NCBI_BLAST__SOAP_Email00 Valid e-mail address. 2010-11-29 19:46:04.175 GMT email@example.org 2010-11-29 19:46:13.15 GMT Sequence00 Query sequence. Either sequence data in any common format or an entry identifier in DB:ID format. 2010-11-29 19:47:13.623 GMT uniprot:wap_rat 2010-11-29 19:47:21.746 GMT Databases11 uniprotkb_swissprotuniprotkb_tremblpdb 2010-11-29 19:45:49.744 GMT List of databases to search. 2010-11-29 19:45:34.132 GMT Sequence_type00 protein 2010-11-29 19:47:37.827 GMT Query sequence type. 2010-11-29 19:47:33.759 GMT Program00 blastp 2010-11-29 19:46:37.896 GMT NCBI BLAST program to use to perform the search. 2010-11-29 19:46:34.453 GMT JobId NCBI BLAST (SOAP) web service at EMBL-EBI job identifier. 2010-11-29 19:48:12.236 GMT Job_Status NCBI BLAST job status. 2010-11-29 19:47:49.643 GMT Result NCBI BLAST result. 2010-11-29 19:48:24.580 GMT runparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl runnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_inputparameters0email0output00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="run" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}run"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="email" qname=">run>email" /><s:basetype optional="true" unbounded="false" typename="string" name="title" qname=">run>title" /><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname=">run>parameters"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="program" qname="InputParameters>program" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters>matrix" /><s:basetype optional="true" unbounded="false" typename="int" name="alignments" qname="InputParameters>alignments" /><s:basetype optional="true" unbounded="false" typename="int" name="scores" qname="InputParameters>scores" /><s:basetype optional="true" unbounded="false" typename="string" name="exp" qname="InputParameters>exp" /><s:basetype optional="true" unbounded="false" typename="int" name="dropoff" qname="InputParameters>dropoff" /><s:basetype optional="true" unbounded="false" typename="string" name="match_scores" qname="InputParameters>match_scores" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters>gapopen" /><s:basetype optional="true" unbounded="false" typename="int" name="gapext" qname="InputParameters>gapext" /><s:basetype optional="true" unbounded="false" typename="string" name="filter" qname="InputParameters>filter" /><s:basetype optional="true" unbounded="false" typename="string" name="seqrange" qname="InputParameters>seqrange" /><s:basetype optional="true" unbounded="false" typename="boolean" name="gapalign" qname="InputParameters>gapalign" /><s:basetype optional="true" unbounded="false" typename="int" name="align" qname="InputParameters>align" /><s:basetype optional="false" unbounded="false" typename="string" name="stype" qname="InputParameters>stype" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters>sequence" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="database" qname="InputParameters>database"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> false email 0 'text/plain' false title 0 'text/plain' false parameters 0 'text/xml' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_outputinput0jobId00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="runResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}runResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">runResponse>jobId" /></s:elements></s:complextype></s:extensions> java.lang.String false input 0 'text/xml' 0 jobId 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_input_2sequence0database1stype0program0output00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname=">run>parameters"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="program" qname="InputParameters>program" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters>matrix" /><s:basetype optional="true" unbounded="false" typename="int" name="alignments" qname="InputParameters>alignments" /><s:basetype optional="true" unbounded="false" typename="int" name="scores" qname="InputParameters>scores" /><s:basetype optional="true" unbounded="false" typename="string" name="exp" qname="InputParameters>exp" /><s:basetype optional="true" unbounded="false" typename="int" name="dropoff" qname="InputParameters>dropoff" /><s:basetype optional="true" unbounded="false" typename="string" name="match_scores" qname="InputParameters>match_scores" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters>gapopen" /><s:basetype optional="true" unbounded="false" typename="int" name="gapext" qname="InputParameters>gapext" /><s:basetype optional="true" unbounded="false" typename="string" name="filter" qname="InputParameters>filter" /><s:basetype optional="true" unbounded="false" typename="string" name="seqrange" qname="InputParameters>seqrange" /><s:basetype optional="true" unbounded="false" typename="boolean" name="gapalign" qname="InputParameters>gapalign" /><s:basetype optional="true" unbounded="false" typename="int" name="align" qname="InputParameters>align" /><s:basetype optional="false" unbounded="false" typename="string" name="stype" qname="InputParameters>stype" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters>sequence" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="database" qname="InputParameters>database"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> false program 0 'text/plain' false matrix 0 'text/plain' false alignments 0 'text/plain' false scores 0 'text/plain' false exp 0 'text/plain' false dropoff 0 'text/plain' false match_scores 0 'text/plain' false gapopen 0 'text/plain' false gapext 0 'text/plain' false filter 0 'text/plain' false seqrange 0 'text/plain' false gapalign 0 'text/plain' false align 0 'text/plain' false stype 0 'text/plain' false sequence 0 'text/plain' false database 1 l('text/plain') 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWorkflow2JobId0Status00net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loop <activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
<script>loop = "" + Status.equals("RUNNING");
if ("true".matches(loop)) {
Thread.sleep(3000);
}</script>
<dependencies />
<classLoaderSharing>workflow</classLoaderSharing>
<localDependencies />
<artifactDependencies />
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
<name>Status</name>
<depth>0</depth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<granularDepth>0</granularDepth>
<name>loop</name>
<depth>0</depth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity> true net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResultparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl getResultnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_inputjobId0type0output00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getResult>jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname=">getResult>type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname=">getResult>parameters"><s:elementtype><s:complextype optional="false" unbounded="false" typename="wsRawOutputParameter" name="" qname="{http://soap.jdispatcher.ebi.ac.uk}wsRawOutputParameter"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="wsRawOutputParameter>name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter>value"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> false jobId 0 'text/plain' false type 0 'text/plain' false parameters 1 'text/xml' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_outputinput0output00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResultResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResultResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="base64Binary" name="output" qname=">getResultResponse>output" /></s:elements></s:complextype></s:extensions> java.lang.String false input 0 'text/xml' 0 output 0 'application/octet-stream' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketype_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity outnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerunparametersrun_inputparametersrun_inputemailrun_outputinputrun_input_2sequencerun_input_2databaserun_input_2styperun_input_2programWorkflow2JobIdgetResultparametersgetResult_inputjobIdgetResult_inputtypegetResult_outputinputJobIdJob_StatusResult NCBI BLAST (SOAP) 2010-11-29 20:00:40.41 GMT Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default. 2010-11-29 20:02:59.610 GMT Hamish McWilliam 2010-11-29 20:00:33.208 GMT Job_StatusJobId00 NCBI BLAST (SOAP) web service at EMBL-EBI job identifier. 2010-11-29 19:44:12.180 GMT Status Job status code. 2010-11-29 19:44:29.316 GMT getStatusparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl getStatusnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatus_inputjobId0output00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getStatus" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getStatus"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getStatus>jobId" /></s:elements></s:complextype></s:extensions> false jobId 0 'text/plain' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatus_outputinput0status00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getStatusResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getStatusResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="status" qname=">getStatusResponse>status" /></s:elements></s:complextype></s:extensions> java.lang.String false input 0 'text/xml' 0 status 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatusparametersgetStatus_inputjobIdgetStatus_outputinputStatus Hamish McWilliam 2010-11-29 19:41:52.325 GMT Job status sub-workflow to allow status polling to work with a document/literal wrapped operation. 2010-11-29 19:43:01.913 GMT Job status 2010-11-29 19:42:11.445 GMT Status sub-workflow 2010-11-29 19:42:05.813 GMT Job Status 2010-11-29 19:42:20.638 GMT