Merge pull request #2313 from opencb/TASK-4667

TASK-4667 - Port Patch 1.6.3.1 -> 1.8.0

opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/hrdetect/HRDetectAnalysis.java

@@ -59,7 +59,7 @@ public class HRDetectAnalysis extends OpenCgaToolScopeStudy {
     public static final String ID = "hr-detect";
     public static final String DESCRIPTION = "Run HRDetect analysis for a given somatic sample.";
 
-    public final static String HRDETECT_SCORES_FILENAME_DEFAULT = "data_matrix.tsv";
+    public final static String HRDETECT_SCORES_FILENAME_DEFAULT = "hrdetect_output.tsv";
 
     @ToolParams
     private HRDetectAnalysisParams hrdetectParams = new HRDetectAnalysisParams();

opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java

@@ -130,7 +130,7 @@ public void run() throws ToolException {
 
         VariantQuery query = new VariantQuery()
                 .study(studyId)
-                .sample(sampleId + ":0/1,1/1")
+                .sample(sampleId)
                 .includeSample(samples)
                 .includeSampleData("GT")
                 .unknownGenotype("./.");

opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

@@ -194,7 +194,9 @@ public void setUp() throws Throwable {
                     null, null, null, token);
 
             Phenotype phenotype = new Phenotype("phenotype", "phenotype", "");
-            Disorder disorder = new Disorder("disorder", "disorder", "", "", Collections.singletonList(phenotype), Collections.emptyMap());
+            Disorder disorder1 = new Disorder("disorder id 1", "disorder name 1", "", "", Collections.singletonList(phenotype), Collections.emptyMap());
+            Disorder disorder2 = new Disorder("disorder id 2", "disorder name 2", "", "", Collections.singletonList(phenotype), Collections.emptyMap());
+            List<Disorder> disorderList = new ArrayList<>(Arrays.asList(disorder1, disorder2));
             List<Individual> individuals = new ArrayList<>(4);
 
             // Father
@@ -208,14 +210,14 @@ public void setUp() throws Throwable {
             // Son
             individuals.add(catalogManager.getIndividualManager()
                     .create(STUDY, new Individual(son, son, new Individual(), new Individual(), new Location(), SexOntologyTermAnnotation.initMale(), null, null, null, null, "",
-                            Collections.emptyList(), false, 0, Collections.emptyList(), Collections.emptyList(), Collections.emptyList(), IndividualInternal.init(), Collections.emptyMap()).setFather(individuals.get(0)).setMother(individuals.get(1)).setDisorders(Collections.singletonList(disorder)), Collections.singletonList(son), new QueryOptions(ParamConstants.INCLUDE_RESULT_PARAM, true), token).first());
+                            Collections.emptyList(), false, 0, Collections.emptyList(), Collections.emptyList(), Collections.emptyList(), IndividualInternal.init(), Collections.emptyMap()).setFather(individuals.get(0)).setMother(individuals.get(1)).setDisorders(disorderList), Collections.singletonList(son), new QueryOptions(ParamConstants.INCLUDE_RESULT_PARAM, true), token).first());
             // Daughter
             individuals.add(catalogManager.getIndividualManager()
                     .create(STUDY, new Individual(daughter, daughter, new Individual(), new Individual(), new Location(), SexOntologyTermAnnotation.initFemale(), null, null, null, null, "",
                             Collections.emptyList(), false, 0, Collections.emptyList(), Collections.emptyList(), Collections.emptyList(), IndividualInternal.init(), Collections.emptyMap()).setFather(individuals.get(0)).setMother(individuals.get(1)), Collections.singletonList(daughter), new QueryOptions(ParamConstants.INCLUDE_RESULT_PARAM, true), token).first());
             catalogManager.getFamilyManager().create(
                     STUDY,
-                    new Family("f1", "f1", Collections.singletonList(phenotype), Collections.singletonList(disorder), null, null, 3, null, null),
+                    new Family("f1", "f1", Collections.singletonList(phenotype), disorderList, null, null, 3, null, null),
                     individuals.stream().map(Individual::getId).collect(Collectors.toList()), new QueryOptions(),
                     token);
 
@@ -814,9 +816,22 @@ public void testMutationalSignatureCatalogueSV() throws Exception {
         params.setSample(cancer_sample);
         params.setId("catalogue-1");
         params.setDescription("Catalogue #1");
-        VariantQuery query = new VariantQuery();
-        query.sample(cancer_sample);
-        query.type(VariantType.SV.name());
+        VariantQuery query = new VariantQuery()
+                .sample(cancer_sample)
+                .type(VariantType.SV.name())
+                //.file("AR2.10039966-01T_vs_AR2.10039966-01G.annot.brass.vcf.gz");
+                .fileData("AR2.10039966-01T_vs_AR2.10039966-01G.annot.brass.vcf.gz:BAS>=0;BKDIST>=-1")
+                .region("1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y");
+
+        //https://ws.opencb.org/opencga-test/webservices/rest/v2/analysis/variant/mutationalSignature/query
+        // ?study=serena@cancer38:test38
+        // &fitting=false
+        // &sample=AR2.10039966-01T
+        // &fileData=AR2.10039966-01T_vs_AR2.10039966-01G.annot.brass.vcf.gz:BAS>=0;BKDIST>=-1;EXT_PS_SOM>=4;EXT_RC_SOM>=0
+        // &region=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y
+        // &type=SV
+
+
         params.setQuery(query.toJson());
         params.setSkip("fitting");
 
@@ -992,8 +1007,12 @@ public void testHRDetect() throws Exception {
         List<HRDetect> hrDetects = sample.getQualityControl().getVariant().getHrDetects();
         for (HRDetect hrDetect : hrDetects) {
             if (hrDetect.getId().equals(hrDetect.getId())) {
+                System.out.println("HRDetect scores for " + hrDetect.getId());
+                for (Map.Entry<String, Object> entry : hrDetect.getScores().entrySet()) {
+                    System.out.println("\t" + entry.getKey() + ": " + entry.getValue());
+                }
                 if (hrDetect.getScores().containsKey("del.mh.prop")) {
-                    Assert.assertEquals(hrDetect.getScores().getFloat("del.mh.prop"), 0.172413793103448f, 0.00001f);
+                    Assert.assertEquals(-1.5702984, hrDetect.getScores().getFloat("del.mh.prop"), 0.00001f);
                     return;
                 }
             }
@@ -1018,12 +1037,23 @@ public void testHRDetectParseResults() throws Exception {
 
         HRDetect hrDetect = HRDetectAnalysis.parseResult(hrdParams, hrdetectOutDir);
         for (Map.Entry<String, Object> entry : hrDetect.getScores().entrySet()) {
-            System.out.println(entry.getKey() + " -> " + entry.getValue());
+            System.out.println(entry.getKey() + ": " + entry.getValue());
         }
         assertTrue(hrDetect.getScores().containsKey("hrd"));
-        assertEquals(-0.102769986f, hrDetect.getScores().getFloat("hrd"), 0.00001f);
+        assertEquals(-1.95208666666667, hrDetect.getScores().getFloat("hrd"), 0.00001f);
         assertTrue(hrDetect.getScores().containsKey("Probability"));
-        assertEquals(0.998444f, hrDetect.getScores().getFloat("Probability"), 0.00001f);
+        assertEquals(4.21293910790655e-05, hrDetect.getScores().getFloat("Probability"), 0.00001f);
+    }
+
+    @Test
+    public void testPedigreeGraph() throws CatalogException {
+        String base64 = "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";
+
+        OpenCGAResult<Family> results = catalogManager.getFamilyManager().search(STUDY, new Query("id", "f1"), QueryOptions.empty(), token);
+        Family family = results.first();
+
+        assertTrue(family.getPedigreeGraph() != null);
+        assertEquals(base64, family.getPedigreeGraph().getBase64());
     }
 
     public void checkExecutionResult(ExecutionResult er) {

opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile

@@ -15,13 +15,16 @@ RUN apt-get update -y && DEBIAN_FRONTEND="noninteractive" TZ="Europe/London" apt
     libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
     gnuplot pandoc samtools bcftools tabix fastqc plink1.9 bwa r-base && \
     ## Installation dependencies using R install.packages() is slower than apt-get but final size is 400GB smaller.
-    R -e "install.packages(c('BiocManager', 'RCircos', 'nnls', 'ggplot2', 'jsonlite', 'optparse', 'knitr', 'configr', 'dplyr', 'rmarkdown', 'tidyr', 'httr', 'kinship2'))" && \
+    R -e "install.packages(c('BiocManager', 'RCircos', 'nnls', 'ggplot2', 'jsonlite', 'optparse', 'knitr', 'configr', 'dplyr', 'rmarkdown', 'tidyr', 'httr', 'kinship2', 'limSolve'))" && \
     R -e "BiocManager::install('BiocStyle')" && \
-    ## signature.tools.lib installation
+    ## signature.tools.lib installation \
     R -e 'install.packages(c("devtools", "getopt"), repos="https://www.stats.bris.ac.uk/R/")' && \
-    git clone https://github.com/Nik-Zainal-Group/signature.tools.lib.git /opt/opencga/signature.tools.lib && \
-#    git checkout tags/v2.3.0 && \
-    git checkout d3d73db497b5b83abc55d6cd55840c34ed542628 && \
+    git clone https://github.com/Nik-Zainal-Group/signature.tools.lib.git /opt/opencga/signature.tools.lib
+
+WORKDIR /opt/opencga/signature.tools.lib
+
+RUN git fetch origin --tags && \
+    git checkout tags/v2.4.1 && \
     sed -i '/Mmusculus/d' DESCRIPTION && \
     sed -i '/Cfamiliaris/d' DESCRIPTION && \
     sed -i '/1000genomes/d' DESCRIPTION && \

opencga-catalog/src/main/java/org/opencb/opencga/catalog/utils/PedigreeGraphUtils.java

@@ -120,7 +120,7 @@ private static File createPedFile(Family family, Path outDir) throws FileNotFoun
             StringBuilder sbDisorders = new StringBuilder();
             if (CollectionUtils.isNotEmpty(disorders) && disorders.size() > 1) {
                 for (Disorder disorder : family.getDisorders()) {
-                    sbDisorders.append("affected.").append(disorder.getId()).append("\t");
+                    sbDisorders.append("\"affected.").append(disorder.getId()).append("\"\t");
                 }
             } else {
                 sbDisorders.append("affected").append("\t");

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/metadata/VariantStorageMetadataManager.java

@@ -185,6 +185,10 @@ public VariantStorageMetadataManager(VariantStorageMetadataDBAdaptorFactory dbAd
         });
     }
 
+    public ObjectMap getConfiguration() {
+        return dbAdaptorFactory.getConfiguration();
+    }
+
     public Lock lockGlobal(long lockDuration, long timeout, String lockName)
             throws StorageEngineException {
         try {

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/GenotypeClass.java

@@ -211,6 +211,25 @@ public enum GenotypeClass implements Predicate<String> {
         return true;
     }),
 
+    /**
+     * Genotypes containing any secondary alternate.
+     * <p>
+     * 1/2, 2/3, ./2, 0/2, ...
+     */
+    SEC(str -> {
+        Genotype gt = parseGenotype(str);
+        if (gt == null) {
+            // Skip invalid genotypes
+            return false;
+        }
+        for (int allele : gt.getAllelesIdx()) {
+            if (allele > 1) {
+                return true;
+            }
+        }
+        return false;
+    }),
+
     /**
      * Genotypes containing reference and secondary alternates only.
      * <p>
@@ -233,6 +252,7 @@ public enum GenotypeClass implements Predicate<String> {
         return hasSecondaryAlternate;
     }),
 
+
     /**
      * Contains the main alternate.
      * <p>

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQuery.java

@@ -9,6 +9,7 @@
 import org.opencb.opencga.storage.core.variant.query.VariantQueryUtils;
 
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
@@ -193,6 +194,12 @@ public VariantQuery includeSampleData(String value) {
         put(VariantQueryParam.INCLUDE_SAMPLE_DATA.key(), value);
         return this;
     }
+
+    public VariantQuery includeSampleData(Collection<String> value) {
+        put(VariantQueryParam.INCLUDE_SAMPLE_DATA.key(), value);
+        return this;
+    }
+
     public String includeSampleData() {
         return getString(VariantQueryParam.INCLUDE_SAMPLE_DATA.key());
     }
@@ -257,6 +264,12 @@ public VariantQuery includeFile(String value) {
         put(VariantQueryParam.INCLUDE_FILE.key(), value);
         return this;
     }
+
+    public VariantQuery includeFile(Collection<String> value) {
+        put(VariantQueryParam.INCLUDE_FILE.key(), value);
+        return this;
+    }
+
     public VariantQuery includeFileAll() {
         return includeFile(ParamConstants.ALL);
     }

opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/adaptors/VariantDBAdaptorTest.java

@@ -2285,7 +2285,12 @@ public void testReturnNoneFiles() {
         queryResult = query(new Query(INCLUDE_FILE.key(), VariantQueryUtils.NONE).append(INCLUDE_SAMPLE.key(), ALL), new QueryOptions());
         assertEquals(allVariants.getResults().size(), queryResult.getResults().size());
         for (Variant variant : queryResult.getResults()) {
-            assertThat(variant.getStudies().get(0).getFiles(), is(Collections.emptyList()));
+            if (variant.getLengthReference() == 0 || variant.getLengthAlternate() == 0) {
+                assertThat(variant.getStudies().get(0).getFiles(), is(not(Collections.emptyList())));
+                assertThat(variant.getStudies().get(0).getFiles().get(0).getCall(), is(not(nullValue())));
+            } else {
+                assertThat(variant.getStudies().get(0).getFiles(), is(Collections.emptyList()));
+            }
             assertThat(new HashSet<>(variant.getStudies().get(0).getSampleDataKeys()), is(FORMAT));
         }
     }

opencga-storage/opencga-storage-core/src/test/resources/hrdetect_output_38.tsv

@@ -1,2 +1,2 @@
 intercept	del.mh.prop	SNV3	SV3	SV5	hrd	SNV8	Probability
-AR2.10039966-01T	-3.364	6.1388694855816	2.93200322296942	-0.876753168376584	1.62647246717118	-0.102769988932733	0.110259929136027	0.998444003582779
+AR2.10039966-01T	-3.364	-1.70122966415816	-0.949832911392405	-0.876753168376584	-1.10515509103169	-1.95208666666667	-0.125665303554577	4.21293910790655e-05