if (data.getFormat() == GFormat.OBO) { return new GraphLoader_OBO_1_2(); } else if (data.getFormat() == GFormat.GAF2) { return new GraphLoader_GAF_2(); } else if (data.getFormat() == GFormat.RDF_XML) { return new RDFLoader(RDFFormat.RDFXML); } else if (data.getFormat() == GFormat.NTRIPLES) { return new RDFLoader(RDFFormat.NTRIPLES); } else if (data.getFormat() == GFormat.TURTLE) { return new RDFLoader(RDFFormat.TURTLE); } else if (data.getFormat() == GFormat.CSV) { return new GraphLoader_CSV(); } else if (data.getFormat() == GFormat.SNOMED_CT_RF2) { return new GraphLoaderSnomedCT_RF2(); } else if (data.getFormat() == GFormat.SLIB) { return new GraphLoader_SLIB(); } else if (data.getFormat() == GFormat.MESH_XML) { return new GraphLoader_MESH_XML(); } else if (data.getFormat() == GFormat.TSV_ANNOT) { return new GraphLoader_TSVannot(); } else if (data.getFormat() == GFormat.WORDNET_DATA) { return new GraphLoader_Wordnet(); } else { throw new SLIB_Ex_Critic("Unknown Graph format " + data.getFormat());
private void loadConf(GDataConf conf) throws SLIB_Ex_Critic { String header = (String) conf.getParameter(PARAM_HEADER); String prefixSubjectParam = (String) conf.getParameter(PARAM_PREFIX_SUBJECT); String prefixObjectParam = (String) conf.getParameter(PARAM_PREFIX_OBJECT); String predicateParam = (String) conf.getParameter(PARAM_PREDICATE); logger.info("file " + conf.getLoc()); logger.info("Skipping header " + skipHeader); logger.info("predicate '" + predicate + "'");
@Override public boolean isValid() { if (uri == null) { return false; } for (GDataConf dataFile : data) { if (!dataFile.isValid()) { return false; } } for (GAction action : actions) { if (!action.isValid()) { return false; } } return true; }
logger.info("Loading from Wordnet data"); if (conf.getFormat() != GFormat.WORDNET_DATA) { throw new SLIB_Ex_Critic("Cannot use " + this.getClass() + " to load file format " + conf.getFormat() + ", required format is " + GFormat.WORDNET_DATA); String filepath = conf.getLoc(); if (conf.getParameter("prefix") != null) { uriPrefix = (String) conf.getParameter("prefix");
public static void main(String[] args) throws SLIB_Exception { String dataloc = "/data/WordNet/WordNet-3.1/dict/"; // We create the graph URIFactory factory = URIFactoryMemory.getSingleton(); URI guri = factory.getURI("http://graph/wordnet/"); G wordnet = new GraphMemory(guri); // We load the data into the graph GraphLoader_Wordnet_Full loader = new GraphLoader_Wordnet_Full(); GDataConf dataNoun = new GDataConf(GFormat.WORDNET_DATA, dataloc + "data.noun"); GDataConf dataVerb = new GDataConf(GFormat.WORDNET_DATA, dataloc + "data.verb"); GDataConf dataAdj = new GDataConf(GFormat.WORDNET_DATA, dataloc + "data.adj"); GDataConf dataAdv = new GDataConf(GFormat.WORDNET_DATA, dataloc + "data.adv"); loader.populate(dataNoun, wordnet); loader.populate(dataVerb, wordnet); loader.populate(dataAdj, wordnet); loader.populate(dataAdv, wordnet); } }
@Override public void populate(GDataConf conf, G g) throws SLIB_Exception { logger.info("-------------------------------------"); logger.info("Loading Annotations using TSV loader."); logger.info("-------------------------------------"); this.g = g; loadConf(conf); loadTSV(conf.getLoc()); logger.info("TSV specification loaded."); logger.info("-------------------------------------"); }
String concept_file = (String) conf.getParameter(ARG_CONCEPT_FILE); String relationship_file = (String) conf.getParameter(ARG_RELATIONSHIP_FILE); String prefix = (String) conf.getParameter(ARG_PREFIX); if (conf.existsParam(ARG_LOAD_INACTIVE_CONCEPTS)) { String load_inactive_concepts = conf.getParameter(ARG_LOAD_INACTIVE_CONCEPTS).toString(); if (conf.existsParam(ARG_LOAD_INACTIVE_RELATIONSHIPS)) { String load_inactive_relationships = conf.getParameter(ARG_LOAD_INACTIVE_RELATIONSHIPS).toString();
private void loadConf(GDataConf conf) throws SLIB_Ex_Critic { String header = (String) conf.getParameter("header"); if (header == null || Util.stringToBoolean(header) == true) { skipHeader = true; } logger.info("Skipping header " + skipHeader); String separator = (String) conf.getParameter("separator"); if (separator == null) { pattern = Pattern.compile("\\t"); } else { pattern = Pattern.compile(separator); } HashMap<Integer, CSV_Mapping> mappingsLocal = (HashMap<Integer, CSV_Mapping>) conf.getParameter("mappings"); HashMap<Integer, CSV_StatementTemplate> statementTemplatesLocal = (HashMap<Integer, CSV_StatementTemplate>) conf.getParameter("statementTemplates"); if (mappingsLocal != null) { this.mappings.putAll(mappingsLocal); } if (statementTemplatesLocal != null) { this.statementTemplates.putAll(statementTemplatesLocal); } if (this.mappings.isEmpty()) { throw new SLIB_Ex_Critic("Please specify a mapping for CSV loader"); } if (this.statementTemplates.isEmpty()) { throw new SLIB_Ex_Critic("Please specify a statement template for CSV loader"); } }
gDataConf.addParameter("mappings", mappings); gDataConf.addParameter("statementTemplates", stmtemplates);
logger.info("Loading from Wordnet data"); if (conf.getFormat() != GFormat.WORDNET_DATA) { throw new SLIB_Ex_Critic("Cannot use " + this.getClass() + " to load file format " + conf.getFormat() + ", required format is " + GFormat.WORDNET_DATA); String filepath = conf.getLoc(); if (conf.getParameter("prefix") != null) { uriPrefix = (String) conf.getParameter("prefix");
public static void main(String[] args) throws Exception { URIFactoryMemory factory = URIFactoryMemory.getSingleton(); G graph = new GraphMemory(factory.getURI("http://mesh")); GraphLoader_MESH_XML loader = new GraphLoader_MESH_XML(); loader.populate(new GDataConf(GFormat.MESH_XML, "/data/mesh/desc2013.xml"), graph); URI dna_barcoding = factory.getURI("http://D058893"); System.out.println(graph); System.out.println(graph.containsVertex(dna_barcoding)); } }
@Override public void populate(GDataConf conf, G g) throws SLIB_Exception { loadConf(conf); logger.info("-------------------------------------"); logger.info(" RDF Loader"); logger.info("-------------------------------------"); logger.info("Populate graph " + g.getURI() + " from " + conf.getLoc()); load(g, conf.getLoc()); logger.info("Graph " + g.getURI() + " populated by RDF data "); logger.info("-------------------------------------"); }
String concept_file = (String) conf.getParameter(ARG_CONCEPT_FILE); String relationship_file = (String) conf.getParameter(ARG_RELATIONSHIP_FILE); String prefix = (String) conf.getParameter(ARG_PREFIX); if (conf.existsParam(ARG_LOAD_INACTIVE_CONCEPTS)) { String load_inactive_concepts = conf.getParameter(ARG_LOAD_INACTIVE_CONCEPTS).toString(); if (conf.existsParam(ARG_LOAD_INACTIVE_RELATIONSHIPS)) { String load_inactive_relationships = conf.getParameter(ARG_LOAD_INACTIVE_RELATIONSHIPS).toString();
private void loadConf(GDataConf conf) throws SLIB_Ex_Critic { String header = (String) conf.getParameter("header"); if (header == null || Util.stringToBoolean(header) == true) { skipHeader = true; } logger.info("Skipping header " + skipHeader); String separator = (String) conf.getParameter("separator"); if (separator == null) { pattern = Pattern.compile("\\t"); } else { pattern = Pattern.compile(separator); } HashMap<Integer, CSV_Mapping> mappingsLocal = (HashMap<Integer, CSV_Mapping>) conf.getParameter("mappings"); HashMap<Integer, CSV_StatementTemplate> statementTemplatesLocal = (HashMap<Integer, CSV_StatementTemplate>) conf.getParameter("statementTemplates"); if (mappingsLocal != null) { this.mappings.putAll(mappingsLocal); } if (statementTemplatesLocal != null) { this.statementTemplates.putAll(statementTemplatesLocal); } if (this.mappings.isEmpty()) { throw new SLIB_Ex_Critic("Please specify a mapping for CSV loader"); } if (this.statementTemplates.isEmpty()) { throw new SLIB_Ex_Critic("Please specify a statement template for CSV loader"); } }
gDataConf.addParameter("mappings", mappings); gDataConf.addParameter("statementTemplates", stmtemplates);
private void loadConf(GDataConf conf) throws SLIB_Ex_Critic { String header = (String) conf.getParameter(PARAM_HEADER); String prefixSubjectParam = (String) conf.getParameter(PARAM_PREFIX_SUBJECT); String prefixObjectParam = (String) conf.getParameter(PARAM_PREFIX_OBJECT); String predicateParam = (String) conf.getParameter(PARAM_PREDICATE); logger.info("file " + conf.getLoc()); logger.info("Skipping header " + skipHeader); logger.info("predicate '" + predicate + "'");
logger.info("Loading from Wordnet data"); if (conf.getFormat() != GFormat.WORDNET_DATA) { throw new SLIB_Ex_Critic("Cannot use " + this.getClass() + " to load file format " + conf.getFormat() + ", required format is " + GFormat.WORDNET_DATA); String filepath = conf.getLoc(); if (conf.getParameter("prefix") != null) { uriPrefix = (String) conf.getParameter("prefix");
public static void main(String[] args) throws Exception { URIFactoryMemory factory = URIFactoryMemory.getSingleton(); G graph = new GraphMemory(factory.getURI("http://mesh")); GraphLoader_MESH_XML loader = new GraphLoader_MESH_XML(); loader.populate(new GDataConf(GFormat.MESH_XML, "/data/mesh/desc2013.xml"), graph); URI dna_barcoding = factory.getURI("http://D058893"); System.out.println(graph); System.out.println(graph.containsVertex(dna_barcoding)); } }
@Override public void populate(GDataConf conf, G g) throws SLIB_Exception { logger.info("-------------------------------------"); logger.info("Loading CSV."); logger.info("-------------------------------------"); this.g = g; loadConf(conf); loadCSV(conf.getLoc()); logger.info("CSV specification loaded."); logger.info("-------------------------------------"); }
if (data.getFormat() == GFormat.OBO) { return new GraphLoader_OBO_1_2(); } else if (data.getFormat() == GFormat.GAF2) { return new GraphLoader_GAF_2(); } else if (data.getFormat() == GFormat.RDF_XML) { return new RDFLoader(RDFFormat.RDFXML); } else if (data.getFormat() == GFormat.NTRIPLES) { return new RDFLoader(RDFFormat.NTRIPLES); } else if (data.getFormat() == GFormat.TURTLE) { return new RDFLoader(RDFFormat.TURTLE); } else if (data.getFormat() == GFormat.CSV) { return new GraphLoader_CSV(); } else if (data.getFormat() == GFormat.SNOMED_CT_RF2) { return new GraphLoaderSnomedCT_RF2(); } else if (data.getFormat() == GFormat.SLIB) { return new GraphLoader_SLIB(); } else if (data.getFormat() == GFormat.MESH_XML) { return new GraphLoader_MESH_XML(); } else if (data.getFormat() == GFormat.TSV_ANNOT) { return new GraphLoader_TSVannot(); } else if (data.getFormat() == GFormat.WORDNET_DATA) { return new GraphLoader_Wordnet(); } else { throw new SLIB_Ex_Critic("Unknown Graph format " + data.getFormat());