp(String opencgaHome, CatalogManager catalogManager, VariantStorageManager variantStorageManager,
-                                   ObjectMap params, Path outDir, String jobId, String token) {
+                                   ObjectMap params, Path outDir, String jobId, boolean dryRun, String token) {
         this.opencgaHome = opencgaHome;
         this.catalogManager = catalogManager;
         this.configuration = catalogManager.getConfiguration();
         this.variantStorageManager = variantStorageManager;
         this.storageConfiguration = variantStorageManager.getStorageConfiguration();
         this.jobId = jobId;
+        this.dryRun = dryRun;
         this.token = token;
         if (params != null) {
             this.params.putAll(params);
@@ -188,13 +190,14 @@ public final ExecutionResult start() throws ToolException {
                 exception = e;
             }
             if (!erm.isClosed()) {
-                privateLogger.error("Unexpected system shutdown!");
+                String message = "Unexpected system shutdown. Job killed by the system.";
+                privateLogger.error(message);
                 try {
                     if (scratchDir != null) {
                         deleteScratchDirectory();
                     }
                     if (exception == null) {
-                        exception = new RuntimeException("Unexpected system shutdown");
+                        exception = new RuntimeException(message);
                     }
                     logException(exception);
                     ExecutionResult result = erm.close(exception);
@@ -243,21 +246,32 @@ public final ExecutionResult start() throws ToolException {
             try {
                 currentStep = "check";
                 privateCheck();
-                check();
-                currentStep = null;
-                erm.setSteps(getSteps());
-                run();
+                if (dryRun) {
+                    logger.info("Dry run enabled. Sleep for 5 seconds and skip execution.");
+                    Thread.sleep(5000);
+                } else {
+                    currentStep = null;
+                    erm.setSteps(getSteps());
+                    run();
+                }
             } catch (ToolException e) {
                 throw e;
             } catch (Exception e) {
                 throw new ToolException(e);
             }
+            Runtime.getRuntime().removeShutdownHook(hook);
         } catch (Throwable e) {
             exception = e;
+            // Do not use a finally block to remove shutdownHook, as finally blocks will be executed even if the JVM is killed,
+            // and this would throw IllegalStateException("Shutdown in progress");
+            try {
+                Runtime.getRuntime().removeShutdownHook(hook);
+            } catch (Exception e1) {
+                e.addSuppressed(e1);
+            }
             throw e;
         } finally {
             deleteScratchDirectory();
-            Runtime.getRuntime().removeShutdownHook(hook);
             stopMemoryMonitor();
             result = erm.close(exception);
             logException(exception);
@@ -308,6 +322,7 @@ private void privateCheck() throws Exception {
         if (toolParams != null) {
             toolParams.updateParams(getParams());
         }
+        check();
     }
 
     /**