TASK-6708 - Port Patch 2.12.7 -> 3.2.1 (Xetabase 1.10.7 -> 2.2.1)

opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java

@@ -81,6 +81,7 @@ public void singleExomiserAnalysis() throws IOException, CatalogException, ToolE
 //        String resourceVersion = "2109";
         String exomiserVersion = "14.0";
         String resourceVersion = "2402";
+        assertTrue(opencga.getOpencgaHome().resolve("analysis").resolve("exomiser").resolve(exomiserVersion).toFile().exists());
         assumeTrue(Paths.get("/opt/opencga/analysis/resources/exomiser/READY-" + resourceVersion).toFile().exists());
 
         prepareExomiserData();
@@ -131,6 +132,7 @@ public void familyExomiserAnalysis() throws IOException, CatalogException, ToolE
 //        String resourceVersion = "2109";
         String exomiserVersion = "14.0";
         String resourceVersion = "2402";
+        assertTrue(opencga.getOpencgaHome().resolve("analysis").resolve("exomiser").resolve(exomiserVersion).toFile().exists());
         assumeTrue(Paths.get("/opt/opencga/analysis/resources/exomiser/READY-" + resourceVersion).toFile().exists());
 
         prepareExomiserData();
@@ -180,6 +182,7 @@ public void trioSingleExomiserAnalysis() throws IOException, CatalogException, T
 //        String resourceVersion = "2109";
         String exomiserVersion = "14.0";
         String resourceVersion = "2402";
+        assertTrue(opencga.getOpencgaHome().resolve("analysis").resolve("exomiser").resolve(exomiserVersion).toFile().exists());
         assumeTrue(Paths.get("/opt/opencga/analysis/resources/exomiser/READY-" + resourceVersion).toFile().exists());
 
         prepareExomiserData();

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

@@ -22,7 +22,6 @@
 import org.opencb.commons.datastore.mongodb.MongoDataStore;
 import org.opencb.commons.datastore.mongodb.MongoDataStoreManager;
 import org.opencb.opencga.analysis.StorageManager;
-import org.opencb.opencga.analysis.clinical.exomiser.ExomiserInterpretationAnalysisTest;
 import org.opencb.opencga.analysis.tools.ToolRunner;
 import org.opencb.opencga.analysis.variant.manager.VariantStorageManager;
 import org.opencb.opencga.catalog.db.mongodb.MongoBackupUtils;
@@ -220,9 +219,9 @@ public Path isolateOpenCGA() throws IOException {
 
         catalogManagerExternalResource.getConfiguration().serialize(
                 new FileOutputStream(conf.resolve("configuration.yml").toFile()));
-        InputStream inputStream = StorageManager.class.getClassLoader().getResourceAsStream("storage-configuration.yml");
-
-        storageConfiguration = StorageConfiguration.load(inputStream, "yml");
+        try (InputStream inputStream = StorageManager.class.getClassLoader().getResourceAsStream("storage-configuration.yml")) {
+            storageConfiguration = StorageConfiguration.load(inputStream, "yml");
+        }
 
         storageConfiguration.getVariant().setDefaultEngine(storageEngine);
         if (storageEngine.equals(HadoopVariantStorageEngine.STORAGE_ENGINE_ID)) {
@@ -259,20 +258,22 @@ public Path isolateOpenCGA() throws IOException {
 
         // Mutational signatue analysis
         Path analysisPath = Files.createDirectories(opencgaHome.resolve("analysis/mutational-signature")).toAbsolutePath();
-        inputStream = new FileInputStream("../opencga-app/app/analysis/mutational-signature/sv_clustering.R");
-        Files.copy(inputStream, analysisPath.resolve("sv_clustering.R"), StandardCopyOption.REPLACE_EXISTING);
+        try (FileInputStream inputStream = new FileInputStream("../opencga-app/app/analysis/mutational-signature/sv_clustering.R")) {
+            Files.copy(inputStream, analysisPath.resolve("sv_clustering.R"), StandardCopyOption.REPLACE_EXISTING);
+        }
 
         // Pedigree graph analysis
         analysisPath = Files.createDirectories(opencgaHome.resolve("analysis/pedigree-graph")).toAbsolutePath();
-        inputStream = new FileInputStream("../opencga-app/app/analysis/pedigree-graph/ped.R");
-        Files.copy(inputStream, analysisPath.resolve("ped.R"), StandardCopyOption.REPLACE_EXISTING);
+        try (FileInputStream inputStream = new FileInputStream("../opencga-app/app/analysis/pedigree-graph/ped.R")) {
+            Files.copy(inputStream, analysisPath.resolve("ped.R"), StandardCopyOption.REPLACE_EXISTING);
+        }
 
         // Exomiser analysis files
         List<String> exomiserVersions = Arrays.asList("13.1", "14.0");
         List<String> exomiserFiles = Arrays.asList("application.properties", "exomiser-analysis.yml", "output.yml");
         for (String exomiserVersion : exomiserVersions) {
             analysisPath = Files.createDirectories(opencgaHome.resolve("analysis/exomiser").resolve(exomiserVersion).toAbsolutePath());
-            Path exomiserPath = Paths.get(ExomiserInterpretationAnalysisTest.class.getClassLoader().getResource("exomiser").getPath());
+            Path exomiserPath = Paths.get("../opencga-app/app/analysis/exomiser");
             for (String exomiserFile : exomiserFiles) {
                 String resource = exomiserVersion + "/" + exomiserFile;
                 Files.copy(exomiserPath.resolve(resource).toAbsolutePath(), analysisPath.resolve(exomiserFile), StandardCopyOption.REPLACE_EXISTING);

opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/manager/operations/RemoveVariantsTest.java

@@ -32,6 +32,7 @@
 import org.opencb.opencga.core.models.sample.Sample;
 import org.opencb.opencga.core.models.study.Study;
 import org.opencb.opencga.core.testclassification.duration.MediumTests;
+import org.opencb.opencga.storage.core.variant.VariantStorageEngine;
 import org.opencb.opencga.storage.core.variant.VariantStorageOptions;
 
 import java.nio.file.Files;
@@ -46,7 +47,6 @@
 import static org.hamcrest.CoreMatchers.anyOf;
 import static org.hamcrest.CoreMatchers.is;
 import static org.junit.Assert.*;
-import static org.opencb.opencga.storage.core.variant.VariantStorageBaseTest.getResourceUri;
 
 /**
  * Created on 10/07/17.
@@ -140,7 +140,7 @@ public void testLoadAndRemoveDifferentChromosomes() throws Exception {
         List<File> files = new ArrayList<>();
         files.add(create("1k.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"));
         files.add(create("10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"));
-        indexFiles(files, new QueryOptions(), outputId);
+        indexFiles(files, new QueryOptions(VariantStorageOptions.LOAD_SPLIT_DATA.key(), VariantStorageEngine.SplitData.CHROMOSOME), outputId);
 
         removeFile(files.get(0), new QueryOptions());
     }