Workflow119count00 20 2009-11-16 22:10:18.95 EST 50 2009-11-16 22:19:22.865 EST graph00 http://bio2rdf 2009-11-16 22:19:42.603 EST sparql_endpoint00 http://localhost:8890/sparql 2009-11-16 22:19:48.551 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 . } 2009-11-17 00:41:05.80 EST o1o2related_insert_logo3o4citation_insert_logo5Search_Pubmed_linksrelated_article_count0pubmed_bmuri_string0citation_bmuris_string00related_bmuris_string00related_ntriples11ncbi_search_pubmed_link_citation_ntriples11net.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_ntriplessparql_endpoint_url0graph0ntriples0sparql_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.InvokeInsert_ntriples_1sparql_endpoint_url0graph0ntriples0sparql_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.InvokeSPARQL_querygraph0sparql_endpoint0sparql_query0bmuris_string00net.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.InvokeSearch_Pubmed_linksrelated_article_countcountSearch_Pubmed_linkspubmed_bmuri_stringSPARQL_querybmuris_stringInsert_ntriplessparql_endpoint_urlsparql_endpointInsert_ntriplesgraphgraphInsert_ntriplesntriplesSearch_Pubmed_linksrelated_ntriplesInsert_ntriples_1sparql_endpoint_urlsparql_endpointInsert_ntriples_1graphgraphInsert_ntriples_1ntriplesSearch_Pubmed_linksncbi_search_pubmed_link_citation_ntriplesSPARQL_querygraphgraphSPARQL_querysparql_endpointsparql_endpointSPARQL_querysparql_querysparql_queryo1Search_Pubmed_linkscitation_bmuris_stringo2Search_Pubmed_linksrelated_bmuris_stringrelated_insert_logInsert_ntriplessparql_insert_ntriples_logo3Search_Pubmed_linksrelated_ntripleso4Search_Pubmed_linksncbi_search_pubmed_link_citation_ntriplescitation_insert_logInsert_ntriples_1sparql_insert_ntriples_logo5SPARQL_querybmuris_string FrancoisBelleau@yahoo.ca 2009-11-16 23:34:45.836 EST Search for citations and related article in PubMed [myexperiment:pubmed_step2_link] 2009-11-16 23:35:12.286 EST graph = http://nur77 bmuri = http://bio2rdf.org/pubmed:18843482 http://bio2rdf.org/pubmed:18466322 http://bio2rdf.org/pubmed:17201484 http://bio2rdf.org/pubmed:14603264 http://bio2rdf.org/pubmed:12629527 2009-11-16 23:37:12.358 EST Search for citations and related article in PubMed [myexperiment:pubmed_step2_get_link] 2009-11-17 00:47:41.540 EST FrancoisBelleau@yahoo.ca 2009-11-16 23:35:32.794 EST Workflow64pubmed_bmuri_string00 bio2rdf 2009-11-16 13:32:10.500 EST http://bio2rdf.org/pubmed:18472304 2009-11-16 17:56:20.664 EST related_article_count00 20 2009-11-16 17:42:59.370 EST related_bmuris_stringo3citation_bmuris_stringncbi_search_pubmed_link_citation_ntripleso2related_ntriplesNCBI_links_from_Pubmedpubmed_bmuri0top_related_count0related_bmuri_list11citation_bmuri_list11related_ntriples_string00ncbi_pubmed2pubmed_citation_ntriples_string00net.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.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') 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.InvokeFlatten_List2inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') 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_String2stringlist1concatenated00net.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.InvokeFlatten_List4inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') 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.InvokeFlatten_List5inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') 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.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.InvokeNCBI_links_from_Pubmedpubmed_bmuriSplit_string_into_string_list_by_regular_expressionsplitNCBI_links_from_Pubmedtop_related_countrelated_article_countFlatten_ListinputlistNCBI_links_from_Pubmedcitation_bmuri_listMerge_String_List_to_a_StringstringlistFlatten_List5outputlistFlatten_List2inputlistNCBI_links_from_Pubmedrelated_bmuri_listMerge_String_List_to_a_String2stringlistFlatten_List4outputlistFlatten_List4inputlistFlatten_List2outputlistFlatten_List5inputlistFlatten_ListoutputlistSplit_string_into_string_list_by_regular_expressionstringpubmed_bmuri_stringSplit_string_into_string_list_by_regular_expressionregexeolvaluerelated_bmuris_stringMerge_String_List_to_a_String2concatenatedo3NCBI_links_from_Pubmedcitation_bmuri_listcitation_bmuris_stringMerge_String_List_to_a_Stringconcatenatedncbi_search_pubmed_link_citation_ntriplesNCBI_links_from_Pubmedncbi_pubmed2pubmed_citation_ntriples_stringo2NCBI_links_from_Pubmedrelated_bmuri_listrelated_ntriplesNCBI_links_from_Pubmedrelated_ntriples_string bio2rdf_subject_fetch_links demo example 2009-11-16 15:48:45.723 EST FrancoisBelleau@yahoo.ca 2009-11-16 14:10:39.952 EST bio2rdf 2009-11-16 13:30:00.651 EST bio2rdf_subject demo example 2009-11-16 14:11:17.703 EST Workflow2pubmed_bmuri00 18472304 2009-11-16 11:13:06.356 EST Pubmed URI for which we search citations and related articles. 2009-11-16 13:37:59.97 EST http://bio2rdf.org/pubmed:18472304 2009-11-16 13:37:14.101 EST Bio2RDF: Towards a mashup to build bioinformatics knowledge systems 2009-11-16 10:49:14.433 EST &cmd=neighbor 2009-11-16 11:12:41.143 EST top_related_count00 20 2009-11-17 00:10:54.484 EST o1o2citation_bmuri_listncbi_pubmed2pubmed_citation_ntriples_stringrelated_bmuri_listrelated_ntriples_stringBuild_NCBI_ELink_urlpubmed_id0elink_url00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true pubmed_id 0 text/plain 0 elink_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_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.InvokeXPath_From_Textxml-text0xpath0nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 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.Invokexpath_LinkSetDbvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity //LinkSetDb 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_by_regexstringlist1regex0filteredlist11net.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' 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.InvokeLinkName_pubmed_pubmed_citedinvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity .*<LinkName>pubmed_pubmed_citedin</LinkName>.* 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.InvokeXPath_From_Text2xml-text0xpath0nodelist11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 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.Invokexpath_Idvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity //Id 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_citation_ntriplespubmed_id_reference0pubmed_id_source0ntriples00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true pubmed_id_source 0 text/plain java.lang.String true pubmed_id_reference 0 text/plain 0 ntriples 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.InvokeFilter_List_of_Strings_by_regex2stringlist1regex0filteredlist11net.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' 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.InvokeLinkName_pubmed_pubmedvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity .*<LinkName>pubmed_pubmed</LinkName>.* 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.InvokeXPath_From_Text3xml-text0xpath0nodelist11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 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.InvokeBuild_citation_bmuripubmed_id0pubmed_bmuri00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true pubmed_id 0 text/plain 0 pubmed_bmuri 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_related_bmuripubmed_id0pubmed_bmuri00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true pubmed_id 0 text/plain 0 pubmed_bmuri 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.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') 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.InvokeFlatten_List2inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity0.8net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') 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_related_ntriplespubmed_id_source0pubmed_id_reference0ntriples00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true pubmed_id_reference 0 text/plain java.lang.String true pubmed_id_source 0 text/plain 0 ntriples 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.InvokeMerge_String_List_to_a_String2stringlist1concatenated00net.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.InvokeSplit_bmuribmuri0id00net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true bmuri 0 text/plain 0 id 0 text/plain 0 namespace 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.InvokeTop_bmuristringlist1item_number0utility_stringlist_select_first_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.InvokeBuild_NCBI_ELink_urlpubmed_idSplit_bmuriidGet_Web_Page_from_URLurlBuild_NCBI_ELink_urlelink_urlXPath_From_Textxml-textGet_Web_Page_from_URLcontentsXPath_From_Textxpathxpath_LinkSetDbvalueFilter_List_of_Strings_by_regexstringlistXPath_From_TextnodelistAsXMLFilter_List_of_Strings_by_regexregexLinkName_pubmed_pubmed_citedinvalueXPath_From_Text2xml-textFilter_List_of_Strings_by_regexfilteredlistXPath_From_Text2xpathxpath_IdvalueBuild_citation_ntriplespubmed_id_referenceFlatten_List2outputlistBuild_citation_ntriplespubmed_id_sourceSplit_bmuriidFilter_List_of_Strings_by_regex2stringlistXPath_From_TextnodelistAsXMLFilter_List_of_Strings_by_regex2regexLinkName_pubmed_pubmedvalueXPath_From_Text3xml-textFilter_List_of_Strings_by_regex2filteredlistXPath_From_Text3xpathxpath_IdvalueBuild_citation_bmuripubmed_idFlatten_List2outputlistBuild_related_bmuripubmed_idTop_bmuriutility_stringlist_select_first_listFlatten_ListinputlistXPath_From_Text3nodelistFlatten_List2inputlistXPath_From_Text2nodelistMerge_String_List_to_a_StringstringlistBuild_citation_ntriplesntriplesBuild_related_ntriplespubmed_id_sourceSplit_bmuriidBuild_related_ntriplespubmed_id_referenceTop_bmuriutility_stringlist_select_first_listMerge_String_List_to_a_String2stringlistBuild_related_ntriplesntriplesSplit_bmuribmuripubmed_bmuriTop_bmuristringlistFlatten_ListoutputlistTop_bmuriitem_numbertop_related_counto1Build_NCBI_ELink_urlelink_urlo2Get_Web_Page_from_URLcontentscitation_bmuri_listBuild_citation_bmuripubmed_bmurincbi_pubmed2pubmed_citation_ntriples_stringMerge_String_List_to_a_Stringconcatenatedrelated_bmuri_listBuild_related_bmuripubmed_bmurirelated_ntriples_stringMerge_String_List_to_a_String2concatenated FrancoisBelleau@yahoo.ca 2009-11-16 12:37:35.404 EST ncbi_pubmed2pubmed 2009-11-17 00:12:48.842 EST ncbi_pubmed2pubmed_ntriples 2009-11-16 13:14:47.361 EST Use NCBI ELink service to get the citations list and related article list from Pubmed for a specific pubmed ID. Returms bmuri list or ntriples for both result set. 2009-11-16 13:16:22.222 EST Workflow5stringlist11item_number00 10 2009-11-16 14:13:23.402 EST utility_stringlist_select_first_listSelect_first_n_stringitem_number0stringlist1outputlist11net.sf.taverna.t2.activitiesbeanshell-activity0.8net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true stringlist 1 text/plain java.lang.String true item_number 0 text/plain 1 outputlist 1 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.InvokeSelect_first_n_stringitem_numberitem_numberSelect_first_n_stringstringliststringlistutility_stringlist_select_first_listSelect_first_n_stringoutputlist utility_select_first 2009-11-16 14:07:53.25 EST FrancoisBelleau@yahoo.ca 2009-11-16 14:14:34.320 EST utility_stringlist_select_first 2009-11-16 14:08:31.750 EST Returns the first n items of a stringlist. 2009-11-16 14:15:05.878 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 2009-01-23 00:06:17.667 EST UserNameHere 2009-01-23 00:06:51.677 EST UserNameHere 2009-01-22 23:12:14.802 EST UserNameHere 2009-11-02 14:01:31.829 EST UserNameHere 2009-10-06 00:34:47.715 EDT UserNameHere 2009-01-23 00:03:55.477 EST UserNameHere 2009-01-23 00:07:17.366 EST UserNameHere 2009-01-23 00:44:07.662 EST UserNameHere 2009-10-06 00:28:07.839 EDT UserNameHere 2009-01-23 00:03:19.809 EST UserNameHere 2009-11-02 14:07:23.431 EST UserNameHere 2009-01-23 00:05:21.845 EST UserNameHere 2009-10-06 00:36:49.673 EDT UserNameHere 2009-01-26 23:10:57.600 EST UserNameHere 2009-01-23 00:08:37.503 EST UserNameHere 2009-01-22 22:42:57.377 EST UserNameHere 2009-10-06 00:23:08.363 EDT UserNameHere 2009-01-25 22:32:29.783 EST UserNameHere 2009-10-20 01:19:54.646 EDT UserNameHere 2009-01-26 23:11:58.183 EST UserNameHere 2009-01-25 22:33:59.715 EST UserNameHere 2009-01-25 22:27:57.661 EST UserNameHere 2009-01-23 00:09:42.877 EST UserNameHere 2009-01-26 23:08:43.41 EST UserNameHere 2009-01-25 22:17:04.902 EST UserNameHere 2009-01-22 22:44:53.200 EST UserNameHere 2009-11-02 14:11:03.534 EST UserNameHere 2009-01-25 22:31:23.275 EST UserNameHere 2009-01-23 00:08:17.891 EST UserNameHere 2009-01-22 22:58:39.533 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 test values: graph=http://labrie sparql_host = localhost sparql_port = 8890 2009-11-02 14:14:41.522 EST FrancoisBelleau@yahoo.ca 2009-10-20 01:20:39.936 EDT test values: graph=http://hexokinase 2009-10-20 01:21:14.365 EDT 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 sparql_insert_ntriples.t2flow 2009-11-02 14:00:03.250 EST 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 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 2009-01-26 23:08:43.41 EST UserNameHere 2009-01-23 00:08:37.503 EST UserNameHere 2009-10-06 00:36:49.673 EDT UserNameHere 2009-01-25 22:27:57.661 EST UserNameHere 2009-01-23 00:03:55.477 EST UserNameHere 2009-01-22 22:42:57.377 EST UserNameHere 2009-01-22 23:12:14.802 EST UserNameHere 2009-10-06 00:28:07.839 EDT UserNameHere 2009-10-20 01:19:54.646 EDT UserNameHere 2009-10-06 00:23:08.363 EDT UserNameHere 2009-01-23 00:08:17.891 EST UserNameHere 2009-01-23 00:05:21.845 EST UserNameHere 2009-01-26 23:11:58.183 EST UserNameHere 2009-01-22 22:44:53.200 EST UserNameHere 2009-11-02 14:07:23.431 EST UserNameHere 2009-01-25 22:32:29.783 EST UserNameHere 2009-01-22 22:58:39.533 EST UserNameHere 2009-11-02 14:01:31.829 EST UserNameHere 2009-01-25 22:31:23.275 EST UserNameHere 2009-01-23 00:07:17.366 EST UserNameHere 2009-11-02 14:11:03.534 EST UserNameHere 2009-01-23 00:06:17.667 EST UserNameHere 2009-01-23 00:03:19.809 EST UserNameHere 2009-01-26 23:10:57.600 EST UserNameHere 2009-01-23 00:06:51.677 EST UserNameHere 2009-01-25 22:33:59.715 EST UserNameHere 2009-01-25 22:17:04.902 EST UserNameHere 2009-01-23 00:44:07.662 EST UserNameHere 2009-01-23 00:53:10.565 EST UserNameHere 2009-10-06 00:34:47.715 EDT UserNameHere 2009-01-23 00:09:42.877 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 test values: graph=http://hexokinase 2009-10-20 01:21:14.365 EDT test values: graph=http://hexokinase sparql_host = localhost sparql_port = 8890 2009-11-02 14:03:31.963 EST FrancoisBelleau@yahoo.ca 2009-10-20 01:20:39.936 EDT sparql_insert_ntriples_1 2009-11-16 23:53:34.858 EST 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 sparql_insert_ntriples.t2flow 2009-11-02 14:00:03.250 EST test values: graph=http://labrie sparql_host = localhost sparql_port = 8890 2009-11-02 14:14:41.522 EST sparql_insert_ntriples 2009-11-09 19:11:40.925 EST Workflow2sparql_query00 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 2009-11-17 00:28:48.97 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 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 ?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 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 SELECT DISTINCT ?seeAlso WHERE { ?s <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso . } 2009-11-17 00:33:30.917 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_bmuris 2009-11-09 11:33:22.596 EST FrancoisBelleau@yahoo.ca 2009-11-09 11:32:51.395 EST 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