analysis: Fix NPE at relatedness tool. #TASK-6722

opencb · Nov 29, 2024 · 5141031 · 5141031
1 parent 1d86756
commit 5141031
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Showing 2 changed files with 16 additions and 4 deletions.
diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/IBDComputation.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/IBDComputation.java
@@ -32,6 +32,7 @@
 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.Analysis;
 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 +118,7 @@ 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);
+        File outFile = runIBD(FILTERED_BASENAME, freqPath, outDir, storageManager.getCatalogManager().getConfiguration().getAnalysis());
 
         if (!outFile.exists()) {
             throw new ToolException("Something wrong happened executing relatedness analysis");
@@ -298,7 +299,7 @@ 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 basename, Path freqPath, Path outDir, Analysis analysisConf) throws ToolException {
         // Input bindings
         List<AbstractMap.SimpleEntry<String, String>> inputBindings = new ArrayList<>();
         inputBindings.add(new AbstractMap.SimpleEntry<>(freqPath.getParent().toString(), "/input"));
@@ -311,8 +312,8 @@ 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);
+            String dockerImageName = PlinkWrapperAnalysisExecutor.getDockerImageName(analysisConf);
+            DockerUtils.run(dockerImageName, inputBindings, outputBinding, plinkParams, null);
         } catch (IOException e) {
             throw new ToolException(e);
         }

diff --git a/...rc/main/java/org/opencb/opencga/analysis/wrappers/plink/PlinkWrapperAnalysisExecutor.java b/...rc/main/java/org/opencb/opencga/analysis/wrappers/plink/PlinkWrapperAnalysisExecutor.java
@@ -3,6 +3,8 @@
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
 import org.opencb.opencga.analysis.wrappers.executors.DockerWrapperAnalysisExecutor;
+import org.opencb.opencga.core.config.Analysis;
+import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.tools.annotations.ToolExecutor;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -21,6 +23,15 @@ public class PlinkWrapperAnalysisExecutor extends DockerWrapperAnalysisExecutor
 
     private Logger logger = LoggerFactory.getLogger(this.getClass());
 
+    public static String getDockerImageName(Analysis analysisConf) throws ToolException {
+        return analysisConf.getOpencgaExtTools().split(":")[0];
+    }
+
+    @Override
+    public String getDockerImageName() throws ToolException {
+        return getDockerImageName(getConfiguration().getAnalysis());
+    }
+
     @Override
     protected void run() throws Exception {
         StringBuilder sb = initCommandLine();