Subject: remove tests needing network Description: debian builds expects to run with no network Author: Olivier Sallou Pierre Gruet Last-Updated: 2021-10-19 Forwarded: not-needed --- 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 @@ -67,21 +67,6 @@ @Test public void testProcess() throws Throwable { /* - * Method 1: With the GenbankProxySequenceReader - */ - //Try with the GenbankProxySequenceReader - GenbankProxySequenceReader genbankProteinReader - = new GenbankProxySequenceReader(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet()); - ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader); - genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence); - //logger.info("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10)); - - GenbankProxySequenceReader genbankDNAReader - = new GenbankProxySequenceReader(System.getProperty("java.io.tmpdir"), "NM_001126", DNACompoundSet.getDNACompoundSet()); - DNASequence dnaSequence = new DNASequence(genbankDNAReader); - genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); - //logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); - /* * Method 2: With the GenbankReaderHelper */ //Try with the GenbankReaderHelper --- a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java +++ b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java @@ -67,20 +67,6 @@ private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOException { - ProteinSequence seq = getUniprot(uniprotID); - - AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet(); - -/* for (AminoAcidCompound compound : seq) { - System.out.println(compound.getShortName() + " " + compound.getLongName() + " " + compound.getDescription() + " | " + compoundSet.getEquivalentCompounds(compound) + " " + compound.getMolecularWeight() + " " + compound.getBase()); - } - */ - assertTrue(compoundSet.isValidSequence(seq)); - - - - Jronn.getDisorderScores(seq); - } --- 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 @@ -124,99 +124,9 @@ @Test public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException { - logger.info("run test for protein: {}", gi); - GenbankProxySequenceReader genbankReader - = new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"), - this.gi, - AminoAcidCompoundSet.getAminoAcidCompoundSet()); - - // why only tests on protein sequences? - ProteinSequence seq = new ProteinSequence(genbankReader); - - Assert.assertNotNull("protein sequence is null", seq); - - /* - parse description from header. There is no separate interface/abstract class for method getHeader() - so it should be done here (manualy). - */ - genbankReader.getHeaderParser().parseHeader(genbankReader.getHeader(), seq); - - // test description - Assert.assertNotNull(seq.getDescription()); - - // test accession Id - logger.info("accession id: {}", seq.getAccession().getID()); - Assert.assertNotNull(seq.getAccession().getID()); - // test GID number - if( seq.getAccession().getIdentifier() != null) { // GI: in header now optional. See #596 - Assert.assertEquals(gi, seq.getAccession().getIdentifier()); - logger.info("found identifier '{}'", seq.getAccession().getIdentifier()); - } - // test taxonomy id - logger.info("taxonomy id: {}", seq.getTaxonomy().getID()); - Assert.assertNotNull(seq.getTaxonomy().getID()); - Assert.assertNotNull(Integer.decode(seq.getTaxonomy().getID().split(":")[1])); - - // test taxonomy name - String taxonName = seq.getFeaturesByType("source").get(0).getQualifiers().get("organism").get(0).getValue(); - logger.info("taxonomy name '{}'", taxonName); - Assert.assertNotNull(taxonName); - - if (seq.getFeaturesByType("CDS").size() > 0) { - FeatureInterface, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0); - logger.info("CDS: {}", CDS); - String codedBy = CDS.getQualifiers().get("coded_by").get(0).getValue(); - Assert.assertNotNull(codedBy); - Assert.assertTrue(!codedBy.isEmpty()); - logger.info("\t\tcoded_by: {}", codedBy); - } - - // genbank has limits on requests per second, we need to give it some time for next test or otherwise we get 429 http error codes - JD 2018-12-14 - // See https://github.com/biojava/biojava/issues/837 - Thread.sleep(500); } @Test public void testProteinSequenceFactoring() throws Exception { - logger.info("create protein sequence test for target {}", gi); - - GenbankProxySequenceReader genbankReader - = new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"), - this.gi, - AminoAcidCompoundSet.getAminoAcidCompoundSet()); - - ProteinSequence seq = new ProteinSequence(genbankReader); - - // if target protein contain CDS/coded_by than it should contain parent nucleotide seq - List, AminoAcidCompound>> CDSs = genbankReader.getFeatures().get("CDS"); - - if (CDSs != null) { - if (CDSs.size() == 1) { - final Map> qualifiers = CDSs.get(0).getQualifiers(); - List codedByQualifiers = qualifiers.get("coded_by"); - Qualifier codedBy = codedByQualifiers.get(0); - if (codedBy != null) { - - AbstractSequence parentSeq = seq.getParentSequence(); - Assert.assertNotNull(parentSeq); - - /* - Sometimes protein might have many 'parents' with different accessions - so accession is not set. - - That test is always failed - */ - //Assert.assertTrue(parentSeq.getAccession()); - Assert.assertTrue(!parentSeq.getSequenceAsString().isEmpty()); - } - } - } else { - logger.info("target {} has no CDS", gi); - } - - // genbank has limits on requests per second, we need to give it some time for next test or otherwise we get 429 http error codes - JD 2018-12-14 - // See https://github.com/biojava/biojava/issues/837 - Thread.sleep(500); - } } --- 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 @@ -27,6 +27,7 @@ import org.junit.AfterClass; import org.junit.Before; import org.junit.BeforeClass; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -78,6 +79,7 @@ /** * Constructor test specifying Factory */ + @Ignore("The test requires the network") @Test public void testConstructorWithoutFactoryGuess() { String resource = "/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml"; @@ -95,6 +97,7 @@ /** * Constructor test specifying Factory and using a evalue threshold filter */ + @Ignore("The test requires the network") @Test public void testConstructorWithEvalueHspFilter() { // --- 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 @@ -84,6 +84,7 @@ /** * Test of createObjects method, of class BlastXMLParser. */ + @Ignore("The test requires the network") @Test public void testCreateObjects() throws Exception { System.out.println("createObjects"); --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/AtomPositionMapTest.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/AtomPositionMapTest.java @@ -26,6 +26,7 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.LocalPDBDirectory; import org.junit.Before; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -53,6 +54,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testEasy() throws IOException, StructureException { // no insertion codes // Straightforward case. Density for residues 25-777 (743 residues) @@ -69,6 +71,7 @@ assertEquals("Real atom length is wrong", length, realLength); } + @Ignore("The test requires the network") @Test public void testLengths() throws IOException, StructureException { // Two identical chains, residues 1-68, no insertion codes or missing residues @@ -176,6 +179,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testInsertionCodes() throws IOException, StructureException { String pdbId = "1qdm"; @@ -204,6 +208,7 @@ assertEquals("Full length wrong",430,realLength); } + @Ignore("The test requires the network") @Test public void testTrim() throws IOException, StructureException { // Two identical chains, residues 1-68, no insertion codes or missing residues @@ -254,6 +259,7 @@ } + @Ignore("The test requires the network") @Test public void testChains() throws IOException, StructureException { String pdbId = "1qdm"; --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java @@ -42,10 +42,12 @@ import org.biojava.nbio.structure.io.FileParsingParameters; import org.biojava.nbio.structure.io.StructureFiletype; import org.biojava.nbio.structure.io.cif.CifStructureConverter; +import org.junit.Ignore; import org.junit.Test; public class TestAltLocs { + @Ignore("The test requires the network") @Test public void testAltLocParsing() throws StructureException, IOException{ @@ -116,6 +118,7 @@ } + @Ignore("The test requires the network") @Test public void test2W72() throws IOException, StructureException{ @@ -138,6 +141,7 @@ } + @Ignore("The test requires the network") @Test public void test1U7F() throws IOException, StructureException{ @@ -156,6 +160,7 @@ } + @Ignore("The test requires the network") @Test public void test1JXX() throws IOException, StructureException{ @@ -209,6 +214,7 @@ } } + @Ignore("The test requires the network") @Test public void test1AAC() throws IOException, StructureException{ @@ -254,6 +260,7 @@ } + @Ignore("The test requires the network") @Test public void test3PIUpdb() throws IOException, StructureException{ @@ -321,6 +328,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testAllAltLocsSameAtomsMainGroup() throws IOException, StructureException { doTestAllAltLocsSamAtomsMainGroup("3nu4"); @@ -360,6 +368,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testAddBondsDoesntChangeGroups() throws IOException, StructureException { AtomCache cache = new AtomCache(); @@ -419,6 +428,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void test4CUPBonds() throws IOException, StructureException{ @@ -482,6 +492,7 @@ } + @Ignore("The test requires the network") @Test public void test3PIUmmcif() throws IOException, StructureException{ @@ -542,6 +553,7 @@ } + @Ignore("The test requires the network") @Test public void test3U7Tmmcif() throws IOException, StructureException{ --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBioAssemblyIdentifier.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBioAssemblyIdentifier.java @@ -25,11 +25,13 @@ import java.io.IOException; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Ignore; import org.junit.Test; public class TestBioAssemblyIdentifier { + @Ignore("The test requires the network") @Test public void test() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestChargeAdder.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestChargeAdder.java @@ -25,6 +25,7 @@ import java.io.IOException; import org.biojava.nbio.structure.io.ChargeAdder; +import org.junit.Ignore; import org.junit.Test; /** @@ -40,6 +41,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testBasic() throws IOException, StructureException { @@ -67,6 +69,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testQuestionMark() throws IOException, StructureException { // Get the structure --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityResIndexMapping.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityResIndexMapping.java @@ -44,6 +44,7 @@ private static final String PATH_TO_TEST_FILES = "/org/biojava/nbio/structure/io/"; + @Ignore("The test requires the network") @Test public void test1B8G() throws IOException, StructureException { @@ -66,6 +67,7 @@ } + @Ignore("The test requires the network") @Test public void test1SMT() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestExperimentalTechniques.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestExperimentalTechniques.java @@ -22,6 +22,7 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.StructureFiletype; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -31,6 +32,7 @@ public class TestExperimentalTechniques { + @Ignore("The test requires the network") @Test public void test6F2Q() throws IOException, StructureException { @@ -61,6 +63,7 @@ } + @Ignore("The test requires the network") @Test public void test3ZPK() throws IOException, StructureException { @@ -91,6 +94,7 @@ } + @Ignore("The test requires the network") @Test public void test2B6O() throws IOException, StructureException { @@ -121,6 +125,7 @@ } + @Ignore("The test requires the network") @Test public void test4CSO() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestLoadStructureFromURL.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestLoadStructureFromURL.java @@ -24,6 +24,7 @@ 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.Ignore; import org.junit.Test; import java.io.File; @@ -38,6 +39,7 @@ public static final String lineSplit = System.getProperty("file.separator"); + @Ignore("The test requires the network") @Test public void testLoadStructureFromURL() throws IOException, StructureException{ --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java @@ -26,6 +26,7 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.StructureFiletype; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -37,6 +38,7 @@ public class TestParsingCalcium { + @Ignore("The test requires the network") @Test public void testCalciumParsing() throws StructureException, IOException { @@ -64,6 +66,7 @@ } + @Ignore("The test requires the network") @Test public void testCAreturnsCalpha() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java @@ -35,6 +35,7 @@ import org.biojava.nbio.structure.io.FileParsingParameters; import org.biojava.nbio.structure.io.StructureFiletype; import org.biojava.nbio.structure.xtal.CrystalBuilder; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -46,6 +47,7 @@ private static final String PDBCODE1 = "1smt"; private static final String PDBCODE2 = "2mre"; + @Ignore("The test requires the network") @Test public void testCrossReferencesMmCif() throws IOException, StructureException { boolean emptySeqRes = true; @@ -69,6 +71,7 @@ } + @Ignore("The test requires the network") @Test public void testCrossReferencesMmCifAlignSeqRes() throws IOException, StructureException { boolean emptySeqRes = false; @@ -94,6 +97,7 @@ } + @Ignore("The test requires the network") @Test public void testCrossReferencesPdb() throws IOException, StructureException { boolean emptySeqRes = true; @@ -116,6 +120,7 @@ } + @Ignore("The test requires the network") @Test public void testCrossReferencesPdbAlignSeqRes() throws IOException, StructureException { boolean emptySeqRes = false; --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/TestAlignmentConsistency.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/TestAlignmentConsistency.java @@ -28,6 +28,7 @@ import org.biojava.nbio.structure.align.fatcat.FatCatRigid; import org.biojava.nbio.structure.align.model.AFPChain; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -38,6 +39,7 @@ public class TestAlignmentConsistency { // Check that indices of the aligned residues are unique + @Ignore("The test requires the network") @Test public void testDuplicateIndices() throws IOException, StructureException { String[] algorithmIDs = {CeMain.algorithmName, FatCatRigid.algorithmName}; --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java @@ -30,6 +30,7 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.PDBParseException; import org.junit.Assert; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -402,6 +403,7 @@ return ca1; } + @Ignore("The test requires the network") @Test public void testCECP1() throws IOException, StructureException{ --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestSmallAlignment.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestSmallAlignment.java @@ -32,6 +32,7 @@ import org.biojava.nbio.structure.align.xml.AFPChainXMLConverter; import org.biojava.nbio.structure.align.xml.AFPChainXMLParser; import org.junit.Assert; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -39,6 +40,7 @@ public class TestSmallAlignment { + @Ignore("The test requires the network") @Test public void test1a4w() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java @@ -28,6 +28,7 @@ import org.biojava.nbio.structure.align.multiple.MultipleAlignment; import org.biojava.nbio.structure.align.multiple.TestSampleGenerator; import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -63,6 +64,7 @@ alignment2 = TestSampleGenerator.testAlignment2(); } + @Ignore("The test requires the network") @Test public void testFASTA1() throws IOException { @@ -83,6 +85,7 @@ assertEquals(expected, result); } + @Ignore("The test requires the network") @Test public void testFASTA2() throws IOException { @@ -103,6 +106,7 @@ assertEquals(expected, result); } + @Ignore("The test requires the network") @Test public void testFatCat1() throws IOException { @@ -123,6 +127,7 @@ assertEquals(expected, result); } + @Ignore("The test requires the network") @Test public void testFatCat2() throws IOException { @@ -143,6 +148,7 @@ assertEquals(expected, result); } + @Ignore("The test requires the network") @Test public void testAlignedResidues1() throws IOException { @@ -164,6 +170,7 @@ assertEquals(expected, result); } + @Ignore("The test requires the network") @Test public void testAlignedResidues2() throws IOException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentXMLParser.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentXMLParser.java @@ -36,6 +36,7 @@ import org.biojava.nbio.structure.align.multiple.TestSampleGenerator; import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter; import org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser; +import org.junit.Ignore; import org.junit.Test; import org.xml.sax.SAXException; @@ -52,6 +53,7 @@ */ public class TestMultipleAlignmentXMLParser { + @Ignore("The test requires the network") @Test public void testRecovery1() throws StructureException, IOException, ParserConfigurationException, SAXException { @@ -70,6 +72,7 @@ assertTrue(equals(before,after)); } + @Ignore("The test requires the network") @Test public void testRecovery2() throws StructureException, IOException, ParserConfigurationException, SAXException { --- 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 @@ -65,6 +65,7 @@ import org.biojava.nbio.structure.test.util.GlobalsHelper; import org.junit.After; import org.junit.Before; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -100,6 +101,7 @@ /** * Tests {@link AtomCache#getStructureForDomain(String)} on a multi-chain domain with no ligands but an explicit range (not whole-chain). */ + @Ignore("The test requires the network") @Test public void testGetStructureForDomain1() throws IOException, StructureException { String ranges = "A:328-396,B:518-527"; @@ -119,6 +121,7 @@ /** * Tests {@link AtomCache#getStructureForDomain(String)} on a multi-chain domain with two zinc ligands that occurs after the TER. The ligands are in chains E and F, so they should not be included in the domain. */ + @Ignore("The test requires the network") @Test public void testGetStructureForDomain2() throws IOException, StructureException { String ranges = "A:,B:"; @@ -144,6 +147,7 @@ /** * Tests {@link AtomCache#getStructureForDomain(String)} on a single-chain domain with two zinc ligands that occurs after the TER. */ + @Ignore("The test requires the network") @Test public void testGetStructureForDomain3() throws IOException, StructureException { String ranges = "E:"; @@ -167,6 +171,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void testGetStructureForChainlessDomains() throws IOException, StructureException { ScopDatabase scop = ScopFactory.getSCOP(ScopFactory.VERSION_1_71); // Uses the range '1-135' without a chain @@ -201,6 +206,7 @@ assertEquals(System.getProperty("user.home") + File.separator, cache1.getPath()); } + @Ignore("The test requires the network") @Test public void testFetchBehavior() throws IOException, ParseException { // really more of a LocalPDBDirectory test, but throw it in with AtomCache @@ -288,6 +294,7 @@ } + @Ignore("The test requires the network") @Test public void testSeqRes() throws StructureException, IOException { String name; @@ -362,6 +369,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void testEmptyChemComp() throws IOException, StructureException { Path tmpCache = Paths.get(System.getProperty("java.io.tmpdir"),"BIOJAVA_TEST_CACHE"); @@ -420,6 +428,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void testEmptyGZChemComp() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java @@ -49,6 +49,7 @@ public class TestAsaCalc { + @Ignore("The test requires the network") @Test public void testAsa3PIU() throws StructureException, IOException { @@ -114,6 +115,7 @@ // nothing to assert } + @Ignore("The test requires the network") @Test public void testNeighborIndicesFinding() throws StructureException, IOException { // important: without this the tests can fail when running in maven (but not in IDE) @@ -161,6 +163,7 @@ } + @Ignore("The test requires the network") @Test public void testPerformance() throws StructureException, IOException { // important: without this the tests can fail when running in maven (but not in IDE) --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/basepairs/TestBasePairParameters.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/basepairs/TestBasePairParameters.java @@ -25,6 +25,7 @@ import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.StructureIO; import org.biojava.nbio.structure.basepairs.BasePairParameters; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -41,6 +42,7 @@ */ public class TestBasePairParameters { + @Ignore("The test requires the network") @Test public void testBasePair() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java @@ -40,6 +40,7 @@ import org.biojava.nbio.structure.StructureIO; import org.biojava.nbio.structure.StructureImpl; import org.biojava.nbio.structure.StructureTools; +import org.junit.Ignore; import org.junit.Test; /** @@ -192,6 +193,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testMergeStructure() throws StructureException, IOException { @@ -248,6 +250,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testDivideInternally() throws StructureException, IOException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitExtractor.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitExtractor.java @@ -28,6 +28,7 @@ import org.biojava.nbio.structure.Structure; import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.StructureIO; +import org.junit.Ignore; import org.junit.Test; /** @@ -45,6 +46,7 @@ * * @see SubunitClustererParameters#getMinimumSequenceLengthFraction() */ + @Ignore("The test requires the network") @Test public void testCollagen() throws StructureException, IOException { @@ -65,6 +67,7 @@ /** * Make sure that only aminoacid chains are extracted: 5B2I. */ + @Ignore("The test requires the network") @Test public void testHistone() throws StructureException, IOException { @@ -82,6 +85,7 @@ /** * Test that all chains from biological assemblies are extracted. */ + @Ignore("The test requires the network") @Test public void testBioAssembly() throws StructureException, IOException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestUnitQuaternions.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestUnitQuaternions.java @@ -36,6 +36,7 @@ import org.biojava.nbio.structure.StructureIO; import org.biojava.nbio.structure.StructureTools; import org.biojava.nbio.structure.geometry.UnitQuaternions; +import org.junit.Ignore; import org.junit.Test; /** @@ -56,6 +57,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testOrientation() throws IOException, StructureException { @@ -158,6 +160,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testOrientationMetricIncrement() throws IOException, StructureException { @@ -228,6 +231,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testRelativeOrientation() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java @@ -39,6 +39,7 @@ import org.custommonkey.xmlunit.XMLUnit; import org.custommonkey.xmlunit.examples.RecursiveElementNameAndTextQualifier; import org.junit.Before; +import org.junit.Ignore; import org.junit.Test; import org.xml.sax.SAXException; @@ -101,6 +102,7 @@ ScopFactory.setScopDatabase(ScopFactory.VERSION_1_75B); } + @Ignore("The test requires the network") @Test public void testCpAsymmetric() throws IOException, StructureException, CompoundNotFoundException { Structure structure = cache.getStructure("1w0p"); @@ -111,6 +113,7 @@ assertEquals("Wrong RMSD", 3.605, afpChain.getTotalRmsdOpt(), 0.001); } + @Ignore("The test requires the network") @Test public void testCpSymmetric2() throws IOException,StructureException, CompoundNotFoundException { String a = "--vRSLNCTLRDSQQ-KSLVMSG---PYELKALHLQgqdmeq-----QVVFSMSFVQGeesndkiPVALGLKEK-NLYLSSVLKdDKPTLQLESVdpknypkkkmekRFVFNKIEInn--KLEFESAQFpnWYISTSqAENmPVFLGGT----KGgqDITDFTMQFV---"; @@ -121,6 +124,7 @@ assertEquals("Wrong RMSD", 2.50569, afpChain.getTotalRmsdOpt(), 0.001); } + @Ignore("The test requires the network") @Test public void testBug1() throws IOException, StructureException, CompoundNotFoundException { /* @@ -142,6 +146,7 @@ assertEquals("Wrong TM-score", 0.69848, afpChain.getTMScore(), 0.001); } + @Ignore("The test requires the network") @Test public void testCpSymmetric1() throws IOException,StructureException, CompoundNotFoundException { //cat 2GG6-best.fasta |tr -d \\n|pbcopy @@ -153,6 +158,7 @@ assertEquals("Wrong RMSD", 3.035, afpChain.getTotalRmsdOpt(), 0.001); } + @Ignore("The test requires the network") @Test public void testFromFasta() throws IOException, StructureException, CompoundNotFoundException { Structure s1 = cache.getStructure("1w0p"); --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/StructureSequenceMatcherTest.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/StructureSequenceMatcherTest.java @@ -29,6 +29,7 @@ import org.biojava.nbio.core.sequence.ProteinSequence; import org.junit.Assert; import org.junit.Before; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -114,6 +115,7 @@ */ } + @Ignore("The test requires the network") @Test public void testSubstructureMatchingProteinSequence() throws CompoundNotFoundException { ProteinSequence seq = new ProteinSequence(seq1.substring(30, 40)); @@ -131,6 +133,7 @@ } } + @Ignore("The test requires the network") @Test public void testGetProteinSequenceForStructure() { Map groupIndexPos = new HashMap(); @@ -157,6 +160,7 @@ } } + @Ignore("The test requires the network") @Test public void testMatchSequenceToStructure() throws StructureException, CompoundNotFoundException { // create modified sequence by removing 10 residues and adding 3 @@ -223,6 +227,7 @@ } } + @Ignore("The test requires the network") @Test public void testRemoveGaps1() throws CompoundNotFoundException { String ungapped = "ACDEFGHIKLMNPQRSTVWY"; --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDifficultMmCIFFiles.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDifficultMmCIFFiles.java @@ -44,6 +44,7 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.cif.CifStructureConverter; import org.biojava.nbio.structure.quaternary.BioAssemblyInfo; +import org.junit.Ignore; import org.junit.Test; /** @@ -63,6 +64,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void test2KSA() throws IOException, StructureException { AtomCache cache = new AtomCache(); @@ -90,6 +92,7 @@ } } + @Ignore("The test requires the network") @Test public void test2BI6() throws IOException, StructureException { @@ -119,6 +122,7 @@ } + @Ignore("The test requires the network") @Test public void test1GQO() throws IOException, StructureException { @@ -163,6 +167,7 @@ } + @Ignore("The test requires the network") @Test public void testResidueNumbers() throws IOException, StructureException { AtomCache cache = new AtomCache(); @@ -234,6 +239,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void test2KLI() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java @@ -30,6 +30,7 @@ import org.biojava.nbio.structure.geometry.CalcPoint; import org.biojava.nbio.structure.geometry.SuperPosition; import org.biojava.nbio.structure.geometry.SuperPositionSVD; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -49,6 +50,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void test4A1Immcif() throws IOException, StructureException { @@ -101,6 +103,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void test4A1I() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java @@ -38,6 +38,7 @@ import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior; import org.biojava.nbio.structure.io.cif.CifStructureConverter; import org.junit.Assert; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -55,6 +56,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testHeaderOnly() throws StructureException, IOException { // Get either PDB or mmCIF with a headerOnly = true. @@ -90,6 +92,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testAlignSeqres() throws StructureException, IOException { // Get either PDB or mmCIF with a headerOnly = false. --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java @@ -43,10 +43,12 @@ import org.biojava.nbio.structure.StructureTools; import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.cif.CifStructureConverter; +import org.junit.Ignore; import org.junit.Test; public class TestMMCIFWriting { + @Ignore("The test requires the network") @Test public void test1SMT() throws IOException, StructureException { // an x-ray structure @@ -58,12 +60,14 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void test2N3J() throws IOException, StructureException { // an NMR structure (multimodel) with 2 chains testRoundTrip("2N3J"); } + @Ignore("The test requires the network") @Test public void test1A2C() throws IOException, StructureException { // a structure with insertion codes --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java @@ -31,6 +31,7 @@ import org.biojava.nbio.structure.StructureIO; import org.biojava.nbio.structure.align.util.AtomCache; import org.junit.BeforeClass; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -52,6 +53,7 @@ StructureIO.setAtomCache(cache); } + @Ignore("The test requires the network") @Test public void test1STP() throws IOException, StructureException{ String pdbId = "1stp"; @@ -68,6 +70,7 @@ } + @Ignore("The test requires the network") @Test public void test4hhb() throws IOException, StructureException{ String pdbId = "4hhb"; @@ -76,6 +79,7 @@ } + @Ignore("The test requires the network") @Test public void test3ZD6() throws IOException, StructureException { // a PDB ID that contains a synthetic entity --- 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 @@ -43,6 +43,7 @@ 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.Ignore; import org.junit.Test; /** @@ -453,6 +454,7 @@ } + @Ignore("The test requires the network") @Test public void testStructureWithBranchedEntities() throws IOException { // Example carbohydrate remediation file to be released in July 2020 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFFeatures.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFFeatures.java @@ -33,12 +33,14 @@ import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.StructureIO; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Ignore; import org.junit.Test; /** * Created by larsonmattr on 10/31/2015. */ public class TestParseMmCIFFeatures { + @Ignore("The test requires the network") @Test public void testSSBond()throws IOException, StructureException { AtomCache cache = new AtomCache(); @@ -71,6 +73,7 @@ } + @Ignore("The test requires the network") @Test public void testSSBondAltLocs() throws IOException, StructureException { AtomCache cache = new AtomCache(); @@ -140,6 +143,7 @@ } + @Ignore("The test requires the network") @Test public void testSites()throws IOException, StructureException { @@ -175,6 +179,7 @@ assertEquals(getDescription(sCif, "AC6"), "BINDING SITE FOR RESIDUE HEM D 148"); } + @Ignore("The test requires the network") @Test public void testSites1a4w()throws IOException, StructureException { AtomCache cache = new AtomCache(); --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFLigands.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFLigands.java @@ -34,6 +34,7 @@ import org.biojava.nbio.structure.chem.ChemCompGroupFactory; import org.biojava.nbio.structure.chem.DownloadChemCompProvider; import org.biojava.nbio.structure.chem.PolymerType; +import org.junit.Ignore; import org.junit.Test; /** @@ -46,6 +47,7 @@ private static final int ATOM_COUNT_3UCB = 114; //number of atoms in 3UCB, including alternate ligand conformations + @Ignore("The test requires the network") @Test public void testLigandConnections()throws IOException, StructureException { AtomCache cache = new AtomCache(); @@ -89,6 +91,7 @@ return count; } + @Ignore("The test requires the network") @Test public void testMultipleConformations()throws IOException, StructureException { AtomCache cache = new AtomCache(); --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseOnAsymId.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseOnAsymId.java @@ -29,12 +29,14 @@ import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.StructureIO; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Ignore; import org.junit.Test; public class TestParseOnAsymId { + @Ignore("The test requires the network") @Test public void test4cup() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java @@ -25,6 +25,7 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.quaternary.BioAssemblyInfo; import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -36,17 +37,20 @@ public class TestQuaternaryStructureProviders { + @Ignore("The test requires the network") @Test public void test1STP() throws IOException, StructureException{ comparePdbVsMmcif("1stp",1, 4); } + @Ignore("The test requires the network") @Test public void test3FAD() throws IOException, StructureException{ comparePdbVsMmcif("3fad",1, 1); comparePdbVsMmcif("3fad",2, 2); } + @Ignore("The test requires the network") @Test public void test5LDH() throws IOException, StructureException{ comparePdbVsMmcif("5LDH",1, 4); @@ -82,16 +86,19 @@ } + @Ignore("The test requires the network") @Test public void test3NTU() throws IOException, StructureException{ comparePdbVsMmcif("3NTU",1, 6); } + @Ignore("The test requires the network") @Test public void test1A29() throws IOException, StructureException{ comparePdbVsMmcif("1A29",1, 1); } + @Ignore("The test requires the network") @Test public void test1EI7() throws IOException, StructureException { @@ -99,6 +106,7 @@ } + @Ignore("The test requires the network") @Test public void testGetNrBioAssemblies5LDH() throws IOException, StructureException { assertEquals("There should be 4 bioassemblies for 5LDH, see github issue #230", 4, StructureIO.getBiologicalAssemblies("5LDH").size()); --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java @@ -95,6 +95,7 @@ } } + @Ignore("The test requires the network") @Test public void test4DOU() throws Exception { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestTitleParsing.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestTitleParsing.java @@ -24,6 +24,7 @@ import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.StructureIO; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -39,6 +40,7 @@ */ public class TestTitleParsing { + @Ignore("The test requires the network") @Test public void test2W6E() throws IOException, StructureException { --- 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 @@ -26,6 +26,7 @@ import org.biojava.nbio.structure.Structure; import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.StructureIO; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -34,6 +35,7 @@ */ public class TestURLBasedFileParsing { + @Ignore("The test requires the network") @Test public void testMMcifURL() throws StructureException, IOException{ String u = "https://files.wwpdb.org/pub/pdb/data/assemblies/mmCIF/divided/nw/4nwr-assembly1.cif.gz"; --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestWriteLargeCoordinatePDB.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestWriteLargeCoordinatePDB.java @@ -30,6 +30,7 @@ import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.StructureIO; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Ignore; import org.junit.Test; public class TestWriteLargeCoordinatePDB { @@ -37,6 +38,7 @@ // This test checks that 'grouping' characters such as commas are not // incorrectly introduced into formatted PDB coordinate fields. // See FileConvert.d3 formatter. + @Ignore("The test requires the network") @Test public void TestWrite5D9Q() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java @@ -37,6 +37,7 @@ import org.biojava.nbio.structure.chem.ZipChemCompProvider; import org.biojava.nbio.structure.io.FileParsingParameters; import org.biojava.nbio.structure.io.PDBFileReader; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -144,6 +145,7 @@ // ZipChemCompProvider.purgeTempFiles(pdbdir.toString()); } + @Ignore("The test requires the network") @Test public void testNormalStructure() throws StructureException, IOException { // we just need this to track where to store PDB files --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestEntityNameAndType.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestEntityNameAndType.java @@ -34,6 +34,7 @@ import org.biojava.nbio.structure.chem.ChemCompGroupFactory; import org.biojava.nbio.structure.chem.DownloadChemCompProvider; import org.biojava.nbio.structure.io.FileParsingParameters; +import org.junit.Ignore; import org.junit.Test; /** * Test to ensure the entity name and type @@ -42,6 +43,7 @@ */ public class TestEntityNameAndType { + @Ignore("The test requires the network") @Test public void testEntityId() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseInternalChainId.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseInternalChainId.java @@ -28,6 +28,7 @@ import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.io.StructureFiletype; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -36,6 +37,7 @@ */ public class TestParseInternalChainId { + @Ignore("The test requires the network") @Test public void test2I13() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseMmcifHeader.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseMmcifHeader.java @@ -34,6 +34,7 @@ import org.biojava.nbio.structure.io.StructureFiletype; import org.biojava.nbio.structure.StructureIO; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Ignore; import org.junit.Test; /** @@ -48,6 +49,7 @@ /** * Test we can parse R-work and R-free effectively. */ + @Ignore("The test requires the network") @Test public void testRfactors() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestBondFinding.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestBondFinding.java @@ -23,6 +23,7 @@ import org.biojava.nbio.structure.io.StructureFiletype; import org.biojava.nbio.structure.chem.ChemCompGroupFactory; import org.biojava.nbio.structure.chem.DownloadChemCompProvider; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -54,6 +55,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void testInterGroupBonds() throws IOException, StructureException { --- 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 @@ -21,6 +21,7 @@ package org.biojava.nbio.structure.io.mmtf; import org.biojava.nbio.structure.io.PDBFileParser; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -66,6 +67,7 @@ return buffer.toByteArray(); } + @Ignore("The test requires the network") @Test public void test3HBX() throws Exception{ String pdbId = "3hbx"; --- 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 @@ -44,6 +44,7 @@ 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.Ignore; import org.junit.Test; import org.rcsb.mmtf.decoder.StructureDataToAdapter; import org.rcsb.mmtf.encoder.AdapterToStructureData; @@ -64,6 +65,7 @@ * @throws IOException an error reading the file * @throws StructureException an error parsing the structure */ + @Ignore("The test requires the network") @Test public void testRoundTrip() throws IOException, StructureException { @@ -352,6 +354,7 @@ } } + @Ignore("The test requires the network") @Test public void testStructWithBranchedEntitiesRoundTrip() throws IOException { // Example carbohydrate remediation file to be released in July 2020 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java @@ -25,6 +25,7 @@ import org.biojava.nbio.structure.chem.DownloadChemCompProvider; import org.biojava.nbio.structure.io.FileParsingParameters; import org.biojava.nbio.structure.io.StructureFiletype; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -95,6 +96,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void microHeterogenity() throws IOException, StructureException { setUpBioJava(); --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestCeSymm.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestCeSymm.java @@ -29,6 +29,7 @@ import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.StructureTools; import org.biojava.nbio.structure.symmetry.internal.CeSymm; +import org.junit.Ignore; import org.junit.Test; /** @@ -41,6 +42,7 @@ */ public class TestCeSymm { + @Ignore("The test requires the network") @Test public void testEasyCases() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java @@ -34,6 +34,7 @@ import org.biojava.nbio.structure.symmetry.internal.RefinerFailedException; import org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector; import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod; +import org.junit.Ignore; import org.junit.Test; /** @@ -42,6 +43,7 @@ */ public class TestSequenceFunctionOrderDetector { + @Ignore("The test requires the network") @Test public void testGetSymmetryOrder() throws IOException, StructureException, RefinerFailedException { // List of alignments to try, along with proper symmetry --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalInfo.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalInfo.java @@ -23,6 +23,7 @@ import org.biojava.nbio.structure.*; import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.StructureFiletype; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -39,6 +40,7 @@ private static final float DELTA = 0.000001f; + @Ignore("The test requires the network") @Test public void test1NMR() throws IOException, StructureException { @@ -63,6 +65,7 @@ } + @Ignore("The test requires the network") @Test public void test1B8G() throws IOException, StructureException { @@ -87,6 +90,7 @@ } + @Ignore("The test requires the network") @Test public void test4M7P() throws IOException, StructureException { @@ -115,6 +119,7 @@ } + @Ignore("The test requires the network") @Test public void test2MBQ() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestInterfaceClustering.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestInterfaceClustering.java @@ -41,12 +41,14 @@ import org.biojava.nbio.structure.contact.StructureInterfaceList; import org.biojava.nbio.structure.io.FileParsingParameters; import org.biojava.nbio.structure.io.PDBFileParser; +import org.junit.Ignore; import org.junit.Test; import javax.vecmath.Matrix4d; public class TestInterfaceClustering { + @Ignore("The test requires the network") @Test public void test3DDO() throws IOException, StructureException { @@ -95,6 +97,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void test1AUY() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueRangeTest.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueRangeTest.java @@ -26,6 +26,7 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior; import org.junit.Before; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -61,6 +62,7 @@ assertNull("End residue should be null", rr.getEnd()); } + @Ignore("The test requires the network") @Test public void testPartialChainWithMap() throws IOException, StructureException { @@ -75,6 +77,7 @@ assertEquals("Wrong end", end, rr.getEnd()); } + @Ignore("The test requires the network") @Test public void testWholeChainWithMap() throws IOException, StructureException { String pdbId = "1cph"; @@ -123,6 +126,7 @@ } } + @Ignore("The test requires the network") @Test public void testLengths() throws IOException, StructureException { String pdbId = "1w0p"; @@ -134,6 +138,7 @@ assertEquals(2, range.getLength()); } + @Ignore("The test requires the network") @Test public void testIterator() throws IOException, StructureException { String pdbId = "2eke"; @@ -158,6 +163,7 @@ assertEquals(expected.length,i); } + @Ignore("The test requires the network") @Test public void testMultiIterator() throws IOException, StructureException { String pdbId = "1qdm"; @@ -283,6 +289,8 @@ assertEquals(rangeStr,55,(int)range.getEnd().getSeqNum()); } + + @Ignore("The test requires the network") @Test public void testPartialRangeLength() throws IOException, StructureException { AtomPositionMap map = new AtomPositionMap(cache.getAtoms("2eke")); @@ -304,6 +312,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testParseAndEqualWithLengths() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java @@ -27,6 +27,7 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.FileParsingParameters; import org.biojava.nbio.structure.io.StructureFiletype; +import org.junit.Ignore; import org.junit.Test; /** @@ -34,6 +35,7 @@ */ public class Test2JA5 { + @Ignore("The test requires the network") @Test public void test2JA5() throws IOException, StructureException { @@ -64,6 +66,7 @@ assertNull(chain); } + @Ignore("The test requires the network") @Test public void test2JA5noHeader() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java @@ -32,6 +32,7 @@ import org.biojava.nbio.structure.io.PDBFileReader; import org.biojava.nbio.structure.io.StructureFiletype; import org.junit.Before; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -69,6 +70,7 @@ } // TODO dmyersturnbull: Which of these syntaxes do we support? We should re-enable after + @Ignore("The test requires the network") @Test public void testAtomCacheNameParsing() throws IOException, StructureException { @@ -183,6 +185,7 @@ } // 1HHB is obsolete with a replacement + @Ignore("The test requires the network") @Test public void testFetchCurrent1HHB() throws IOException, StructureException { @@ -199,6 +202,7 @@ } // Fetching obsolete directly + @Ignore("The test requires the network") @Test public void testFetchObsolete() throws IOException, StructureException { cache.setFetchBehavior(FetchBehavior.FETCH_FILES); @@ -221,6 +225,7 @@ } + @Ignore("The test requires the network") @Test public void testGetScopDomain() throws IOException, StructureException { String name = "d2gs2a_"; --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomIterator.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomIterator.java @@ -31,9 +31,11 @@ import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.StructureIO; import org.biojava.nbio.structure.StructureTools; +import org.junit.Ignore; import org.junit.Test; public class TestAtomIterator { + @Ignore("The test requires the network") @Test public void test5frf() throws IOException, StructureException { // 5frf: 10 models; residues -2-105, binds a ZN; 1615 atoms/model --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java @@ -30,6 +30,7 @@ import org.biojava.nbio.structure.io.FileParsingParameters; import org.biojava.nbio.structure.io.StructureFiletype; import org.junit.BeforeClass; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -65,6 +66,7 @@ } + @Ignore("The test requires the network") @Test public void testStructConnModels() throws IOException, StructureException { Structure s = StructureIO.getStructure("1cdr"); @@ -75,6 +77,7 @@ assertTrue(areBonded(atomOne, atomTwo)); } + @Ignore("The test requires the network") @Test public void testIntraResidueBonds() throws StructureException, IOException { @@ -101,6 +104,7 @@ } } + @Ignore("The test requires the network") @Test public void testPeptideBonds() throws StructureException, IOException { @@ -116,6 +120,7 @@ assertTrue(areBonded(carboxylC, aminoN)); } + @Ignore("The test requires the network") @Test public void testDisulfideBonds() throws StructureException, IOException { @@ -127,6 +132,7 @@ assertTrue(areBonded(atom1, atom2)); } + @Ignore("The test requires the network") @Test public void testLigandBonds() throws StructureException, IOException { @@ -143,6 +149,7 @@ * @throws IOException * @throws StructureException */ + @Ignore("The test requires the network") @Test public void testNucleotideBonds() throws IOException, StructureException { Structure bio = StructureIO.getStructure("4y60"); @@ -175,6 +182,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testHeavyAtomBondMissing() throws IOException, StructureException { assertEquals(0, countAtomsWithoutBonds("3jtm")); @@ -192,6 +200,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testHydrogenToProteinBondMissing() throws IOException, StructureException { assertEquals(0, countAtomsWithoutBonds("4txr")); @@ -203,6 +212,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testAltLocBondMissing() throws IOException, StructureException { assertEquals(0, countAtomsWithoutBonds("4cup")); @@ -290,16 +300,19 @@ * Each of the following PDB IDs used to make formBonds() crash. */ + @Ignore("The test requires the network") @Test public void test145D() throws IOException, StructureException { StructureIO.getStructure("145D"); } + @Ignore("The test requires the network") @Test public void test1APJ() throws IOException, StructureException { StructureIO.getStructure("1APJ"); } + @Ignore("The test requires the network") @Test public void test1BDX() throws IOException, StructureException { StructureIO.getStructure("1BDX"); @@ -310,6 +323,7 @@ * @throws IOException an error getting the required file * @throws StructureException an error parsing the required file */ + @Ignore("The test requires the network") @Test public void testDeuterated() throws IOException, StructureException { // The terminal Hydrogen D3 - is missing (from the CCD) @@ -325,6 +339,7 @@ * @throws IOException an error getting the required file * @throws StructureException an error parsing the required file */ + @Ignore("The test requires the network") @Test public void testWeirdCase() throws IOException, StructureException { assertEquals(6, countAtomsWithoutBonds("1IU6")); @@ -336,6 +351,7 @@ * @throws IOException an error getting the required file * @throws StructureException an error parsing the required file */ + @Ignore("The test requires the network") @Test public void testSSBonds() throws IOException, StructureException { for(String pdbCode : new String[]{"3ZXW","1NTY", "4H2I", "2K6D", "2MLM"}){ --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java @@ -31,12 +31,14 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.FileParsingParameters; import org.biojava.nbio.structure.io.StructureFiletype; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; public class TestCloning { + @Ignore("The test requires the network") @Test public void test1a4wCloning() throws StructureException, IOException { @@ -57,6 +59,7 @@ } + @Ignore("The test requires the network") @Test public void testAsymUnitCloning() throws StructureException, IOException { @@ -76,6 +79,7 @@ compareCloned(s, c); } + @Ignore("The test requires the network") @Test public void testBioUnitCloning() throws StructureException, IOException { @@ -88,6 +92,7 @@ } + @Ignore("The test requires the network") @Test public void testBiounitEntitiesFlatChains() throws StructureException, IOException { Structure s; @@ -107,6 +112,7 @@ } + @Ignore("The test requires the network") @Test public void testBiounitEntitiesMultimodel() throws StructureException, IOException { Structure s; @@ -133,6 +139,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void test3piuCloning() throws StructureException, IOException { @@ -188,6 +195,7 @@ } + @Ignore("The test requires the network") @Test public void testBondCloning() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDNAAlignment.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDNAAlignment.java @@ -31,6 +31,7 @@ import org.biojava.nbio.structure.align.ce.CeMain; import org.biojava.nbio.structure.align.model.AFPChain; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Ignore; import org.junit.Test; /** make sure DNA alignments fail gracefully @@ -41,6 +42,7 @@ public class TestDNAAlignment { + @Ignore("The test requires the network") @Test public void test1() throws IOException { String name1="1l3s.A"; --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestNucleotides.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestNucleotides.java @@ -32,6 +32,7 @@ import org.biojava.nbio.structure.io.FileParsingParameters; import org.biojava.nbio.structure.io.PDBFileReader; import org.junit.BeforeClass; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -54,6 +55,7 @@ cache = new AtomCache(); } + @Ignore("The test requires the network") @Test public void test3T5N() throws IOException, StructureException{ @@ -112,6 +114,7 @@ } + @Ignore("The test requires the network") @Test public void test1OFX() throws StructureException, IOException { Structure s = getStructure("1OFX"); @@ -136,6 +139,7 @@ return cache.getStructure(pdbId); } + @Ignore("The test requires the network") @Test public void test1REP() throws StructureException, IOException{ --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java @@ -25,6 +25,7 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.FileParsingParameters; import org.junit.BeforeClass; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.LoggerFactory; @@ -63,6 +64,7 @@ } + @Ignore("The test requires the network") @Test public void testIntraChainContacts() throws StructureException, IOException { @@ -125,6 +127,7 @@ } + @Ignore("The test requires the network") @Test public void testInterChainContacts3HBX() throws StructureException, IOException { @@ -161,6 +164,7 @@ } + @Ignore("The test requires the network") @Test public void testIntraChainContactsVsDistMatrix1SMT() throws IOException, StructureException { @@ -175,6 +179,7 @@ checkContactsVsDistMatrix(chain, cutoff); } + @Ignore("The test requires the network") @Test public void testIntraChainContactsVsDistMatrix2TRX() throws IOException, StructureException { @@ -189,6 +194,7 @@ checkContactsVsDistMatrix(chain, cutoff); } + @Ignore("The test requires the network") @Test public void testIntraChainContactsVsDistMatrix1SU4() throws IOException, StructureException { @@ -233,6 +239,7 @@ } + @Ignore("The test requires the network") @Test public void testInterChainContactsVsDistMatrix2TRX() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/Test1DARSeqAlign.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/Test1DARSeqAlign.java @@ -27,6 +27,7 @@ import org.biojava.nbio.structure.chem.ChemCompProvider; import org.biojava.nbio.structure.chem.DownloadChemCompProvider; import org.biojava.nbio.structure.io.FileParsingParameters; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -39,6 +40,7 @@ */ public class Test1DARSeqAlign { + @Ignore("The test requires the network") @Test public void test1DAR() throws StructureException, IOException { AtomCache cache = new AtomCache(); --- 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 @@ -28,6 +28,7 @@ import org.biojava.nbio.structure.Structure; import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -41,6 +42,7 @@ */ public class TestDSSPParser { + @Ignore("The test requires the network") @Test public void testDSSPParser() throws IOException, StructureException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestSecStrucCalc.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestSecStrucCalc.java @@ -28,6 +28,7 @@ import org.biojava.nbio.structure.Structure; import org.biojava.nbio.structure.StructureException; import org.biojava.nbio.structure.align.util.AtomCache; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -49,6 +50,7 @@ */ public class TestSecStrucCalc { + @Ignore("The test requires the network") @Test public void testSecStrucPred() throws StructureException, IOException { @@ -89,6 +91,7 @@ * @throws StructureException * @throws IOException */ + @Ignore("The test requires the network") @Test public void testMultiModelPred() throws StructureException, IOException { --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/ChemCompTest.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/ChemCompTest.java @@ -27,6 +27,7 @@ import org.biojava.nbio.structure.chem.PolymerType; import org.biojava.nbio.structure.chem.ReducedChemCompProvider; import org.biojava.nbio.structure.chem.ResidueType; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -48,6 +49,7 @@ assertTrue (" is not amino ", cc.getResidueType().equals(ResidueType.lPeptideLinking)); } + @Ignore("The test requires the network") @Test public void testMEA(){ @@ -88,6 +90,7 @@ ChemCompGroupFactory.setChemCompProvider(oldProvider); } + @Ignore("The test requires the network") @Test public void testPRR(){ @@ -113,6 +116,7 @@ } + @Ignore("The test requires the network") @Test public void testChangingProviders(){ --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java @@ -22,6 +22,7 @@ import org.biojava.nbio.structure.PDBStatus.Status; import org.junit.Assert; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -41,6 +42,7 @@ *3HHB CURRENT replaces=1HHB * */ + @Ignore("The test requires the network") @Test public void testGetStatus() throws IOException { Assert.assertEquals(Status.REMOVED, PDBStatus.getStatus("1HHB")); @@ -48,6 +50,7 @@ Assert.assertEquals(Status.CURRENT, PDBStatus.getStatus("4HHB")); } + @Ignore("The test requires the network") @Test public void testGetStatusMultipleIds() throws IOException { String[] ids = {"1HHB", "3HHB", "4HHB"}; @@ -57,6 +60,7 @@ Assert.assertEquals(Status.CURRENT, statuses[2]); } + @Ignore("The test requires the network") @Test public void testGetCurrent() throws IOException { Assert.assertEquals("4HHB", PDBStatus.getCurrent("1HHB")); --- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java +++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java @@ -23,6 +23,7 @@ import com.google.common.collect.Range; import org.biojava.nbio.genome.util.ChromosomeMappingTools; import org.junit.Assert; +import org.junit.Ignore; import org.junit.Test; import java.util.ArrayList; @@ -34,6 +35,7 @@ */ public class TestGenomeMapping { + @Ignore("The test requires the network") @Test public void testGenomeMappingToolGetCDSRanges(){ @@ -58,6 +60,7 @@ } + @Ignore("The test requires the network") @Test public void testGenomeMappingToolGetCDSRangesSERINC2(){ --- a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ModifiedCompoundSerializationTest.java +++ b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ModifiedCompoundSerializationTest.java @@ -31,6 +31,7 @@ import org.biojava.nbio.structure.Structure; import org.junit.Assert; import org.junit.Before; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -57,6 +58,7 @@ //strucs = ProteinModificationParserTest.setUpLongTest(); } + @Ignore("The test requires the network") @Test public void testMulti() { int count = 0; @@ -72,12 +74,14 @@ } } + @Ignore("The test requires the network") @Test public void test1CAD(){ String pdbId = "1CAD"; testXMLSerialization(pdbId); } + @Ignore("The test requires the network") @Test public void test1a4w(){ String pdbId = "1a4w"; @@ -124,6 +128,7 @@ } + @Ignore("The test requires the network") @Test public void test1UIS(){ String pdbId = "1UIS"; @@ -135,6 +140,7 @@ // testXMLSerialization(pdbId); // } + @Ignore("The test requires the network") @Test public void test1CDG(){ String pdbId = "1CDG"; --- a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java +++ b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java @@ -25,6 +25,7 @@ import org.biojava.nbio.structure.*; import org.junit.Assert; import org.junit.Before; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -326,6 +327,7 @@ return strucs; } + @Ignore("The test requires the network") @Test public void testParser() throws IOException, StructureException { multiTest(); @@ -446,6 +448,7 @@ * Note: if you change this unit test, also change the cook book: * http://www.biojava.org/wiki/BioJava:CookBook3:ProtMod */ + @Ignore("The test requires the network") @Test public void testCookBookTestCases() throws StructureException, IOException { // identify all modificaitons from PDB:1CAD and print them --- 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 @@ -24,6 +24,7 @@ import org.biojava.nbio.structure.chem.ChemComp; import org.biojava.nbio.structure.chem.DownloadChemCompProvider; import org.biojava.nbio.structure.io.LocalPDBDirectory; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -48,6 +49,7 @@ assertEquals(cc.getId(), id); } + @Ignore("The test requires the network") @Test public void testWeDontCacheGarbage() { // see #703 --- a/biojava-core/src/test/java/org/biojava/nbio/core/util/FileDownloadUtilsTest.java +++ b/biojava-core/src/test/java/org/biojava/nbio/core/util/FileDownloadUtilsTest.java @@ -12,6 +12,7 @@ import java.io.IOException; import java.nio.file.Files; +import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Nested; import org.junit.jupiter.api.Test; @@ -156,6 +157,7 @@ class URLMethods { final String availableUrl = "https://www.google.com"; + @Disabled("Requires network access") @Test void pingGoogleOK(){ assertTrue(FileDownloadUtils.ping(availableUrl, 1000)); --- a/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/symmetry/TestJmolSymmetryScriptGenerator.java +++ b/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/symmetry/TestJmolSymmetryScriptGenerator.java @@ -39,6 +39,7 @@ import org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod; import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn; import org.junit.Before; +import org.junit.Ignore; import org.junit.Test; /** @@ -50,6 +51,7 @@ public void setUp() { } + @Ignore("Requires network access") @Test public void testPolygon() throws IOException, StructureException { Structure struc = StructureIO.getStructure("4hhb"); @@ -64,4 +66,4 @@ String expected = "draw polyhedronD30 line{30.02,-39.95,0.59}{29.24,-0.53,40.00}{30.02,38.89,0.59}{30.80,-0.53,-38.82}{30.02,-39.95,0.59}{-30.00,-39.95,-0.60}{-30.79,-0.53,38.81}{-30.00,38.89,-0.60}{-29.22,-0.53,-40.01}{-30.00,-39.95,-0.60}width 0.45 color [x42ffd9] off;draw polyhedronD31 line{29.24,-0.53,40.00}{-30.79,-0.53,38.81}width 0.45 color [x42ffd9] off;draw polyhedronD32 line{30.02,38.89,0.59}{-30.00,38.89,-0.60}width 0.45 color [x42ffd9] off;draw polyhedronD33 line{30.80,-0.53,-38.82}{-29.22,-0.53,-40.01}width 0.45 color [x42ffd9] off;"; assertEquals(expected, poly); } -} \ No newline at end of file +} --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java @@ -100,7 +100,8 @@ reduced = id.reduce(full); assertEquals("wrong length for chainName=A", 94, StructureTools.getRepresentativeAtomArray(reduced).length); - try { + // Skipping the following, which depends on certificates that will expire in the foreseeable future. + /*try { url = new URL("https://files.rcsb.org/download/1B8G.pdb.gz"); id = new URLIdentifier(url); @@ -110,6 +111,6 @@ } catch(UnknownHostException e) { logger.error("Unable to connect to rcsb.org"); // still pass - } + }*/ } }