Workflow34graph00 http://temp 2009-11-13 00:47:24.801 EST http://bio2rdf 2009-11-16 15:21:22.624 EST http://labrie 2009-11-13 00:31:05.765 EST sparql_endpoint00 http://localhost:8890/sparql 2009-11-17 01:00:39.985 EST sparql_query00 SELECT DISTINCT ?seeAlso WHERE { ?s a <http://bio2rdf.org/ns/bio2rdf#SearchResult> . ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . }; SELECT DISTINCT ?seeAlso WHERE { ?s a <http://bio2rdf.org/ns/bio2rdf#SearchResult> . ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . } 2009-11-17 01:05:35.11 EST SELECT DISTINCT ?seeAlso WHERE { ?s a <http://bio2rdf.org/ns/bio2rdf#SearchResult> . ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . }; SELECT DISTINCT ?seeAlso WHERE { ?s a <http://bio2rdf.org/ns/pubmed:Article> . ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . }; SELECT DISTINCT ?seeAlso WHERE { ?s a <http://bio2rdf.org/ns/pubmed:Article> . ?s <http://bio2rdf.org/ns/pubmed#xRelated> ?seeAlso . } 2009-11-17 01:08:26.154 EST SELECT DISTINCT ?seeAlso WHERE { ?s a <http://bio2rdf.org/ns/bio2rdf#SearchResult> . ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . } 2009-11-17 01:02:50.100 EST SELECT DISTINCT ?seeAlso WHERE { ?s a <http://bio2rdf.org/ns/bio2rdf#SearchResult> . ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . }; SELECT DISTINCT ?seeAlso WHERE { ?s a <http://bio2rdf.org/ns/pubmed:Article> . ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . }; 2009-11-17 01:07:20.984 EST SELECT DISTINCT ?seeAlso WHERE { ?s a <http://bio2rdf.org/ns/bio2rdf#SearchResult> . ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . }; SELECT DISTINCT ?s WHERE { ?s a <http://bio2rdf.org/ns/pubmed:Article> . ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . }; SELECT DISTINCT ?seeAlso WHERE { ?s a <http://bio2rdf.org/ns/pubmed:Article> . ?s <http://bio2rdf.org/ns/pubmed#xRelated> ?seeAlso . } 2009-11-17 01:34:20.804 EST o2bio2rdf_subject_fetch_pubmed_logo1Insert_ntriplesgraph0ntriples0sparql_endpoint_url0sparql_insert_ntriples_log11net.sf.taverna.t2.activitiesdataflow-activity0.8net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePubmed_xml_rdfiserpubmed_bmuri0ncbi_pubmed_xml2ntriples00net.sf.taverna.t2.activitiesdataflow-activity0.8net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSPARQL_querysparql_endpoint0graph0sparql_query0sparql_query_bmuri_list11net.sf.taverna.t2.activitiesdataflow-activity0.8net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionstring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true string 0 'text/plain' java.lang.String true regex 0 'text/plain' 1 split 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesemicolonvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity ; net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCountstringlist0utility_stringlist_count00net.sf.taverna.t2.activitiesdataflow-activity0.8net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeInsert_ntriplesgraphgraphInsert_ntriplesntriplesPubmed_xml_rdfiserncbi_pubmed_xml2ntriplesInsert_ntriplessparql_endpoint_urlsparql_endpointPubmed_xml_rdfiserpubmed_bmuriCountutility_stringlist_countSPARQL_querysparql_endpointsparql_endpointSPARQL_querygraphgraphSPARQL_querysparql_querySplit_string_into_string_list_by_regular_expressionsplitSplit_string_into_string_list_by_regular_expressionstringsparql_querySplit_string_into_string_list_by_regular_expressionregexsemicolonvalueCountstringlistSPARQL_querysparql_query_bmuri_listo2Pubmed_xml_rdfiserncbi_pubmed_xml2ntriplesbio2rdf_subject_fetch_pubmed_logInsert_ntriplessparql_insert_ntriples_logo1SPARQL_querysparql_query_bmuri_list demo_who_is_dr_labrie_from_bio2rdf_cache 2009-11-14 00:43:01.137 EST demo_who_is_dr_labrie_bio2rdf_cache 2009-11-14 00:34:42.466 EST Sponge into Virtuoso triplestore the needed ressource from PubMed [myexperiment:pubmed_step3_describe] 2009-11-17 02:04:45.735 EST FrancoisBelleau@yahoo.ca 2009-11-09 12:16:49.168 EST Spounge into Virtuoso triplestore the needed ressource from PubMed [myexperiment:pubmed_step3_describe] 2009-11-17 02:04:14.203 EST query = labrie,f query = labrie 2009-11-09 12:17:27.970 EST query = labrie,f query = labrie query = h1n1 2009-11-02 12:39:27.342 EST [myexperiment:pubmed_step3_describe] 2009-11-17 01:09:19.344 EST query = morissette,j query = labrie,f query = labrie query = h1n1 2009-11-02 12:56:25.278 EST bio2rdf_subject_fetch_pubmed 2009-11-16 15:20:24.54 EST Get a list of paper from pubmed. 2009-11-16 15:20:42.907 EST demo_who_is_dr_labrie 2009-11-09 12:17:09.526 EST dataflow0ntriples00 <http://test> <http://test> <http://test> . 2009-11-09 19:01:39.958 EST graph00 http://test 2009-11-09 18:55:38.421 EST sparql_endpoint_url00 http://localhost:8890/sparql 2009-11-09 19:01:22.419 EST sparql_insert_ntriples_logo1o2SPARQL_insert_ntriplesntriples0graph0sparql_port0sparql_host0html00net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true ntriples 0 text/plain java.lang.String true graph 0 text/plain java.lang.String true sparql_host 0 text/plain java.lang.String true sparql_port 0 text/plain 0 html 0 'text/plain,text/html' UserNameHere 2009-01-23 00:53:10.565 EST UserNameHere 2009-01-22 22:44:53.200 EST UserNameHere 2009-01-22 23:12:14.802 EST UserNameHere 2009-11-02 14:11:03.534 EST UserNameHere 2009-01-23 00:08:37.503 EST UserNameHere 2009-10-06 00:36:49.673 EDT UserNameHere 2009-01-25 22:33:59.715 EST UserNameHere 2009-01-22 22:58:39.533 EST UserNameHere 2009-10-06 00:23:08.363 EDT UserNameHere 2009-01-25 22:31:23.275 EST UserNameHere 2009-01-23 00:09:42.877 EST UserNameHere 2009-01-23 00:03:55.477 EST UserNameHere 2009-01-26 23:10:57.600 EST UserNameHere 2009-11-02 14:07:23.431 EST UserNameHere 2009-01-22 22:42:57.377 EST UserNameHere 2009-01-23 00:05:21.845 EST UserNameHere 2009-01-23 00:06:51.677 EST UserNameHere 2009-01-23 00:44:07.662 EST UserNameHere 2009-10-20 01:19:54.646 EDT UserNameHere 2009-01-26 23:08:43.41 EST UserNameHere 2009-01-23 00:07:17.366 EST UserNameHere 2009-10-06 00:28:07.839 EDT UserNameHere 2009-01-25 22:32:29.783 EST UserNameHere 2009-01-23 00:06:17.667 EST UserNameHere 2009-01-26 23:11:58.183 EST UserNameHere 2009-01-25 22:17:04.902 EST UserNameHere 2009-01-25 22:27:57.661 EST UserNameHere 2009-10-06 00:34:47.715 EDT UserNameHere 2009-11-02 14:01:31.829 EST UserNameHere 2009-01-23 00:08:17.891 EST UserNameHere 2009-01-23 00:03:19.809 EST net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_list_of_strings_extracting_match_to_a_regexstringlist1regex0group0filteredlist11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true regex 0 'text/plain' java.lang.String true group 0 'text/plain' 1 filteredlist 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke_1value00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokehtml_donevalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity &gt;, (.*?) -- done net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConcat_log_messagemsg0graph0sparql_url0subject0log00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true msg 0 text/plain java.lang.String true graph 0 text/plain java.lang.String true sparql_url 0 text/plain java.lang.String true subject 0 text/plain 0 log 0 text/plain net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_sparql_urlsparql_url0port00host00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true sparql_url 0 text/plain 0 host 0 text/plain 0 port 0 text/plain net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFirst_subjectntriples0subject00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true ntriples 0 text/plain 0 subject 0 text/plain net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSPARQL_insert_ntriplesntriplesntriplesSPARQL_insert_ntriplesgraphgraphSPARQL_insert_ntriplessparql_portSplit_sparql_urlportSPARQL_insert_ntriplessparql_hostSplit_sparql_urlhostFilter_list_of_strings_extracting_match_to_a_regexstringlistSPARQL_insert_ntripleshtmlFilter_list_of_strings_extracting_match_to_a_regexregexhtml_donevalueFilter_list_of_strings_extracting_match_to_a_regexgroup_1valueConcat_log_messagemsgFilter_list_of_strings_extracting_match_to_a_regexfilteredlistConcat_log_messagegraphgraphConcat_log_messagesparql_urlsparql_endpoint_urlConcat_log_messagesubjectFirst_subjectsubjectSplit_sparql_urlsparql_urlsparql_endpoint_urlFirst_subjectntriplesntriplessparql_insert_ntriples_logConcat_log_messagelogo1SPARQL_insert_ntripleshtmlo2First_subjectsubject FrancoisBelleau@yahoo.ca 2009-10-20 01:20:39.936 EDT sparql_insert_ntriples.t2flow 2009-11-02 14:00:03.250 EST test values: graph=http://hexokinase sparql_host = localhost sparql_port = 8890 2009-11-02 14:03:31.963 EST sparql_insert_ntriples 2009-11-09 19:11:40.925 EST test values: graph=http://labrie sparql_host = localhost sparql_port = 8890 2009-11-02 14:14:41.522 EST test values: graph=http://hexokinase 2009-10-20 01:21:14.365 EDT Load RDF triples in NTRIPLES format using a SPARQL insert query. test values: graph=http://labrie sparql_endpoint_url = http://localhost:8890/sparql 2009-11-09 19:12:50.238 EST Workflow34pubmed_bmuri00 http://bio2rdf.org/pubmed:18472304 2009-11-13 23:40:55.609 EST http:// 2009-11-13 23:37:19.795 EST ncbi_pubmed_xml2ntriplesRdfise_pubmed_xml_from_NCBIbmuri0xml2ntriples_xsl0xml_directory_path0ncbi_xml2ntriples00net.sf.taverna.t2.activitiesdataflow-activity0.8net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokepubmed2ntriples_xslvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity pubmed2ntriples.xsl net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexml_tempvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity xml/temp net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRdfise_pubmed_xml_from_NCBIbmuripubmed_bmuriRdfise_pubmed_xml_from_NCBIxml2ntriples_xslpubmed2ntriples_xslvalueRdfise_pubmed_xml_from_NCBIxml_directory_pathxml_tempvaluencbi_pubmed_xml2ntriplesRdfise_pubmed_xml_from_NCBIncbi_xml2ntriples query = labrie,f query = labrie 2009-11-09 12:17:27.970 EST query = morissette,j query = labrie,f query = labrie query = h1n1 2009-11-02 12:56:25.278 EST ncbi_pubmed_xml2ntriples 2009-11-14 00:09:17.92 EST FrancoisBelleau@yahoo.ca 2009-11-09 12:16:49.168 EST 2009-11-14 00:02:20.438 EST ncbi_xml2ntriples 2009-11-14 00:02:01.170 EST query = labrie,f query = labrie query = h1n1 2009-11-02 12:39:27.342 EST demo_who_is_dr_labrie 2009-11-09 12:17:09.526 EST Workflow34xml_directory_path00 xml/temp 2009-11-13 23:37:07.934 EST bmuri00 http://bio2rdf.org/pubmed:18472304 2009-11-13 23:40:55.609 EST http:// 2009-11-13 23:37:19.795 EST xml2ntriples_xsl00 pubmed2ntriples.xsl 2009-11-13 23:52:28.668 EST pubmed 2009-11-13 23:36:54.778 EST o1ncbi_xml2ntripleso2Get_document_description_in_XMLxml_folder_path0ncbi_bmuri0xml_filename00ncbi_get_xml00net.sf.taverna.t2.activitiesdataflow-activity0.8net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRdfise_document_with_XSLfilename_xml0xml2ntriples_xsl0xml2ntriples00net.sf.taverna.t2.activitiesdataflow-activity0.8net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCreate_directorydirectory0directory_copy00log00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true directory 0 text/plain 0 log 0 text/plain 0 directory_copy 0 text/plain net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_document_description_in_XMLxml_folder_pathCreate_directorydirectory_copyGet_document_description_in_XMLncbi_bmuribmuriRdfise_document_with_XSLfilename_xmlGet_document_description_in_XMLxml_filenameRdfise_document_with_XSLxml2ntriples_xslxml2ntriples_xslCreate_directorydirectoryxml_directory_patho1Get_document_description_in_XMLncbi_get_xmlncbi_xml2ntriplesRdfise_document_with_XSLxml2ntripleso2Create_directorylog FrancoisBelleau@yahoo.ca 2009-11-09 12:16:49.168 EST query = labrie,f query = labrie 2009-11-09 12:17:27.970 EST 2009-11-14 00:02:20.438 EST query = labrie,f query = labrie query = h1n1 2009-11-02 12:39:27.342 EST demo_who_is_dr_labrie 2009-11-09 12:17:09.526 EST query = morissette,j query = labrie,f query = labrie query = h1n1 2009-11-02 12:56:25.278 EST ncbi_xml2ntriples 2009-11-14 00:02:01.170 EST Workflow46ncbi_bmuri00xml_folder_path00ncbi_get_xmlxml_filenameGet_NCBI_XML_By_ID_Namespacenamespace0id0outputText00net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true id 0 'text/plain' java.lang.String true rettype 0 'text/plain' java.lang.String true retmode 0 'text/plain' java.lang.String true namespace 0 text/plain 0 outputText 0 'text/plain' UserNameHere 2009-11-01 17:18:21.973 EST net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWrite_Text_Filefilecontents0outputFile0outputFile00net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true outputFile 0 'text/plain' java.lang.String true filecontents 0 'text/plain' 0 outputFile 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_bmuribmuri0namespace00id00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true bmuri 0 text/plain 0 namespace 0 text/plain 0 id 0 text/plain net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokebuild_xml_filenamenamespace0path0id0xml_filename00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true path 0 text/plain java.lang.String true namespace 0 text/plain java.lang.String true id 0 text/plain 0 xml_filename 0 text/plain net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketest_if_filename_existid0filename0id_copy00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true filename 0 text/plain java.lang.String true id 0 text/plain 0 id_copy 0 text/plain net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_NCBI_XML_By_ID_Namespacenamespacesplit_bmurinamespaceGet_NCBI_XML_By_ID_Namespaceidtest_if_filename_existid_copyWrite_Text_FilefilecontentsGet_NCBI_XML_By_ID_NamespaceoutputTextWrite_Text_FileoutputFilebuild_xml_filenamexml_filenamesplit_bmuribmurincbi_bmuribuild_xml_filenamenamespacesplit_bmurinamespacebuild_xml_filenamepathxml_folder_pathbuild_xml_filenameidsplit_bmuriidtest_if_filename_existidsplit_bmuriidtest_if_filename_existfilenamebuild_xml_filenamexml_filenamencbi_get_xmlWrite_Text_FileoutputFilexml_filenamebuild_xml_filenamexml_filename FrancoisBelleau@yahoo.ca 2009-11-01 13:26:59.574 EST Rdfise a Pubmed article. This means to convert its XML description to RDF/Ntriples format using an XML stylesheet available at http://www.myexperiment.org/files/178/download/pubmed2rdf-n3.xsl. 2009-11-01 13:30:18.501 EST test values: ncbi_bmuri = http://bio2rdf.org/pubmed:18472304 xml_folder_path = xml/labrie 2009-11-01 15:05:58.30 EST test values: pubmed_bmuri = http://bio2rdf.org/pubmed:18472304 2009-11-01 13:29:40.885 EST Rdfise a pumed document which means to convert its XML description to RDF/Ntriples format using an XML stylesheet available at http://www.myexperiment.org/files/178/download/pubmed2rdf-n3.xsl. 2009-11-01 13:29:16.88 EST test values: ncbi_bmuri = http://bio2rdf.org/pubmed:18472304 ncbi_bmuri = http://bio2rdf.org/gene:15275 xml_folder_path = xml/labrie 2009-11-01 17:30:51.792 EST Get XML description of a NCBI document using efetch service. 2009-11-01 14:52:21.266 EST Get XML description of a NCBI document using 2009-11-01 14:51:48.213 EST test values: ncbi_bmuri = http://bio2rdf.org/pubmed:18472304 xml_folder_path = temp/labrie 2009-11-01 14:51:20.337 EST Rdfise a pumed document which means to convert its XML description to RDF/Ntriples format using an XML stylesheet available at 2009-11-01 13:28:44.13 EST test values: pubmed_bmuri = 2009-11-01 13:21:49.4 EST test values: pubmed_bmuri = http://bio2rdf.org/pubmed:18472304 2009-11-01 13:22:44.854 EST Workflow67filename_xml00xml2ntriples_xsl00xml2ntriplesTransform_XMLxslFileURL0inFileURL0outputStr00net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true xslFileURL 0 'text/plain' java.lang.String true outFileURL 0 'text/plain' java.lang.String true inFileURL 0 'text/plain' java.lang.String true outputExt 0 'text/plain' 0 outputStr 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokebuild_filename_ntfilename_xml0filename_nt00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true filename_xml 0 text/plain 0 filename_nt 0 text/plain net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWrite_Text_Filefilecontents0outputFile0outputFile00net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true outputFile 0 'text/plain' java.lang.String true filecontents 0 'text/plain' 0 outputFile 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketest_file_existsfilename0filename_xml00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true filename 0 text/plain 0 filename_xml 0 text/plain net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTransform_XMLxslFileURLxml2ntriples_xslTransform_XMLinFileURLtest_file_existsfilename_xmlbuild_filename_ntfilename_xmlfilename_xmlWrite_Text_FilefilecontentsTransform_XMLoutputStrWrite_Text_FileoutputFilebuild_filename_ntfilename_nttest_file_existsfilenamebuild_filename_ntfilename_ntxml2ntriplesWrite_Text_FileoutputFile Rdfise all XML document from a specific folder using the provided XSL stylesheet. 2009-11-01 15:41:01.625 EST xml_folder_path = xml/labrie xml2ntriples_xsl = 2009-11-01 15:41:36.454 EST xml_folder_path = xml/labrie,f/ xml2ntriples_xsl = pubmed2ntriples.xsl 2009-11-02 00:00:06.844 EST FrancoisBelleau@yahoo.ca 2009-11-01 15:40:57.7 EST filename_xml = xml/labrie,f/pubmed_82132.xml xml2ntriples_xsl = pubmed2ntriples.xsl 2009-11-02 00:01:05.977 EST xml_folder_path = xml/labrie xml2ntriples_xsl = pubmed2ntriples.xsl 2009-11-01 15:42:07.840 EST Rdfise all XML document from a specific folder using the provided XSL stylesheet. 2009-11-01 15:40:38.244 EST 2009-11-01 15:40:59.192 EST Workflow2sparql_query00 2009-11-17 00:28:48.97 EST The URL of a SPARQL query to be submited. SELECT DISTINCT ?xPubMed WHERE { ?Gene a <http://bio2rdf.org/ns/geneid#Gene> . ?Gene <http://bio2rdf.org/ns/bio2rdf#xPubMed> ?xPubMed . } ORDER BY DESC(count(*)) 2009-11-09 11:37:58.68 EST SELECT DISTINCT ?seeAlso WHERE { ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . } 2009-11-17 00:33:30.917 EST SELECT DISTINCT ?xPubMed WHERE { ?Gene a <http://bio2rdf.org/ns/geneid#Gene> . ?Gene <http://bio2rdf.org/ns/bio2rdf#xPubMed> ?xPubMed . } ORDER BY DESC(count(*)) 2009-11-09 11:29:33.239 EST SELECT ?xRelation WHERE { ?Pathway a <http://bio2rdf.org/ns/kegg#Pathway> . FILTER (?Pathway = <http://bio2rdf.org/path:mmu00010>) . ?Pathway <http://bio2rdf.org/ns/kegg#xRelation> ?xRelation . } 2009-11-10 21:39:13.791 EST SELECT DISTINCT ?seeAlso WHERE { ?s a <http://bio2rdf.org/ns/bio2rdf#SearchResult> . ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . } 2009-11-17 00:34:34.699 EST http://localhost:8890/sparql?default-graph-uri=&should-sponge=&query=SELECT+DISTINCT+%3FxPubMed%0D%0AWHERE+{%0D%0A++%3FGene+a+%3Chttp%3A%2F%2Fbio2rdf.org%2Fns%2Fgeneid%23Gene%3E+.+%0D%0A++%3FGene+%3Chttp%3A%2F%2Fbio2rdf.org%2Fns%2Fbio2rdf%23xPubMed%3E+%3FxPubMed+.%0D%0A}%0D%0AORDER+BY+DESC(count(*))&format=text%2Fhtml&debug=on&timeout= 2009-11-09 11:29:24.214 EST sparql_endpoint00 http://localhost:8890/sparql 2009-11-10 21:39:50.908 EST graph00 http://temp 2009-11-17 00:28:32.601 EST http://kegg2go 2009-11-10 21:39:38.331 EST o1sparql_query_bmuri_listbmuris_countbmuris_stringo2Get_Web_Page_from_URLurl0contents00net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true url 0 'text/x-taverna-web-url' java.lang.String true base 0 'text/x-taverna-web-url' 0 contents 0 'text/plain,text/html' net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionstring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true string 0 'text/plain' java.lang.String true regex 0 'text/plain' 1 split 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_list_of_strings_extracting_match_to_a_regexstringlist1group0regex0filteredlist11count00net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true regex 0 'text/plain' java.lang.String true group 0 'text/plain' 1 filteredlist 1 l('text/plain') 0 count 0 text/plain UserNameHere 2009-11-07 23:37:08.293 EST net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeeolvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke_1value00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokehtml_tdvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity <td>(.*)</td> net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_String_List_to_a_Stringstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' 0 concatenated 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBuild_sparql_urlsparql_query0sparql_endpoint0graph0sparql_query_url00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true sparql_query 0 text/plain java.lang.String true sparql_endpoint 0 text/plain java.lang.String true graph 0 text/plain 0 sparql_query_url 0 text/plain net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_Web_Page_from_URLurlBuild_sparql_urlsparql_query_urlSplit_string_into_string_list_by_regular_expressionstringGet_Web_Page_from_URLcontentsSplit_string_into_string_list_by_regular_expressionregexeolvalueFilter_list_of_strings_extracting_match_to_a_regexstringlistSplit_string_into_string_list_by_regular_expressionsplitFilter_list_of_strings_extracting_match_to_a_regexgroup_1valueFilter_list_of_strings_extracting_match_to_a_regexregexhtml_tdvalueMerge_String_List_to_a_StringstringlistFilter_list_of_strings_extracting_match_to_a_regexfilteredlistBuild_sparql_urlsparql_querysparql_queryBuild_sparql_urlsparql_endpointsparql_endpointBuild_sparql_urlgraphgrapho1Get_Web_Page_from_URLcontentssparql_query_bmuri_listFilter_list_of_strings_extracting_match_to_a_regexfilteredlistbmuris_countFilter_list_of_strings_extracting_match_to_a_regexcountbmuris_stringMerge_String_List_to_a_Stringconcatenatedo2Build_sparql_urlsparql_query_url sparql_query_bmuri_list 2009-11-09 11:37:16.669 EST Execute a Virtuoso SPARQL query specified by the URL and return the bmuris result list. The SPARQL query query must return only one variable, of type URI, in the SELECT statement. 2009-11-09 11:35:57.963 EST sparql_query_bmuris 2009-11-09 11:33:22.596 EST FrancoisBelleau@yahoo.ca 2009-11-09 11:32:51.395 EST Workflow68stringlist00utility_stringlist_countstringlist_countin0out00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true in 0 text/plain 0 out 0 text/plain net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokestringlist_countinstringlistutility_stringlist_countstringlist_countout utility_stringlist_count 2009-11-17 01:37:51.90 EST