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TASK-5113 - SVs not being displayed in genome plot (circos) #2362

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merged 8 commits into from
Dec 4, 2023
Merged

TASK-5113 - SVs not being displayed in genome plot (circos) #2362

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72ebe63
analysis: take into account the assembly when executing genome/circos…
jtarraga Nov 17, 2023
8c41819
Merge branch 'release-2.12.x' into TASK-5113
jtarraga Nov 23, 2023
f5dd58f
analysis: add genome version when calling the R script to plot the Ci…
jtarraga Nov 23, 2023
88cd07b
Merge branch 'release-2.12.x' into TASK-5113
jtarraga Dec 1, 2023
02986a8
Merge branch 'release-2.12.x' into TASK-5113
jtarraga Dec 4, 2023
7128554
server: use permissions 777 for tmp directory when running circos plo…
jtarraga Dec 4, 2023
426258a
Merge branch 'release-2.12.x' into TASK-5113
jtarraga Dec 4, 2023
00c9e60
Merge branch 'TASK-5113' of https://github.com/opencb/opencga into TA…
jtarraga Dec 4, 2023
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5 changes: 5 additions & 0 deletions ...cga-analysis/src/main/java/org/opencb/opencga/analysis/variant/circos/CircosAnalysis.java
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Expand Up @@ -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;
Expand All @@ -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();
Expand All @@ -58,6 +61,8 @@ protected void check() throws Exception {
// }
//
// addAttribute("sampleName", sampleName);

assembly = ResourceUtils.getAssembly(catalogManager, study, token);
}

@Override
Expand Down
14 changes: 12 additions & 2 deletions ...src/main/java/org/opencb/opencga/analysis/variant/circos/CircosLocalAnalysisExecutor.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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();
Expand Down Expand Up @@ -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
Expand All @@ -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()
Expand Down
1 change: 1 addition & 0 deletions ...ysis/src/main/java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotAnalysis.java
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Expand Up @@ -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;
Expand Down
18 changes: 13 additions & 5 deletions .../java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotLocalAnalysisExecutor.java
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Expand Up @@ -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;
Expand All @@ -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;
Expand Down Expand Up @@ -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());

Expand Down Expand Up @@ -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()
Expand Down
6 changes: 4 additions & 2 deletions opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/VariantWebService.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);
Expand Down Expand Up @@ -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) {
Expand Down
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