public IntactSolrSearchResult(SolrDocumentList results, String [] fieldNames, List<FacetField> facetFields){ super(results, fieldNames, facetFields); mitabReader = new PsimiTabReader(); }
public ClusteredMitabFilter(InteractionExporter exporter, String mitab){ super(exporter, mitab); this.mitabReader = new PsimiTabReader(); }
public NonClusteredMitabFilter(InteractionExporter exporter, String mitab){ super(exporter, mitab); this.mitabReader = new PsimiTabReader(); }
public IntactSolrSearchResult(SolrDocumentList results, String [] fieldNames){ super(results, fieldNames); this.mitabReader = new PsimiTabReader(); }
public NonClusteredMitabFilter(InteractionExporter exporter){ super(exporter); this.mitabReader = new PsimiTabReader(); }
public ClusteredMitabFilter(InteractionExporter exporter){ super(exporter); this.mitabReader = new PsimiTabReader(); }
public MitabLineMapper() { this.psimitabReader = new PsimiTabReader(); }
public void setComplexProperties(String complexProperties) throws IOException { this.complexProperties = complexProperties; initialiseMapOfPsicquicClients(); this.reader = new PsimiTabReader(); } }
protected AbstractInteractionDocumentBuilder( ColumnBasedDocumentDefinition documentDefinition ) { this.documentDefinition = documentDefinition; this.rowReader = new DefaultRowReader(this.documentDefinition); this.mitabReader = new PsimiTabReader(); }
public void setBinaryInteractionIterator(Reader r, boolean hasHeader) throws ClusterServiceException { if ( r != null ) { final PsimiTabReader reader = new PsimiTabReader( ); try { this.binaryInteractionIterator = reader.iterate( r ); } catch ( Exception e ) { throw new ClusterServiceException( "An error occured while read MITAB data", e ); } } }
public void setBinaryInteractionIterator(InputStream inputStream, boolean hasHeader) throws ClusterServiceException { if ( inputStream != null ) { final PsimiTabReader reader = new PsimiTabReader( ); try { this.binaryInteractionIterator = reader.iterate( inputStream ); } catch ( Exception e ) { throw new ClusterServiceException( "An error occured while read MITAB data", e ); } } }
public PsimiTabIterator(Reader psiMiTabInteractionsReader) { boolean isHeader = true; if (psiMiTabInteractionsReader == null) { throw new IllegalArgumentException("You must give a non null input stream."); } if (psiMiTabInteractionsReader instanceof BufferedReader) { this.interactionStreamReader = (BufferedReader) psiMiTabInteractionsReader; } else { this.interactionStreamReader = new BufferedReader(psiMiTabInteractionsReader); } this.mReader = new PsimiTabReader(); try { do { String firstLine = interactionStreamReader.readLine(); if(firstLine == null){ nextLine = null; isHeader = false; } else if (!firstLine.isEmpty() && !firstLine.startsWith("#")) { //This line is not a comment, we read nextLine = mReader.readLine(firstLine); lineIndex++; isHeader = false; } } while (isHeader); } catch (Exception e) { closeStreamReader(); throw new RuntimeException("Error while reading the header line.", e); } }
public List<BinaryInteraction> getInteractions(String query, int firstResult, int maxNumberOfResults) throws IOException { List<BinaryInteraction> results = new ArrayList<BinaryInteraction>(Math.min(2048, maxNumberOfResults)); String url = service.getRestUrl(); PsicquicSimpleClient client = new PsicquicSimpleClient(url); InputStream is = client.getByQuery(query, PsicquicSimpleClient.MITAB25, firstResult, maxNumberOfResults); PsimiTabReader tabReader = new PsimiTabReader(); BufferedReader in = new BufferedReader(new InputStreamReader(is)); String str; while ((str = in.readLine()) != null) { BinaryInteraction interaction = null; try { interaction = tabReader.readLine(str); } catch (PsimiTabException e) { throw new IOException("Impossible to read the mitab line", e); } results.add(interaction); } in.close(); return results; } }
public AbstractInteractionCluster( Reader r, boolean hasHeader ) throws ClusterServiceException { if ( r == null ) { throw new IllegalArgumentException( "You must give a non null MITAB Reader" ); } String [] dbNames; if (mappingIdDbNames.contains(",")){ dbNames = mappingIdDbNames.split(","); } else { dbNames = new String [] {mappingIdDbNames}; } this.binary2Encore = new Binary2Encore(dbNames); final PsimiTabReader reader = new PsimiTabReader( ); try { this.binaryInteractionIterator = reader.iterate( r ); } catch ( Exception e ) { throw new ClusterServiceException( "An error occured while read MITAB data", e ); } }
PsimiTabReader reader = new PsimiTabReader(); Collection<BinaryInteraction> interactions = reader.read(inputStream); Tab2Xml tab2Xml = new Tab2Xml();
@Override public void open(ExecutionContext executionContext) throws ItemStreamException { if (clusteredMitabFile == null){ throw new ItemStreamException("The Mitab cluster score item processor needs a clustered mitab file containing the scores to be able to process the non clustered MITAB file"); } PsimiTabReader mitabReader = new PsimiTabReader(); try { Iterator<BinaryInteraction> binaryInteractionIterator = mitabReader.iterate(clusteredMitabFile); while (binaryInteractionIterator.hasNext()){ BinaryInteraction binary = binaryInteractionIterator.next(); Interactor interactorA = binary.getInteractorA(); Interactor interactorB = binary.getInteractorB(); List<Confidence> confidences = binary.getConfidenceValues(); String firstInteractor = extractInteractorIdentifier(interactorA); String secondInteractor = extractInteractorIdentifier(interactorB); Double score = extractClusterScoreFrom(confidences); if (score != null){ scores.put(new BinaryPair(firstInteractor, secondInteractor), score); } } } catch (IOException e) { throw new ItemStreamException("Impossible to read the clustered mitab file " + clusteredMitabFile.getAbsolutePath(), e); } }
public SolrDocumentConverter(SolrServer solrServer, FieldEnricher fieldEnricher) { super(); this.fieldEnricher = fieldEnricher != null ? fieldEnricher : new BaseFieldEnricher(); try { this.schemaInfo = IntactSolrUtils.retrieveSchemaInfo(solrServer); } catch (IOException e) { throw new RuntimeException("Problem fetching schema info from solr server: "+solrServer); } rowReader = new DefaultRowReader(MitabDocumentDefinitionFactory.mitab27()); mitabReader = new PsimiTabReader(); confidenceSelectiveAdder = new ConfidenceScoreSelectiveAdder(FieldNames.INTACT_SCORE_NAME.toLowerCase()); geneSelectiveAdder = new GeneNameSelectiveAdder(); idATypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ID_A, InteractionKeys.KEY_INTERACTOR_TYPE_A); idBTypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ID_B, InteractionKeys.KEY_INTERACTOR_TYPE_B); altidATypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ALTID_A, InteractionKeys.KEY_INTERACTOR_TYPE_A); altidBTypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ALTID_B, InteractionKeys.KEY_INTERACTOR_TYPE_B); binarySelectiveAdder = new BinaryIdSelectiveAdder(); // override the static initializeKeyMap with the field enricher initialized overrideKeyMap(); }
public SolrDocumentConverter(SolrServer solrServer) { super(); this.fieldEnricher = new BaseFieldEnricher(); try { this.schemaInfo = IntactSolrUtils.retrieveSchemaInfo(solrServer); } catch (IOException e) { throw new RuntimeException("Problem fetching schema info from solr server: "+solrServer); } rowReader = new DefaultRowReader(MitabDocumentDefinitionFactory.mitab27()); mitabReader = new PsimiTabReader(); confidenceSelectiveAdder = new ConfidenceScoreSelectiveAdder(FieldNames.INTACT_SCORE_NAME.toLowerCase()); geneSelectiveAdder = new GeneNameSelectiveAdder(); idATypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ID_A, InteractionKeys.KEY_INTERACTOR_TYPE_A); idBTypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ID_B, InteractionKeys.KEY_INTERACTOR_TYPE_B); altidATypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ALTID_A, InteractionKeys.KEY_INTERACTOR_TYPE_A); altidBTypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ALTID_B, InteractionKeys.KEY_INTERACTOR_TYPE_B); binarySelectiveAdder = new BinaryIdSelectiveAdder(); // override the static initializeKeyMap with the field enricher initialized overrideKeyMap(); }
public SolrDocumentConverter(SolrServer solrServer, OntologySearcher ontologySearcher) { super(); this.fieldEnricher = ontologySearcher != null ? new OntologyFieldEnricher(ontologySearcher) : new BaseFieldEnricher(); try { this.schemaInfo = IntactSolrUtils.retrieveSchemaInfo(solrServer); } catch (IOException e) { throw new RuntimeException("Problem fetching schema info from solr server: "+solrServer); } rowReader = new DefaultRowReader(MitabDocumentDefinitionFactory.mitab27()); mitabReader = new PsimiTabReader(); confidenceSelectiveAdder = new ConfidenceScoreSelectiveAdder(FieldNames.INTACT_SCORE_NAME.toLowerCase()); geneSelectiveAdder = new GeneNameSelectiveAdder(); idATypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ID_A, InteractionKeys.KEY_INTERACTOR_TYPE_A); idBTypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ID_B, InteractionKeys.KEY_INTERACTOR_TYPE_B); altidATypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ALTID_A, InteractionKeys.KEY_INTERACTOR_TYPE_A); altidBTypeSelectiveAdder = new ByInteractorTypeRowDataAdder(InteractionKeys.KEY_ALTID_B, InteractionKeys.KEY_INTERACTOR_TYPE_B); binarySelectiveAdder = new BinaryIdSelectiveAdder(); // override the static initializeKeyMap with the field enricher initialized overrideKeyMap(); }
/** * Execute takslet step * @param arg0 * @param arg1 * @return * @throws Exception */ public RepeatStatus execute(StepContribution arg0, ChunkContext arg1) throws Exception { // do some checking there this.checkOutputMitabFile(); this.checkInputMitabFile(); /* Get mitab file */ PsimiTabReader mitabReader = new PsimiTabReader(); InteractionClusterScore interactionClusterScore = new InteractionClusterScore(); interactionClusterScore.setScoreName(scoreName); /* Get binaryInteractions from mitab file */ interactionClusterScore.setBinaryInteractionIterator(mitabReader.iterate(mitabInputFile)); /* Run cluster using list of binary interactions as input */ interactionClusterScore.setMappingIdDbNames(databaseToCluster); interactionClusterScore.runService(); /* Save mitab clustered data in files */ saveMitabOutputFile(interactionClusterScore); /* task finsihed */ return RepeatStatus.FINISHED; }