diff --git a/cv-rule-reader/pom.xml b/cv-rule-reader/pom.xml index 89279f2..a48c692 100644 --- a/cv-rule-reader/pom.xml +++ b/cv-rule-reader/pom.xml @@ -4,7 +4,7 @@ psidev.psi.tools master-pom - 2.0.13 + 2.0.14-SNAPSHOT cv-rule-reader @@ -22,7 +22,7 @@ org.jvnet.jaxb2.maven2 maven-jaxb2-plugin - 0.7.4 + 0.15.1 ${project.basedir}/src/main/resources/ ${project.basedir}/src/main/resources/ @@ -47,17 +47,24 @@ + + javax.xml.bind + jaxb-api + + com.sun.xml.bind jaxb-impl + - stax - stax + com.sun.xml.bind + jaxb-core + - javax.xml.bind - jaxb-api + org.glassfish.jaxb + jaxb-xjc diff --git a/cv-rule-reader/src/test/java/psidev/psi/tools/cvrReader/MockMemoryStreamHandler.java b/cv-rule-reader/src/test/java/psidev/psi/tools/cvrReader/MockMemoryStreamHandler.java index 15c4692..2a788de 100644 --- a/cv-rule-reader/src/test/java/psidev/psi/tools/cvrReader/MockMemoryStreamHandler.java +++ b/cv-rule-reader/src/test/java/psidev/psi/tools/cvrReader/MockMemoryStreamHandler.java @@ -36,7 +36,7 @@ public class MockMemoryStreamHandler extends URLStreamHandler { public static final String MEMORY_PROTOCOL = "memory"; - private static Map url2content = new HashMap(); + private static Map url2content = new HashMap<>(); public static void addContent( URL url, String content ) { url2content.put( url.toString(), content ); @@ -64,15 +64,12 @@ public InputStream getInputStream() throws IOException { */ public static void initHandler() { try { - URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory() { - - public URLStreamHandler createURLStreamHandler( String protocol ) { - if ( "memory".equals( protocol ) ) { - return new MockMemoryStreamHandler(); - } - return null; + URL.setURLStreamHandlerFactory(protocol -> { + if ( "memory".equals( protocol ) ) { + return new MockMemoryStreamHandler(); } - } ); + return null; + }); } catch ( Throwable ex ) { // we just ignore this exception, because m2 does not fork properly // and URL does not like double handler definitions. diff --git a/object-rule-reader/pom.xml b/object-rule-reader/pom.xml index 6534e65..feca7cb 100644 --- a/object-rule-reader/pom.xml +++ b/object-rule-reader/pom.xml @@ -4,7 +4,7 @@ psidev.psi.tools master-pom - 2.0.13 + 2.0.14-SNAPSHOT object-rule-reader @@ -20,9 +20,9 @@ - com.sun.tools.xjc.maven2 - maven-jaxb-plugin - 1.0 + org.jvnet.jaxb2.maven2 + maven-jaxb2-plugin + 0.15.1 psidev.psi.tools.objectRuleReader.mapping.jaxb @@ -50,17 +50,24 @@ + + javax.xml.bind + jaxb-api + + com.sun.xml.bind jaxb-impl + - stax - stax + com.sun.xml.bind + jaxb-core + - javax.xml.bind - jaxb-api + org.glassfish.jaxb + jaxb-xjc diff --git a/object-rule-reader/src/main/java/psidev/psi/tools/objectRuleReader/ObjectRuleReader.java b/object-rule-reader/src/main/java/psidev/psi/tools/objectRuleReader/ObjectRuleReader.java index 6aed46b..92f1b91 100644 --- a/object-rule-reader/src/main/java/psidev/psi/tools/objectRuleReader/ObjectRuleReader.java +++ b/object-rule-reader/src/main/java/psidev/psi/tools/objectRuleReader/ObjectRuleReader.java @@ -129,9 +129,7 @@ public ObjectRuleList read( String s ) throws ObjectRuleReaderException { public ObjectRuleList read( File file ) throws ObjectRuleReaderException { try { return unmarshall( file ); - } catch ( JAXBException e ) { - throw new ObjectRuleReaderException( e ); - } catch ( FileNotFoundException e ) { + } catch (JAXBException | FileNotFoundException e ) { throw new ObjectRuleReaderException( e ); } } @@ -147,9 +145,7 @@ public ObjectRuleList read( InputStream is ) throws ObjectRuleReaderException { public ObjectRuleList read( URL url ) throws ObjectRuleReaderException { try { return unmarshall( url ); - } catch ( JAXBException e ) { - throw new ObjectRuleReaderException( e ); - } catch ( FileNotFoundException e ) { + } catch (JAXBException | FileNotFoundException e ) { throw new ObjectRuleReaderException( e ); } } diff --git a/object-rule-reader/src/test/java/psidev/psi/tools/objectRuleReader/MockMemoryStreamHandler.java b/object-rule-reader/src/test/java/psidev/psi/tools/objectRuleReader/MockMemoryStreamHandler.java index 051f41b..761ae12 100755 --- a/object-rule-reader/src/test/java/psidev/psi/tools/objectRuleReader/MockMemoryStreamHandler.java +++ b/object-rule-reader/src/test/java/psidev/psi/tools/objectRuleReader/MockMemoryStreamHandler.java @@ -36,7 +36,7 @@ public class MockMemoryStreamHandler extends URLStreamHandler { public static final String MEMORY_PROTOCOL = "memory"; - private static Map url2content = new HashMap(); + private static Map url2content = new HashMap<>(); public static void addContent( URL url, String content ) { url2content.put( url.toString(), content ); @@ -64,15 +64,12 @@ public InputStream getInputStream() throws IOException { */ public static void initHandler() { try { - URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory() { - - public URLStreamHandler createURLStreamHandler( String protocol ) { - if ( "memory".equals( protocol ) ) { - return new MockMemoryStreamHandler(); - } - return null; + URL.setURLStreamHandlerFactory(protocol -> { + if ( "memory".equals( protocol ) ) { + return new MockMemoryStreamHandler(); } - } ); + return null; + }); } catch ( Throwable ex ) { // we just ignore this exception, because m2 does not fork properly // and URL does not like double handler definitions. diff --git a/ontology-config-reader/pom.xml b/ontology-config-reader/pom.xml index dca0055..fb3c5d1 100644 --- a/ontology-config-reader/pom.xml +++ b/ontology-config-reader/pom.xml @@ -4,7 +4,7 @@ psidev.psi.tools master-pom - 2.0.13 + 2.0.14-SNAPSHOT ontology-config-reader @@ -20,9 +20,9 @@ - com.sun.tools.xjc.maven2 - maven-jaxb-plugin - 1.0 + org.jvnet.jaxb2.maven2 + maven-jaxb2-plugin + 0.15.1 psidev.psi.tools.ontologyCfgReader.mapping.jaxb @@ -50,17 +50,24 @@ + + javax.xml.bind + jaxb-api + + com.sun.xml.bind jaxb-impl + - stax - stax + com.sun.xml.bind + jaxb-core + - javax.xml.bind - jaxb-api + org.glassfish.jaxb + jaxb-xjc diff --git a/ontology-config-reader/src/main/java/psidev/psi/tools/ontologyConfigReader/OntologyConfigReader.java b/ontology-config-reader/src/main/java/psidev/psi/tools/ontologyConfigReader/OntologyConfigReader.java index 7d99bde..bbbfb5a 100644 --- a/ontology-config-reader/src/main/java/psidev/psi/tools/ontologyConfigReader/OntologyConfigReader.java +++ b/ontology-config-reader/src/main/java/psidev/psi/tools/ontologyConfigReader/OntologyConfigReader.java @@ -129,9 +129,7 @@ public CvSourceList read( String s ) throws OntologyConfigReaderException { public CvSourceList read( File file ) throws OntologyConfigReaderException { try { return unmarshall( file ); - } catch ( JAXBException e ) { - throw new OntologyConfigReaderException( e ); - } catch ( FileNotFoundException e ) { + } catch (JAXBException | FileNotFoundException e ) { throw new OntologyConfigReaderException( e ); } } @@ -147,9 +145,7 @@ public CvSourceList read( InputStream is ) throws OntologyConfigReaderException public CvSourceList read( URL url ) throws OntologyConfigReaderException { try { return unmarshall( url ); - } catch ( JAXBException e ) { - throw new OntologyConfigReaderException( e ); - } catch ( FileNotFoundException e ) { + } catch (JAXBException | FileNotFoundException e ) { throw new OntologyConfigReaderException( e ); } } diff --git a/ontology-config-reader/src/test/java/psidev/psi/tools/ontologyConfigReader/MockMemoryStreamHandler.java b/ontology-config-reader/src/test/java/psidev/psi/tools/ontologyConfigReader/MockMemoryStreamHandler.java index f5b2565..373e159 100755 --- a/ontology-config-reader/src/test/java/psidev/psi/tools/ontologyConfigReader/MockMemoryStreamHandler.java +++ b/ontology-config-reader/src/test/java/psidev/psi/tools/ontologyConfigReader/MockMemoryStreamHandler.java @@ -36,7 +36,7 @@ public class MockMemoryStreamHandler extends URLStreamHandler { public static final String MEMORY_PROTOCOL = "memory"; - private static Map url2content = new HashMap(); + private static Map url2content = new HashMap<>(); public static void addContent( URL url, String content ) { url2content.put( url.toString(), content ); @@ -64,15 +64,12 @@ public InputStream getInputStream() throws IOException { */ public static void initHandler() { try { - URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory() { - - public URLStreamHandler createURLStreamHandler( String protocol ) { - if ( "memory".equals( protocol ) ) { - return new MockMemoryStreamHandler(); - } - return null; + URL.setURLStreamHandlerFactory(protocol -> { + if ( "memory".equals( protocol ) ) { + return new MockMemoryStreamHandler(); } - } ); + return null; + }); } catch ( Throwable ex ) { // we just ignore this exception, because m2 does not fork properly // and URL does not like double handler definitions. diff --git a/ontology-manager/pom.xml b/ontology-manager/pom.xml index 3a3a2b2..3b86d6e 100644 --- a/ontology-manager/pom.xml +++ b/ontology-manager/pom.xml @@ -4,7 +4,7 @@ psidev.psi.tools master-pom - 2.0.13 + 2.0.14-SNAPSHOT ontology-manager @@ -17,6 +17,7 @@ 2.13 + 2.13.4 @@ -28,17 +29,17 @@ com.fasterxml.jackson.core jackson-databind - 2.9.8 + ${jackson.version} com.fasterxml.jackson.core jackson-core - 2.9.8 + ${jackson.version} com.fasterxml.jackson.core jackson-annotations - 2.9.8 + ${jackson.version} @@ -60,9 +61,64 @@ ojdbc14 oracle + + proteomics + proteomics-common + + + obo + obo + + + obo + bbop + + + org.geneontology + oboedit + + + org.geneontology + org.geneontology + + + jcvsii + jcvsii + + + com.ice + tar + + + xerces + xercesImpl + + + proteomics + proteomics-common + 1.5 + + + + obo + obo + 2.0 + + + + obo + bbop + 2.0 + + + org.geneontology + org.geneontology + 1.101 + + uk.ac.ebi.pride.utilities @@ -82,18 +138,6 @@ commons-logging - - log4j - log4j - 1.2.15 - - - javax.jms - jms - - - - commons-lang commons-lang diff --git a/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/OntologyManagerContext.java b/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/OntologyManagerContext.java index 50cdf52..70d97b0 100644 --- a/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/OntologyManagerContext.java +++ b/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/OntologyManagerContext.java @@ -22,12 +22,7 @@ public class OntologyManagerContext { private static ThreadLocal instance = - new ThreadLocal() { - @Override - protected OntologyManagerContext initialValue() { - return new OntologyManagerContext(); - } - }; + ThreadLocal.withInitial(() -> new OntologyManagerContext()); public static OntologyManagerContext getInstance() { return instance.get(); diff --git a/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/OntologyUtils.java b/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/OntologyUtils.java index bc8874c..7b589c2 100644 --- a/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/OntologyUtils.java +++ b/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/OntologyUtils.java @@ -39,7 +39,7 @@ public static Collection getAccessions( Collection terms if ( terms == null ) { return Collections.EMPTY_LIST; } - Collection accessions = new ArrayList( terms.size() ); + Collection accessions = new ArrayList<>(terms.size()); for ( OntologyTermI term : terms ) { accessions.add( term.getTermAccession() ); } @@ -55,7 +55,7 @@ public static Collection getTermNames( Collection terms if ( terms == null ) { return Collections.EMPTY_LIST; } - Collection names = new ArrayList( terms.size() ); + Collection names = new ArrayList<>(terms.size()); for ( OntologyTermI term : terms ) { names.add( term.getPreferredName() ); names.addAll( term.getNameSynonyms() ); diff --git a/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/local/AbstractOboLoader.java b/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/local/AbstractOboLoader.java index 75918ee..928183c 100644 --- a/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/local/AbstractOboLoader.java +++ b/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/local/AbstractOboLoader.java @@ -5,7 +5,6 @@ import psidev.psi.tools.ontology_manager.OntologyManagerContext; import psidev.psi.tools.ontology_manager.interfaces.OntologyTermI; import uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader; -import uk.ac.ebi.ols.loader.parser.OBOFormatParser; import uk.ac.ebi.ols.model.interfaces.Term; import uk.ac.ebi.ols.model.interfaces.TermRelationship; import uk.ac.ebi.ols.model.interfaces.TermSynonym; @@ -57,22 +56,20 @@ protected O buildOntology() { O ontology = createNewOntology(); // 1. convert and index all terms (note: at this stage we don't handle the hierarchy) - for ( Iterator iterator = ontBean.getTerms().iterator(); iterator.hasNext(); ) { - Term term = ( Term ) iterator.next(); - + for (Term term : ontBean.getTerms()) { // convert term into a OboTerm - T ontologyTerm = createNewOntologyTerm( term ); + T ontologyTerm = createNewOntologyTerm(term); final Collection synonyms = term.getSynonyms(); - if( synonyms != null ) { - for ( TermSynonym synonym : synonyms ) { - ontologyTerm.getNameSynonyms().add( synonym.getSynonym() ); + if (synonyms != null) { + for (TermSynonym synonym : synonyms) { + ontologyTerm.getNameSynonyms().add(synonym.getSynonym()); } } - ontology.addTerm( ontologyTerm ); + ontology.addTerm(ontologyTerm); - if ( term.isObsolete() ) { - ontology.addObsoleteTerm( ontologyTerm ); + if (term.isObsolete()) { + ontology.addObsoleteTerm(ontologyTerm); } } buildTermRelationships(ontology); @@ -82,15 +79,11 @@ protected O buildOntology() { protected void buildTermRelationships(O ontology) { // 2. build hierarchy based on the relations of the Terms - for ( Iterator iterator = ontBean.getTerms().iterator(); iterator.hasNext(); ) { - Term term = ( Term ) iterator.next(); - - if ( term.getRelationships() != null ) { - for ( Iterator iterator1 = term.getRelationships().iterator(); iterator1.hasNext(); ) { - TermRelationship relation = ( TermRelationship ) iterator1.next(); - - ontology.addLink( relation.getObjectTerm().getIdentifier(), - relation.getSubjectTerm().getIdentifier() ); + for (Term term : ontBean.getTerms()) { + if (term.getRelationships() != null) { + for (TermRelationship relation : term.getRelationships()) { + ontology.addLink(relation.getObjectTerm().getIdentifier(), + relation.getSubjectTerm().getIdentifier()); } } } @@ -146,11 +139,7 @@ public O parseOboFileFromJar( String jarURI ) { private File getRegistryFile() throws OntologyLoaderException { File ontologyDirectory = OntologyManagerContext.getInstance().getOntologyDirectory(); - File[] registry = ontologyDirectory.listFiles( new FileFilter() { - public boolean accept( File pathname ) { - return ONTOLOGY_REGISTRY_NAME.equals( pathname.getName() ); - } - } ); + File[] registry = ontologyDirectory.listFiles(pathname -> ONTOLOGY_REGISTRY_NAME.equals( pathname.getName() )); if ( registry.length == 1 ) { // found our file @@ -257,10 +246,7 @@ public O parseOboFile( URL url ) throws OntologyLoaderException { } else { log.info( "The file is empty" ); } - } catch ( IOException e ) { - // optional, so just display message in the log - log.error( "Error while deserializing the map", e ); - } catch ( ClassNotFoundException e ) { + } catch (IOException | ClassNotFoundException e ) { // optional, so just display message in the log log.error( "Error while deserializing the map", e ); } diff --git a/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/local/OntologyTemplateImpl.java b/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/local/OntologyTemplateImpl.java index e136c78..96ada4b 100644 --- a/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/local/OntologyTemplateImpl.java +++ b/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/local/OntologyTemplateImpl.java @@ -27,7 +27,7 @@ public abstract class OntologyTemplateImpl implements O /** * Pool of all term contained in that ontology. */ - protected Collection ontologyTerms = new ArrayList( 1024 ); + protected Collection ontologyTerms = new ArrayList<>(1024); // TODO introduce an interface for querying/updating the relationship // TODO replace the hashmap by a Lucene index -> using a different interface !! @@ -35,17 +35,17 @@ public abstract class OntologyTemplateImpl implements O /** * Represent the relationship: child -> parents. */ - protected final Map> parents = new HashMap>(); + protected final Map> parents = new HashMap<>(); /** * Represent the relationship: parent -> children. */ - protected final Map> children = new HashMap>(); + protected final Map> children = new HashMap<>(); /** * Mapping of all OboTerm by their ID. */ - protected Map id2ontologyTerm = new HashMap( 1024 ); + protected Map id2ontologyTerm = new HashMap<>(1024); /** * Collection of root terms of that ontology. A root term is defined as follow: term having no parent. @@ -55,7 +55,7 @@ public abstract class OntologyTemplateImpl implements O /** * List of all obsolete term found while loading the ontology. */ - protected Collection obsoleteTerms = new ArrayList(); + protected Collection obsoleteTerms = new ArrayList<>(); ///////////////////////////// // Public methods @@ -101,11 +101,11 @@ public void addLink( String parentId, String childId ) { } if ( !children.containsKey( parent ) ) { - children.put( parent, new HashSet() ); + children.put( parent, new HashSet<>() ); } if ( !parents.containsKey( child ) ) { - parents.put( child, new HashSet() ); + parents.put( child, new HashSet<>() ); } children.get( parent ).add( child ); @@ -162,13 +162,11 @@ public Collection getRoots() { } // it wasn't precalculated, then do it here... - roots = new HashSet(); + roots = new HashSet<>(); - for ( Iterator iterator = ontologyTerms.iterator(); iterator.hasNext(); ) { - T ontologyTerm = iterator.next(); - - if ( !hasParent( ontologyTerm ) ) { - roots.add( ontologyTerm ); + for (T ontologyTerm : ontologyTerms) { + if (!hasParent(ontologyTerm)) { + roots.add(ontologyTerm); } } @@ -230,7 +228,7 @@ public Set getDirectChildren( T term ) { } public Set getAllParents( T term ) { - Set parents = new HashSet(); + Set parents = new HashSet<>(); getAllParents( term, parents ); return parents; } @@ -244,7 +242,7 @@ protected void getAllParents( T term, Set parents ) { } public Set getAllChildren( T term ) { - Set children = new HashSet(); + Set children = new HashSet<>(); getAllChildren( term, children ); return children; } diff --git a/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/ols/AbstractOlsOntology.java b/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/ols/AbstractOlsOntology.java index bdccb53..147557c 100644 --- a/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/ols/AbstractOlsOntology.java +++ b/ontology-manager/src/main/java/psidev/psi/tools/ontology_manager/impl/ols/AbstractOlsOntology.java @@ -121,7 +121,7 @@ public void loadOntology( String ontologyID, String name, String version, String this.ontologyID = ontologyID; try { Map roots = olsClient.getRootTerms( ontologyID ); - rootAccs = new HashSet(); + rootAccs = new HashSet<>(); rootAccs.addAll( roots.keySet() ); } catch ( RemoteException e ) { throw new IllegalStateException( "RemoteException while trying to connect to OLS." ); @@ -151,7 +151,7 @@ public void setOntologyDirectory( File directory ) { * @return a Set of OntologyTerms that are valid (in terms of the validator). */ public Set getValidTerms( String accession, boolean allowChildren, boolean useTerm ) { - Set validTerms = new HashSet(); + Set validTerms = new HashSet<>(); T term = getTermForAccession( accession ); if ( term != null ) { if ( useTerm ) { @@ -506,7 +506,7 @@ public Set getDirectParents( T term ) { * @return a Set of OntologyTermIs of the direct parents of the given term. */ public Set getAllParents( T term ) { - Set allParents = new HashSet(); + Set allParents = new HashSet<>(); addParents( term, allParents ); return allParents; } @@ -626,7 +626,7 @@ public Set getAllChildren( T term ) { * @return a Set of OntologyTermI objects representing the result contained in the Map. */ private Set olsMap2TermSet( Map results ) { - Set terms = new HashSet(); + Set terms = new HashSet<>(); for ( Object o : results.keySet() ) { Object v = results.get( o ); if ( o instanceof String && v instanceof String ) { @@ -648,7 +648,7 @@ private Set olsMap2TermSet( Map results ) { // This has issues finding all the child terms if the tree changes relationship types -> use getValidIDs2 @Deprecated public Set getValidIDsOld( String id, boolean allowChildren, boolean useTerm ) { - Set terms = new HashSet(); + Set terms = new HashSet<>(); try { if ( useTerm ) { String result = olsClient.getTermById( id, ontologyID ); @@ -681,7 +681,7 @@ public Set getValidIDsOld( String id, boolean allowChildren, boolean use @Deprecated protected Set getValidIDs2( String id, boolean allowChildren, boolean useTerm ) { - Set terms = new HashSet(); + Set terms = new HashSet<>(); try { if ( useTerm ) { String result = olsClient.getTermById( id, ontologyID ); @@ -880,7 +880,7 @@ public synchronized Set getDirectParentsIDs( String id ) { @Deprecated public Set getAllChildTerms( String id ) throws RemoteException { - Set retVal = new TreeSet(); + Set retVal = new TreeSet<>(); appendChildTerms( retVal, getChildTerms( id ) ); return retVal; } diff --git a/ontology-manager/src/test/java/psidev/psi/tools/ontology_manager/OntologyManagerTest.java b/ontology-manager/src/test/java/psidev/psi/tools/ontology_manager/OntologyManagerTest.java index 263c0a3..1d042d5 100644 --- a/ontology-manager/src/test/java/psidev/psi/tools/ontology_manager/OntologyManagerTest.java +++ b/ontology-manager/src/test/java/psidev/psi/tools/ontology_manager/OntologyManagerTest.java @@ -36,9 +36,6 @@ public void setup() throws OntologyLoaderException, IOException { om.loadOntologies(is); is.close(); Assert.assertNotNull( om ); -// for ( String id : om.getOntologyIDs() ) { -// System.out.println( id ); -// } } private File getTargetDirectory() { diff --git a/pom.xml b/pom.xml index 9dc35b6..2176a62 100755 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ psidev.psi.tools master-pom pom - 2.0.13 + 2.0.14-SNAPSHOT PSI :: Tools :: Master pom @@ -14,7 +14,7 @@ Samuel Kerrien skerrien@ebi.ac.uk Proteomics Services Team - EBI - http://www.ebi.ac.uk/intact + https://www.ebi.ac.uk/intact 0 @@ -22,7 +22,7 @@ Florian Reisinger florian@ebi.ac.uk Proteomics Services Team - EBI - http://www.ebi.ac.uk/proteomics + https://www.ebi.ac.uk/proteomics 0 @@ -30,7 +30,7 @@ Bruno Aranda baranda@ebi.ac.uk Proteomics Services Team - EBI - http://www.ebi.ac.uk/intact + https://www.ebi.ac.uk/intact 0 @@ -38,7 +38,7 @@ Marine Dumousseau marine@ebi.ac.uk Proteomics Services Team - EBI - http://www.ebi.ac.uk/intact + https://www.ebi.ac.uk/intact 0 @@ -96,8 +96,8 @@ maven-compiler-plugin 3.10.1 - 1.5 - 1.5 + 1.8 + 1.8 @@ -148,7 +148,7 @@ maven-javadoc-plugin 2.10.3 - 1.5 + 1.8 true @@ -169,15 +169,15 @@ org.apache.maven.plugins maven-jxr-plugin - 2.5 + 3.3.0 org.apache.maven.plugins maven-pmd-plugin - 2.4 + 3.19.0 - 1.5 + 1.8 utf-8 true @@ -207,29 +207,44 @@ commons-logging commons-logging - 1.1 + 1.2 commons-lang commons-lang - 2.3 + 2.6 - - com.sun.xml.bind - jaxb-impl - 2.1.3 - + stax stax 1.2.0 + javax.xml.bind jaxb-api - 2.1 + 2.3.1 + + + + com.sun.xml.bind + jaxb-impl + 2.3.1 + + + + com.sun.xml.bind + jaxb-core + 2.3.0 + + + + org.glassfish.jaxb + jaxb-xjc + 2.3.2 @@ -243,17 +258,13 @@ - - nexus-ebi-repo-old - http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/ - nexus-ebi-release-repo - http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/ + https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/ nexus-ebi-snapshot-repo - http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/ + https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/ @@ -262,7 +273,7 @@ pst-release EBI Nexus Repository - http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release + https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release diff --git a/validator/pom.xml b/validator/pom.xml index b30cdb5..f9cec8e 100644 --- a/validator/pom.xml +++ b/validator/pom.xml @@ -4,7 +4,7 @@ psidev.psi.tools master-pom - 2.0.13 + 2.0.14-SNAPSHOT validator diff --git a/validator/src/main/java/psidev/psi/tools/validator/Context.java b/validator/src/main/java/psidev/psi/tools/validator/Context.java index 5ec52c3..77cf4af 100644 --- a/validator/src/main/java/psidev/psi/tools/validator/Context.java +++ b/validator/src/main/java/psidev/psi/tools/validator/Context.java @@ -40,7 +40,7 @@ public void setContext( String context ) { } public String toString() { - StringBuffer sb = new StringBuffer( 128 ); + StringBuilder sb = new StringBuilder( 128 ); sb.append( "Context(" ); if ( context != null ) { sb.append( context ); diff --git a/validator/src/main/java/psidev/psi/tools/validator/Validator.java b/validator/src/main/java/psidev/psi/tools/validator/Validator.java index e6bf6c4..1fab503 100644 --- a/validator/src/main/java/psidev/psi/tools/validator/Validator.java +++ b/validator/src/main/java/psidev/psi/tools/validator/Validator.java @@ -98,22 +98,22 @@ public static void setValidationSuccessReporting(boolean validationSuccessReport * The set of rules specific to that Validator. * List of ObjectRuleS */ - private Set rules = new HashSet (); + private Set rules = new HashSet<>(); /** * The map containing the set of Rules excluded by each imported object rule file */ - private Map> excludedRules = new HashMap>(); + private Map> excludedRules = new HashMap<>(); /** * The list contains all the excluded rules (recursively) for one import. It will be cleaned at each time we start the first import */ - private Stack> stackOfExcludedRulesPerImport = new Stack>(); + private Stack> stackOfExcludedRulesPerImport = new Stack<>(); /** * Contains the URL for the rules to import */ - private HashMap urlsForTheImportedRules = new HashMap(); + private HashMap urlsForTheImportedRules = new HashMap<>(); /** * The type of the file to import in the object-rule config file is a resource @@ -401,7 +401,7 @@ private boolean processExcludedRulesDuringImport(Import importedRules){ Exclude exclusion = importedRules.getExclude(); if (exclusion.getRule() != null){ - Set excludedRulesDuringImport = new HashSet(); + Set excludedRulesDuringImport = new HashSet<>(); if (!this.stackOfExcludedRulesPerImport.isEmpty()){ excludedRulesDuringImport.addAll(this.stackOfExcludedRulesPerImport.peek()); @@ -445,36 +445,36 @@ private void importRulesFromFile(String urlName, String typeOfImport) throws Val if (typeOfImport != null){ - if (typeOfImport.toLowerCase().equals(RESOURCE)){ - //URL url = Validator.class.getClassLoader().getResource( urlName ); - URL url = this.getClass().getClassLoader().getResource( urlName ); - - if (url != null){ - InputStream is = url.openStream(); - setObjectRules(is); - isImportDone = true; - is.close(); - } - else{ - log.warn(" The file (" + urlName + ") to import is a resource (" + typeOfImport + ") but was not found. Try to load this url as a local file and if not, try to read the url on internet."); - } - } - else if (typeOfImport.toLowerCase().equals(LOCAL_FILE)){ - if (isALocalFile(urlName)){ - loadLocalFileFrom(urlName); + switch (typeOfImport.toLowerCase()) { + case RESOURCE: + //URL url = Validator.class.getClassLoader().getResource( urlName ); + URL url = this.getClass().getClassLoader().getResource(urlName); + + if (url != null) { + InputStream is = url.openStream(); + setObjectRules(is); + isImportDone = true; + is.close(); + } else { + log.warn(" The file (" + urlName + ") to import is a resource (" + typeOfImport + ") but was not found. Try to load this url as a local file and if not, try to read the url on internet."); + } + break; + case LOCAL_FILE: + if (isALocalFile(urlName)) { + loadLocalFileFrom(urlName); + isImportDone = true; + } else { + log.warn(" The file (" + urlName + ") to import is a local file (" + typeOfImport + ") but was not found. Try to read the url on internet."); + } + break; + case FILE: + loadFileFrom(urlName); isImportDone = true; - } - else { - log.warn(" The file (" + urlName + ") to import is a local file (" + typeOfImport + ") but was not found. Try to read the url on internet."); - } - } - else if (typeOfImport.toLowerCase().equals(FILE)){ - loadFileFrom(urlName); - isImportDone = true; - } - else { - log.warn(" The type of the file (" + urlName + ") to import " + typeOfImport + " is not known. You can choose 'resource' (resource of the validator), 'file' (local file on your machine), or 'url' (look on internet)." + - " First we will try to load this file as a resource. If not found, we will look the local files and then we will try on internet."); + break; + default: + log.warn(" The type of the file (" + urlName + ") to import " + typeOfImport + " is not known. You can choose 'resource' (resource of the validator), 'file' (local file on your machine), or 'url' (look on internet)." + + " First we will try to load this file as a resource. If not found, we will look the local files and then we will try on internet."); + break; } } else { @@ -606,7 +606,7 @@ public void setUserPreferences( UserPreferences userPreferences ) { * @throws ValidatorException Exception while trying to validate the input. */ public Collection validate( Collection col ) throws ValidatorException { - Collection messages = new ArrayList(); + Collection messages = new ArrayList<>(); for ( ObjectRule rule : rules ) { messages.addAll( validate( col, rule ) ); } @@ -621,7 +621,7 @@ public Collection validate( Collection col ) throws Validat * @throws ValidatorException Exception while trying to validate the input. */ public Collection validate( Object objectToCheck ) throws ValidatorException { - Collection messages = new ArrayList(); + Collection messages = new ArrayList<>(); for ( ObjectRule rule : rules ) { if ( rule.canCheck( objectToCheck ) ) { // apply only if rule can handle this object messages.addAll( rule.check( objectToCheck ) ); @@ -638,7 +638,7 @@ public Collection validate( Object objectToCheck ) throws Vali * @throws ValidatorException Exception while trying to validate the input. */ public Collection validate( Object objectToCheck, ObjectRule rule ) throws ValidatorException { - Collection messages = new ArrayList(); + Collection messages = new ArrayList<>(); if ( rule.canCheck( objectToCheck ) ) { // apply only if rule can handle this object messages.addAll( rule.check( objectToCheck ) ); } @@ -654,7 +654,7 @@ public Collection validate( Object objectToCheck, ObjectRule r * @throws ValidatorException Exception while trying to validate the input. */ private Collection validate( Collection col, ObjectRule rule ) throws ValidatorException { - Collection messages = new ArrayList(); + Collection messages = new ArrayList<>(); for ( Object aCol : col ) { if ( rule.canCheck( aCol ) ) { // apply only if rule can handle this object messages.addAll( rule.check( aCol ) ); @@ -677,7 +677,7 @@ public Collection checkCvMappingRules() throws ValidatorExcept return cvRuleManager.checkCvMapping(); } else { log.warn( "The CvRuleManager has not been set up yet." ); - return new ArrayList(); + return new ArrayList<>(); } } @@ -690,7 +690,7 @@ public Collection checkCvMappingRules() throws ValidatorExcept * @throws ValidatorException Exception while trying to validate the input. */ public Collection checkCvMapping( Collection col, String xPath ) throws ValidatorException { - Collection messages = new ArrayList(); + Collection messages = new ArrayList<>(); // Run cv mapping check if ( cvRuleManager != null ) { for ( CvRule rule : cvRuleManager.getCvRules() ) { @@ -716,7 +716,7 @@ public Collection checkCvMapping( Collection col, String xP * @throws ValidatorException Exception while trying to validate the input. */ public Collection checkCvMapping( Object o, String xPath ) throws ValidatorException { - Collection messages = new ArrayList(); + Collection messages = new ArrayList<>(); // Run cv mapping check if ( cvRuleManager != null ) { for ( CvRule rule : cvRuleManager.getCvRules() ) { diff --git a/validator/src/main/java/psidev/psi/tools/validator/ValidatorContext.java b/validator/src/main/java/psidev/psi/tools/validator/ValidatorContext.java index b1bdc4b..d20278c 100644 --- a/validator/src/main/java/psidev/psi/tools/validator/ValidatorContext.java +++ b/validator/src/main/java/psidev/psi/tools/validator/ValidatorContext.java @@ -12,13 +12,7 @@ public class ValidatorContext { private ValidatorConfig validatorConfig; - private static ThreadLocal instance = new - ThreadLocal() { - @Override - protected ValidatorContext initialValue() { - return new ValidatorContext(); - } - }; + private static ThreadLocal instance = ThreadLocal.withInitial(() -> new ValidatorContext()); private ValidatorContext(){ this.validatorConfig = new ValidatorConfig(); diff --git a/validator/src/main/java/psidev/psi/tools/validator/ValidatorCvContext.java b/validator/src/main/java/psidev/psi/tools/validator/ValidatorCvContext.java index 8dce7ce..dd9c49a 100644 --- a/validator/src/main/java/psidev/psi/tools/validator/ValidatorCvContext.java +++ b/validator/src/main/java/psidev/psi/tools/validator/ValidatorCvContext.java @@ -42,13 +42,7 @@ public class ValidatorCvContext { public static final Log log = LogFactory.getLog( ValidatorCvContext.class); - private static ThreadLocal instance = new - ThreadLocal() { - @Override - protected ValidatorCvContext initialValue() { - return new ValidatorCvContext(); - } - }; + private static ThreadLocal instance = ThreadLocal.withInitial(() -> new ValidatorCvContext()); public static ValidatorCvContext getInstance() { return instance.get(); @@ -59,14 +53,14 @@ public static void removeInstance() { } private ValidatorCvContext() { - notRecognisedTerms = new HashMap>(); - recognisedTerms = new HashMap>(); + notRecognisedTerms = new HashMap<>(); + recognisedTerms = new HashMap<>(); } public void resetRecognised() { - recognisedTerms = new HashMap>(); + recognisedTerms = new HashMap<>(); } public boolean isRecognised(String xpath, String term) { @@ -75,7 +69,7 @@ public boolean isRecognised(String xpath, String term) { public void addRecognised(String xpath, String term) { if (recognisedTerms.get(xpath) == null) { - Set newSet = new HashSet(); + Set newSet = new HashSet<>(); recognisedTerms.put(xpath, newSet); } recognisedTerms.get(xpath).add(term); @@ -96,7 +90,7 @@ public Set getRecognisedTerms(String xpath) { public void resetNotRecognised() { - notRecognisedTerms = new HashMap>(); + notRecognisedTerms = new HashMap<>(); } public boolean isNotRecognised(String xpath, String term) { @@ -105,7 +99,7 @@ public boolean isNotRecognised(String xpath, String term) { public void addNotRecognised(String xpath, String term) { if (notRecognisedTerms.get(xpath) == null) { - Set newSet = new HashSet(); + Set newSet = new HashSet<>(); notRecognisedTerms.put(xpath, newSet); } notRecognisedTerms.get(xpath).add(term); diff --git a/validator/src/main/java/psidev/psi/tools/validator/ValidatorMessage.java b/validator/src/main/java/psidev/psi/tools/validator/ValidatorMessage.java index 642ad86..0af4baa 100644 --- a/validator/src/main/java/psidev/psi/tools/validator/ValidatorMessage.java +++ b/validator/src/main/java/psidev/psi/tools/validator/ValidatorMessage.java @@ -3,6 +3,8 @@ import psidev.psi.tools.validator.rules.Rule; import psidev.psi.tools.validator.schema.SaxMessage; +import java.util.Objects; + /** * The definition of a Validator message. * @@ -121,7 +123,7 @@ public boolean equals( Object o ) { final ValidatorMessage that = (ValidatorMessage) o; - if ( context != null ? !context.equals( that.context ) : that.context != null ) { + if (!Objects.equals(context, that.context)) { return false; } if ( level != that.level ) { @@ -130,7 +132,7 @@ public boolean equals( Object o ) { if ( !message.equals( that.message ) ) { return false; } - if ( rule != null ? !rule.equals( that.rule ) : that.rule != null ) { + if (!Objects.equals(rule, that.rule)) { return false; } @@ -147,7 +149,7 @@ public int hashCode() { } public String toString() { - final StringBuffer sb = new StringBuffer(); + final StringBuilder sb = new StringBuilder(); sb.append( "ValidatorMessage" ); sb.append( "{message='" ).append( message ).append( '\'' ); sb.append( ", level=" ).append( level ); diff --git a/validator/src/main/java/psidev/psi/tools/validator/rules/AbstractRule.java b/validator/src/main/java/psidev/psi/tools/validator/rules/AbstractRule.java index eb1f824..ed4ca48 100644 --- a/validator/src/main/java/psidev/psi/tools/validator/rules/AbstractRule.java +++ b/validator/src/main/java/psidev/psi/tools/validator/rules/AbstractRule.java @@ -38,7 +38,7 @@ public abstract class AbstractRule implements Rule { /** * A collection of tips. */ - private Collection howToFixTips = new ArrayList( 1 ); + private Collection howToFixTips = new ArrayList<>(1); /** * Map of needed ontologies @@ -101,9 +101,8 @@ public String toString() { if ( howToFixTips != null && !howToFixTips.isEmpty() ) { sb.append( "Tip" ).append( ( howToFixTips.size() > 1 ? "s" : "" ) ).append( ':' ).append( NEW_LINE ); - for ( Iterator iterator = howToFixTips.iterator(); iterator.hasNext(); ) { - String tip = iterator.next(); - sb.append( "\t* " ).append( tip ).append( NEW_LINE ); + for (String tip : howToFixTips) { + sb.append("\t* ").append(tip).append(NEW_LINE); } } diff --git a/validator/src/main/java/psidev/psi/tools/validator/rules/cvmapping/CvRule.java b/validator/src/main/java/psidev/psi/tools/validator/rules/cvmapping/CvRule.java index c24f5cf..284eda9 100644 --- a/validator/src/main/java/psidev/psi/tools/validator/rules/cvmapping/CvRule.java +++ b/validator/src/main/java/psidev/psi/tools/validator/rules/cvmapping/CvRule.java @@ -5,11 +5,9 @@ import psidev.psi.tools.validator.rules.Rule; import psidev.psi.tools.validator.MessageLevel; import psidev.psi.tools.cvrReader.mapping.jaxb.CvTerm; -import psidev.psi.tools.cvrReader.mapping.jaxb.CvMappingRule; import java.util.Collection; import java.util.List; -import java.util.Map; /** * CV Mapping Rule that is configured via XML. diff --git a/validator/src/main/java/psidev/psi/tools/validator/rules/cvmapping/CvRuleImpl.java b/validator/src/main/java/psidev/psi/tools/validator/rules/cvmapping/CvRuleImpl.java index e4b415d..da1dc67 100644 --- a/validator/src/main/java/psidev/psi/tools/validator/rules/cvmapping/CvRuleImpl.java +++ b/validator/src/main/java/psidev/psi/tools/validator/rules/cvmapping/CvRuleImpl.java @@ -125,7 +125,7 @@ public Collection check( Object object, String prefixXpath ) t throw new ValidatorException( "Cannot validate a null object." ); } - Collection messages = new ArrayList(); + Collection messages = new ArrayList<>(); if( status.equals( MappingRuleStatus.INVALID_XPATH )) { // do not run the rule as it is not valid. return messages; @@ -535,12 +535,12 @@ private Map> checkValuesAgainstCvTerms( final final Recommendation level ) { Map> result2termCount = - new HashMap>( valueResults.size() ); + new HashMap<>(valueResults.size()); // check that each match (term used in the XML) has at least one matching CV term amongst those specified. for ( XPathResult valueResult : valueResults ) { // for each term used in the XML - Map term2count = new HashMap( getCVTerms().size() ); + Map term2count = new HashMap<>(getCVTerms().size()); result2termCount.put( valueResult, term2count ); // for each XPath expression @@ -767,7 +767,7 @@ public boolean equals( Object o ) { CV cv = ( CV ) o; - return accession.equals(cv.accession) && !(name != null ? !name.equals(cv.name) : cv.name != null); + return accession.equals(cv.accession) && !(!Objects.equals(name, cv.name)); } @Override @@ -786,7 +786,7 @@ public int hashCode() { * @return */ private Map calculateCvTermUsage( Map> result2termCount ) { - Map term2count = new HashMap(); + Map term2count = new HashMap<>(); for ( Map.Entry> e : result2termCount.entrySet() ) { Map t2c = e.getValue(); @@ -870,13 +870,6 @@ protected ValidatorMessage buildMessage( String xpath, Recommendation level, Str private String printCvTerm( CvTerm cv ) { StringBuilder sb = new StringBuilder( 512 ); -// sb.append( "CvTerm(" ); -// sb.append( '\'' ).append( cv.getTermAccession() ).append( '\'' ).append( ',' ).append( ' ' ); -// sb.append( '\'' ).append( cv.getTermName() ).append( '\'' ).append( ',' ).append( ' ' ); -// sb.append( "allowChildren:" ).append( cv.isAllowChildren() ).append( ',' ).append( ' ' ); -// sb.append( "useTerm:" ).append( cv.isUseTerm() ).append( ',' ).append( ' ' ); -// sb.append( "repeatable:" ).append( cv.isIsRepeatable() ); -// sb.append( ")" ); if ( cv.isUseTerm() && cv.isAllowChildren() ) { sb.append(cv.getTermAccession()).append(" (").append(cv.getTermName()).append(")"); @@ -947,7 +940,7 @@ private String removeXpathPrefix( String xpath, String prefixXpath ) { public String toString() { - StringBuffer sb = new StringBuffer( 256 ); + StringBuilder sb = new StringBuilder( 256 ); sb.append("[Rule: ID="); sb.append(this.getId()); diff --git a/validator/src/main/java/psidev/psi/tools/validator/schema/SaxMessage.java b/validator/src/main/java/psidev/psi/tools/validator/schema/SaxMessage.java index 03c0001..dcb6ebc 100755 --- a/validator/src/main/java/psidev/psi/tools/validator/schema/SaxMessage.java +++ b/validator/src/main/java/psidev/psi/tools/validator/schema/SaxMessage.java @@ -134,7 +134,7 @@ public int hashCode() { public String toString() { - final StringBuffer sb = new StringBuffer(); + final StringBuilder sb = new StringBuilder(); sb.append( "SaxMessage" ); sb.append( "{publicId='" ).append( publicId ).append( '\'' ); sb.append( ", systemId='" ).append( systemId ).append( '\'' ); diff --git a/validator/src/main/java/psidev/psi/tools/validator/schema/SaxReport.java b/validator/src/main/java/psidev/psi/tools/validator/schema/SaxReport.java index 458bbe7..0343a04 100755 --- a/validator/src/main/java/psidev/psi/tools/validator/schema/SaxReport.java +++ b/validator/src/main/java/psidev/psi/tools/validator/schema/SaxReport.java @@ -24,7 +24,7 @@ public class SaxReport { private boolean valid = true; - private List messages = new ArrayList(); + private List messages = new ArrayList<>(); public SaxReport() { } diff --git a/validator/src/main/java/psidev/psi/tools/validator/util/ValidatorReport.java b/validator/src/main/java/psidev/psi/tools/validator/util/ValidatorReport.java index 099fd75..12fd096 100644 --- a/validator/src/main/java/psidev/psi/tools/validator/util/ValidatorReport.java +++ b/validator/src/main/java/psidev/psi/tools/validator/util/ValidatorReport.java @@ -32,10 +32,10 @@ public class ValidatorReport { private static final String NEW_LINE = System.getProperty( "line.separator" ); - Collection cvRulesNotChecked = new ArrayList(); - Collection cvRulesInvalidXpath = new ArrayList(); - Collection cvRulesValidXpath = new ArrayList(); - Collection cvRulesValid = new ArrayList(); + Collection cvRulesNotChecked = new ArrayList<>(); + Collection cvRulesInvalidXpath = new ArrayList<>(); + Collection cvRulesValidXpath = new ArrayList<>(); + Collection cvRulesValid = new ArrayList<>(); public ValidatorReport( Collection allCvRules ) { splitCvRulesByStatus( allCvRules ); diff --git a/validator/src/test/java/SPEValidator.java b/validator/src/test/java/SPEValidator.java index 4be6565..6683fdb 100755 --- a/validator/src/test/java/SPEValidator.java +++ b/validator/src/test/java/SPEValidator.java @@ -52,7 +52,7 @@ public Collection validate( Object experiment ) throws Validat if( experiment == null ) throw new IllegalArgumentException( "You must give a non null experiment" ); - final Collection messages = new ArrayList(); + final Collection messages = new ArrayList<>(); // Run Object Rules messages.addAll( super.validate( experiment ) ); diff --git a/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/ChestOfDrawers.java b/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/ChestOfDrawers.java index 3cf4d12..a0cd949 100644 --- a/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/ChestOfDrawers.java +++ b/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/ChestOfDrawers.java @@ -11,7 +11,7 @@ * @since specify the maven artifact version */ public class ChestOfDrawers { - Collection drawers = new ArrayList( ); + Collection drawers = new ArrayList<>(); public Collection getDrawers() { return drawers; diff --git a/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/Drawer.java b/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/Drawer.java index 05aa37c..230451c 100644 --- a/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/Drawer.java +++ b/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/Drawer.java @@ -12,7 +12,7 @@ */ public class Drawer { - Collection objects = new ArrayList( ); + Collection objects = new ArrayList<>(); ////////////////// // Constructors diff --git a/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/Garage.java b/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/Garage.java index 9bbe6bd..aea90f6 100644 --- a/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/Garage.java +++ b/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/house/Garage.java @@ -15,7 +15,7 @@ public class Garage { float depth; float width; Car car = null; - Collection bikes = new ArrayList(); + Collection bikes = new ArrayList<>(); ////////////////// // Constructors diff --git a/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/protein/Protein.java b/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/protein/Protein.java index fd9fc34..0b27a99 100644 --- a/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/protein/Protein.java +++ b/validator/src/test/java/psidev/psi/tools/validator/rules/cvmapping/protein/Protein.java @@ -35,13 +35,13 @@ public class Protein { public Protein( String name, CrossReference... references ) { this.name = name; - this.references = new ArrayList(); + this.references = new ArrayList<>(); this.references.addAll( Arrays.asList( references ) ); } public Protein( String name, Modification... modifications ) { this.name = name; - this.modifications = new ArrayList( ); + this.modifications = new ArrayList<>(); this.modifications.addAll( Arrays.asList( modifications ) ); } diff --git a/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/Rule3.java b/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/Rule3.java index 7a67225..2afe1bd 100644 --- a/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/Rule3.java +++ b/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/Rule3.java @@ -35,6 +35,6 @@ public boolean canCheck(Object t) { @Override public Collection check(Object o) throws ValidatorException { - return new ArrayList(); + return new ArrayList<>(); } } diff --git a/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/imex/Rule1.java b/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/imex/Rule1.java index 9a9dd90..3bd67b0 100644 --- a/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/imex/Rule1.java +++ b/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/imex/Rule1.java @@ -35,6 +35,6 @@ public boolean canCheck(Object t) { @Override public Collection check(Object o) throws ValidatorException { - return new ArrayList(); + return new ArrayList<>(); } } diff --git a/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/imex/Rule2.java b/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/imex/Rule2.java index 95dde34..567ea23 100644 --- a/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/imex/Rule2.java +++ b/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/imex/Rule2.java @@ -35,6 +35,6 @@ public boolean canCheck(Object t) { @Override public Collection check(Object o) throws ValidatorException { - return new ArrayList(); + return new ArrayList<>(); } } diff --git a/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/mimix/Rule4.java b/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/mimix/Rule4.java index 6d5984a..c55b8e7 100644 --- a/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/mimix/Rule4.java +++ b/validator/src/test/java/psidev/psi/tools/validator/rules/objectRules/mimix/Rule4.java @@ -35,6 +35,6 @@ public boolean canCheck(Object t) { @Override public Collection check(Object o) throws ValidatorException { - return new ArrayList(); + return new ArrayList<>(); } } diff --git a/validator/src/test/java/psidev/psi/tools/validator/schema/SaxValidatorHandlerTest.java b/validator/src/test/java/psidev/psi/tools/validator/schema/SaxValidatorHandlerTest.java index 3048086..7e8111d 100644 --- a/validator/src/test/java/psidev/psi/tools/validator/schema/SaxValidatorHandlerTest.java +++ b/validator/src/test/java/psidev/psi/tools/validator/schema/SaxValidatorHandlerTest.java @@ -15,11 +15,9 @@ */ package psidev.psi.tools.validator.schema; -import junit.framework.TestCase; import junit.framework.Assert; import org.junit.Test; -import java.io.File; import java.io.InputStream; /**