Test 1: RoblibServices TN

A dsid TN2 will be ingested when dsid TN added to object having cmodel islandora:sp_biological_entity_taxa_cmodel.

Create Workflow with Taverna Workbench (2.5)
- Add soap service to Workbench Available services

Create workflow using soap service above

Set web service security to “HTTP user and password”

Save workflow to file .t2flow

WF_TN_2input.t2flow

Add Datastreams to content model islandora:sp_biological_entity_taxa_cmodel

DSID “Trigger-Datastreams”, text/xml

Trigger-Datastreams.xml

<methods>
  <method type="addDatastream">
    <trigger id="TN">
      <t2flow id="T2flow-TN"></t2flow>
    </trigger>
  </method>
</methods>

DSID “T2flow-TN”, application/vnd.taverna.t2flow+xml
WF_TN_2input.t2flow

Start php_listener and taverna server
Add a DSID TN to an object (i.e. islandora:123) with cmodel islandora:sp_biological_entity_taxa_cmodel (i.e. by Fedora admin web interface)
Refresh object DS list to see TN2 added

Listener log

03/Jun/2014, 12:43:13, INFO, MODIFY_OBJECT, islandora:123, TN, fedoraAdmin, Method: addDatastream, (connect)
03/Jun/2014, 12:43:13, INFO, SERVER_INFO, , , , Content Models: islandora:sp_biological_entity_taxa_cmodel, (connect)
03/Jun/2014, 12:43:13, INFO, MODIFY_OBJECT, islandora:123, TN, fedoraAdmin, Found a child method: addDatastream, (connect)
03/Jun/2014, 12:43:13, INFO, MODIFY_OBJECT, islandora:123, TN, fedoraAdmin, Modifing object with workflow defined in Trigger-Datastreams addDatastream, (connect)
03/Jun/2014, 12:43:13, INFO, MODIFY_OBJECT, islandora:123, TN, fedoraAdmin, Matching Trigger  trigger, (connect)
03/Jun/2014, 12:43:13, INFO, SERVER_INFO, , , , Names of t2flows T2flow-TN, (connect)
03/Jun/2014, 12:43:14, INFO, SERVER_INFO, , , , uuid = 670c3ec4-a045-4315-963d-cb08c498532e, (connect)
03/Jun/2014, 12:43:14, INFO, SERVER_INFO, , , , added input pid = islandora:123, (connect)
03/Jun/2014, 12:43:14, INFO, SERVER_INFO, , , , added input dsid = TN, (connect)
03/Jun/2014, 12:43:39, INFO, SOAP_LOG, islandora:123, TN, , Function tn starting..., (soap_serv)
03/Jun/2014, 12:43:39, INFO, SOAP_LOG, islandora:123, TN, , Fedora object successfully fetched, (soap_serv)
03/Jun/2014, 12:43:39, INFO, SOAP_LOG, islandora:123, TN, , Image class loaded, (soap_serv)
03/Jun/2014, 12:43:39, INFO, PROCESS_DATASTREAM, islandora:123, TN2, , Starting processing, (soap_serv)
03/Jun/2014, 12:43:40, INFO, COMPLETE_DATASTREAM, islandora:123, TN2, , Finished processing, (soap_serv)
03/Jun/2014, 12:43:40, INFO, SOAP_LOG, islandora:123, TN, , tn function successful, (soap_serv)
03/Jun/2014, 12:43:40, INFO, MODIFY_OBJECT, islandora:123, TN2, fedoraAdmin, Method: addDatastream, (connect)
03/Jun/2014, 12:43:40, INFO, SERVER_INFO, , , , Content Models: islandora:sp_biological_entity_taxa_cmodel, (connect)
03/Jun/2014, 12:43:40, INFO, MODIFY_OBJECT, islandora:123, TN2, fedoraAdmin, Found a child method: addDatastream, (connect)
03/Jun/2014, 12:43:40, INFO, MODIFY_OBJECT, islandora:123, TN2, fedoraAdmin, Modifing object with workflow defined in Trigger-Datastreams addDatastream, (connect)
03/Jun/2014, 12:43:40, INFO, SERVER_INFO, , , , Content Models: fedora-system:FedoraObject-3.0, (connect)
03/Jun/2014, 12:43:47, INFO, SERVER_INFO, , , , deleting workflow 670c3ec4-a045-4315-963d-cb08c498532e islandora:123 TN, (connect)

Taverna server log

20140603T124314.207 INFO  Webapp TavernaServerSupport - <?xml version="1.0" encoding="UTF-8" standalone="yes"?><ts:workflow .......
20140603T124314.535 INFO  forker StdOut - Subprocess(out):Creating run from workflow <cab0a9d1-76eb-4774-a678-3e25fadc6b89> for <tavAdmin>
20140603T124314.539 INFO  forker StdOut - Subprocess(out):about to create /tmp/670c3ec4-a045-4315-963d-cb08c498532e
20140603T124314.596 INFO  Worker PasswordIssuer - issued new password of length 8
20140603T124314.692 INFO  Performance CallTimeLogger - call to execution(TavernaServer.submitWorkflow(..)) took 594.124ms
20140603T124314.720 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 16.964ms
20140603T124314.727 INFO  Performance CallTimeLogger - call to execution(RunREST.getInputs(..)) took 5.145ms
20140603T124314.748 INFO  Performance CallTimeLogger - call to execution(InputREST.setInput(..)) took 18.612ms
20140603T124314.765 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 7.232ms
20140603T124314.786 INFO  Performance CallTimeLogger - call to execution(InputREST.setInput(..)) took 15.633ms
20140603T124314.805 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 7.791ms
20140603T124314.815 INFO  Performance CallTimeLogger - call to execution(RunREST.getSecurity()) took 7.490ms
20140603T124314.950 INFO  Performance CallTimeLogger - call to execution(RunSecurityREST.addCredential(..)) took 128.926ms
20140603T124314.968 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 7.844ms
20140603T124314.974 INFO  Worker RemoteRunDelegate - setting status of run 670c3ec4-a045-4315-963d-cb08c498532e to Operating
20140603T124315.105 INFO  Worker SecurityContextDelegate - issuing self-referential credential for https://123.123.123.124:8443/tavernaserver/rest/runs/670c3ec4-a045-4315-963d-cb08c498532e/#tavernaserver
20140603T124315.152 INFO  Worker SecurityContextDelegate - constructing merged keystore
20140603T124315.315 INFO  Worker SecurityContextDelegate - transfering merged truststore with 1 entries
20140603T124315.319 INFO  Worker SecurityContextDelegate - transfering merged keystore with 2 entries
20140603T124315.325 INFO  Worker SecurityContextDelegate - transferring serviceURL->alias map with 2 entries
20140603T124315.344 INFO  forker StdOut - Subprocess(out):security dir location: /tmp/29872@fc2/.taverna-server-security/670c3ec4-a045-4315-963d-cb08c498532e
20140603T124315.346 INFO  forker StdOut - Subprocess(out):password of length 36 will be written to subprocess stdin
20140603T124315.374 INFO  Atom EventDAO - stored 1 notification events
20140603T124315.375 INFO  forker StdOut - Subprocess(out):starting [/usr/bin/time, /bin/sh, /var/lib/tomcat7/webapps/tavernaserver/WEB-INF/classes/util/taverna-commandline-enterprise-2.5.0/executeworkflow.sh, -logfile, /tmp/670c3ec4-a045-4315-963d-cb08c498532e/logs/detail.log, -cmdir, /tmp/29872@fc2/.taverna-server-security/670c3ec4-a045-4315-963d-cb08c498532e, -cmpassword, -inputfile, pid, /tmp/670c3ec4-a045-4315-963d-cb08c498532e/.tav_in_3637079194144617447.tmp, -inputfile, dsid, /tmp/670c3ec4-a045-4315-963d-cb08c498532e/.tav_in_7020461184459761713.tmp, -outputdir, /tmp/670c3ec4-a045-4315-963d-cb08c498532e/out, /tmp/670c3ec4-a045-4315-963d-cb08c498532e/.wf_3207203763033582579.t2flow] in directory /tmp/670c3ec4-a045-4315-963d-cb08c498532e with environment {TERM=xterm, INTERACTION_WEBDAV=/tavernaserver/rest/runs/670c3ec4-a045-4315-963d-cb08c498532e/wd/interactions, SHELL=/bin/false, INTERACTION_FEED=/tavernaserver/rest/runs/670c3ec4-a045-4315-963d-cb08c498532e/interaction, RAVEN_APPHOME=/tmp/670c3ec4-a045-4315-963d-cb08c498532e, LANGUAGE=en_US:en, PATH=/usr/lib/jvm/java-7-openjdk-amd64/jre/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin, INTERACTION_PORT=8443, MAIL=/var/mail/tomcat7, INTERACTION_HOST=https://123.123.123.124, USER=tomcat7, HOME=/usr/share/tomcat7, LOGNAME=tomcat7, TAVERNA_RUN_ID=670c3ec4-a045-4315-963d-cb08c498532e, USERNAME=tomcat7, LANG=en_US.UTF-8}
20140603T124315.376 INFO  Performance CallTimeLogger - call to execution(RunREST.setStatus(..)) took 403.280ms
20140603T124316.396 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 7.881ms
20140603T124318.420 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 7.925ms
20140603T124320.437 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 4.432ms
20140603T124322.285 INFO  Performance CallTimeLogger - call to execution(RunDatabaseDAO.getPotentiallyNotifiable()) took 4.991ms
20140603T124322.459 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 10.022ms
20140603T124324.486 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 8.126ms
20140603T124326.510 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 8.071ms
20140603T124328.571 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 24.934ms
20140603T124330.606 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 8.870ms
20140603T124330.886 INFO  Performance CallTimeLogger - call to execution(RunREST.getStatus()) took 5.914ms
20140603T124332.396 INFO  Performance CallTimeLogger - call to execution(RunDatabaseDAO.getPotentiallyNotifiable()) took 107.838ms
20140603T124332.909 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 8.306ms
20140603T124334.934 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 8.421ms
20140603T124336.952 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 4.246ms
20140603T124338.967 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 5.246ms
20140603T124340.988 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 8.251ms
20140603T124342.509 INFO  Performance CallTimeLogger - call to execution(RunDatabaseDAO.getPotentiallyNotifiable()) took 107.648ms
20140603T124343.010 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 6.681ms
20140603T124345.033 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 6.730ms
20140603T124347.055 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 6.676ms
20140603T124347.059 INFO  forker StdOut - Subprocess(out):workflow exited, code=0
20140603T124347.612 INFO  Performance CallTimeLogger - call to execution(RunREST.getStatus()) took 552.327ms
20140603T124347.626 INFO  Performance CallTimeLogger - call to execution(RunDatabaseDAO.getPotentiallyNotifiable()) took 15.646ms
20140603T124347.641 INFO  Performance CallTimeLogger - call to execution(TavernaServer.getRunResource(..)) took 6.745ms
20140603T124347.770 INFO  Performance CallTimeLogger - call to execution(RunDatabaseDAO.markFinished(..)) took 140.947ms
20140603T124347.813 INFO  Atom EventDAO - stored 1 notification events
20140603T124347.849 INFO  Performance CallTimeLogger - call to execution(RunREST.destroy()) took 204.589ms
20140603T124348.365 INFO  Performance CallTimeLogger - call to execution(RunDatabaseDAO.doClean()) took 4.090ms