diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 3eb9f4994e..a5c43b5839 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -81,5 +81,11 @@ org.glassfish.jaxb jaxb-runtime + + io.github.jensdietrich.saflate + saflate-network-junit4 + 1.0.0 + test + \ No newline at end of file diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java index a49dae544a..87571dd2e4 100644 --- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java +++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java @@ -22,12 +22,11 @@ import java.io.File; import java.net.URL; + +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.core.search.io.blast.BlastXMLParser; -import org.junit.After; -import org.junit.AfterClass; -import org.junit.Before; -import org.junit.BeforeClass; -import org.junit.Test; +import org.junit.*; + import static org.junit.Assert.*; /** @@ -40,7 +39,8 @@ */ public class SearchIOTest { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); public SearchIOTest() { } diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java index 45de0dbd19..5ba918db62 100644 --- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java +++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java @@ -24,23 +24,22 @@ import java.net.URL; import java.util.ArrayList; import java.util.List; + +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.core.search.io.Hit; import org.biojava.nbio.core.search.io.Hsp; import org.biojava.nbio.core.search.io.Result; -import org.junit.After; -import org.junit.AfterClass; -import org.junit.Before; -import org.junit.BeforeClass; -import org.junit.Test; +import org.junit.*; + import static org.junit.Assert.*; -import org.junit.Ignore; /** * * @author Paolo Pavan */ public class BlastXMLParserTest { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); public BlastXMLParserTest() { } diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java index d6018a5eaf..2ce30347e3 100644 --- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java +++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java @@ -20,6 +20,7 @@ */ package org.biojava.nbio.core.sequence.io; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.core.sequence.DNASequence; import org.biojava.nbio.core.sequence.ProteinSequence; import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; @@ -39,7 +40,8 @@ * @author Scooter Willis */ public class GenbankCookbookTest { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); private final static Logger logger = LoggerFactory.getLogger(GenbankCookbookTest.class); public GenbankCookbookTest() { diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java index 6883637a49..e9f7e40b7e 100644 --- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java +++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java @@ -20,6 +20,7 @@ */ package org.biojava.nbio.core.sequence.loader; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.core.exceptions.CompoundNotFoundException; import org.biojava.nbio.core.sequence.ProteinSequence; import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; @@ -30,6 +31,7 @@ import org.biojava.nbio.core.sequence.template.AbstractSequence; import org.junit.Assert; import org.junit.Before; +import org.junit.Rule; import org.junit.Test; import org.junit.runner.RunWith; import org.junit.runners.Parameterized; @@ -55,6 +57,8 @@ */ @RunWith(Parameterized.class) public class GenbankProxySequenceReaderTest { + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); private String gi; private final static Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReaderTest.class); diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 8c770abe7a..47b39ff70c 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -60,6 +60,12 @@ org.apache.logging.log4j log4j-core + + io.github.jensdietrich.saflate + saflate-network-junit4 + 1.0.0 + test + A module which only has the purpose to run slow running integration tests. diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java index 8ab3f29fb3..2c32067e66 100644 --- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java +++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java @@ -38,6 +38,7 @@ import java.util.regex.Matcher; import java.util.regex.Pattern; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.core.util.ConcurrencyTools; import org.biojava.nbio.structure.ResidueNumber; import org.biojava.nbio.structure.ResidueRange; @@ -59,7 +60,8 @@ * */ public class EcodInstallationTest { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); private static final Logger logger = LoggerFactory.getLogger(EcodInstallationTest.class); private static final String VERSION = "develop204"; // Should be updated periodically diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierIntegrationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierIntegrationTest.java index 1a66090ccd..9c83e5c12d 100644 --- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierIntegrationTest.java +++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierIntegrationTest.java @@ -1,5 +1,6 @@ package org.biojava.nbio.structure.test.io.cif; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.structure.AminoAcidImpl; import org.biojava.nbio.structure.Atom; import org.biojava.nbio.structure.AtomImpl; @@ -13,6 +14,7 @@ import org.biojava.nbio.structure.StructureImpl; import org.biojava.nbio.structure.StructureTools; import org.biojava.nbio.structure.io.cif.CifStructureConverter; +import org.junit.Rule; import org.junit.Test; import java.io.ByteArrayInputStream; @@ -26,6 +28,8 @@ import static org.junit.Assert.assertNotNull; public class CifFileSupplierIntegrationTest { + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); @Test public void test1SMT() throws IOException { // an x-ray structure diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java index 08946e3e0a..993c3e1aa3 100644 --- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java +++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java @@ -25,6 +25,7 @@ import java.io.IOException; import java.util.*; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.structure.Structure; import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.io.StructureFiletype; @@ -42,6 +43,7 @@ import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults; import org.biojava.nbio.structure.symmetry.core.Stoichiometry; import org.junit.Ignore; +import org.junit.Rule; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -55,7 +57,8 @@ * */ public class TestQuatSymmetryDetectorExamples { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); private static final Logger logger = LoggerFactory.getLogger(TestQuatSymmetryDetectorExamples.class); /** diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 3151924f82..69bbb6a40f 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -122,6 +122,13 @@ org.junit.vintage junit-vintage-engine + + io.github.jensdietrich.saflate + saflate-network-junit4 + 1.0.0 + test + + diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java index 82e26bd802..beb3a430ae 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java @@ -20,8 +20,10 @@ */ package org.biojava.nbio.structure; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.structure.PDBStatus.Status; import org.junit.Assert; +import org.junit.Rule; import org.junit.Test; import java.io.IOException; @@ -31,6 +33,8 @@ * */ public class PDBStatusTest { + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); /** * Test {@link PDBStatus#getStatus(String)}. diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestLoadStructureFromURL.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestLoadStructureFromURL.java index 5ba56deb19..ffa8901b2a 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestLoadStructureFromURL.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestLoadStructureFromURL.java @@ -20,10 +20,12 @@ */ package org.biojava.nbio.structure; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.align.util.UserConfiguration; import org.biojava.nbio.structure.io.PDBFileReader; import org.biojava.nbio.structure.io.StructureFiletype; +import org.junit.Rule; import org.junit.Test; import java.io.File; @@ -34,7 +36,8 @@ public class TestLoadStructureFromURL { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); public static final String lineSplit = System.getProperty("file.separator"); diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java index 57fc673340..58d72e6a3a 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java @@ -40,6 +40,7 @@ import java.util.Locale; import java.util.zip.GZIPOutputStream; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.core.util.FileDownloadUtils; import org.biojava.nbio.structure.AtomPositionMap; import org.biojava.nbio.structure.Chain; @@ -65,6 +66,7 @@ import org.biojava.nbio.structure.test.util.GlobalsHelper; import org.junit.After; import org.junit.Before; +import org.junit.Rule; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -76,7 +78,8 @@ * @since 3.0.6 */ public class AtomCacheTest { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); private static Logger logger = LoggerFactory.getLogger(AtomCacheTest.class); private AtomCache cache; diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/chem/TestDownloadChemCompProvider.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/chem/TestDownloadChemCompProvider.java index d690021cc9..be56453669 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/chem/TestDownloadChemCompProvider.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/chem/TestDownloadChemCompProvider.java @@ -20,10 +20,12 @@ */ package org.biojava.nbio.structure.chem; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.core.util.FlatFileCache; import org.biojava.nbio.structure.chem.ChemComp; import org.biojava.nbio.structure.chem.DownloadChemCompProvider; import org.biojava.nbio.structure.io.LocalPDBDirectory; +import org.junit.Rule; import org.junit.Test; import static org.junit.Assert.*; @@ -35,7 +37,8 @@ import java.util.zip.GZIPOutputStream; public class TestDownloadChemCompProvider { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); @Test public void testProtectedIDs(){ diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java index 26bf9c3ac8..9607a19549 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java @@ -34,6 +34,7 @@ import java.util.List; import java.util.zip.GZIPInputStream; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.structure.Chain; import org.biojava.nbio.structure.EntityInfo; import org.biojava.nbio.structure.EntityType; @@ -43,6 +44,7 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.cif.CifStructureConverter; import org.biojava.nbio.structure.xtal.CrystalCell; +import org.junit.Rule; import org.junit.Test; /** @@ -56,7 +58,8 @@ * */ public class TestNonDepositedFiles { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); @Test public void test1B8GnoSeqresPdb() throws IOException, StructureException { diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java index 2adb5ab358..07d40b13d3 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java @@ -23,9 +23,11 @@ import java.io.IOException; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.structure.Structure; import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.StructureIO; +import org.junit.Rule; import org.junit.Test; import static org.junit.Assert.*; @@ -33,7 +35,8 @@ * Created by ap3 on 31/07/2015. */ public class TestURLBasedFileParsing { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); @Test public void testMMcifURL() throws StructureException, IOException{ diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java index e0b576d79a..aee77f3423 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java @@ -20,7 +20,9 @@ */ package org.biojava.nbio.structure.io.mmtf; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.structure.io.PDBFileParser; +import org.junit.Rule; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -39,7 +41,8 @@ * */ public class TestMmtfPerformance { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); private static final Logger logger = LoggerFactory.getLogger(TestMmtfPerformance.class); private static final int NUMBER_OF_REPEATS = 10; diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java index e362c2a35f..f63e1ed196 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java @@ -29,6 +29,7 @@ import java.util.List; import java.util.Map; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.structure.Atom; import org.biojava.nbio.structure.Bond; import org.biojava.nbio.structure.Chain; @@ -44,6 +45,7 @@ import org.biojava.nbio.structure.io.cif.CifStructureConverter; import org.biojava.nbio.structure.quaternary.BioAssemblyInfo; import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation; +import org.junit.Rule; import org.junit.Test; import org.rcsb.mmtf.decoder.StructureDataToAdapter; import org.rcsb.mmtf.encoder.AdapterToStructureData; @@ -57,8 +59,8 @@ * */ public class TestMmtfRoundTrip { - - /** + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); /** * Test that we can round trip a simple structure. * * @throws IOException an error reading the file diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java index 57612fc8d6..99a3f2c093 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java @@ -25,9 +25,11 @@ import java.util.List; import java.util.zip.GZIPInputStream; +import nz.ac.wgtn.saflate.network.junit4.SanitiseNetworkDependenciesRule; import org.biojava.nbio.structure.Structure; import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Rule; import org.junit.Test; import static org.junit.Assert.*; @@ -40,7 +42,8 @@ * */ public class TestDSSPParser { - + @Rule + public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule(); @Test public void testDSSPParser() throws IOException, StructureException { diff --git a/pom.xml b/pom.xml index 6c96f9f9d4..3e1fee472e 100644 --- a/pom.xml +++ b/pom.xml @@ -470,6 +470,13 @@ 2.3.5 runtime + + io.github.jensdietrich.saflate + saflate-network-junit4 + 1.0.0 + test + +