analysis: Fix some analysis tests #TASK-5663

opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/PedigreeGraphAnalysis.java

@@ -57,7 +57,7 @@ protected void check() throws Exception {
         OpenCGAResult<Family> familyResult = catalogManager.getFamilyManager().get(study, pedigreeParams.getFamilyId(),
                 QueryOptions.empty(), token);
         if (familyResult.getNumResults() != 1) {
-            throw new ToolException("Unable to compute the pedigree graph imae. Family '" + pedigreeParams.getFamilyId() +  "' not found");
+            throw new ToolException("Unable to compute the pedigree graph image. Family '" + pedigreeParams.getFamilyId() +  "' not found");
         }
         family = familyResult.first();
 

opencga-analysis/src/test/java/org/opencb/opencga/analysis/family/FamilyAnalysisTest.java

@@ -1,6 +1,8 @@
 package org.opencb.opencga.analysis.family;
 
 import org.apache.commons.lang3.StringUtils;
+import org.hamcrest.CoreMatchers;
+import org.hamcrest.MatcherAssert;
 import org.junit.*;
 import org.junit.rules.ExpectedException;
 import org.opencb.biodata.models.clinical.Disorder;
@@ -184,8 +186,8 @@ public void updateTest() throws CatalogException {
                 .first();
 
         PedigreeGraph pedigreeGraph = updatedFamily.getPedigreeGraph();
-        assertTrue(pedigreeGraph.getBase64().startsWith("iVBORw0KGgoAAAANSUhEUgAAAeAAAAHg"));
-        assertTrue(pedigreeGraph.getBase64().endsWith("5UIf81hI8AAAAASUVORK5CYII="));
+        MatcherAssert.assertThat(pedigreeGraph.getBase64(), CoreMatchers.startsWith("iVBORw0KGgoAAAANSUhEUgAAAeAAAAHg="));
+        MatcherAssert.assertThat(pedigreeGraph.getBase64(), CoreMatchers.endsWith("5UIf81hI8AAAAASUVORK5CYII="));
     }
 
     @Test
@@ -207,8 +209,8 @@ public void testPedigreeGraphAnalysis() throws ToolException, IOException {
                 sessionIdUser);
 
         String b64Image = PedigreeGraphUtils.getB64Image(outDir);
-        assertTrue(b64Image.startsWith("iVBORw0KGgoAAAANSUhEUgAAAeAAAAHg"));
-        assertTrue(b64Image.endsWith("s3Rj5UIf81hI8AAAAASUVORK5CYII="));
+        MatcherAssert.assertThat(b64Image, CoreMatchers.startsWith("iVBORw0KGgoAAAANSUhEUgAAAeAAAAHg"));
+        MatcherAssert.assertThat(b64Image, CoreMatchers.endsWith("s3Rj5UIf81hI8AAAAASUVORK5CYII="));
 
         assertEquals(family.getPedigreeGraph().getBase64(), b64Image);
     }

opencga-analysis/src/test/java/org/opencb/opencga/analysis/rga/RgaEngineTest.java

@@ -15,16 +15,17 @@
 import org.opencb.opencga.catalog.managers.CatalogManager;
 import org.opencb.opencga.core.config.Configuration;
 import org.opencb.opencga.core.config.storage.StorageConfiguration;
-import org.opencb.opencga.core.models.analysis.knockout.*;
+import org.opencb.opencga.core.models.analysis.knockout.KnockoutByIndividual;
 import org.opencb.opencga.core.testclassification.duration.MediumTests;
 import org.opencb.opencga.storage.core.StorageEngineFactory;
+import org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageTest;
 
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.List;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 @Category(MediumTests.class)
 public class RgaEngineTest {
@@ -38,7 +39,10 @@ public class RgaEngineTest {
 
     private List<KnockoutByIndividual> knockoutByIndividualList = new ArrayList<>(2);
 
-    @Rule
+    @Rule(order = 0)
+    public HadoopVariantStorageTest.HadoopSolrSupport solrSupport = new HadoopVariantStorageTest.HadoopSolrSupport();
+
+    @Rule(order = 1)
     public RgaSolrExtenalResource solr = new RgaSolrExtenalResource();
 
     @Before

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

@@ -168,8 +168,6 @@ public void setUp() throws Throwable {
 //        System.setProperty("opencga.log.level", "INFO");
 //        Configurator.reconfigure();
         if (!indexed) {
-            indexed = true;
-
             opencga.after();
             opencga.before(storageEngine);
 
@@ -251,6 +249,7 @@ public void setUp() throws Throwable {
             if (storageEngine.equals(HadoopVariantStorageEngine.STORAGE_ENGINE_ID)) {
                 VariantHbaseTestUtils.printVariants(((VariantHadoopDBAdaptor) engine.getDBAdaptor()), Paths.get(opencga.createTmpOutdir("_hbase_print_variants")).toUri());
             }
+            indexed = true;
         }
         // Reset engines
         opencga.getStorageEngineFactory().close();
@@ -279,7 +278,8 @@ public void setUpCatalogManager() throws IOException, CatalogException {
 
         String projectId = catalogManager.getProjectManager().create(new ProjectCreateParams()
                         .setId(PROJECT)
-                        .setDescription("Project about some genomes").setOrganism(new ProjectOrganism("hsapiens", "grch38")),
+                        .setDescription("Project about some genomes")
+                        .setOrganism(new ProjectOrganism("hsapiens", "GRCh38")),
                 new QueryOptions(ParamConstants.INCLUDE_RESULT_PARAM, true), token).first().getId();
         catalogManager.getStudyManager().create(projectId, STUDY, null, "Phase 1", "Done", null, null, null, null, null, token);
 
@@ -1013,6 +1013,7 @@ public void testHRDetect() throws Exception {
         toolRunner.execute(HRDetectAnalysis.class, hrdParams, new ObjectMap(ParamConstants.STUDY_PARAM, CANCER_STUDY), hrdetectOutDir, null, token);
 
         java.io.File hrDetectFile = hrdetectOutDir.resolve(HRDetectAnalysis.HRDETECT_SCORES_FILENAME_DEFAULT).toFile();
+        assertTrue("File missing : " + hrDetectFile, hrDetectFile.exists());
         byte[] bytes = Files.readAllBytes(hrDetectFile.toPath());
         System.out.println(new String(bytes));
         assertTrue(hrDetectFile.exists());

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

@@ -11,8 +11,12 @@
 import org.opencb.opencga.core.models.family.PedigreeGraph;
 import org.opencb.opencga.core.models.individual.Individual;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.PrintWriter;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.*;
@@ -85,11 +89,8 @@ public static String getB64Image(Path outDir) throws IOException {
         if (!imgFile.exists()) {
             throw new IOException("Pedigree graph image file (" + PEDIGREE_IMAGE_FILENAME + ") not found at " + outDir);
         }
-
-        FileInputStream fileInputStreamReader = new FileInputStream(imgFile);
-        byte[] bytes = new byte[(int) imgFile.length()];
-        fileInputStreamReader.read(bytes);
-        return new String(Base64.getEncoder().encode(bytes), StandardCharsets.UTF_8);
+        byte[] bytes = Files.readAllBytes(imgFile.toPath());
+        return Base64.getEncoder().encodeToString(bytes);
     }
 
     public static Object getJsonPedigreeGraph(Path outDir) throws IOException {
@@ -107,9 +108,7 @@ public static String getTsvPedigreeGraph(Path outDir) throws IOException {
             throw new IOException("Pedigree graph TSV file (" + PEDIGREE_TSV_FILENAME + ") not found at " + outDir);
         }
 
-        FileInputStream fileInputStreamReader = new FileInputStream(tsvFile);
-        byte[] bytes = new byte[(int) tsvFile.length()];
-        fileInputStreamReader.read(bytes);
+        byte[] bytes = Files.readAllBytes(tsvFile.toPath());
         return new String(bytes, StandardCharsets.UTF_8);
     }
 

opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/HadoopVariantStorageSearchIntersectTest.java

@@ -33,10 +33,10 @@
 @Category(LongTests.class)
 public class HadoopVariantStorageSearchIntersectTest extends VariantStorageSearchIntersectTest implements HadoopVariantStorageTest {
 
-    @ClassRule
+    @ClassRule(order = 0)
     public static HadoopSolrSupport solrSupport = new HadoopSolrSupport();
 
-    @ClassRule
+    @ClassRule(order = 1)
     public static ExternalResource externalResource = new HadoopExternalResource();
 
     @Override