test: Migration JUNIT4 -> JUNIT5 TemporalFolder and ExpectedException…

… Rules #TASK-5174
opencb · Feb 20, 2024 · e70dc9c · e70dc9c
1 parent 111f46c
commit e70dc9c
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Showing 62 changed files with 262 additions and 210 deletions.
diff --git a/biodata-formats/src/test/java/org/opencb/biodata/formats/GafParserTest.java b/biodata-formats/src/test/java/org/opencb/biodata/formats/GafParserTest.java
@@ -1,12 +1,10 @@
 package org.opencb.biodata.formats;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.formats.gaf.GafParser;
 import org.opencb.biodata.models.core.AnnotationEvidence;
 import org.opencb.biodata.models.core.FeatureOntologyTermAnnotation;
-import org.opencb.commons.utils.FileUtils;
 
-import java.io.BufferedReader;
 import java.io.IOException;
 import java.nio.file.Path;
 import java.nio.file.Paths;

diff --git a/biodata-formats/src/test/java/org/opencb/biodata/formats/OboFileParserTest.java b/biodata-formats/src/test/java/org/opencb/biodata/formats/OboFileParserTest.java
@@ -1,6 +1,6 @@
 package org.opencb.biodata.formats;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.formats.obo.OboParser;
 import org.opencb.biodata.models.core.OntologyTerm;
 import org.opencb.commons.utils.FileUtils;

diff --git a/...st/java/org/opencb/biodata/formats/alignment/samtools/io/SamtoolsFlagstatsParserTest.java b/...st/java/org/opencb/biodata/formats/alignment/samtools/io/SamtoolsFlagstatsParserTest.java
@@ -1,6 +1,6 @@
 package org.opencb.biodata.formats.alignment.samtools.io;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.formats.alignment.samtools.SamtoolsFlagstats;
 
 import java.io.ByteArrayInputStream;

diff --git a/...a-formats/src/test/java/org/opencb/biodata/formats/annotation/io/VepFormatReaderTest.java b/...a-formats/src/test/java/org/opencb/biodata/formats/annotation/io/VepFormatReaderTest.java
@@ -19,8 +19,7 @@
 
 package org.opencb.biodata.formats.annotation.io;
 
-import org.junit.Ignore;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.formats.variant.annotation.io.VepFormatReader;
 import org.opencb.biodata.models.variant.avro.VariantAnnotation;
 //import org.opencb.biodata.models.variant.annotation.VariantAnnotation;

diff --git a/biodata-formats/src/test/java/org/opencb/biodata/formats/feature/gtf/io/GtfReaderTest.java b/biodata-formats/src/test/java/org/opencb/biodata/formats/feature/gtf/io/GtfReaderTest.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.formats.feature.gtf.io;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.formats.feature.gtf.Gtf;
 
 import java.io.StringReader;

diff --git a/biodata-formats/src/test/java/org/opencb/biodata/formats/pedigree/PedigreeParserTest.java b/biodata-formats/src/test/java/org/opencb/biodata/formats/pedigree/PedigreeParserTest.java
@@ -1,6 +1,6 @@
 package org.opencb.biodata.formats.pedigree;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.models.clinical.pedigree.Pedigree;
 
 import java.nio.file.Path;

diff --git a/biodata-formats/src/test/java/org/opencb/biodata/formats/pubmed/PubMedParserTest.java b/biodata-formats/src/test/java/org/opencb/biodata/formats/pubmed/PubMedParserTest.java
@@ -2,7 +2,7 @@
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.formats.pubmed.v233jaxb.PubmedArticle;
 import org.opencb.biodata.formats.pubmed.v233jaxb.PubmedArticleSet;
 

diff --git a/...ats/src/test/java/org/opencb/biodata/formats/variant/VariantAggregatedVcfFactoryTest.java b/...ats/src/test/java/org/opencb/biodata/formats/variant/VariantAggregatedVcfFactoryTest.java
@@ -16,7 +16,7 @@
 
 package org.opencb.biodata.formats.variant;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.formats.variant.vcf4.VariantAggregatedVcfFactory;
 import org.opencb.biodata.formats.variant.vcf4.VariantVcfFactory;
 import org.opencb.biodata.models.variant.StudyEntry;

diff --git a/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java b/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java
@@ -20,7 +20,7 @@
 package org.opencb.biodata.formats.variant.annotation.io;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAvro;
 import org.opencb.commons.utils.FileUtils;

diff --git a/...a-formats/src/test/java/org/opencb/biodata/formats/variant/clinvar/ClinvarParserTest.java b/...a-formats/src/test/java/org/opencb/biodata/formats/variant/clinvar/ClinvarParserTest.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.formats.variant.clinvar;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.formats.variant.clinvar.rcv.ClinvarParser;
 import org.opencb.biodata.formats.variant.clinvar.rcv.v64jaxb.PublicSetType;
 import org.opencb.biodata.formats.variant.clinvar.rcv.v64jaxb.ReleaseType;

diff --git a/...ormats/src/test/java/org/opencb/biodata/formats/variant/vcf4/io/VariantVcfReaderTest.java b/...ormats/src/test/java/org/opencb/biodata/formats/variant/vcf4/io/VariantVcfReaderTest.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.formats.variant.vcf4.io;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.formats.variant.io.VariantReader;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.formats.variant.vcf4.VariantAggregatedVcfFactory;

diff --git a/...est/java/org/opencb/biodata/models/clinical/interpretation/VariantClassificationTest.java b/...est/java/org/opencb/biodata/models/clinical/interpretation/VariantClassificationTest.java
@@ -1,7 +1,7 @@
 package org.opencb.biodata.models.clinical.interpretation;
 
 import org.apache.commons.lang3.StringUtils;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.models.clinical.ClinicalAcmg;
 import org.opencb.biodata.models.clinical.ClinicalProperty;
 

diff --git a/biodata-models/src/test/java/org/opencb/biodata/models/core/RegionTest.java b/biodata-models/src/test/java/org/opencb/biodata/models/core/RegionTest.java
@@ -1,6 +1,6 @@
 package org.opencb.biodata.models.core;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
 import static org.junit.Assert.assertEquals;
 

diff --git a/biodata-models/src/test/java/org/opencb/biodata/models/feature/GenotypeTest.java b/biodata-models/src/test/java/org/opencb/biodata/models/feature/GenotypeTest.java
@@ -17,7 +17,8 @@
 package org.opencb.biodata.models.feature;
 
 import org.junit.Rule;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
 import org.junit.rules.ExpectedException;
 import org.opencb.biodata.models.variant.Genotype;
 
@@ -98,23 +99,38 @@ public void testParse() {
 
     @Test
     public void testParseFail1() {
-        thrown.expect(IllegalArgumentException.class);
-        thrown.expectMessage("Unknown allele");
-        new Genotype("AAA|T", "A", Arrays.asList("G", "C", "T")).getAllelesIdx();
+        IllegalArgumentException thrown = Assertions.assertThrows(IllegalArgumentException.class, () -> {
+            new Genotype("AAA|T", "A", Arrays.asList("G", "C", "T")).getAllelesIdx();
+        });
+        Assertions.assertEquals("Unable to parse genotype 'AAA|T'. Unknown allele \"AAA\". REF=A,ALT=G,C,T", thrown.getMessage());
     }
 
     @Test
     public void testParseFail2() {
+        /*
         thrown.expect(IllegalArgumentException.class);
         thrown.expectMessage("Empty allele");
         new Genotype("A|T|", "A", Arrays.asList("G", "C", "T")).getAllelesIdx();
+
+         */
+
+        IllegalArgumentException thrown = Assertions.assertThrows(IllegalArgumentException.class, () -> {
+            new Genotype("A|T|", "A", Arrays.asList("G", "C", "T")).getAllelesIdx();
+
+        });
+        Assertions.assertEquals("Unable to parse genotype 'A|T|'. Empty allele: REF=A,ALT=G,C,T", thrown.getMessage());
     }
 
     @Test
     public void testParseFail3() {
-        thrown.expect(IllegalArgumentException.class);
+      /*  thrown.expect(IllegalArgumentException.class);
         thrown.expectMessage("Empty allele");
-        new Genotype("|C", "A", Arrays.asList("G", "C", "T")).getAllelesIdx();
+        new Genotype("|C", "A", Arrays.asList("G", "C", "T")).getAllelesIdx();*/
+
+        IllegalArgumentException thrown = Assertions.assertThrows(IllegalArgumentException.class, () -> {
+            new Genotype("|C", "A", Arrays.asList("G", "C", "T")).getAllelesIdx();
+        });
+        Assertions.assertEquals("Unable to parse genotype '|C'. Empty allele: REF=A,ALT=G,C,T", thrown.getMessage());
     }
 
     @Test

diff --git a/biodata-models/src/test/java/org/opencb/biodata/models/variant/VariantBuilderTest.java b/biodata-models/src/test/java/org/opencb/biodata/models/variant/VariantBuilderTest.java
@@ -1,7 +1,8 @@
 package org.opencb.biodata.models.variant;
 
 import org.apache.commons.lang3.RandomStringUtils;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.models.variant.avro.*;
 import org.opencb.biodata.models.variant.protobuf.VariantProto;
 
@@ -240,14 +241,19 @@ public void buildIndelVariantNoEnd_large() {
         assertEquals(100 + ref.length() - 1, variant.getEnd().intValue());
     }
 
-    @Test(expected = IllegalArgumentException.class)
+    @Test
     public void buildIncompleteSV() throws Exception {
-        new VariantBuilder("1:1000:<DEL>").build();
+        IllegalArgumentException thrown = Assertions.assertThrows(IllegalArgumentException.class, () -> {
+            new VariantBuilder("1:1000:<DEL>").build();
+        });
+
     }
 
-    @Test(expected = IllegalArgumentException.class)
+    @Test
     public void buildIncompleteSV_2() throws Exception {
-        new VariantBuilder("1:1000:A:<DEL>").build();
+        IllegalArgumentException thrown = Assertions.assertThrows(IllegalArgumentException.class, () -> {
+            new VariantBuilder("1:1000:A:<DEL>").build();
+        });
     }
 
 

diff --git a/.../src/test/java/org/opencb/biodata/models/variant/VariantTransformToEnsemblFormatTest.java b/.../src/test/java/org/opencb/biodata/models/variant/VariantTransformToEnsemblFormatTest.java
@@ -16,7 +16,7 @@
 
 package org.opencb.biodata.models.variant;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
 import static org.junit.Assert.assertEquals;
 

diff --git a/biodata-models/src/test/java/org/opencb/biodata/models/variant/stats/VariantStatsTest.java b/biodata-models/src/test/java/org/opencb/biodata/models/variant/stats/VariantStatsTest.java
@@ -1,6 +1,6 @@
 package org.opencb.biodata.models.variant.stats;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
 import static org.junit.Assert.*;
 

diff --git a/biodata-tools/src/test/java/org/opencb/biodata/tools/alignment/BamManagerTest.java b/biodata-tools/src/test/java/org/opencb/biodata/tools/alignment/BamManagerTest.java
@@ -1,9 +1,10 @@
 package org.opencb.biodata.tools.alignment;
 
 import htsjdk.samtools.*;
-import org.junit.Assume;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Assumptions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.models.alignment.RegionCoverage;
 import org.opencb.biodata.models.core.Region;
 import org.opencb.biodata.tools.alignment.exceptions.AlignmentCoverageException;
@@ -32,9 +33,9 @@ public class BamManagerTest {
     Path bamPath;
     Path bwPath;
 
-    @Before
+    @BeforeEach
     public void init() throws URISyntaxException, IOException {
-        Assume.assumeTrue(bamCoverageExists());
+        Assumptions.assumeTrue(bamCoverageExists());
 
         inputPath = Paths.get(getClass().getResource("/HG00096.chrom20.small.bam").toURI());
         bamPath = Paths.get("/tmp/" + inputPath.toFile().getName());
@@ -80,14 +81,14 @@ public void testQuery() throws Exception {
         AlignmentOptions options = new AlignmentOptions().setLimit(5);
         Region region = new Region("20", 60000, 65000);
         List<SAMRecord> query = bamManager.query(region, options);
-        assertEquals(5, query.size());
+        Assertions.assertEquals(5, query.size());
 
         options.setLimit(3);
         query = bamManager.query(region, options);
         for (SAMRecord sam: query) {
             System.out.println(sam.toString());
         }
-        assertEquals(3, query.size());
+        Assertions.assertEquals(3, query.size());
     }
 
     @Test

diff --git a/...encb/biodata/tools/alignment/converters/SAMRecordToProtoReadAlignmentBiConverterTest.java b/...encb/biodata/tools/alignment/converters/SAMRecordToProtoReadAlignmentBiConverterTest.java
@@ -2,7 +2,7 @@
 
 import ga4gh.Reads;
 import htsjdk.samtools.*;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
 import java.io.IOException;
 import java.net.URISyntaxException;

diff --git a/...-tools/src/test/java/org/opencb/biodata/tools/alignment/filters/SamRecordFiltersTest.java b/...-tools/src/test/java/org/opencb/biodata/tools/alignment/filters/SamRecordFiltersTest.java
@@ -1,7 +1,7 @@
 package org.opencb.biodata.tools.alignment.filters;
 
 import htsjdk.samtools.SAMRecord;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.models.core.Region;
 import org.opencb.biodata.tools.alignment.AlignmentOptions;
 import org.opencb.biodata.tools.alignment.BamManager;

diff --git a/...pencb/biodata/tools/alignment/iterators/SAMRecordToProtoReadAlignmentBiConverterTest.java b/...pencb/biodata/tools/alignment/iterators/SAMRecordToProtoReadAlignmentBiConverterTest.java
@@ -1,7 +1,7 @@
 package org.opencb.biodata.tools.alignment.iterators;
 
 import htsjdk.samtools.SAMRecord;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.models.core.Region;
 import org.opencb.biodata.tools.alignment.AlignmentOptions;
 import org.opencb.biodata.tools.alignment.BamManager;

diff --git a/...est/java/org/opencb/biodata/tools/alignment/tasks/AlignmentGlobalStatsCalculatorTest.java b/...est/java/org/opencb/biodata/tools/alignment/tasks/AlignmentGlobalStatsCalculatorTest.java
@@ -2,7 +2,7 @@
 
 import htsjdk.samtools.SAMRecord;
 import org.ga4gh.models.ReadAlignment;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.tools.alignment.BamManager;
 import org.opencb.biodata.tools.alignment.AlignmentOptions;
 import org.opencb.biodata.tools.alignment.iterators.BamIterator;

diff --git a/biodata-tools/src/test/java/org/opencb/biodata/tools/commons/ChunkFrequencyManagerTest.java b/biodata-tools/src/test/java/org/opencb/biodata/tools/commons/ChunkFrequencyManagerTest.java
@@ -1,6 +1,6 @@
 package org.opencb.biodata.tools.commons;
 
-import org.junit.Before;
+import org.junit.jupiter.api.BeforeEach;
 import org.opencb.biodata.models.core.Region;
 import org.opencb.biodata.tools.alignment.BamUtils;
 import org.opencb.biodata.tools.feature.WigUtils;
@@ -19,7 +19,7 @@ public class ChunkFrequencyManagerTest {
     int chunkSize = 1000;
     int windowSize = 100;
 
-    @Before
+    @BeforeEach
     public void init() throws Exception {
         bamPath = Paths.get(getClass().getResource("/HG00096.chrom20.small.bam").toURI());
         coverageWigPath = Paths.get("/tmp/" + bamPath.toFile().getName() + ".bam.coverage.wig");

diff --git a/biodata-tools/src/test/java/org/opencb/biodata/tools/feature/BigWigManagerTest.java b/biodata-tools/src/test/java/org/opencb/biodata/tools/feature/BigWigManagerTest.java
@@ -1,9 +1,8 @@
 package org.opencb.biodata.tools.feature;
 
 import org.broad.igv.bbfile.*;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.models.core.Region;
-import org.opencb.biodata.tools.commons.ChunkFrequencyManager;
 
 import java.nio.file.Path;
 import java.nio.file.Paths;

diff --git a/biodata-tools/src/test/java/org/opencb/biodata/tools/pedigree/ModeOfInheritanceTest.java b/biodata-tools/src/test/java/org/opencb/biodata/tools/pedigree/ModeOfInheritanceTest.java
@@ -1,7 +1,7 @@
 package org.opencb.biodata.tools.pedigree;
 
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
 import org.opencb.biodata.models.clinical.Disorder;
 import org.opencb.biodata.models.clinical.pedigree.Member;
 import org.opencb.biodata.models.clinical.pedigree.Pedigree;
@@ -36,7 +36,7 @@ public class ModeOfInheritanceTest {
     Disorder disorder3;
     Disorder disorder4;
 
-    @Before
+    @BeforeEach
     public void before() {
         disorder1 = new Disorder("disease1", "disease1", "", "", Collections.emptyList(), Collections.emptyMap());
         disorder2 = new Disorder("disease2", "disease2", "", "", Collections.emptyList(), Collections.emptyMap());