TASK-5513 Fix the Docker image configuration for OpenCGA analysis

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

@@ -23,6 +23,7 @@
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;
 import org.opencb.opencga.core.config.Configuration;
+import org.opencb.opencga.core.config.ConfigurationUtils;
 import org.opencb.opencga.core.exceptions.ToolExecutorException;
 import org.opencb.opencga.storage.core.StorageEngineFactory;
 

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

@@ -17,7 +17,7 @@
 package org.opencb.opencga.analysis.clinical;
 
 import org.opencb.commons.datastore.core.ObjectMap;
-import org.opencb.opencga.analysis.ConfigurationUtils;
+import org.opencb.opencga.core.config.ConfigurationUtils;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;
 import org.opencb.opencga.core.config.Configuration;

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

@@ -23,7 +23,7 @@
 import org.opencb.biodata.models.clinical.interpretation.Software;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
-import org.opencb.opencga.analysis.ConfigurationUtils;
+import org.opencb.opencga.core.config.ConfigurationUtils;
 import org.opencb.opencga.analysis.tools.OpenCgaTool;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java

@@ -38,6 +38,8 @@
 import org.opencb.opencga.core.common.GitRepositoryState;
 import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.core.common.TimeUtils;
+import org.opencb.opencga.core.config.ConfigurationUtils;
+import org.opencb.opencga.core.config.Docker;
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.models.clinical.ClinicalAnalysis;
 import org.opencb.opencga.core.models.clinical.Interpretation;
@@ -136,13 +138,21 @@ protected void run() throws ToolException {
 
     protected void saveInterpretation(String studyId, ClinicalAnalysis clinicalAnalysis) throws ToolException, StorageEngineException,
             CatalogException, IOException {
+        // Get Docker image name and version
+        String dockerImage = ConfigurationUtils.getDockerImage(Docker.EXOMISER_IMAGE_KEY, configuration);
+        String dockerVersion = "";
+        String[] split = dockerImage.split(":");
+        String dockerName = split[0];
+        if (split.length > 1) {
+            dockerVersion = split[1];
+        }
         // Interpretation method
         InterpretationMethod method = new InterpretationMethod(getId(), GitRepositoryState.getInstance().getBuildVersion(),
                 GitRepositoryState.getInstance().getCommitId(), Collections.singletonList(
                 new Software()
                         .setName("Exomiser")
-                        .setRepository("Docker: " + ExomiserWrapperAnalysisExecutor.DOCKER_IMAGE_NAME)
-                        .setVersion(ExomiserWrapperAnalysisExecutor.DOCKER_IMAGE_VERSION)));
+                        .setRepository("Docker: " + dockerName)
+                        .setVersion(dockerVersion)));
 
         // Analyst
         ClinicalAnalyst analyst = clinicalInterpretationManager.getAnalyst(studyId, token);

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

@@ -28,12 +28,9 @@
 import org.opencb.opencga.core.tools.annotations.ToolParams;
 import org.opencb.opencga.core.tools.family.PedigreeGraphAnalysisExecutor;
 
-@Tool(id = PedigreeGraphAnalysis.ID, resource = Enums.Resource.FAMILY)
+@Tool(id = PedigreeGraphAnalysisExecutor.ID, resource = Enums.Resource.FAMILY)
 public class PedigreeGraphAnalysis extends OpenCgaToolScopeStudy {
 
-    public static final String ID = "pedigree-graph";
-    public static final String DESCRIPTION = "Compute the family pedigree graph image.";
-
     @ToolParams
     private PedigreeGraphAnalysisParams pedigreeParams = new PedigreeGraphAnalysisParams();
 

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

@@ -25,6 +25,8 @@
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.utils.PedigreeGraphUtils;
 import org.opencb.opencga.core.api.ParamConstants;
+import org.opencb.opencga.core.config.ConfigurationUtils;
+import org.opencb.opencga.core.config.Docker;
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.models.family.Family;
@@ -59,11 +61,12 @@ public List<String> getSteps() {
     @Override
     protected void run() throws ToolException {
         step("pull-docker", () -> {
+            String dockerImage = ConfigurationUtils.getDockerImage(Docker.OPENCGA_EXT_TOOLS_IMAGE_KEY, configuration);
             // Be sure docker is alive and that opencga-ext-tools is downloaded
             logger.info("Checking if docker daemon is alive");
             DockerUtils.checkDockerDaemonAlive();
-            logger.info("Pulling docker '{}'", PedigreeGraphUtils.R_DOCKER_IMAGE);
-            new Command("docker pull " + PedigreeGraphUtils.R_DOCKER_IMAGE).run();
+            logger.info("Pulling docker '{}'", dockerImage);
+            new Command("docker pull " + dockerImage).run();
         });
 
         step(getId(), () -> {

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

@@ -16,31 +16,22 @@
 
 package org.opencb.opencga.analysis.family;
 
-import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.opencb.biodata.models.clinical.Disorder;
-import org.opencb.commons.utils.DockerUtils;
-import org.opencb.opencga.analysis.StorageToolExecutor;
+import org.opencb.opencga.core.config.ConfigurationUtils;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.utils.PedigreeGraphUtils;
-import org.opencb.opencga.core.common.GitRepositoryState;
+import org.opencb.opencga.core.config.Configuration;
 import org.opencb.opencga.core.exceptions.ToolException;
-import org.opencb.opencga.core.models.individual.Individual;
 import org.opencb.opencga.core.tools.annotations.ToolExecutor;
 import org.opencb.opencga.core.tools.family.PedigreeGraphAnalysisExecutor;
 import org.opencb.opencga.storage.core.exceptions.StorageEngineException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.io.PrintWriter;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.*;
 
-@ToolExecutor(id="opencga-local", tool = PedigreeGraphAnalysis.ID,
+@ToolExecutor(id="opencga-local", tool = PedigreeGraphAnalysisExecutor.ID,
         framework = ToolExecutor.Framework.LOCAL, source = ToolExecutor.Source.STORAGE)
 public class PedigreeGraphLocalAnalysisExecutor extends PedigreeGraphAnalysisExecutor {
 
@@ -51,8 +42,10 @@ public class PedigreeGraphLocalAnalysisExecutor extends PedigreeGraphAnalysisExe
     @Override
     public void run() throws ToolException, CatalogException, IOException, StorageEngineException {
         opencgaHome = Paths.get(getExecutorParams().getString("opencgaHome"));
+        Configuration configuration = ConfigurationUtils.loadConfiguration(opencgaHome.toAbsolutePath().toString());
 
          // Run R script for fitting signature
-        PedigreeGraphUtils.createPedigreeGraph(getFamily(), opencgaHome.resolve("analysis/" + PedigreeGraphAnalysis.ID), getOutDir());
+        PedigreeGraphUtils.createPedigreeGraph(getFamily(), opencgaHome.resolve("analysis/" + PedigreeGraphAnalysisExecutor.ID),
+                getOutDir(), configuration);
     }
 }

opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/IBDComputation.java

@@ -30,8 +30,9 @@
 import org.opencb.opencga.analysis.individual.qc.IndividualQcUtils;
 import org.opencb.opencga.analysis.variant.manager.VariantStorageManager;
 import org.opencb.opencga.analysis.variant.relatedness.RelatednessAnalysis;
-import org.opencb.opencga.analysis.wrappers.plink.PlinkWrapperAnalysisExecutor;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
+import org.opencb.opencga.core.config.ConfigurationUtils;
+import org.opencb.opencga.core.config.Docker;
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.models.family.Family;
 import org.opencb.opencga.core.models.individual.Individual;
@@ -117,7 +118,9 @@ public static RelatednessReport compute(String study, Family family, List<String
         } catch (IOException e) {
             throw new ToolException("Something wrong happened when copying files during the relatedness analysis execution");
         }
-        File outFile = runIBD(FILTERED_BASENAME, freqPath, outDir);
+        String dockerImage = ConfigurationUtils.getDockerImage(Docker.OPENCGA_EXT_TOOLS_IMAGE_KEY,
+                storageManager.getCatalogManager().getConfiguration());
+        File outFile = runIBD(dockerImage, FILTERED_BASENAME, freqPath, outDir);
 
         if (!outFile.exists()) {
             throw new ToolException("Something wrong happened executing relatedness analysis");
@@ -298,7 +301,7 @@ public static void filterFamilyTpedFile(Path tPedPath, Path tPedFilteredPath, Pa
         bw.close();
     }
 
-    private static File runIBD(String basename, Path freqPath, Path outDir) throws ToolException {
+    private static File runIBD(String dockerImage, String basename, Path freqPath, Path outDir) throws ToolException {
         // Input bindings
         List<AbstractMap.SimpleEntry<String, String>> inputBindings = new ArrayList<>();
         inputBindings.add(new AbstractMap.SimpleEntry<>(freqPath.getParent().toString(), "/input"));
@@ -311,8 +314,7 @@ private static File runIBD(String basename, Path freqPath, Path outDir) throws T
         String plinkParams = "plink1.9 --tfile /output/" + basename + " --genome rel-check --read-freq /input/" + FREQ_FILENAME
                 + " --out /output/" + basename;
         try {
-            PlinkWrapperAnalysisExecutor plinkExecutor = new PlinkWrapperAnalysisExecutor();
-            DockerUtils.run(plinkExecutor.getDockerImageName(), inputBindings, outputBinding, plinkParams, null);
+            DockerUtils.run(dockerImage, inputBindings, outputBinding, plinkParams, null);
         } catch (IOException e) {
             throw new ToolException(e);
         }

opencga-analysis/src/main/java/org/opencb/opencga/analysis/individual/qc/IndividualQcUtils.java

@@ -24,12 +24,13 @@
 import org.opencb.commons.exec.Command;
 import org.opencb.commons.utils.DockerUtils;
 import org.opencb.opencga.analysis.variant.manager.VariantStorageManager;
-import org.opencb.opencga.analysis.wrappers.plink.PlinkWrapperAnalysisExecutor;
 import org.opencb.opencga.catalog.db.api.IndividualDBAdaptor;
 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.ConfigurationUtils;
+import org.opencb.opencga.core.config.Docker;
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.common.InternalStatus;
@@ -85,7 +86,9 @@ public static void selectMarkers(String basename, String study, List<String> sam
 
         exportData(tpedFile, tfamFile, query, storageManager, token);
         if (tpedFile.exists() && tpedFile.length() > 0) {
-            pruneVariants(basename, outputBinding);
+            String dockerImage = ConfigurationUtils.getDockerImage(Docker.OPENCGA_EXT_TOOLS_IMAGE_KEY,
+                    storageManager.getCatalogManager().getConfiguration());
+            pruneVariants(dockerImage, basename, outputBinding);
         }
 
         if (!tpedFile.exists() || tpedFile.length() == 0) {
@@ -362,12 +365,11 @@ private static void exportData(File tpedFile, File tfamFile, Query query, Varian
         }
     }
 
-    private static void pruneVariants(String basename, AbstractMap.SimpleEntry<String, String> outputBinding) throws ToolException {
+    private static void pruneVariants(String dockerImage, String basename, AbstractMap.SimpleEntry<String, String> outputBinding) throws ToolException {
         // Variant pruning using PLINK in docker
         String plinkParams = "plink1.9 --tfile /data/output/" + basename + " --indep 50 5 2 --out /data/output/" + basename;
         try {
-            PlinkWrapperAnalysisExecutor plinkExecutor = new PlinkWrapperAnalysisExecutor();
-            DockerUtils.run(plinkExecutor.getDockerImageName(), null, outputBinding, plinkParams, null);
+            DockerUtils.run(dockerImage, null, outputBinding, plinkParams, null);
         } catch (IOException e) {
             throw new ToolException(e);
         }

opencga-analysis/src/main/java/org/opencb/opencga/analysis/individual/qc/InferredSexComputation.java

@@ -20,7 +20,6 @@
 import org.opencb.biodata.models.core.Region;
 import org.opencb.commons.utils.DockerUtils;
 import org.opencb.opencga.analysis.alignment.AlignmentStorageManager;
-import org.opencb.opencga.analysis.variant.mutationalSignature.MutationalSignatureLocalAnalysisExecutor;
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.models.file.File;
 
@@ -88,13 +87,13 @@ public static double[] computeRatios(String study, File bwFile, String assembly,
         return new double[]{1.0d * means[1] / means[0], 1.0d * means[2] / means[0]};
     }
 
-    public static java.io.File plot(File inputFile, Path outDir) throws ToolException {
+    public static java.io.File plot(File inputFile, Path outDir, String dockerImage) throws ToolException {
         // Execute R script in docker
         AbstractMap.SimpleEntry<String, String> outputBinding = new AbstractMap.SimpleEntry<>(outDir.toAbsolutePath().toString(),
                 "/data/output");
         String rParams = "R CMD Rscript --vanilla /data/input/" + inputFile.getName();
         try {
-            DockerUtils.run(MutationalSignatureLocalAnalysisExecutor.R_DOCKER_IMAGE, null, outputBinding, rParams, null);
+            DockerUtils.run(dockerImage, null, outputBinding, rParams, null);
         } catch (IOException e) {
             throw new ToolException(e);
         }

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

@@ -22,7 +22,6 @@
 import org.apache.commons.lang3.time.StopWatch;
 import org.opencb.commons.datastore.core.Event;
 import org.opencb.commons.datastore.core.ObjectMap;
-import org.opencb.opencga.analysis.ConfigurationUtils;
 import org.opencb.opencga.analysis.variant.manager.VariantStorageManager;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;
@@ -31,6 +30,7 @@
 import org.opencb.opencga.core.common.MemoryUsageMonitor;
 import org.opencb.opencga.core.common.TimeUtils;
 import org.opencb.opencga.core.config.Configuration;
+import org.opencb.opencga.core.config.ConfigurationUtils;
 import org.opencb.opencga.core.config.storage.StorageConfiguration;
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.models.common.Enums;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/circos/CircosLocalAnalysisExecutor.java

@@ -32,8 +32,9 @@
 import org.opencb.opencga.analysis.StorageToolExecutor;
 import org.opencb.opencga.analysis.variant.manager.VariantStorageManager;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
-import org.opencb.opencga.core.common.GitRepositoryState;
 import org.opencb.opencga.core.common.TimeUtils;
+import org.opencb.opencga.core.config.ConfigurationUtils;
+import org.opencb.opencga.core.config.Docker;
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.exceptions.ToolExecutorException;
 import org.opencb.opencga.core.models.variant.CircosAnalysisParams;
@@ -59,9 +60,8 @@
         framework = ToolExecutor.Framework.LOCAL, source = ToolExecutor.Source.STORAGE)
 public class CircosLocalAnalysisExecutor extends CircosAnalysisExecutor implements StorageToolExecutor {
 
-    public final static String R_DOCKER_IMAGE = "opencb/opencga-ext-tools:"
-            + GitRepositoryState.getInstance().getBuildVersion();
     private VariantStorageManager storageManager;
+    private String dockerImage;
 
     private File snvsFile;
     private File rearrsFile;
@@ -96,6 +96,8 @@ public VariantStorageManager getVariantStorageManager() throws ToolExecutorExcep
 
     @Override
     public void run() throws ToolException, IOException, CatalogException {
+        dockerImage = ConfigurationUtils.getDockerImage(Docker.OPENCGA_EXT_TOOLS_IMAGE_KEY,
+                storageManager.getCatalogManager().getConfiguration());
 
         // Create query
         Query query = new Query();
@@ -160,7 +162,7 @@ public void run() throws ToolException, IOException, CatalogException {
                     + " " + getCircosParams().getTitle();
 
             StopWatch stopWatch = StopWatch.createStarted();
-            String cmdline = DockerUtils.run(R_DOCKER_IMAGE, inputBindings, outputBinding, scriptParams, null);
+            String cmdline = DockerUtils.run(dockerImage, inputBindings, outputBinding, scriptParams, null);
             logger.info("Docker command line: " + cmdline);
             logger.info("Execution time: " + TimeUtils.durationToString(stopWatch));
         } else {

opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotLocalAnalysisExecutor.java

@@ -34,10 +34,12 @@
 import org.opencb.opencga.analysis.StorageToolExecutor;
 import org.opencb.opencga.analysis.variant.manager.VariantStorageManager;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
-import org.opencb.opencga.core.common.GitRepositoryState;
 import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.core.common.TimeUtils;
+import org.opencb.opencga.core.config.ConfigurationUtils;
+import org.opencb.opencga.core.config.Docker;
 import org.opencb.opencga.core.exceptions.ToolException;
+import org.opencb.opencga.core.exceptions.ToolExecutorException;
 import org.opencb.opencga.core.tools.annotations.ToolExecutor;
 import org.opencb.opencga.core.tools.variant.GenomePlotAnalysisExecutor;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;
@@ -59,9 +61,7 @@
         framework = ToolExecutor.Framework.LOCAL, source = ToolExecutor.Source.STORAGE)
 public class GenomePlotLocalAnalysisExecutor extends GenomePlotAnalysisExecutor implements StorageToolExecutor {
 
-    public final static String R_DOCKER_IMAGE = "opencb/opencga-ext-tools:"
-            + GitRepositoryState.getInstance().getBuildVersion();
-
+    private String dockerImage;
     private GenomePlotConfig plotConfig;
 
     private File snvsFile;
@@ -79,7 +79,8 @@ public class GenomePlotLocalAnalysisExecutor extends GenomePlotAnalysisExecutor
 
     @Override
     public void run() throws ToolException, IOException, CatalogException {
-
+        dockerImage = ConfigurationUtils.getDockerImage(Docker.OPENCGA_EXT_TOOLS_IMAGE_KEY,
+                getVariantStorageManager().getCatalogManager().getConfiguration());
         plotConfig = JacksonUtils.getDefaultObjectMapper().readerFor(GenomePlotConfig.class).readValue(getConfigFile());
 
         // Create query
@@ -145,7 +146,7 @@ public void run() throws ToolException, IOException, CatalogException {
                     + " " + plotConfig.getTitle();
 
             StopWatch stopWatch = StopWatch.createStarted();
-            String cmdline = DockerUtils.run(R_DOCKER_IMAGE, inputBindings, outputBinding, scriptParams, null);
+            String cmdline = DockerUtils.run(dockerImage, inputBindings, outputBinding, scriptParams, null);
             logger.info("Docker command line: " + cmdline);
             logger.info("Execution time: " + TimeUtils.durationToString(stopWatch));
         } else {