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fixes biojava/biojava#910 for network flaky tests #1022

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fixes biojava/biojava#910 for network flaky tests #1022

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6 changes: 6 additions & 0 deletions biojava-core/pom.xml
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Expand Up @@ -81,5 +81,11 @@
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
</dependency>
<dependency>
<groupId>io.github.jensdietrich.saflate</groupId>
<artifactId>saflate-network-junit4</artifactId>
<version>1.0.0</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
12 changes: 6 additions & 6 deletions biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java
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Expand Up @@ -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.*;

/**
Expand All @@ -40,7 +39,8 @@
*/

public class SearchIOTest {

@Rule
public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule();
public SearchIOTest() {
}

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13 changes: 6 additions & 7 deletions biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java
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Expand Up @@ -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() {
}

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4 changes: 3 additions & 1 deletion biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
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Expand Up @@ -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;
Expand All @@ -39,7 +40,8 @@
* @author Scooter Willis <willishf at gmail dot com>
*/
public class GenbankCookbookTest {

@Rule
public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule();
private final static Logger logger = LoggerFactory.getLogger(GenbankCookbookTest.class);

public GenbankCookbookTest() {
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4 changes: 4 additions & 0 deletions ...e/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
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Expand Up @@ -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;
Expand All @@ -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;
Expand All @@ -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);
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6 changes: 6 additions & 0 deletions biojava-integrationtest/pom.xml
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Expand Up @@ -60,6 +60,12 @@
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>io.github.jensdietrich.saflate</groupId>
<artifactId>saflate-network-junit4</artifactId>
<version>1.0.0</version>
<scope>test</scope>
</dependency>
</dependencies>
<description>A module which only has the purpose to run slow running integration tests.

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4 changes: 3 additions & 1 deletion ...egrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
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Expand Up @@ -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;
Expand All @@ -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

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4 changes: 4 additions & 0 deletions .../src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierIntegrationTest.java
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@@ -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;
Expand All @@ -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;
Expand All @@ -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
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5 changes: 4 additions & 1 deletion .../test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java
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Expand Up @@ -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;
Expand All @@ -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;
Expand All @@ -55,7 +57,8 @@
*
*/
public class TestQuatSymmetryDetectorExamples {

@Rule
public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule();
private static final Logger logger = LoggerFactory.getLogger(TestQuatSymmetryDetectorExamples.class);

/**
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7 changes: 7 additions & 0 deletions biojava-structure/pom.xml
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Expand Up @@ -122,6 +122,13 @@
<groupId>org.junit.vintage</groupId>
<artifactId>junit-vintage-engine</artifactId>
</dependency>
<dependency>
<groupId>io.github.jensdietrich.saflate</groupId>
<artifactId>saflate-network-junit4</artifactId>
<version>1.0.0</version>
<scope>test</scope>
</dependency>


</dependencies>

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4 changes: 4 additions & 0 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java
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Expand Up @@ -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;
Expand All @@ -31,6 +33,8 @@
*
*/
public class PDBStatusTest {
@Rule
public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule();

/**
* Test {@link PDBStatus#getStatus(String)}.
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5 changes: 4 additions & 1 deletion biojava-structure/src/test/java/org/biojava/nbio/structure/TestLoadStructureFromURL.java
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Expand Up @@ -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;
Expand All @@ -34,7 +36,8 @@


public class TestLoadStructureFromURL {

@Rule
public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule();
public static final String lineSplit = System.getProperty("file.separator");


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5 changes: 4 additions & 1 deletion biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
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Expand Up @@ -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;
Expand All @@ -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;
Expand All @@ -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;

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5 changes: 4 additions & 1 deletion ...structure/src/test/java/org/biojava/nbio/structure/chem/TestDownloadChemCompProvider.java
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Expand Up @@ -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.*;

Expand All @@ -35,7 +37,8 @@
import java.util.zip.GZIPOutputStream;

public class TestDownloadChemCompProvider {

@Rule
public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule();
@Test
public void testProtectedIDs(){

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5 changes: 4 additions & 1 deletion biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java
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Expand Up @@ -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;
Expand All @@ -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;

/**
Expand All @@ -56,7 +58,8 @@
*
*/
public class TestNonDepositedFiles {

@Rule
public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule();
@Test
public void test1B8GnoSeqresPdb() throws IOException, StructureException {

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5 changes: 4 additions & 1 deletion biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java
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Expand Up @@ -23,17 +23,20 @@

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.*;

/**
* Created by ap3 on 31/07/2015.
*/
public class TestURLBasedFileParsing {

@Rule
public SanitiseNetworkDependenciesRule rule = new SanitiseNetworkDependenciesRule();
@Test
public void testMMcifURL() throws StructureException, IOException{

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5 changes: 4 additions & 1 deletion biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java
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Expand Up @@ -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;
Expand All @@ -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;
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6 changes: 4 additions & 2 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
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Expand Up @@ -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;
Expand All @@ -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;
Expand All @@ -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
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