Merge pull request #2362 from opencb/TASK-5113

TASK-5113 SVs not being displayed in genome plot (circos)
opencb · Dec 4, 2023 · 3487daf · 3487daf
2 parents 6120687 + 00c9e60
commit 3487daf
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Showing 5 changed files with 35 additions and 9 deletions.
diff --git a/...cga-analysis/src/main/java/org/opencb/opencga/analysis/variant/circos/CircosAnalysis.java b/...cga-analysis/src/main/java/org/opencb/opencga/analysis/variant/circos/CircosAnalysis.java
@@ -16,6 +16,7 @@
 
 package org.opencb.opencga.analysis.variant.circos;
 
+import org.opencb.opencga.analysis.ResourceUtils;
 import org.opencb.opencga.analysis.tools.OpenCgaTool;
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.models.common.Enums;
@@ -34,6 +35,8 @@ public class CircosAnalysis extends OpenCgaTool {
     private String study;
     private CircosAnalysisParams circosParams;
 
+    private String assembly;
+
     @Override
     protected void check() throws Exception {
         super.check();
@@ -58,6 +61,8 @@ protected void check() throws Exception {
 //        }
 //
 //        addAttribute("sampleName", sampleName);
+
+        assembly = ResourceUtils.getAssembly(catalogManager, study, token);
     }
 
     @Override

diff --git a/...src/main/java/org/opencb/opencga/analysis/variant/circos/CircosLocalAnalysisExecutor.java b/...src/main/java/org/opencb/opencga/analysis/variant/circos/CircosLocalAnalysisExecutor.java
@@ -28,8 +28,10 @@
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.utils.DockerUtils;
+import org.opencb.opencga.analysis.ResourceUtils;
 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.exceptions.ToolException;
@@ -93,7 +95,7 @@ public VariantStorageManager getVariantStorageManager() throws ToolExecutorExcep
     }
 
     @Override
-    public void run() throws ToolException, IOException {
+    public void run() throws ToolException, IOException, CatalogException {
 
         // Create query
         Query query = new Query();
@@ -128,7 +130,6 @@ public void run() throws ToolException, IOException {
             throw new ToolException("Error launching threads when executing the Circos analysis", e);
         }
 
-
         if (MapUtils.isEmpty(errors)) {
             // Execute R script
             // circos.R ./snvs.tsv ./indels.tsv ./cnvs.tsv ./rearrs.tsv SampleId
@@ -138,10 +139,19 @@ public void run() throws ToolException, IOException {
             AbstractMap.SimpleEntry<String, String> outputBinding = new AbstractMap.SimpleEntry<>(getOutDir()
                     .toAbsolutePath().toString(),
                     DOCKER_OUTPUT_PATH);
+
+            // Get genome version
+            String genomeVersion = "hg38";
+            String assembly = ResourceUtils.getAssembly(storageManager.getCatalogManager(), getStudy(), getToken());
+            if (StringUtils.isNotEmpty(assembly) && assembly.toUpperCase(Locale.ROOT).equals("GRCH37")) {
+                genomeVersion = "hg19";
+            }
+
             String scriptParams = "R CMD Rscript --vanilla " + DOCKER_INPUT_PATH + "/circos.R"
                     + (plotCopynumber ? "" : " --no_copynumber")
                     + (plotIndels ? "" : " --no_indels")
                     + (plotRearrangements ? "" : " --no_rearrangements")
+                    + " --genome_version " + genomeVersion
                     + " --out_path " + DOCKER_OUTPUT_PATH
                     + " " + DOCKER_OUTPUT_PATH + "/" + snvsFile.getName()
                     + " " + DOCKER_OUTPUT_PATH + "/" + indelsFile.getName()

diff --git a/...ysis/src/main/java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotAnalysis.java b/...ysis/src/main/java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotAnalysis.java
@@ -21,6 +21,7 @@
 import org.opencb.biodata.models.clinical.qc.GenomePlotConfig;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.analysis.AnalysisUtils;
+import org.opencb.opencga.analysis.ResourceUtils;
 import org.opencb.opencga.analysis.tools.OpenCgaToolScopeStudy;
 import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.core.exceptions.ToolException;

diff --git a/.../java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotLocalAnalysisExecutor.java b/.../java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotLocalAnalysisExecutor.java
@@ -30,8 +30,10 @@
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.utils.DockerUtils;
+import org.opencb.opencga.analysis.ResourceUtils;
 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;
@@ -46,10 +48,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
-import java.util.AbstractMap;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 import java.util.concurrent.*;
 
 import static org.opencb.opencga.analysis.wrappers.executors.DockerWrapperAnalysisExecutor.DOCKER_INPUT_PATH;
@@ -79,7 +78,7 @@ public class GenomePlotLocalAnalysisExecutor extends GenomePlotAnalysisExecutor
     private Logger logger = LoggerFactory.getLogger(this.getClass());
 
     @Override
-    public void run() throws ToolException, IOException {
+    public void run() throws ToolException, IOException, CatalogException {
 
         plotConfig = JacksonUtils.getDefaultObjectMapper().readerFor(GenomePlotConfig.class).readValue(getConfigFile());
 
@@ -125,10 +124,19 @@ public void run() throws ToolException, IOException {
             inputBindings.add(new AbstractMap.SimpleEntry<>(rScriptPath, DOCKER_INPUT_PATH));
             AbstractMap.SimpleEntry<String, String> outputBinding = new AbstractMap.SimpleEntry<>(getOutDir()
                     .toAbsolutePath().toString(), DOCKER_OUTPUT_PATH);
+
+            // Get genome version
+            String genomeVersion = "hg38";
+            String assembly = ResourceUtils.getAssembly(storageManager.getCatalogManager(), getStudy(), getToken());
+            if (StringUtils.isNotEmpty(assembly) && assembly.toUpperCase(Locale.ROOT).equals("GRCH37")) {
+                genomeVersion = "hg19";
+            }
+
             String scriptParams = "R CMD Rscript --vanilla " + DOCKER_INPUT_PATH + "/circos.R"
                     + (plotCopynumber ? "" : " --no_copynumber")
                     + (plotIndels ? "" : " --no_indels")
                     + (plotRearrangements ? "" : " --no_rearrangements")
+                    + " --genome_version " + genomeVersion
                     + " --out_path " + DOCKER_OUTPUT_PATH
                     + " " + DOCKER_OUTPUT_PATH + "/" + snvsFile.getName()
                     + " " + DOCKER_OUTPUT_PATH + "/" + indelsFile.getName()

diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/VariantWebService.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/VariantWebService.java
@@ -30,6 +30,7 @@
 import org.opencb.commons.annotations.DataField;
 import org.opencb.commons.datastore.core.*;
 import org.opencb.opencga.analysis.AnalysisUtils;
+import org.opencb.opencga.analysis.ResourceUtils;
 import org.opencb.opencga.analysis.family.qc.FamilyQcAnalysis;
 import org.opencb.opencga.analysis.individual.qc.IndividualQcAnalysis;
 import org.opencb.opencga.analysis.individual.qc.IndividualQcUtils;
@@ -1330,6 +1331,7 @@ public Response circos(
             if (!outDir.exists()) {
                 return createErrorResponse(new Exception("Error creating temporal directory for Circos analysis"));
             }
+            Runtime.getRuntime().exec("chmod 777 " + outDir.getAbsolutePath());
 
             // Create and set up Circos executor
             CircosLocalAnalysisExecutor executor = new CircosLocalAnalysisExecutor(study, params, variantManager);
@@ -1361,13 +1363,13 @@ public Response circos(
             } else {
                 return createErrorResponse(new Exception("Error plotting Circos graph"));
             }
-        } catch (ToolException | IOException e) {
+        } catch (ToolException | IOException | CatalogException e) {
             return createErrorResponse(e);
         } finally {
             if (outDir != null) {
                 // Delete temporal directory
                 try {
-                    if (outDir.exists() && !params.getTitle().startsWith("no.delete.")) {
+                    if (outDir.exists()) {
                         FileUtils.deleteDirectory(outDir);
                     }
                 } catch (IOException e) {