diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java index f60eb7ad87da207d084a55c54a2f0c2fed0c6d22..fcf345ef25ea6ea9c898b2fe16b20de7fd018877 100644 --- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java +++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java @@ -83,8 +83,8 @@ public class MiriamConnectorImpl extends CachableInterface implements MiriamConn public String getUrlString(final MiriamData miriamData) { if (miriamData.getDataType() == null) { throw new InvalidArgumentException("Data type cannot be empty."); - } else if (miriamData.getDataType().getUris().size() == 0) { - throw new InvalidArgumentException("Url for " + miriamData.getDataType() + " cannot be retreived."); + } else if (miriamData.getDataType().getUris().isEmpty()) { + throw new InvalidArgumentException("Url for " + miriamData.getDataType() + " cannot be retrieved."); } String query = LINK_DB_PREFIX + miriamData.getDataType().getUris().get(0) + "\n" + miriamData.getResource(); String result = getCacheValue(query); @@ -162,8 +162,7 @@ public class MiriamConnectorImpl extends CachableInterface implements MiriamConn * @param string identifier in the format NAME:IDENTIFIER. Where NAME is the name * from {@link MiriamType#getCommonName()} and IDENTIFIER is resource * identifier. - * @return <code>true</code> if identifier can be transformed into - * {@link MiriamData} + * @return <code>true</code> if identifier can be transformed into {@link MiriamData} */ @Override public boolean isValidIdentifier(final String string) { @@ -179,8 +178,7 @@ public class MiriamConnectorImpl extends CachableInterface implements MiriamConn * Checks if {@link MiriamType} is valid. * * @param type type to be checked - * @return <code>true</code> if {@link MiriamType} is valid, <code>false</code> - * otherwise + * @return <code>true</code> if {@link MiriamType} is valid, <code>false</code> otherwise */ @Override public boolean isValidMiriamType(final MiriamType type) { diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java index 2b34837e9dd83824f21f9fe1aac7fb1fb67e4461..34655cfe5df8cc06dfee66b6c0759707eb78eb81 100644 --- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java +++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java @@ -172,7 +172,7 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions { assertTrue(SbgnUtil.isValid(tempFile)); } - isDescribedBy + @Test public void importExportZ() throws Exception { Compartment compartment = createCompartment(); diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java index 9d9bb94a7da90418a643685b1f6d0a9f08d3e339..ce6428dd066b246d9d00f121c2c6cda15809ef3f 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java @@ -6700,7 +6700,7 @@ public enum MiriamType { * @param uris {@link #uris} * @param classes {@link #validClass} * @param registryIdentifier {@link #registryIdentifier} - * @param requiredClasses {@link #requiredClasses} + * @param requiredClasses {@link #requiredClass} */ MiriamType(final String commonName, final String dbHomePage, final String[] uris, final Class<?>[] classes, final String registryIdentifier, final Class<?>[] requiredClasses, final String namespace, final String exampleIdentifier) { @@ -6772,8 +6772,7 @@ public enum MiriamType { * @param generalIdentifier identifier in the format NAME:IDENTIFIER. Where NAME is the name * from {@link MiriamType#commonName} and IDENTIFIER is resource * identifier. - * @return {@link MiriamData} representing generalIdentifier, when identifier is - * invalid InvalidArgumentException is thrown + * @return {@link MiriamData} representing generalIdentifier, when identifier is invalid InvalidArgumentException is thrown */ public static MiriamData getMiriamDataFromIdentifier(final String generalIdentifier) { int index = generalIdentifier.indexOf(":"); diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java index 6b289f3310ff3d1dd722edb3b666040d6d172ccd..7702778bf162dff21ee42b2243554dc031f91923 100644 --- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java +++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java @@ -29,7 +29,7 @@ public class BiopaxFactory { */ public MiriamData createMiriamData(final BiopaxPublication publication) { if ("PubMed".equals(publication.getDb())) { - if (publication.getId() == null || publication.getId().equals("")) { + if (publication.getId() == null || publication.getId().isEmpty()) { return null; } else { if (StringUtils.isNumeric(publication.getId().trim())) { @@ -50,8 +50,7 @@ public class BiopaxFactory { * @param biopaxData {@link BiopaxData} where annotations are stored * @param biopaxReference list of references (to data in {@link BiopaxData}) that we want to * convert into {@link MiriamData} - * @return list of {@link MiriamData} that are referenced in {@link BiopaxData} - * with identifier given in biopaxReference. + * @return list of {@link MiriamData} that are referenced in {@link BiopaxData} with identifier given in biopaxReference. */ public Collection<MiriamData> getMiriamData(final BiopaxData biopaxData, final Collection<String> biopaxReference) { List<MiriamData> result = new ArrayList<>();