/** * Creates a new DataSource with the given id and empty description. Adds * the new DataSource to the list of DataSources of this graph. * * @param id * id of the new DataSource * @return created DataSource * @throws NullValueException * if any parameter is null. * @throws EmptyStringException * if id parameter is an empty string. * @throws UnsupportedOperationException * for read-only graphs */ public DataSource createDataSource(String id) throws NullValueException, EmptyStringException, UnsupportedOperationException { return createDataSource(id, ""); }
/** * Creates a new DataSource with the given id, full name and empty * description. Adds the new DataSource to the list of DataSources of this * graph. * * @param id * id of the new DataSource * @param fullname * full name of the new DataSource * @return created DataSource * @throws NullValueException * if any parameter is null. * @throws EmptyStringException * if id parameter is an empty string. * @throws UnsupportedOperationException * for read-only graphs */ public DataSource createDataSource(String id, String fullname) throws NullValueException, EmptyStringException, UnsupportedOperationException { return createDataSource(id, fullname, ""); }
public DataSource safeFetchDataSource(String id) { DataSource dataSource = metaData.getDataSource(id); if (dataSource == null) { dataSource = metaData.getFactory().createDataSource(id); } return dataSource; }
protected static DataSource createDataSource(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ DataSource dataSource = meta.getDataSource(type); if(dataSource == null)dataSource = meta.getFactory().createDataSource(type); return dataSource; }
protected static DataSource createDataSource(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ DataSource dataSource = meta.getDataSource(type); if(dataSource == null)dataSource = meta.getFactory().createDataSource(type); return dataSource; }
/** * Get cv * * @param graph * @param type * @return */ public static DataSource createDataSource(final ONDEXGraph graph, final String type) { ONDEXGraphMetaData meta = graph.getMetaData(); DataSource dataSource = meta.getDataSource(type); if (dataSource == null) dataSource = meta.getFactory().createDataSource(type); return dataSource; }
/** * Get cv * * @param graph * @param type * @return */ public static DataSource createDataSource(final ONDEXGraph graph, final String type) { ONDEXGraphMetaData meta = graph.getMetaData(); DataSource dataSource = meta.getDataSource(type); if (dataSource == null) dataSource = meta.getFactory().createDataSource(type); return dataSource; }
errorReport.append(arguments[1]); dataSource = graph.getMetaData().getFactory() .createDataSource(arguments[1]); errorReport.append("\n"); errorReport
/** * Adds concept data sources to drop down box */ private void populateRestrictDataSource() { restrictDataSource.setEnabled(withinDataSource.isSelected()); // check only for data sources with concepts Set<DataSource> dataSources = new HashSet<DataSource>(); for (DataSource dataSource : graph.getMetaData().getDataSources()) { if (graph.getConceptsOfDataSource(dataSource).size() > 0) { dataSources.add(dataSource); } } // sort data sources DataSource[] array = dataSources.toArray(new DataSource[0]); Arrays.sort(array); // dummy data source DataSource none = graph.getMetaData().getDataSource("NONE"); if (none == null) none = graph.getMetaData().getFactory().createDataSource("NONE"); // add data source to drop-down box restrictDataSource.removeActionListener(this); restrictDataSource.removeAll(); restrictDataSource.addItem(none); for (DataSource dataSource : array) { restrictDataSource.addItem(dataSource); } restrictDataSource.addActionListener(this); restrictDataSource.setSelectedIndex(0); restrictDataSource.revalidate(); }
public static void initialiseMetaData(ONDEXGraph g) { graph = g; ONDEXGraphMetaData metaData = graph.getMetaData(); dataSource = metaData.getFactory().createDataSource("BCSDB", "bacterial carbohydrate structure database"); cc = metaData.getConceptClass("Taxon"); et = metaData.getEvidenceType("IMPD"); external = metaData.getDataSource("TX"); // as used by NCBI Taxonomy parser taxidAttributeName = metaData.getAttributeName("TAXID"); }
public static void initialiseMetaData(ONDEXGraph g) { graph = g; ONDEXGraphMetaData metaData = graph.getMetaData(); // required metadata for a publication dataSource = metaData.getFactory().createDataSource("OGLYCBASE", "o-linked glycoprotein database"); nlm = metaData.getDataSource("NLM"); cc = metaData.getConceptClass("Publication"); // see entries of et = metaData.getEvidenceType("IMPD"); // Attributes for publication authorsAttributeName = metaData.getAttributeName("AUTHORS"); citationAttributeName = metaData.getAttributeName("JOURNAL_REF"); yearPublishedAttributeName = metaData.getAttributeName("YEAR"); }
/** * sets the ONDEXGraph and starts the parser */ public void start() throws InvalidPluginArgumentException { if (args.getUniqueValue(ArgumentNames.CV_ARG) != null) { cvToUse = (String) args.getUniqueValue(ArgumentNames.CV_ARG); if (graph.getMetaData().getDataSource(cvToUse) == null) { graph.getMetaData().getFactory().createDataSource(cvToUse); fireEventOccurred(new DataSourceMissingEvent( "The specified DataSource is not part of the metadata, therefore creating new one.", "[Parser - start]")); } } taxidToUse = (String) args.getUniqueValue(ArgumentNames.TAXID_TO_USE_ARG); try { ReadAllFiles(); // clean up to enable execute from scratch SinkFactory.getInstance().clearCache(); TransformerFactory.instanceRegister.clear(); } catch (Exception e) { e.printStackTrace(); } }
dataSourceGGID = graph.getMetaData().getFactory().createDataSource("GGID", "GENEGO ID", "GeneGO ID for the Regulation Object");
public static void initialiseMetaData(ONDEXGraph g) { graph = g; ONDEXGraphMetaData metaData = graph.getMetaData(); // required metadata for a publication dataSource = metaData.getFactory().createDataSource("CARBBANK", "carbbank"); cc = metaData.getConceptClass("Publication"); // see entries of et = metaData.getEvidenceType("IMPD"); // Attributes for publication analyticalMethodAttributeName = metaData.getFactory().createAttributeName("analyticalmethod","experimental techniqes used in publication", Set.class); antigenInformationAttributeName = metaData.getFactory().createAttributeName("antigeninformation","information about antigens used in publication",Set.class); authorsAttributeName = metaData.getAttributeName("AUTHORS"); citationAttributeName = metaData.getAttributeName("JOURNAL_REF"); articleTitleAttributeName = metaData.getAttributeName("AbstractHeader"); }
public static void initialiseMetaData(ONDEXGraph g) { graph = g; ONDEXGraphMetaData metaData = graph.getMetaData(); // required metadata for a publication dataSource = metaData.getFactory().createDataSource("BCSDB", "bacterial carbohydrate structure database"); cc = metaData.getConceptClass("Publication"); // see entries of et = metaData.getEvidenceType("IMPD"); // Attributes for publication authorsAttributeName = metaData.getAttributeName("AUTHORS"); citationAttributeName = metaData.getAttributeName("JOURNAL_REF"); yearPublishedAttributeName = metaData.getAttributeName("YEAR"); articleTitleAttributeName = metaData.getAttributeName("AbstractHeader"); urlAttributeName = metaData.getAttributeName("URL"); publisherAttributeName = metaData.getFactory().createAttributeName("publisher","publisher of journal",String.class); analyticalMethodAttributeName = metaData.getFactory().createAttributeName("analyticalmethod","experimental techniqes used in publication",String.class); keywordsAttributeName = metaData.getFactory().createAttributeName("keywords","publication keywords",String.class); }
public static void initialiseMetaData(ONDEXGraph g) { graph = g; ONDEXGraphMetaData metaData = graph.getMetaData(); dataSource = metaData.getFactory().createDataSource("BCSDB", "bacterial carbohydrate structure database"); ccsd = metaData.getDataSource("CCSD"); cc = metaData.getConceptClass("Comp"); et = metaData.getEvidenceType("IMPD"); linearStructureAttributeName = metaData.getFactory().createAttributeName("linearBCSDB","structure in BCSDB linear format",String.class); structureTypeAttributeName = metaData.getFactory().createAttributeName("typeBCSDB","structure type according to BCSDB classification",String.class); molecularMassAttributeName = metaData.getFactory().createAttributeName("molmass","molecular mass",String.class); aglyconInfoAttributeName = metaData.getFactory().createAttributeName("alglyconinfo","info about biochemical entity to which glycan is bound",String.class); molecularFormulaAttributeName = metaData.getFactory().createAttributeName("molformula","molecular formula",String.class); trivialNameAttributeName = metaData.getFactory().createAttributeName("trivialname","trivial name",String.class); }
m = (M) md.getDataSource(id); if (m == null) { m = (M) md.getFactory().createDataSource(id);
public static void initialiseMetaData(ONDEXGraph g) { graph = g; ONDEXGraphMetaData metaData = graph.getMetaData(); // required metadata for a glycoprotein dataSource = metaData.getFactory().createDataSource("OGLYCBASE", "o-linked glycoprotein database"); cc = metaData.getFactory().createConceptClass("Glycoprotein"); et = metaData.getEvidenceType("IMPD"); // Attributes for glycoprotein oglycbaseIDAttributeName = metaData.getFactory().createAttributeName("oglycbaseID", "accession number in OGlycBASE", String.class); proteinNameAttributeName = metaData.getFactory().createAttributeName("proteinname", "name of protein", String.class); oglycanInfoAttributeName = metaData.getFactory().createAttributeName("oglycaninfo", "notes about glycosylation", String.class); experimentalGlycosylatedSerinePositionsAttributeName = metaData.getFactory().createAttributeName("expgserpos" , "experimentally determined positions of glycosylated serine residues", String[].class); predictedGlycosylatedSerinePositionsAttributeName = metaData.getFactory().createAttributeName("pregserpos" , "experimentally determined positions of glycosylated serine residues", String[].class); experimentalGlycosylatedThreoninePositionsAttributeName = metaData.getFactory().createAttributeName("expgthrpos" , "experimentally determined positions of glycosylated threonine residues", String[].class); predictedGlycosylatedThreoninePositionsAttributeName = metaData.getFactory().createAttributeName("pregthrpos" , "experimentally determined positions of glycosylated threonine residues", String[].class); experimentalGlycosylatedAsparaginePositionsAttributeName = metaData.getFactory().createAttributeName("expgasnpos" , "experimentally determined positions of glycosylated asparagine residues", String[].class); predictedGlycosylatedAsparaginePositionsAttributeName = metaData.getFactory().createAttributeName("pregasnpos" , "experimentally determined positions of glycosylated asparagine residues", String[].class); experimentalGlycosylatedTryptophanPositionsAttributeName = metaData.getFactory().createAttributeName("expgtrppos" , "experimentally determined positions of glycosylated tryptophan residues", String[].class); predictedGlycosylatedTryptophanPositionsAttributeName = metaData.getFactory().createAttributeName("pregtrppos" , "experimentally determined positions of glycosylated tryptophan residues", String[].class); sequenceLengthAttributeName = metaData.getFactory().createAttributeName("seqlen" , "number of residues in protein sequence", Integer.class); sequenceAttributeName = metaData.getFactory().createAttributeName("seq" , "amino-acid sequence", String.class); sequenceByGlycosylationAttributeName = metaData.getFactory().createAttributeName("gseq" , "amino-acid sequence with glycosylation info", String.class); commentsAttributeName = metaData.getFactory().createAttributeName("comments" , "comments", HashSet.class); }
dataSource = graph.getMetaData().getDataSource(id); if (dataSource == null) { dataSource = graph.getMetaData().getFactory().createDataSource(id);
ONDEXGraphMetaData metaData = graph.getMetaData(); dataSource = metaData.getFactory().createDataSource("CARBBANK", "carbbank"); ccsd = metaData.getDataSource("CCSD"); cc = metaData.getConceptClass("Comp");