Changeset 638


Ignore:
Timestamp:
Apr 16, 2012, 2:23:17 PM (5 years ago)
Author:
rob.hooft@…
Message:
  • More final variables
Location:
trunk/code/conceptwiki
Files:
9 edited

Legend:

Unmodified
Added
Removed
  • trunk/code/conceptwiki/common/common-api/src/main/java/nl/nbic/conceptwiki/common/impl/ConceptImpl.java

    r525 r638  
    276276         * @return  the builder instance this method was called on.
    277277         */
    278         public Builder deleted(boolean isDeleted) {
     278        public Builder deleted(final boolean isDeleted) {
    279279            this.deleted = isDeleted;
    280280            return this;
  • trunk/code/conceptwiki/exports/exports-mapping-uri/src/main/java/nl/nbic/conceptwiki/exports/uri_mapping/URIMapping.java

    r489 r638  
    2929     * @param args the command line arguments
    3030     */
    31     public static void main(String[] args) {
    32         ApplicationContext ctx = new ClassPathXmlApplicationContext(CONTEXT_CONFIGURATION);
    33         URIMapping mapping = ctx.getBean(URIMapping.class);
     31    public static void main(final String[] args) {
     32        final ApplicationContext ctx = new ClassPathXmlApplicationContext(CONTEXT_CONFIGURATION);
     33        final URIMapping mapping = ctx.getBean(URIMapping.class);
    3434        mapping.run();
    3535    }
  • trunk/code/conceptwiki/imports/imports-chemspider/src/main/java/nl/nbic/conceptwiki/imports/chemspider/ChemSpiderImport.java

    r636 r638  
    290290       
    291291        final ChemspiderEntry entry = entries.get(st.getSubject());
    292         String objectValue = st.getObject().stringValue();
     292        final String objectValue = st.getObject().stringValue();
    293293       
    294294        switch (ChemspiderPredicate.valueOf(st.getPredicate().getLocalName().toUpperCase())) {
  • trunk/code/conceptwiki/imports/imports-common/src/main/java/nl/nbic/conceptwiki/imports/common/AbstractImportProducer.java

    r513 r638  
    4646        jms.send(new MessageCreator() {
    4747
    48             public Message createMessage(Session session) throws JMSException {
     48            public Message createMessage(final Session session) throws JMSException {
    4949                final Message msg = converter.toMessage(payload, session);
    5050                msg.setJMSType(type.toString());
  • trunk/code/conceptwiki/imports/imports-common/src/main/java/nl/nbic/conceptwiki/imports/common/ConceptWikiConsumer.java

    r513 r638  
    5353
    5454    @Override
    55     public void onMessage(Message msg) {
     55    public void onMessage(final Message msg) {
    5656        try {
    5757            System.err.println("onMessage");
    5858            Concept receivedConcept;
    5959            Concept existingConcept;
    60             MessageType type = MessageType.valueOf(msg.getJMSType());
     60            final MessageType type = MessageType.valueOf(msg.getJMSType());
    6161            switch (type) {
    6262                case CREATE_OR_UPDATE:
     
    8787                    throw new UnsupportedOperationException("Not supported yet.");
    8888            }
    89         } catch (JMSException ex) {
     89        } catch (final JMSException ex) {
    9090            // Log the error
    9191            // TODO decide on further handling.
     
    9898     * @param branch the Branch.
    9999     */
    100     private synchronized void setBranch(Branch branch) {
     100    private synchronized void setBranch(final Branch branch) {
    101101        this.branch = branch;
    102102    }
  • trunk/code/conceptwiki/imports/imports-umls/src/main/java/nl/nbic/conceptwiki/imports/umls/UMLSImport.java

    r628 r638  
    424424                // addLabel
    425425                // API already :-)
    426                 Set<Concept> sources = Sets.newHashSet();
     426                final Set<Concept> sources = Sets.newHashSet();
    427427                sources.add(conceptsUMLSSources.get(sourceName));               
    428428                //FIXME: enable the following code to run the complete UMLS import
     
    462462            }
    463463
    464             Concept umlsConcept = getUMLSConcept(thisCUI);
     464            final Concept umlsConcept = getUMLSConcept(thisCUI);
    465465           
    466466            if (umlsConcept != null) {
     
    495495                        .notations(notations).urls(urls).build();
    496496                               
    497                 Concept newUmlsConcept = conceptService.createConcept(concept,
     497                final Concept newUmlsConcept = conceptService.createConcept(concept,
    498498                        nlmBranch.getId());
    499499            }
     
    546546                        getUMLSConcept(cui);
    547547               
    548                 Set<Concept> sources = Sets.newHashSet();
     548                final Set<Concept> sources = Sets.newHashSet();
    549549                sources.add(conceptsUMLSSources.get(sourceName));
    550550               
     
    820820
    821821            while (counter < cocCount) {
    822                 Transaction tx = graphTemplate.getGraphDb().beginTx();
     822                final Transaction tx = graphTemplate.getGraphDb().beginTx();
    823823                LOGGER.info("counter: {}", counter);
    824824
     
    973973                        "SELECT ui, sty_rl, def FROM SRDEF WHERE rt='STY'");
    974974        // Create the source of UMLS Semantic Network Semantic Types concept
    975         Set<Concept> sources = Sets.newHashSet();
     975        final Set<Concept> sources = Sets.newHashSet();
    976976        sources.add(collectionConceptUMLSSemanticNetworkSemanticTypes);
    977977
     
    11101110       
    11111111        for (String tui: conceptsSemanticNetworkNodeTypesWithID.keySet()) {
    1112             Concept snNodeConcept = conceptsSemanticNetworkNodeTypesWithID.get(tui);
     1112            final Concept snNodeConcept = conceptsSemanticNetworkNodeTypesWithID.get(tui);
    11131113            tagStorageService.createTag(snNodeConcept.getUuid());
    11141114        }
    11151115       
    11161116        for (String tui: conceptsSemanticNetworkRelationTypesWithID.keySet()) {
    1117             Concept snRelationConcept = conceptsSemanticNetworkRelationTypesWithID.get(tui);
     1117            final Concept snRelationConcept = conceptsSemanticNetworkRelationTypesWithID.get(tui);
    11181118            tagStorageService.createTag(snRelationConcept.getUuid());
    11191119        }
     
    12231223        final Transaction tx = graphTemplate.getGraphDb().beginTx();
    12241224       
    1225         Concept result = getOrCreateConceptWithOnePreferredLabel(preferredLabelEng);
     1225        final Concept result = getOrCreateConceptWithOnePreferredLabel(preferredLabelEng);
    12261226        tagStorageService.createTag(result.getUuid());
    12271227       
     
    12381238     */
    12391239    private Concept getUMLSConcept(final String umlsID) {
    1240         List<Concept> resultConcepts = conceptService.getConceptsByNotation(umlsID, QueryScopeImpl.LITE_SCOPE, 10);
     1240        final List<Concept> resultConcepts = conceptService.getConceptsByNotation(umlsID, QueryScopeImpl.LITE_SCOPE, 10);
    12411241        if (resultConcepts.isEmpty()) {
    12421242            return null;
  • trunk/code/conceptwiki/imports/imports-umls/src/main/java/nl/nbic/conceptwiki/imports/umls/UMLSLanguageMapper.java

    r439 r638  
    3131    public UMLSLanguageMapper() {
    3232
    33         ApplicationContext applicationContext = new ClassPathXmlApplicationContext(
     33        final ApplicationContext applicationContext = new ClassPathXmlApplicationContext(
    3434                "/nl/nbic/conceptwiki/imports/imports-umls-context.xml");
    3535
     
    7070     * @return The corresponding <code>Language</code> object.
    7171     */
    72     public Language getLanguageImpl(String UMLSLatCode) {
     72    public Language getLanguageImpl(final String UMLSLatCode) {
    7373        return languageMapperForUMLSLat.get(UMLSLatCode);
    7474    }
  • trunk/code/conceptwiki/storage/storage-neo4j/src/main/java/nl/nbic/conceptwiki/storage/neo4j/impl/ConceptStorageServiceImpl.java

    r634 r638  
    277277    @Override
    278278    public List<Concept> getConceptsByLabel(final String text, final QueryScope scope, final int limit,
    279                                             final Language language, int branchId) {
     279                                            final Language language, final int branchId) {
    280280        final Node node = labelStorageService.getLabel(new LabelImpl(LabelType.HIDDEN, text, language));
    281281       
  • trunk/code/conceptwiki/storage/storage-solr/src/main/java/nl/nbic/conceptwiki/storage/solr/impl/ConceptSearchServiceImpl.java

    r632 r638  
    139139            // TODO evaluate the use of a explicit commit vs. an (server side) autocommit strategy 
    140140            solrServer.commit();
    141         } catch (SolrServerException e) {
     141        } catch (final SolrServerException e) {
    142142            logger.warn("{}", e.getLocalizedMessage());
    143         } catch (IOException e) {
     143        } catch (final IOException e) {
    144144            logger.warn("{}", e.getLocalizedMessage());
    145145        }
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