} catch (FileNotFoundException fnfe) { Parser.propagateEventOccurred( new DataFileMissingEvent(fnfe.getMessage(), "AbstractTPParser(ConceptWriter conceptWriter, ParserArguments pa)")); } catch (IOException ioe) { Parser.propagateEventOccurred(
ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("FASTA file missing :"+file, "parseFastaFile(ONDEXGraph graph, String fileName, WriteFastaFile write)")); return; } else if (!file.canRead()) { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("FASTA file has no read permissions :"+file, "parseFastaFile(ONDEXGraph graph, String fileName, WriteFastaFile write)")); return;
ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("File does not exit: "+fileName, "parsePublications()"));
Parser.propagateEventOccurred(goe); } catch (FileNotFoundException fnfe) { Parser.propagateEventOccurred(new DataFileMissingEvent(fnfe .getMessage(), ONDEXParser.getCurrentMethodName())); } catch (IOException ioe) {
"[Validator - validate]")); } catch (FileNotFoundException fnfe) { fireEventOccurred(new DataFileMissingEvent(fnfe.getMessage(), "[Validator - validate]")); } catch (IOException ioe) {
.getUniqueValue(FileArgumentDefinition.INPUT_DIR)); if (path == null || !path.exists()) { fireEventOccurred(new DataFileMissingEvent("The directory is missing :" + path.getAbsolutePath(), getCurrentMethodName())); return; fireEventOccurred(new DataFileMissingEvent("Transcription factor file not found in :" + path.getAbsolutePath(), getCurrentMethodName())); return; fireEventOccurred(new DataFileMissingEvent("TF Peptide file not found in :" + path.getAbsolutePath(), getCurrentMethodName()));
Parser.propagateEventOccurred(new DataFileMissingEvent(fnfe .getMessage(), ONDEXParser.getCurrentMethodName())); } catch (IOException ioe) {
"[Validator - validate]")); } catch (FileNotFoundException fnfe) { fireEventOccurred(new DataFileMissingEvent(fnfe .getMessage(), "[Validator - validate]")); } catch (IOException ioe) {
.getUniqueValue(FileArgumentDefinition.INPUT_DIR)); if (!dir.exists()) { fireEventOccurred(new DataFileMissingEvent(dir.getAbsolutePath(), "[Parser - start]")); return; fireEventOccurred(new DataFileMissingEvent(fileNodes .getAbsolutePath(), "[Parser - start]")); } catch (IOException ioe) { fireEventOccurred(new DataFileMissingEvent(fileNames .getAbsolutePath(), "[Parser - start]")); } catch (IOException ioe) { fireEventOccurred(new DataFileMissingEvent(fileNodes .getAbsolutePath(), "[Parser - start]")); } catch (IOException ioe) {
ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("Directory does not exits: "+sequenceDir, Parser.getCurrentMethodName())); return null; ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("Gene sequence data missing: with prefix "+dna_file_prefix+" in directory "+ sequenceDir, Parser.getCurrentMethodName())); }else { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Gene sequence data version: "+fileName.substring(dna_file_prefix.length())+" detected", Parser.getCurrentMethodName()));
System.out.println(numTF + " TFs were parsed from DPTF."); } catch (FileNotFoundException fnfe) { parser.fireEventOccurred(new DataFileMissingEvent( fnfe.getMessage(), "[Parser - start()]")); } catch (IOException ioe) {
ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("Directory does not exits: "+sequenceDir, Parser.getCurrentMethodName())); return null; ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("Protein sequence data missing: with prefix \"TAIR7_pep\" in directory " + sequenceDir, Parser.getCurrentMethodName())); }else { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Protein sequence data version: "+fileName.substring("TAIR7_pep".length())+" detected", Parser.getCurrentMethodName()));
File dir = new File(tairReleaseDir); if (!dir.exists()) { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("Directory does not exits: "+tairReleaseDir, Parser.getCurrentMethodName())); ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent(Parser.TAIRX+"_NCBI_mapping_mRNA is missing from dir: "+tairReleaseDir, Parser.getCurrentMethodName())); ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent(Parser.TAIRX+"_NCBI_mapping_prot is missing from dir: "+tairReleaseDir, Parser.getCurrentMethodName()));
fireEventOccurred(new DataFileMissingEvent( fileToRead.getAbsolutePath() + " can not be found.", "[Parser - start]", Level.ERROR)); fireEventOccurred(new DataFileMissingEvent( fileToRead.getAbsolutePath() + " can not be read.", "[Parser - start]"));
writer.close(); } catch (FileNotFoundException fnfe) { fireEventOccurred(new DataFileMissingEvent(fnfe.getMessage(), getCurrentMethodName())); } catch (IOException ioe) {
fireEventOccurred(new DataFileMissingEvent(fnfe.getMessage(), "[Parser - start]")); } catch (IOException ioe) { fireEventOccurred(new DataFileErrorEvent(ioe.getMessage(), "[Parser - start]"));
writer.close(); } catch (FileNotFoundException fnfe) { this.fireEventOccurred(new DataFileMissingEvent(fnfe.getMessage(), "[Export - start]"));
fireEventOccurred(new DataFileMissingEvent(fnfe.getMessage(), "[Parser - start]")); } catch (IOException ioe) { fireEventOccurred(new DataFileErrorEvent(ioe.getMessage(), "[Parser - start]"));
parser.fireEventOccurred(new DataFileMissingEvent(fnfe .getMessage(), "[Parser - start()]")); } catch (IOException ioe) {
fireEventOccurred(new DataFileMissingEvent(fnfe.getMessage(), "[Parser - start]")); } catch (IOException ioe) { ioe.printStackTrace();