Hi to all
I'm having some problems with Taverna 2.2.0 updated version (taverna
2.2.1 + provenance) (on Fedora 13 java version "1.6.0_22" 64bits)
Sometimes after opening Taverna, some WSDL services don't appear
(services in a WSDL file), if I remove .taverna-2.2.0/ everything gets
ok after some runs everything gets back to the same. The logs say that
the WSDL service are being parsed (each file has around 100/150 services)
I've two logs, one from a working startup and another from a nonworking
startup (missing WSDL), the only difference is that on the non working,
taverna does the following
INFO 2011-04-19 15:03:52,200
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter:766) - DB
cleared DYNAMIC
INFO 2011-04-19 15:03:53,843
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:93) -
Deletion of workflow run '029e9162-2f9b-409b-9a7a-b63b8c529e3d' from
provenance database and Reference Manager's store completed.
I've noticed that on my laptop (java 1.6.0_24) without Taverna update I
have the same DB cleared DYNAMIC *but* the processes are loaded normally.
If necessary for debugging I'm running the following workflow:
http://www.myexperiment.org/workflows/2066.html
Any suggestions ?! Is this some sort of bug ?!
Jorge
PS: Can't wait for Taverna 2.3 :)
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INFO 2011-04-19 15:03:36,411
(net.sf.taverna.t2.workbench.ui.impl.Workbench:487) - Using Nimbus look and feel
INFO 2011-04-19 15:03:36,582
(net.sf.taverna.t2.workbench.ui.credentialmanager.startup.InitialiseSSLStartupHook:47)
- Initialising SSL socket factory for SSL connections from Taverna.
INFO 2011-04-19 15:03:37,193
(net.sf.taverna.t2.provenance.api.ProvenanceAccess:185) - Provenance being
captured using: derby
WARN 2011-04-19 15:03:39,306
(net.sf.taverna.raven.repository.impl.ArtifactImpl:85) - Unable to find a
version for the dependency log4j:log4j - skipping
WARN 2011-04-19 15:03:39,325
(net.sf.taverna.raven.repository.impl.ArtifactImpl:85) - Unable to find a
version for the dependency junit:junit - skipping
WARN 2011-04-19 15:03:39,570 (net.sf.taverna.raven.plugins.PluginManager:85) -
HTTP status 503 while getting plugins
http://www.mygrid.org.uk/taverna/updates/2.2.0/plugins/official/pluginlist.xml
WARN 2011-04-19 15:03:40,118 (net.sf.taverna.raven.plugins.PluginManager:85) -
HTTP status 503 while getting plugins
http://www.mygrid.org.uk/taverna/updates/2.2.0/plugins/3rdparty/pluginlist.xml
WARN 2011-04-19 15:03:40,638 (net.sf.taverna.raven.plugins.PluginManager:85) -
HTTP status 503 while getting plugins
http://www.mygrid.org.uk/taverna/updates/2.2.0/plugins/prototype/pluginlist.xml
INFO 2011-04-19 15:03:40,914
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating WSDL
service http://rsg.pml.ac.uk/wps/generic.wsdl
INFO 2011-04-19 15:03:40,914
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating WSDL
service http://rsg.pml.ac.uk/wps/raster.wsdl
INFO 2011-04-19 15:03:40,916
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Parsing
wsdl:http://rsg.pml.ac.uk/wps/generic.wsdl WSDL service
http://rsg.pml.ac.uk/wps/generic.wsdl
INFO 2011-04-19 15:03:40,918
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Parsing
wsdl:http://rsg.pml.ac.uk/wps/raster.wsdl WSDL service
http://rsg.pml.ac.uk/wps/raster.wsdl
INFO 2011-04-19 15:03:40,925
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating WSDL
service http://rsg.pml.ac.uk/wps/vector.wsdl
INFO 2011-04-19 15:03:40,927
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Parsing
wsdl:http://rsg.pml.ac.uk/wps/vector.wsdl WSDL service
http://rsg.pml.ac.uk/wps/vector.wsdl
INFO 2011-04-19 15:03:40,927
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating
Template service SpreadsheetImport
INFO 2011-04-19 15:03:40,929
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating
Template service String constant
INFO 2011-04-19 15:03:40,932
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating
Template service Beanshell
INFO 2011-04-19 15:03:40,934
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 1
services Template service SpreadsheetImport
INFO 2011-04-19 15:03:40,934
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating
Template service Rshell
INFO 2011-04-19 15:03:40,935
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 1
services Template service String constant
INFO 2011-04-19 15:03:40,935
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 1
services Template service Rshell
INFO 2011-04-19 15:03:40,935
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 1
services Template service Beanshell
INFO 2011-04-19 15:03:40,940
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating
Template service Nested workflow
INFO 2011-04-19 15:03:40,940
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 1
services Template service Nested workflow
INFO 2011-04-19 15:03:40,940
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating Local
workers provider
INFO 2011-04-19 15:03:41,954
(net.sf.taverna.t2.workbench.models.graph.svg.SVGUtil:89) - Using XML parser
null
INFO 2011-04-19 15:03:42,259
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 53
services Local workers provider
INFO 2011-04-19 15:03:43,401
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:77) -
Starting deletion of workflow run 'fb8b2485-42e8-468f-abf3-fab2ce0c8559' (run
id fb8b2485-42e8-468f-abf3-fab2ce0c8559).
INFO 2011-04-19 15:03:44,003
(net.sf.taverna.t2.provenance.api.ProvenanceAccess:185) - Provenance being
captured using: derby
INFO 2011-04-19 15:03:44,355
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter:766) - DB cleared
DYNAMIC
INFO 2011-04-19 15:03:45,254
(net.sf.taverna.t2.workbench.run.ResultsPerspectiveComponent:394) - retrieved
previous run, workflow run id: 16f0f8b1-3bec-450e-81e7-ad3e7f22213b date:
2011-04-18 10:44:19.76
INFO 2011-04-19 15:03:45,737
(net.sf.taverna.t2.workbench.run.ResultsPerspectiveComponent:394) - retrieved
previous run, workflow run id: 3c937ac7-085f-43ee-a7c6-f8d4c7c3f138 date:
2011-04-18 09:03:06.617
INFO 2011-04-19 15:03:47,183
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:93) -
Deletion of workflow run 'fb8b2485-42e8-468f-abf3-fab2ce0c8559' from provenance
database and Reference Manager's store completed.
INFO 2011-04-19 15:03:47,183
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:77) -
Starting deletion of workflow run '5884d17d-1243-4ee4-8120-31506b791e2e' (run
id 5884d17d-1243-4ee4-8120-31506b791e2e).
INFO 2011-04-19 15:03:47,244
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter:766) - DB cleared
DYNAMIC
INFO 2011-04-19 15:03:50,339
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:93) -
Deletion of workflow run '5884d17d-1243-4ee4-8120-31506b791e2e' from provenance
database and Reference Manager's store completed.
INFO 2011-04-19 15:03:50,340
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:77) -
Starting deletion of workflow run '07e41a2e-da94-4b9b-b202-3dd37869add8' (run
id 07e41a2e-da94-4b9b-b202-3dd37869add8).
INFO 2011-04-19 15:03:50,436
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter:766) - DB cleared
DYNAMIC
INFO 2011-04-19 15:03:52,111
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:93) -
Deletion of workflow run '07e41a2e-da94-4b9b-b202-3dd37869add8' from provenance
database and Reference Manager's store completed.
INFO 2011-04-19 15:03:52,111
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:77) -
Starting deletion of workflow run '029e9162-2f9b-409b-9a7a-b63b8c529e3d' (run
id 029e9162-2f9b-409b-9a7a-b63b8c529e3d).
INFO 2011-04-19 15:03:52,200
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter:766) - DB cleared
DYNAMIC
INFO 2011-04-19 15:03:53,843
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:93) -
Deletion of workflow run '029e9162-2f9b-409b-9a7a-b63b8c529e3d' from provenance
database and Reference Manager's store completed.
INFO 2011-04-19 15:03:53,844
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:77) -
Starting deletion of workflow run 'da00e72e-9d5c-46ba-a880-18699017742d' (run
id da00e72e-9d5c-46ba-a880-18699017742d).
INFO 2011-04-19 15:03:53,880
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter:766) - DB cleared
DYNAMIC
INFO 2011-04-19 15:03:57,806
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:93) -
Deletion of workflow run 'da00e72e-9d5c-46ba-a880-18699017742d' from provenance
database and Reference Manager's store completed.
INFO 2011-04-19 15:03:57,806
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:77) -
Starting deletion of workflow run 'b09235e3-e90b-44d9-8900-2bcab7becdfb' (run
id b09235e3-e90b-44d9-8900-2bcab7becdfb).
INFO 2011-04-19 15:03:57,864
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter:766) - DB cleared
DYNAMIC
INFO 2011-04-19 15:03:59,565
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:93) -
Deletion of workflow run 'b09235e3-e90b-44d9-8900-2bcab7becdfb' from provenance
database and Reference Manager's store completed.
INFO 2011-04-19 15:03:59,566
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:77) -
Starting deletion of workflow run '9253d8e9-166e-4471-bddd-c932f854bf2e' (run
id 9253d8e9-166e-4471-bddd-c932f854bf2e).
INFO 2011-04-19 15:03:59,605
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter:766) - DB cleared
DYNAMIC
INFO 2011-04-19 15:04:01,441
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:93) -
Deletion of workflow run '9253d8e9-166e-4471-bddd-c932f854bf2e' from provenance
database and Reference Manager's store completed.
INFO 2011-04-19 15:04:01,442
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:77) -
Starting deletion of workflow run 'e410e20d-909d-42b2-90cf-59645d6f434d' (run
id e410e20d-909d-42b2-90cf-59645d6f434d).
INFO 2011-04-19 15:04:01,484
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter:766) - DB cleared
DYNAMIC
INFO 2011-04-19 15:04:03,212
(net.sf.taverna.t2.workbench.run.cleanup.DeleteWorkflowRunsThread:93) -
Deletion of workflow run 'e410e20d-909d-42b2-90cf-59645d6f434d' from provenance
database and Reference Manager's store completed.
INFO 2011-04-19 15:04:08,031
(net.sf.taverna.t2.workbench.helper.HelpCollator:168) - Attempting to register
net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2011-04-19 15:04:08,431
(net.sf.taverna.t2.workbench.helper.HelpCollator:89) - Read external help set
from http://www.mygrid.org.uk/taverna/helpset/2.2/helpset.hs
INFO 2011-04-19 15:04:08,432
(net.sf.taverna.t2.workbench.helper.HelpCollator:132) - EmptyHelp set to false
INFO 2011-04-19 15:04:08,432
(net.sf.taverna.t2.workbench.helper.HelpCollator:181) - Refused to register
component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2011-04-19 15:04:14,110
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 15 WSDL
operations:http://rsg.pml.ac.uk/wps/generic.wsdl WSDL service
http://rsg.pml.ac.uk/wps/generic.wsdl
INFO 2011-04-19 15:04:14,134
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 15
services WSDL service http://rsg.pml.ac.uk/wps/generic.wsdl
INFO 2011-04-19 15:04:25,486
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating WSDL
service http://localhost/test4.wsdl
INFO 2011-04-19 15:04:25,487
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Parsing
wsdl:http://localhost/test4.wsdl WSDL service http://localhost/test4.wsdl
INFO 2011-04-19 15:22:14,983
(net.sf.taverna.t2.workbench.ui.impl.Workbench:487) - Using Nimbus look and feel
INFO 2011-04-19 15:22:15,142
(net.sf.taverna.t2.workbench.ui.credentialmanager.startup.InitialiseSSLStartupHook:47)
- Initialising SSL socket factory for SSL connections from Taverna.
WARN 2011-04-19 15:22:15,817 (net.sf.taverna.raven.plugins.PluginManager:85) -
HTTP status 503 while getting plugins
http://www.mygrid.org.uk/taverna/updates/2.2.0/plugins/official/pluginlist.xml
WARN 2011-04-19 15:22:16,365 (net.sf.taverna.raven.plugins.PluginManager:85) -
HTTP status 503 while getting plugins
http://www.mygrid.org.uk/taverna/updates/2.2.0/plugins/3rdparty/pluginlist.xml
WARN 2011-04-19 15:22:16,903 (net.sf.taverna.raven.plugins.PluginManager:85) -
HTTP status 503 while getting plugins
http://www.mygrid.org.uk/taverna/updates/2.2.0/plugins/prototype/pluginlist.xml
WARN 2011-04-19 15:22:18,526
(net.sf.taverna.raven.repository.impl.ArtifactImpl:85) - Unable to find a
version for the dependency log4j:log4j - skipping
WARN 2011-04-19 15:22:18,542
(net.sf.taverna.raven.repository.impl.ArtifactImpl:85) - Unable to find a
version for the dependency junit:junit - skipping
WARN 2011-04-19 15:22:18,794 (net.sf.taverna.raven.plugins.PluginManager:85) -
HTTP status 503 while getting plugins
http://www.mygrid.org.uk/taverna/updates/2.2.0/plugins/official/pluginlist.xml
WARN 2011-04-19 15:22:19,315 (net.sf.taverna.raven.plugins.PluginManager:85) -
HTTP status 503 while getting plugins
http://www.mygrid.org.uk/taverna/updates/2.2.0/plugins/3rdparty/pluginlist.xml
INFO 2011-04-19 15:22:19,494
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating WSDL
service http://localhost/test4.wsdl
INFO 2011-04-19 15:22:19,496
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Parsing
wsdl:http://localhost/test4.wsdl WSDL service http://localhost/test4.wsdl
INFO 2011-04-19 15:22:19,494
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating WSDL
service http://rsg.pml.ac.uk/wps/generic.wsdl
INFO 2011-04-19 15:22:19,500
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Parsing
wsdl:http://rsg.pml.ac.uk/wps/generic.wsdl WSDL service
http://rsg.pml.ac.uk/wps/generic.wsdl
INFO 2011-04-19 15:22:19,521
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating WSDL
service http://rsg.pml.ac.uk/wps/raster.wsdl
INFO 2011-04-19 15:22:19,521
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Parsing
wsdl:http://rsg.pml.ac.uk/wps/raster.wsdl WSDL service
http://rsg.pml.ac.uk/wps/raster.wsdl
INFO 2011-04-19 15:22:19,533
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating WSDL
service http://rsg.pml.ac.uk/wps/vector.wsdl
INFO 2011-04-19 15:22:19,533
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Parsing
wsdl:http://rsg.pml.ac.uk/wps/vector.wsdl WSDL service
http://rsg.pml.ac.uk/wps/vector.wsdl
INFO 2011-04-19 15:22:19,536
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating
Template service SpreadsheetImport
INFO 2011-04-19 15:22:19,537
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating
Template service Nested workflow
INFO 2011-04-19 15:22:19,538
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating
Template service Beanshell
INFO 2011-04-19 15:22:19,539
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating
Template service String constant
INFO 2011-04-19 15:22:19,540
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating
Template service Rshell
INFO 2011-04-19 15:22:19,541
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Updating Local
workers provider
INFO 2011-04-19 15:22:19,552
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 1
services Template service Nested workflow
INFO 2011-04-19 15:22:19,552
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 1
services Template service Beanshell
INFO 2011-04-19 15:22:19,553
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 1
services Template service String constant
INFO 2011-04-19 15:22:19,553
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 1
services Template service SpreadsheetImport
INFO 2011-04-19 15:22:19,553
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 1
services Template service Rshell
WARN 2011-04-19 15:22:19,837 (net.sf.taverna.raven.plugins.PluginManager:85) -
HTTP status 503 while getting plugins
http://www.mygrid.org.uk/taverna/updates/2.2.0/plugins/prototype/pluginlist.xml
INFO 2011-04-19 15:22:20,535
(net.sf.taverna.t2.workbench.models.graph.svg.SVGUtil:89) - Using XML parser
null
INFO 2011-04-19 15:22:20,877
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 53
services Local workers provider
INFO 2011-04-19 15:22:22,190
(net.sf.taverna.t2.provenance.api.ProvenanceAccess:185) - Provenance being
captured using: derby
INFO 2011-04-19 15:22:52,507
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 15 WSDL
operations:http://rsg.pml.ac.uk/wps/generic.wsdl WSDL service
http://rsg.pml.ac.uk/wps/generic.wsdl
INFO 2011-04-19 15:22:52,527
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 15
services WSDL service http://rsg.pml.ac.uk/wps/generic.wsdl
INFO 2011-04-19 15:22:54,067
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 95 WSDL
operations:http://rsg.pml.ac.uk/wps/vector.wsdl WSDL service
http://rsg.pml.ac.uk/wps/vector.wsdl
INFO 2011-04-19 15:22:54,070
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 95
services WSDL service http://rsg.pml.ac.uk/wps/vector.wsdl
INFO 2011-04-19 15:22:54,275
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 107 WSDL
operations:http://rsg.pml.ac.uk/wps/raster.wsdl WSDL service
http://rsg.pml.ac.uk/wps/raster.wsdl
INFO 2011-04-19 15:22:54,278
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 107
services WSDL service http://rsg.pml.ac.uk/wps/raster.wsdl
INFO 2011-04-19 15:22:59,748
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 273 WSDL
operations:http://localhost/test4.wsdl WSDL service http://localhost/test4.wsdl
INFO 2011-04-19 15:22:59,751
(net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:131) - Found 273
services WSDL service http://localhost/test4.wsdl
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