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From: Stian Soiland-R. <soi...@cs...> - 2016-11-09 14:02:54
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Hi folks - apologies for the spam. I am part of arranging the below webinar about large-scale Galaxy genomics workflows; which I think might also be interesting to Taverna users: We would like to invite you to attend the 8th webinar in BioExcel’s webinar series on computational methods and applications for biomolecular research, which will take place on 16th November 2016: # Webinar: Large-scale analytical workflows on the cloud using Galaxy and Globus http://bioexcel.eu/webinar-8-2016-11-16-workflows-galaxy-globus/ Presenter: Ravi Madduri When: Wed 16th November 2016 16:00 CET (2016-11-16 15:00 UTC) Registration: Free - https://attendee.gotowebinar.com/register/5808939110698431491 BioExcel webinars include an audience Q&A session during which attendees can ask questions and make suggestions. They are a great opportunity to interact with the main code developers. This is the first webinar from the BioExcel Workflows Interest Group, welcoming users (and potential users) of Scientific Workflow systems for data analysis and pipe-lining of biomolecular simulation and modelling tools; in particular using Galaxy, Apache Taverna, KNIME, COMPSs and Common Workflow Language. This interest group covers pros and cons of these workflow system, practical workflow design and setup, also covers deployment questions on HPC/cloud infrastructure, like the use of Docker for packaging command line codes. In this BioExcel webinar we are delighted to have Ravi Madduri from Argonne National Laboratory and University of Chicago present Globus Genomics, a system developed for rapid analysis of large quantities of next-generation sequencing (NGS) genomic data, combining Galaxy workflows with cloud technologies like Amazon EC2 and Globus File Transfer. Ravi will also present the technologies used to achieve large-scale analytical Galaxy workflows on the cloud. We think this will be of interest not just for the genomics community, but for any scientific workflow users who need to consider distributed deployments, data management and scalability; and so we hope you would like to attend this webinar. (more: http://bioexcel.eu/webinar-8-2016-11-16-workflows-galaxy-globus/ ) ## Register for webinar Title: Large-scale analytical workflows on the cloud using Galaxy and Globus Date: Wed 16th November 2016 (2016-11-16) Time: 16:00 CET Please register at https://attendee.gotowebinar.com/register/5808939110698431491. You will then receive an email with details of how you can connect to the webinar. -- Stian Soiland-Reyes, eScience Lab School of Computer Science The University of Manchester http://orcid.org/0000-0001-9842-9718 |
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From: Stian Soiland-R. <soi...@cs...> - 2014-11-06 13:55:39
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The taverna-users list is now read-only as it has moved to Apache. If you attempt to send to this list, you will receive this response: Your post has not been sent to the taverna-users list, as this mailing list has moved to us...@ta... See http://mail-archives.apache.org/mod_mbox/incubator-taverna-users/ for details. You need to subscribe to the new list by sending a blank email to use...@ta... -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 |
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From: Stian Soiland-R. <soi...@cs...> - 2014-11-05 16:40:07
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Hi, As you might have heard, the Taverna mailing lists are moving to apache.org. I have now invited every subscriber on tav...@li... to us...@ta... and everyone on tav...@li... to de...@ta... My apologies if you have received multiple invitations - you might have been subscribed with several addresses. As mentioned before, you will have to respond to the 'ezmlm' email, which looks like this: > Subject: confirm subscribe to de...@ta... > > Hi! This is the ezmlm program. I'm managing the > de...@ta... mailing list. > ... Your email client might have sorted this under 'Social' or "Lists". You need to REPLY to that email (not this one!) to remain on the Taverna lists. >From tomorrow I will make the taverna-* lists on Sourceforge read-only, that is you can only post to the new apache lists. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 |
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From: Stian Soiland-R. <soi...@cs...> - 2014-11-03 15:47:03
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Hi! We are moving these mailing lists to Apache Incubator infrastructure: tav...@li... tav...@li... tav...@li... The new lists are at: de...@ta... us...@ta... co...@ta... A confirmation step is required by you to remain on the list, see below. For details and archives, see: http://mail-archives.apache.org/mod_mbox/incubator-taverna-dev/ http://mail-archives.apache.org/mod_mbox/incubator-taverna-users/ http://mail-archives.apache.org/mod_mbox/incubator-taverna-commits/ We will by the end of this week make the old sourceforge lists read-only. As a convenience, tomorrow I am going to go through the current subscriber lists on Sourceforge and mass-invite you based on the email address you are currently subscribed with - when you get one of these emails then you simply just need to REPLY to that email to CONFIRM. (You will get two emails if you are on both lists). If you want to subscribe with a different email address, then subscribe manually as detailed below. If for some reason you would prefer to leave the Taverna lists, then simply ignore the invitation email from incubator.apache.org. To sign up to the new lists yourself, you need to send an empty email to the -subscribe version of the list address. E.g. to subscribe, send an email to: dev...@ta... and/or use...@ta... If you would prefer to sign up to the digest email instead, then email to: dev...@ta... and/or use...@ta... You will then need to REPLY to the CONFIRMATION email that comes back from dev...@ta... (or equivalent). -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 |
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From: Stian Soiland-R. <soi...@cs...> - 2014-10-31 09:15:14
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Day 2 starting, #Taverna2014 day 2 starting: http://www.youtube.com/watch?v=HYk67AV1F8A https://plus.google.com/events/cd990a54geq52inrbnaukmu435k On 30 October 2014 15:09, Stian Soiland-Reyes <soi...@cs...> wrote: > Thanks for following! My machine is the camera machine, so I might not > see any questions right away. I'll put the slides on the wiki later as > it is not always shown nicely from projector. > > On 30 October 2014 14:54, Suresh Marru <sm...@ap...> wrote: >> Thank you for sharing Stian, its clear enough to follow the workshop. >> >> Suresh >> >> On Oct 30, 2014, at 10:50 AM, Stian Soiland-Reyes <soi...@cs...> wrote: >> >>> Second half of #Taverna2014 (Sorry about the break - G+ playing up..) >>> >>> https://plus.google.com/events/cr9sjhtn8d5dp1o210cl0eppndo >>> >>> http://www.youtube.com/watch?v=kOquYEYSEzo >>> >>> On 30 October 2014 09:57, Stian Soiland-Reyes >>> <soi...@cs...> wrote: >>>> http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Open+Development+Workshop >>>> >>>> has now started. >>>> >>>> You can join this remotely using Google+ Hangout: >>>> >>>> https://plus.google.com/events/c95g675ghuirlefopj97of52018 >>>> >>>> >>>> >>>> or follow the Youtube stream (which should allow rewinds): >>>> http://www.youtube.com/watch?v=CrgCiEBLKVo >>>> >>>> >>>> Twitter hashtag: #taverna2014 >>>> >>>> >>>> Please feel free to raise questions on Google Hangout chat. >>>> >>>> -- >>>> Stian Soiland-Reyes, myGrid team >>>> School of Computer Science >>>> The University of Manchester >>>> http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 >>> >>> >>> >>> -- >>> Stian Soiland-Reyes, myGrid team >>> School of Computer Science >>> The University of Manchester >>> http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 >> > > > > -- > Stian Soiland-Reyes, myGrid team > School of Computer Science > The University of Manchester > http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 |
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From: Alan R W. <ala...@ma...> - 2014-10-30 18:25:00
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On 27-Oct-14 20:33, Deniz .. wrote: > Hi all, Hello > I want to make a condition that when a service isn`t available at the > run time, workflow can choose other alternative services that I defined > before. Is taverna has any property like that? How can I make this > condition in a service workflow? This was attempted in Taverna 1, but there were problems making it work in practice. Normally you would use a multiplexing service to redirect to the actual service. One possible way would be to ping the service in the workflow and then effectively branch on the response you got. So you would ping Service A, and if it was available go down the route of calling A, otherwise call B. The best solution though depends on exactly why the service is unavailable and how similar the replacement service is. > Could you help or direct me please, > Thank you > Deniz Alan |
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From: Stian Soiland-R. <soi...@cs...> - 2014-10-30 14:51:08
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Second half of #Taverna2014 (Sorry about the break - G+ playing up..) https://plus.google.com/events/cr9sjhtn8d5dp1o210cl0eppndo http://www.youtube.com/watch?v=kOquYEYSEzo On 30 October 2014 09:57, Stian Soiland-Reyes <soi...@cs...> wrote: > http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Open+Development+Workshop > > has now started. > > You can join this remotely using Google+ Hangout: > > https://plus.google.com/events/c95g675ghuirlefopj97of52018 > > > > or follow the Youtube stream (which should allow rewinds): > http://www.youtube.com/watch?v=CrgCiEBLKVo > > > Twitter hashtag: #taverna2014 > > > Please feel free to raise questions on Google Hangout chat. > > -- > Stian Soiland-Reyes, myGrid team > School of Computer Science > The University of Manchester > http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 |
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From: Stian Soiland-R. <soi...@cs...> - 2014-10-30 09:58:27
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http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Open+Development+Workshop has now started. You can join this remotely using Google+ Hangout: https://plus.google.com/events/c95g675ghuirlefopj97of52018 or follow the Youtube stream (which should allow rewinds): http://www.youtube.com/watch?v=CrgCiEBLKVo Twitter hashtag: #taverna2014 Please feel free to raise questions on Google Hangout chat. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 |
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From: Deniz .. <dul...@ho...> - 2014-10-27 20:33:39
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Hi all, I want to make a condition that when a service isn`t available at the run time, workflow can choose other alternative services that I defined before. Is taverna has any property like that? How can I make this condition in a service workflow? Could you help or direct me please, Thank you Deniz |
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From: Muhammad U. <11m...@se...> - 2014-10-24 16:08:50
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I want to make following kind of workflow [A] ---> [B] ----> if(output of [B] condition) then [A] ---> [C][D][E] else [A] ---> [F][G][H] Output of A is given to B If output of B matches a condition than give input of A to CDE otherwise to FGH How can I make this workflow? -- Muhammad Usama 2011-NUST-MS-CS-009 |
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From: Stian Soiland-R. <soi...@cs...> - 2014-10-20 11:02:17
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I am proud to announce that Taverna has been accepted as an Apache Incubator project: https://www.mail-archive.com/ge...@in.../msg45542.html The Apache Software Foundation is a non-profit organization, forming a community of open-source software projects with strong emphasis on openness, collaboration and a consensus-based development process. Well-known Apache projects include the Apache HTTP server, Tomcat, Maven, Jena, CXF and OpenOffice. http://www.apache.org/ Taverna will participate in the Apache Incubator process, with assigned mentors that help assure that we follow the Apache guidelines. http://incubator.apache.org/incubation/Process_Description.html Practically this means that the Taverna code base, mailing lists and website will be migrated to the Apache infrastructure, and future releases will be called Apache Taverna. Apache Taverna development will follow a clear open process, with important decisions (such as approving a release) done by voting on the new de...@ta... mailing list, which will be open to anyone. We will move all members of the current taverna-hackers and taverna-users lists to the new Incubator lists when the Apache infrastructure for Taverna has been established. The Taverna team is thrilled by this move, and hope that this will encourage further involvement in Taverna project. At the Taverna Open Development workshop on the 30th of October 2014 we will discuss Apache Taverna in detail. Registration is still open, see: http://taverna2014.eventbrite.co.uk/ -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 |
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From: Alan R W. <ala...@ma...> - 2014-10-15 14:46:33
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On 15/10/2014 14:46, Deniz .. wrote: > Thank you very much Alan. I have already tried to remove first line of > the XML document. This time it gives no error but creates an emty file > as an output. OK > If so, I`m waiting Jorge`s reply. I hope he has seen our messages here. You can try e-mailing him directly. > Thank you, > Deniz Alan |
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From: Deniz .. <dul...@ho...> - 2014-10-15 13:46:09
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Thank you very much Alan. I have already tried to remove first line of the XML document. This time it gives no error but creates an emty file as an output. If so, I`m waiting Jorge`s reply. I hope he has seen our messages here. Thank you, Deniz |
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From: Alan R W. <ala...@ma...> - 2014-10-15 12:29:11
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On 15/10/2014 13:20, Deniz .. wrote: > Hello again Alan, > The former was my Apache server error log. This is the PYWPS server > error log: > Thank you.. > Deniz > > error log: > > Traceback (most recent call last): > File "C:/pywps\wps.py", line 87, in <module> > if wps.parseRequest(inputQuery): > File "C:/pywps\pywps\__init__.py", line 213, in parseRequest > self.inputs = self.parser.parse(queryStringObject) > File "C:/pywps\pywps\Parser\Post.py", line 108, in parse > firstChild = self.isSoapFirstChild(self.document) > File "C:/pywps\pywps\Parser\Post.py", line 232, in isSoapFirstChild > soapCls = Soap.SOAP(firstChild) > File "C:/pywps\pywps\Soap.py", line 284, in __init__ > raise pywps.NoApplicableCode(e.message) > NoApplicableCode: <?xml version="1.0" encoding="utf-8"?> > <ExceptionReport version="1.0.0" xmlns="http://www.opengis.net/ows/1.1" > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" > xsi:schemaLocation="http://www.opengis.net/ows/1.1 > http://schemas.opengis.net/ows/1.1.0/owsExceptionReport.xsd"> > <Exception exceptionCode="NoApplicableCode"> > <ExceptionText> > u'XML declaration allowed only at the start of the > document, line 1, column 118' > </ExceptionText> > </Exception> > </ExceptionReport> I think this is what Jorge will need. It looks to me as if somehow the XML inside the SOAP message sent by Taverna is being unescaped in Soap.py. That confuses it as it has a full XML document inside another full XML document (the SOAP message itself). I could suggest a hack of removing the first line from the XML document, but do not try that until you have asked Jorge. Alan |
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From: Deniz .. <dul...@ho...> - 2014-10-15 12:20:22
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Hello again Alan,
The former was my Apache server error log. This is the PYWPS server error log:
Thank you..
Deniz
error log:
Traceback (most recent call last):
File "C:/pywps\wps.py", line 87, in <module>
if wps.parseRequest(inputQuery):
File "C:/pywps\pywps\__init__.py", line 213, in parseRequest
self.inputs = self.parser.parse(queryStringObject)
File "C:/pywps\pywps\Parser\Post.py", line 108, in parse
firstChild = self.isSoapFirstChild(self.document)
File "C:/pywps\pywps\Parser\Post.py", line 232, in isSoapFirstChild
soapCls = Soap.SOAP(firstChild)
File "C:/pywps\pywps\Soap.py", line 284, in __init__
raise pywps.NoApplicableCode(e.message)
NoApplicableCode: <?xml version="1.0" encoding="utf-8"?>
<ExceptionReport version="1.0.0" xmlns="http://www.opengis.net/ows/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.opengis.net/ows/1.1 http://schemas.opengis.net/ows/1.1.0/owsExceptionReport.xsd">
<Exception exceptionCode="NoApplicableCode">
<ExceptionText>
u'XML declaration allowed only at the start of the document, line 1, column 118'
</ExceptionText>
</Exception>
</ExceptionReport>
PyWPS [2014-10-15 14:53:50,888] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 14:53:50,959] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
PyWPS [2014-10-15 14:53:50,970] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 14:53:50,971] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
PyWPS [2014-10-15 14:54:09,355] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 14:54:09,397] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
PyWPS [2014-10-15 14:54:09,407] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 14:54:09,408] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
PyWPS [2014-10-15 14:54:35,727] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 14:54:35,769] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
PyWPS [2014-10-15 14:54:35,779] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 14:54:35,780] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
PyWPS [2014-10-15 14:54:37,529] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 14:54:37,569] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
PyWPS [2014-10-15 14:54:37,581] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 14:54:37,582] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
PyWPS [2014-10-15 15:00:25,117] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 15:00:25,158] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
PyWPS [2014-10-15 15:00:25,170] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 15:00:25,171] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
Traceback (most recent call last):
File "C:/pywps\wps.py", line 87, in <module>
if wps.parseRequest(inputQuery):
File "C:/pywps\pywps\__init__.py", line 213, in parseRequest
self.inputs = self.parser.parse(queryStringObject)
File "C:/pywps\pywps\Parser\Post.py", line 104, in parse
raise pywps.NoApplicableCode(e.message)
NoApplicableCode: <?xml version="1.0" encoding="utf-8"?>
<ExceptionReport version="1.0.0" xmlns="http://www.opengis.net/ows/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.opengis.net/ows/1.1 http://schemas.opengis.net/ows/1.1.0/owsExceptionReport.xsd">
<Exception exceptionCode="NoApplicableCode">
<ExceptionText>
'no element found: line 1, column 0'
</ExceptionText>
</Exception>
</ExceptionReport>
Traceback (most recent call last):
File "C:/pywps\wps.py", line 87, in <module>
if wps.parseRequest(inputQuery):
File "C:/pywps\pywps\__init__.py", line 213, in parseRequest
self.inputs = self.parser.parse(queryStringObject)
File "C:/pywps\pywps\Parser\Post.py", line 104, in parse
raise pywps.NoApplicableCode(e.message)
NoApplicableCode: <?xml version="1.0" encoding="utf-8"?>
<ExceptionReport version="1.0.0" xmlns="http://www.opengis.net/ows/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.opengis.net/ows/1.1 http://schemas.opengis.net/ows/1.1.0/owsExceptionReport.xsd">
<Exception exceptionCode="NoApplicableCode">
<ExceptionText>
'no element found: line 1, column 0'
</ExceptionText>
</Exception>
</ExceptionReport>
PyWPS [2014-10-15 15:03:48,763] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 15:03:48,805] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
PyWPS [2014-10-15 15:03:48,815] INFO: Reading processes from directory [C:/pywps/pywps_processes]
PyWPS [2014-10-15 15:03:48,816] INFO: Following processes are imported: ['returner', 'dummyprocess', 'complexVector', 'complexRaster', 'firstInstance', 'secondInstance', 'asyncprocess', 'bboxprocess', 'complexprocess', 'complexprocessows', 'flagsprocess', 'lineagereturn', 'literalprocess', 'noinputsprocess', 'nomimetypesprocess', 'referencedefault', 'returnWCS', 'ultimatequestionprocess', 'ogrbuffer']
Traceback (most recent call last):
File "C:/pywps\wps.py", line 87, in <module>
if wps.parseRequest(inputQuery):
File "C:/pywps\pywps\__init__.py", line 213, in parseRequest
self.inputs = self.parser.parse(queryStringObject)
File "C:/pywps\pywps\Parser\Post.py", line 108, in parse
firstChild = self.isSoapFirstChild(self.document)
File "C:/pywps\pywps\Parser\Post.py", line 232, in isSoapFirstChild
soapCls = Soap.SOAP(firstChild)
File "C:/pywps\pywps\Soap.py", line 284, in __init__
raise pywps.NoApplicableCode(e.message)
NoApplicableCode: <?xml version="1.0" encoding="utf-8"?>
<ExceptionReport version="1.0.0" xmlns="http://www.opengis.net/ows/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.opengis.net/ows/1.1 http://schemas.opengis.net/ows/1.1.0/owsExceptionReport.xsd">
<Exception exceptionCode="NoApplicableCode">
<ExceptionText>
u'XML declaration allowed only at the start of the document, line 1, column 118'
</ExceptionText>
</Exception>
</ExceptionReport>
|
|
From: Deniz .. <dul...@ho...> - 2014-10-15 12:12:36
|
Thank you again Alan..I attached the error log file of my wps server. Thank you! Deniz Error log: [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] Premature end of script headers: pywps.cgi [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: XML\\ declaration\\ allowed\\ only\\ at\\ the\\ start\\ of\\ the\\ document\\,\\ line\\ 1\\,\\ column\\ 118\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: XML\\ declaration\\ allowed\\ only\\ at\\ the\\ start\\ of\\ the\\ document\\,\\ line\\ 1\\,\\ column\\ 118\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] Traceback (most recent call last):\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] File "C:/Program Files (x86)/Apache Software Foundation/Apache2.2/cgi-bin/pywps.cgi", line 11, in <module>\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] import wps\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] File "C:/pywps\\wps.py", line 100, in <module>\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] wps.parser.isSoapExecute)\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\response.py", line 40, in response\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] response = soap.getResponse(response,soapVersion,isSoapExecute,isPromoteStatus)\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\Soap.py", line 405, in getResponse\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] return self.doSOAPFault(exceptionReportTree,soapVersion)\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\Soap.py", line 345, in doSOAPFault\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] if (int(soapVersion)==11):#\r [Tue Sep 30 21:27:14 2014] [error] [client 127.0.0.1] TypeError: int() argument must be a string or a number, not 'NoneType'\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] Premature end of script headers: pywps.cgi [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: XML\\ declaration\\ allowed\\ only\\ at\\ the\\ start\\ of\\ the\\ document\\,\\ line\\ 1\\,\\ column\\ 118\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: XML\\ declaration\\ allowed\\ only\\ at\\ the\\ start\\ of\\ the\\ document\\,\\ line\\ 1\\,\\ column\\ 118\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] Traceback (most recent call last):\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] File "C:/Program Files (x86)/Apache Software Foundation/Apache2.2/cgi-bin/pywps.cgi", line 11, in <module>\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] import wps\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] File "C:/pywps\\wps.py", line 100, in <module>\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] wps.parser.isSoapExecute)\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\response.py", line 40, in response\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] response = soap.getResponse(response,soapVersion,isSoapExecute,isPromoteStatus)\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\Soap.py", line 405, in getResponse\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] return self.doSOAPFault(exceptionReportTree,soapVersion)\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\Soap.py", line 345, in doSOAPFault\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] if (int(soapVersion)==11):#\r [Tue Sep 30 21:37:19 2014] [error] [client 127.0.0.1] TypeError: int() argument must be a string or a number, not 'NoneType'\r [Tue Sep 30 22:02:27 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: no\\ element\\ found\\:\\ line\\ 1\\,\\ column\\ 0\r [Tue Sep 30 22:02:27 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: no\\ element\\ found\\:\\ line\\ 1\\,\\ column\\ 0\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] Premature end of script headers: pywps.cgi [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: XML\\ declaration\\ allowed\\ only\\ at\\ the\\ start\\ of\\ the\\ document\\,\\ line\\ 1\\,\\ column\\ 118\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: XML\\ declaration\\ allowed\\ only\\ at\\ the\\ start\\ of\\ the\\ document\\,\\ line\\ 1\\,\\ column\\ 118\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] Traceback (most recent call last):\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] File "C:/Program Files (x86)/Apache Software Foundation/Apache2.2/cgi-bin/pywps.cgi", line 11, in <module>\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] import wps\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] File "C:/pywps\\wps.py", line 100, in <module>\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] wps.parser.isSoapExecute)\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\response.py", line 40, in response\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] response = soap.getResponse(response,soapVersion,isSoapExecute,isPromoteStatus)\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\Soap.py", line 405, in getResponse\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] return self.doSOAPFault(exceptionReportTree,soapVersion)\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\Soap.py", line 345, in doSOAPFault\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] if (int(soapVersion)==11):#\r [Tue Sep 30 22:02:32 2014] [error] [client 127.0.0.1] TypeError: int() argument must be a string or a number, not 'NoneType'\r [Wed Oct 01 15:35:13 2014] [error] [client 127.0.0.1] (OS 2)The system cannot find the file specified. : couldn't create child process: 720002: wps.py, referer: http://pywps.wald.intevation.org/documentation/process.html [Wed Oct 01 15:35:13 2014] [error] [client 127.0.0.1] (OS 2)The system cannot find the file specified. : couldn't spawn child process: C:/Program Files (x86)/Apache Software Foundation/Apache2.2/cgi-bin/wps.py, referer: http://pywps.wald.intevation.org/documentation/process.html [Wed Oct 01 15:35:18 2014] [error] [client 127.0.0.1] (OS 2)The system cannot find the file specified. : couldn't create child process: 720002: wps.py, referer: http://pywps.wald.intevation.org/documentation/process.html [Wed Oct 01 15:35:18 2014] [error] [client 127.0.0.1] (OS 2)The system cannot find the file specified. : couldn't spawn child process: C:/Program Files (x86)/Apache Software Foundation/Apache2.2/cgi-bin/wps.py, referer: http://pywps.wald.intevation.org/documentation/process.html httpd.exe: Could not reliably determine the server's fully qualified domain name, using 127.0.0.1 for ServerName [Sun Oct 12 18:28:24 2014] [warn] pid file C:/Program Files (x86)/Apache Software Foundation/Apache2.2/logs/httpd.pid overwritten -- Unclean shutdown of previous Apache run? [Sun Oct 12 18:28:24 2014] [notice] Apache/2.2.25 (Win32) configured -- resuming normal operations [Sun Oct 12 18:28:24 2014] [notice] Server built: Jul 10 2013 01:52:12 [Sun Oct 12 18:28:24 2014] [notice] Parent: Created child process 1992 httpd.exe: Could not reliably determine the server's fully qualified domain name, using 127.0.0.1 for ServerName httpd.exe: Could not reliably determine the server's fully qualified domain name, using 127.0.0.1 for ServerName [Sun Oct 12 18:28:24 2014] [notice] Child 1992: Child process is running [Sun Oct 12 18:28:24 2014] [notice] Child 1992: Acquired the start mutex. [Sun Oct 12 18:28:24 2014] [notice] Child 1992: Starting 64 worker threads. [Sun Oct 12 18:28:24 2014] [notice] Child 1992: Starting thread to listen on port 80. [Tue Oct 14 21:31:19 2014] [notice] Parent: Received shutdown signal -- Shutting down the server. [Tue Oct 14 21:31:19 2014] [notice] Child 1992: Exit event signaled. Child process is ending. [Tue Oct 14 21:31:20 2014] [notice] Child 1992: Released the start mutex [Tue Oct 14 21:31:21 2014] [notice] Child 1992: All worker threads have exited. [Tue Oct 14 21:31:21 2014] [notice] Child 1992: Child process is exiting [Tue Oct 14 21:31:22 2014] [notice] Parent: Child process exited successfully. httpd.exe: Could not reliably determine the server's fully qualified domain name, using 127.0.0.1 for ServerName [Wed Oct 15 14:21:11 2014] [notice] Apache/2.2.25 (Win32) configured -- resuming normal operations [Wed Oct 15 14:21:11 2014] [notice] Server built: Jul 10 2013 01:52:12 [Wed Oct 15 14:21:11 2014] [notice] Parent: Created child process 1788 httpd.exe: Could not reliably determine the server's fully qualified domain name, using 127.0.0.1 for ServerName httpd.exe: Could not reliably determine the server's fully qualified domain name, using 127.0.0.1 for ServerName [Wed Oct 15 14:21:11 2014] [notice] Child 1788: Child process is running [Wed Oct 15 14:21:11 2014] [notice] Child 1788: Acquired the start mutex. [Wed Oct 15 14:21:11 2014] [notice] Child 1788: Starting 64 worker threads. [Wed Oct 15 14:21:11 2014] [notice] Child 1788: Starting thread to listen on port 80. [Wed Oct 15 14:23:55 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: No\\ query\\ string\\ found\\.\r [Wed Oct 15 14:23:56 2014] [error] [client 127.0.0.1] File does not exist: C:/Program Files (x86)/Apache Software Foundation/Apache2.2/htdocs/favicon.ico [Wed Oct 15 14:23:56 2014] [error] [client 127.0.0.1] File does not exist: C:/Program Files (x86)/Apache Software Foundation/Apache2.2/htdocs/favicon.ico [Wed Oct 15 14:45:35 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: no\\ element\\ found\\:\\ line\\ 1\\,\\ column\\ 0\r [Wed Oct 15 14:45:35 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: no\\ element\\ found\\:\\ line\\ 1\\,\\ column\\ 0\r [Wed Oct 15 14:47:08 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: no\\ element\\ found\\:\\ line\\ 1\\,\\ column\\ 0\r [Wed Oct 15 14:47:08 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: no\\ element\\ found\\:\\ line\\ 1\\,\\ column\\ 0\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] Premature end of script headers: pywps.cgi [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: XML\\ declaration\\ allowed\\ only\\ at\\ the\\ start\\ of\\ the\\ document\\,\\ line\\ 1\\,\\ column\\ 118\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: XML\\ declaration\\ allowed\\ only\\ at\\ the\\ start\\ of\\ the\\ document\\,\\ line\\ 1\\,\\ column\\ 118\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] Traceback (most recent call last):\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] File "C:/Program Files (x86)/Apache Software Foundation/Apache2.2/cgi-bin/pywps.cgi", line 11, in <module>\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] import wps\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] File "C:/pywps\\wps.py", line 100, in <module>\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] wps.parser.isSoapExecute)\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\response.py", line 40, in response\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] response = soap.getResponse(response,soapVersion,isSoapExecute,isPromoteStatus)\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\Soap.py", line 405, in getResponse\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] return self.doSOAPFault(exceptionReportTree,soapVersion)\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\Soap.py", line 345, in doSOAPFault\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] if (int(soapVersion)==11):#\r [Wed Oct 15 14:50:52 2014] [error] [client 127.0.0.1] TypeError: int() argument must be a string or a number, not 'NoneType'\r [Wed Oct 15 14:53:52 2014] [error] [client 127.0.0.1] File does not exist: C:/Program Files (x86)/Apache Software Foundation/Apache2.2/htdocs/favicon.ico [Wed Oct 15 14:53:52 2014] [error] [client 127.0.0.1] File does not exist: C:/Program Files (x86)/Apache Software Foundation/Apache2.2/htdocs/favicon.ico [Wed Oct 15 15:01:55 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: no\\ element\\ found\\:\\ line\\ 1\\,\\ column\\ 0\r [Wed Oct 15 15:01:55 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: no\\ element\\ found\\:\\ line\\ 1\\,\\ column\\ 0\r [Wed Oct 15 15:01:56 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: no\\ element\\ found\\:\\ line\\ 1\\,\\ column\\ 0\r [Wed Oct 15 15:01:56 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: no\\ element\\ found\\:\\ line\\ 1\\,\\ column\\ 0\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] Premature end of script headers: pywps.cgi [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: XML\\ declaration\\ allowed\\ only\\ at\\ the\\ start\\ of\\ the\\ document\\,\\ line\\ 1\\,\\ column\\ 118\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] PyWPS NoApplicableCode: Locator: None; Value: XML\\ declaration\\ allowed\\ only\\ at\\ the\\ start\\ of\\ the\\ document\\,\\ line\\ 1\\,\\ column\\ 118\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] Traceback (most recent call last):\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] File "C:/Program Files (x86)/Apache Software Foundation/Apache2.2/cgi-bin/pywps.cgi", line 11, in <module>\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] import wps\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] File "C:/pywps\\wps.py", line 100, in <module>\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] wps.parser.isSoapExecute)\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\response.py", line 40, in response\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] response = soap.getResponse(response,soapVersion,isSoapExecute,isPromoteStatus)\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\Soap.py", line 405, in getResponse\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] return self.doSOAPFault(exceptionReportTree,soapVersion)\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] File "C:/pywps\\pywps\\Soap.py", line 345, in doSOAPFault\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] if (int(soapVersion)==11):#\r [Wed Oct 15 15:03:52 2014] [error] [client 127.0.0.1] TypeError: int() argument must be a string or a number, not 'NoneType'\r |
|
From: Alan W. <ala...@ma...> - 2014-10-14 18:45:16
|
Thanks Deniz, The important bit was: POST /cgi-bin/pywps.cgi? HTTP/1.0 Content-Type: text/xml; charset=utf-8 Accept: application/soap+xml, application/dime, multipart/related, text/* User-Agent: Axis/1.4 Host: localhost Cache-Control: no-cache Pragma: no-cache SOAPAction: "http://localhost/cgi-bin/pywps.cgi?/ExecuteProcess_ogrbuffer" Content-Length: 1546 <?xml version="1.0" encoding="UTF-8"?><soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><soapenv:Body><ns1:ExecuteProcess_ogrbuffer xmlns:ns1="http://www.opengis.net/wps/1.0.0"><data xmlns=""><?xml version="1.0" encoding="UTF-8"?> <ogr:FeatureCollection xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://ogr.maptools.org/ singlePoint.xsd" xmlns:ogr="http://ogr.maptools.org/" xmlns:gml="http://www.opengis.net/gml"> <gml:boundedBy> <gml:Box> <gml:coord><gml:X>348757.095296754</gml:X><gml:Y>239942.9447343307</gml:Y></gml:coord> <gml:coord><gml:X>348757.095296754</gml:X><gml:Y>239942.9447343307</gml:Y></gml:coord> </gml:Box> </gml:boundedBy> <gml:featureMember> <ogr:singlePoint fid="F0"> <ogr:geometryProperty><gml:Point><gml:coordinates>348757.095296754036099,239942.944734330725623,741.989222523751437</gml:coordinates></gml:Point></ogr:geometryProperty> <ogr:cat>1</ogr:cat> </ogr:singlePoint> </gml:featureMember> </ogr:FeatureCollection></data><size xmlns="">0.5</size></ns1:ExecuteProcess_ogrbuffer></soapenv:Body></soapenv:Envelope> I was worried that it would not be encoded correctly but it looks valid to me. So we need to check with Jorge if that is what _should_ be sent for an XML file. Are there logs from your WPS server saying what it receives and what errors it detected? It only told Taverna that: The server encountered an internal error or misconfiguration and was unable to complete your request Alan |
|
From: Deniz .. <dul...@ho...> - 2014-10-14 18:28:29
|
Alan, are these parts enough? If not, how can I send full files? There is a limit for file transfering. Is there any other error file I should send?
Thank you,
Deniz
The last two log files:
log 3:
WARN 2014-09-30 21:41:13,479 (org.biomoby.shared.MobyDataType:129) - Cannot parse MOBY Datatype Ontology: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:41:13,479 (System.err:139) - org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:41:13,479 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:257)
ERROR 2014-09-30 21:41:13,480 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.getDataTypes(CentralDigestCachedImpl.java:785)
ERROR 2014-09-30 21:41:13,480 (System.err:139) - at org.biomoby.shared.MobyDataType.getDataType(MobyDataType.java:122)
ERROR 2014-09-30 21:41:13,480 (System.err:139) - at org.biomoby.shared.MobyDataType.getParent(MobyDataType.java:264)
ERROR 2014-09-30 21:41:13,480 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.findDatatypeDescriptions(BiomobyQueryHelper.java:258)
ERROR 2014-09-30 21:41:13,481 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.findServiceDescriptionsAsync(BiomobyQueryHelper.java:221)
ERROR 2014-09-30 21:41:13,481 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider.findServiceDescriptionsAsync(BiomobyServiceProvider.java:60)
ERROR 2014-09-30 21:41:13,481 (System.err:139) - at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
ERROR 2014-09-30 21:41:13,481 (System.err:139) - Caused by: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:41:13,482 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
ERROR 2014-09-30 21:41:13,482 (System.err:139) - at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1807)
ERROR 2014-09-30 21:41:13,482 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.getResourceURL(CentralDigestCachedImpl.java:438)
ERROR 2014-09-30 21:41:13,482 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:140)
ERROR 2014-09-30 21:41:13,483 (System.err:139) - ... 7 more
ERROR 2014-09-30 21:41:13,483 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:41:13,483 (System.err:139) - at org.apache.axis.AxisFault.makeFault(AxisFault.java:101)
ERROR 2014-09-30 21:41:13,483 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154)
ERROR 2014-09-30 21:41:13,484 (System.err:139) - at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
ERROR 2014-09-30 21:41:13,484 (System.err:139) - at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
ERROR 2014-09-30 21:41:13,484 (System.err:139) - at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
ERROR 2014-09-30 21:41:13,484 (System.err:139) - at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
ERROR 2014-09-30 21:41:13,484 (System.err:139) - at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
ERROR 2014-09-30 21:41:13,485 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2767)
ERROR 2014-09-30 21:41:13,485 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2443)
ERROR 2014-09-30 21:41:13,485 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2366)
ERROR 2014-09-30 21:41:13,485 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247)
ERROR 2014-09-30 21:41:13,486 (System.err:139) - ... 10 more
ERROR 2014-09-30 21:41:13,486 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:41:13,486 (System.err:139) - at java.net.DualStackPlainSocketImpl.connect0(Native Method)
ERROR 2014-09-30 21:41:13,486 (System.err:139) - at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:79)
ERROR 2014-09-30 21:41:13,487 (System.err:139) - at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
ERROR 2014-09-30 21:41:13,487 (System.err:139) - at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
ERROR 2014-09-30 21:41:13,487 (System.err:139) - at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
ERROR 2014-09-30 21:41:13,487 (System.err:139) - at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
ERROR 2014-09-30 21:41:13,488 (System.err:139) - at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
ERROR 2014-09-30 21:41:13,488 (System.err:139) - at java.net.Socket.connect(Socket.java:579)
ERROR 2014-09-30 21:41:13,488 (System.err:139) - at java.net.Socket.connect(Socket.java:528)
ERROR 2014-09-30 21:41:13,488 (System.err:139) - at java.net.Socket.<init>(Socket.java:425)
ERROR 2014-09-30 21:41:13,488 (System.err:139) - at java.net.Socket.<init>(Socket.java:208)
ERROR 2014-09-30 21:41:13,489 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:149)
ERROR 2014-09-30 21:41:13,489 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:120)
ERROR 2014-09-30 21:41:13,489 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191)
ERROR 2014-09-30 21:41:13,489 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404)
ERROR 2014-09-30 21:41:13,490 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138)
ERROR 2014-09-30 21:41:13,490 (System.err:139) - ... 19 more
DEBUG 2014-09-30 21:41:13,500 (org.apache.axis.transport.http.HTTPSender:125) - Enter: HTTPSender::invoke
DEBUG 2014-09-30 21:41:34,508 (org.apache.axis.transport.http.HTTPSender:146) - java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:41:34,512 (org.biomoby.shared.MobyException:86) - ; nested exception is:
java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:41:34,512 (org.biomoby.shared.MobyException:86) - ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
WARN 2014-09-30 21:41:34,513 (org.biomoby.shared.MobyDataType:129) - Cannot parse MOBY Datatype Ontology: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:41:34,513 (System.err:139) - org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:41:34,514 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:257)
ERROR 2014-09-30 21:41:34,514 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.getDataTypes(CentralDigestCachedImpl.java:785)
ERROR 2014-09-30 21:41:34,515 (System.err:139) - at org.biomoby.shared.MobyDataType.getDataType(MobyDataType.java:122)
ERROR 2014-09-30 21:41:34,515 (System.err:139) - at org.biomoby.shared.MobyDataType.getParent(MobyDataType.java:264)
ERROR 2014-09-30 21:41:34,516 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.findDatatypeDescriptions(BiomobyQueryHelper.java:258)
ERROR 2014-09-30 21:41:34,516 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.findServiceDescriptionsAsync(BiomobyQueryHelper.java:221)
ERROR 2014-09-30 21:41:34,516 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider.findServiceDescriptionsAsync(BiomobyServiceProvider.java:60)
ERROR 2014-09-30 21:41:34,517 (System.err:139) - at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
ERROR 2014-09-30 21:41:34,517 (System.err:139) - Caused by: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:41:34,518 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
ERROR 2014-09-30 21:41:34,518 (System.err:139) - at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1807)
ERROR 2014-09-30 21:41:34,518 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.getResourceURL(CentralDigestCachedImpl.java:438)
ERROR 2014-09-30 21:41:34,519 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:140)
ERROR 2014-09-30 21:41:34,519 (System.err:139) - ... 7 more
ERROR 2014-09-30 21:41:34,519 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:41:34,520 (System.err:139) - at org.apache.axis.AxisFault.makeFault(AxisFault.java:101)
ERROR 2014-09-30 21:41:34,520 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154)
ERROR 2014-09-30 21:41:34,521 (System.err:139) - at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
ERROR 2014-09-30 21:41:34,521 (System.err:139) - at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
ERROR 2014-09-30 21:41:34,522 (System.err:139) - at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
ERROR 2014-09-30 21:41:34,522 (System.err:139) - at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
ERROR 2014-09-30 21:41:34,522 (System.err:139) - at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
ERROR 2014-09-30 21:41:34,523 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2767)
ERROR 2014-09-30 21:41:34,523 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2443)
ERROR 2014-09-30 21:41:34,523 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2366)
ERROR 2014-09-30 21:41:34,524 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247)
ERROR 2014-09-30 21:41:34,524 (System.err:139) - ... 10 more
ERROR 2014-09-30 21:41:34,524 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:41:34,525 (System.err:139) - at java.net.DualStackPlainSocketImpl.connect0(Native Method)
ERROR 2014-09-30 21:41:34,526 (System.err:139) - at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:79)
ERROR 2014-09-30 21:41:34,526 (System.err:139) - at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
ERROR 2014-09-30 21:41:34,526 (System.err:139) - at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
ERROR 2014-09-30 21:41:34,527 (System.err:139) - at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
ERROR 2014-09-30 21:41:34,527 (System.err:139) - at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
ERROR 2014-09-30 21:41:34,527 (System.err:139) - at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
ERROR 2014-09-30 21:41:34,527 (System.err:139) - at java.net.Socket.connect(Socket.java:579)
ERROR 2014-09-30 21:41:34,527 (System.err:139) - at java.net.Socket.connect(Socket.java:528)
ERROR 2014-09-30 21:41:34,528 (System.err:139) - at java.net.Socket.<init>(Socket.java:425)
ERROR 2014-09-30 21:41:34,528 (System.err:139) - at java.net.Socket.<init>(Socket.java:208)
ERROR 2014-09-30 21:41:34,528 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:149)
ERROR 2014-09-30 21:41:34,528 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:120)
ERROR 2014-09-30 21:41:34,529 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191)
log 4:
INFO 2014-09-30 16:31:06,930 (net.sf.taverna.t2.workbench.ui.servicepanel.ServiceTreeClickListener:147) - java.lang.String
INFO 2014-09-30 16:31:08,064 (net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProvider:54) - Flushed cache for WSDL http://localhost/pywps.wsdl
INFO 2014-09-30 16:31:18,926 (net.sf.taverna.t2.workbench.helper.HelpCollator:214) - Attempting to register net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2014-09-30 16:31:18,926 (net.sf.taverna.t2.workbench.helper.HelpCollator:227) - Refused to register component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2014-09-30 16:31:22,808 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 16:31:22,812 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 16:31:23,833 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 16:31:27,573 (net.sf.taverna.t2.workbench.helper.HelpCollator:214) - Attempting to register net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2014-09-30 16:31:27,573 (net.sf.taverna.t2.workbench.helper.HelpCollator:227) - Refused to register component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2014-09-30 16:31:34,828 (net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:138) - Updating WSDL service http://localhost/pywps.wsdl
INFO 2014-09-30 16:31:34,828 (net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:138) - Parsing wsdl:http://localhost/pywps.wsdl WSDL service http://localhost/pywps.wsdl
INFO 2014-09-30 16:31:34,866 (net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:138) - Found 19 WSDL operations:http://localhost/pywps.wsdl WSDL service http://localhost/pywps.wsdl
INFO 2014-09-30 16:31:34,866 (net.sf.taverna.t2.workbench.ui.servicepanel.ServicePanel:138) - Found 19 services WSDL service http://localhost/pywps.wsdl
INFO 2014-09-30 16:31:58,727 (net.sf.taverna.t2.workbench.ui.dndhandler.ServiceTransferHandler:119) - Importing a transferable
INFO 2014-09-30 16:31:58,756 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 16:32:02,947 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 16:32:02,950 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 16:32:06,908 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 16:32:06,913 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 16:32:06,931 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 16:32:10,008 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 16:32:10,011 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 16:32:10,013 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 16:32:14,931 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 16:32:14,935 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 16:32:14,937 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 16:32:17,571 (net.sf.taverna.t2.workbench.edits.impl.EditManagerImpl:153) - Undoing an edit
INFO 2014-09-30 16:32:17,589 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 16:32:17,592 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 16:32:17,594 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 16:32:18,337 (net.sf.taverna.t2.workbench.edits.impl.EditManagerImpl:153) - Undoing an edit
INFO 2014-09-30 16:32:18,352 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 16:32:18,355 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 16:32:18,357 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 16:32:22,201 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 16:32:22,203 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 16:32:22,204 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 16:32:25,137 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 16:32:25,139 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 16:32:25,141 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 16:32:27,329 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 16:32:27,332 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 16:32:27,333 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 16:32:36,664 (net.sf.taverna.t2.workbench.helper.HelpCollator:214) - Attempting to register net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2014-09-30 16:32:36,664 (net.sf.taverna.t2.workbench.helper.HelpCollator:227) - Refused to register component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2014-09-30 16:32:36,669 (net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker:94) - Returning cached report for endpoint http://localhost/pywps.wsdl: OK Responded OK {endpoint=http://localhost/pywps.wsdl}
INFO 2014-09-30 16:32:36,670 (net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker:94) - Returning cached report for endpoint http://localhost/cgi-bin/pywps.cgi?: OK Responded OK {endpoint=http://localhost/cgi-bin/pywps.cgi?}
INFO 2014-09-30 16:32:53,178 (net.sf.taverna.t2.workbench.helper.HelpCollator:214) - Attempting to register net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2014-09-30 16:32:53,179 (net.sf.taverna.t2.workbench.helper.HelpCollator:227) - Refused to register component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2014-09-30 16:32:53,184 (net.sf.taverna.t2.reference.ui.CopyWorkflowSwingWorker:50) - CopyWorkflowSwingWorker: copying of the workflow started.
INFO 2014-09-30 16:32:53,319 (net.sf.taverna.t2.reference.ui.CopyWorkflowSwingWorker:52) - CopyWorkflowSwingWorker: copying of the workflow finished.
INFO 2014-09-30 16:32:55,361 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 16:32:55,363 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 16:32:55,364 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 16:32:55,494 (net.sf.taverna.t2.provenance.lineageservice.EventProcessor:204) - new workflow structure with ID 92e533de-5b8c-4c5d-920b-dc079f2bd005
DEBUG 2014-09-30 16:32:55,785 (org.apache.axis.transport.http.HTTPSender:125) - Enter: HTTPSender::invoke
DEBUG 2014-09-30 16:32:55,787 (org.apache.axis.transport.http.HTTPSender:484) - XML sent:
DEBUG 2014-09-30 16:32:55,787 (org.apache.axis.transport.http.HTTPSender:485) - ---------------------------------------------------
DEBUG 2014-09-30 16:32:55,787 (org.apache.axis.transport.http.HTTPSender:519) - POST /cgi-bin/pywps.cgi? HTTP/1.0
Content-Type: text/xml; charset=utf-8
Accept: application/soap+xml, application/dime, multipart/related, text/*
User-Agent: Axis/1.4
Host: localhost
Cache-Control: no-cache
Pragma: no-cache
SOAPAction: "http://localhost/cgi-bin/pywps.cgi?/ExecuteProcess_ogrbuffer"
Content-Length: 1546
<?xml version="1.0" encoding="UTF-8"?><soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><soapenv:Body><ns1:ExecuteProcess_ogrbuffer xmlns:ns1="http://www.opengis.net/wps/1.0.0"><data xmlns=""><?xml version="1.0" encoding="UTF-8"?>
<ogr:FeatureCollection xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://ogr.maptools.org/ singlePoint.xsd" xmlns:ogr="http://ogr.maptools.org/" xmlns:gml="http://www.opengis.net/gml">
<gml:boundedBy>
<gml:Box>
<gml:coord><gml:X>348757.095296754</gml:X><gml:Y>239942.9447343307</gml:Y></gml:coord>
<gml:coord><gml:X>348757.095296754</gml:X><gml:Y>239942.9447343307</gml:Y></gml:coord>
</gml:Box>
</gml:boundedBy>
<gml:featureMember>
<ogr:singlePoint fid="F0">
<ogr:geometryProperty><gml:Point><gml:coordinates>348757.095296754036099,239942.944734330725623,741.989222523751437</gml:coordinates></gml:Point></ogr:geometryProperty>
<ogr:cat>1</ogr:cat>
</ogr:singlePoint>
</gml:featureMember>
</ogr:FeatureCollection></data><size xmlns="">0.5</size></ns1:ExecuteProcess_ogrbuffer></soapenv:Body></soapenv:Envelope>
DEBUG 2014-09-30 16:32:55,986 (org.apache.axis.transport.http.HTTPSender:627) - HTTP/1.1 500 Internal Server Error
DEBUG 2014-09-30 16:32:55,986 (org.apache.axis.transport.http.HTTPSender:627) - Date Tue, 30 Sep 2014 13:32:55 GMT
DEBUG 2014-09-30 16:32:55,986 (org.apache.axis.transport.http.HTTPSender:627) - Server Apache/2.2.25 (Win32)
DEBUG 2014-09-30 16:32:55,986 (org.apache.axis.transport.http.HTTPSender:627) - Content-Length 534
DEBUG 2014-09-30 16:32:55,986 (org.apache.axis.transport.http.HTTPSender:627) - Connection close
DEBUG 2014-09-30 16:32:55,986 (org.apache.axis.transport.http.HTTPSender:627) - Content-Type text/html; charset=iso-8859-1
DEBUG 2014-09-30 16:32:55,987 (org.apache.axis.transport.http.HTTPSender:146) - (500)Internal Server Error
ERROR 2014-09-30 16:32:55,988 (net.sf.taverna.t2.activities.wsdl.WSDLActivity:318) - Error invoking WSDL service ExecuteProcess_ogrbuffer
AxisFault
faultCode: {http://xml.apache.org/axis/}HTTP
faultSubcode:
faultString: (500)Internal Server Error
faultActor:
faultNode:
faultDetail:
{}:return code: 500
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>500 Internal Server Error</title>
</head><body>
<h1>Internal Server Error</h1>
<p>The server encountered an internal error or
misconfiguration and was unable to complete
your request.</p>
<p>Please contact the server administrator,
ad...@SE... and inform them of the time the error occurred,
and anything you might have done that may have
caused the error.</p>
<p>More information about this error may be available
in the server error log.</p>
</body></html>
{http://xml.apache.org/axis/}HttpErrorCode:500
(500)Internal Server Error
at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:744)
at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:144)
at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:1910)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invokeCall(WSDLSOAPInvoker.java:198)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invoke(WSDLSOAPInvoker.java:139)
at net.sf.taverna.t2.activities.wsdl.T2WSDLSOAPInvoker.invoke(T2WSDLSOAPInvoker.java:281)
at net.sf.taverna.t2.activities.wsdl.WSDLActivity$1.run(WSDLActivity.java:289)
at java.lang.Thread.run(Thread.java:724)
WARN 2014-09-30 16:32:55,988 (net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke:236) - Failed (INVOCATION) invoking net.sf.taverna.t2.activities.wsdl.WSDLActivity@50105fcd for job DispatchJobEvent facade7:Workflow1:ExecuteProcess_ogrbuffer[]: An error occurred invoking the WSDL service
AxisFault
faultCode: {http://xml.apache.org/axis/}HTTP
faultSubcode:
faultString: (500)Internal Server Error
faultActor:
faultNode:
faultDetail:
{}:return code: 500
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>500 Internal Server Error</title>
</head><body>
<h1>Internal Server Error</h1>
<p>The server encountered an internal error or
misconfiguration and was unable to complete
your request.</p>
<p>Please contact the server administrator,
ad...@SE... and inform them of the time the error occurred,
and anything you might have done that may have
caused the error.</p>
<p>More information about this error may be available
in the server error log.</p>
</body></html>
{http://xml.apache.org/axis/}HttpErrorCode:500
(500)Internal Server Error
at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:744)
at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:144)
at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:1910)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invokeCall(WSDLSOAPInvoker.java:198)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invoke(WSDLSOAPInvoker.java:139)
at net.sf.taverna.t2.activities.wsdl.T2WSDLSOAPInvoker.invoke(T2WSDLSOAPInvoker.java:281)
at net.sf.taverna.t2.activities.wsdl.WSDLActivity$1.run(WSDLActivity.java:289)
at java.lang.Thread.run(Thread.java:724)
WARN 2014-09-30 16:47:12,608 (net.sf.taverna.raven.plugins.PluginManager:85) - Could not fetch plugins from non-existing host
java.net.UnknownHostException: http
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:579)
at java.net.Socket.connect(Socket.java:528)
at java.net.Socket.<init>(Socket.java:425)
at java.net.Socket.<init>(Socket.java:280)
at org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:80)
at org.apache.commons.httpclient.protocol.ControllerThreadSocketFactory$1.doit(ControllerThreadSocketFactory.java:91)
at org.apache.commons.httpclient.protocol.ControllerThreadSocketFactory$SocketTask.run(ControllerThreadSocketFactory.java:158)
at java.lang.Thread.run(Thread.java:724)
WARN 2014-09-30 17:17:22,908 (net.sf.taverna.raven.plugins.PluginManager:85) - Could not fetch plugins from non-existing host
java.net.UnknownHostException: http
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:579)
at java.net.Socket.connect(Socket.java:528)
at java.net.Socket.<init>(Socket.java:425)
at java.net.Socket.<init>(Socket.java:280)
at org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:80)
at org.apache.commons.httpclient.protocol.ControllerThreadSocketFactory$1.doit(ControllerThreadSocketFactory.java:91)
at org.apache.commons.httpclient.protocol.ControllerThreadSocketFactory$SocketTask.run(ControllerThreadSocketFactory.java:158)
at java.lang.Thread.run(Thread.java:724)
WARN 2014-09-30 17:47:33,226 (net.sf.taverna.raven.plugins.PluginManager:85) - Could not fetch plugins from non-existing host
java.net.UnknownHostException: http
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:579)
at java.net.Socket.connect(Socket.java:528)
at java.net.Socket.<init>(Socket.java:425)
at java.net.Socket.<init>(Socket.java:280)
at org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:80)
at org.apache.commons.httpclient.protocol.ControllerThreadSocketFactory$1.doit(ControllerThreadSocketFactory.java:91)
at org.apache.commons.httpclient.protocol.ControllerThreadSocketFactory$SocketTask.run(ControllerThreadSocketFactory.java:158)
at java.lang.Thread.run(Thread.java:724)
INFO 2014-09-30 18:09:04,123 (net.sf.taverna.t2.workbench.ui.servicepanel.ServiceTreeClickListener:147) - net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription
INFO 2014-09-30 18:09:04,129 (net.sf.taverna.t2.workbench.helper.HelpCollator:198) - Looking for id: net.sf.taverna.t2.activities.wsdl.WSDLActivity
WARN 2014-09-30 18:17:43,299 (net.sf.taverna.raven.plugins.PluginManager:85) - Could not fetch plugins from non-existing host
java.net.UnknownHostException: http
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:579)
at java.net.Socket.connect(Socket.java:528)
at java.net.Socket.<init>(Socket.java:425)
at java.net.Socket.<init>(Socket.java:280)
at org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:80)
at org.apache.commons.httpclient.protocol.ControllerThreadSocketFactory$1.doit(ControllerThreadSocketFactory.java:91)
at org.apache.commons.httpclient.protocol.ControllerThreadSocketFactory$SocketTask.run(ControllerThreadSocketFactory.java:158)
at java.lang.Thread.run(Thread.java:724)
INFO 2014-09-30 18:33:04,427 (net.sf.taverna.t2.workbench.helper.HelpCollator:214) - Attempting to register net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2014-09-30 18:33:04,427 (net.sf.taverna.t2.workbench.helper.HelpCollator:227) - Refused to register component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2014-09-30 18:33:18,451 (net.sf.taverna.t2.workbench.helper.HelpCollator:214) - Attempting to register net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2014-09-30 18:33:18,451 (net.sf.taverna.t2.workbench.helper.HelpCollator:227) - Refused to register component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2014-09-30 18:33:18,454 (net.sf.taverna.t2.reference.ui.CopyWorkflowSwingWorker:50) - CopyWorkflowSwingWorker: copying of the workflow started.
INFO 2014-09-30 18:33:18,593 (net.sf.taverna.t2.reference.ui.CopyWorkflowSwingWorker:52) - CopyWorkflowSwingWorker: copying of the workflow finished.
INFO 2014-09-30 18:33:20,885 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 18:33:20,888 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 18:33:20,890 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
DEBUG 2014-09-30 18:33:21,805 (org.apache.axis.transport.http.HTTPSender:125) - Enter: HTTPSender::invoke
DEBUG 2014-09-30 18:33:21,807 (org.apache.axis.transport.http.HTTPSender:484) - XML sent:
DEBUG 2014-09-30 18:33:21,807 (org.apache.axis.transport.http.HTTPSender:485) - ---------------------------------------------------
DEBUG 2014-09-30 18:33:21,808 (org.apache.axis.transport.http.HTTPSender:519) - POST /cgi-bin/pywps.cgi? HTTP/1.0
Content-Type: text/xml; charset=utf-8
Accept: application/soap+xml, application/dime, multipart/related, text/*
User-Agent: Axis/1.4
Host: localhost
Cache-Control: no-cache
Pragma: no-cache
SOAPAction: "http://localhost/cgi-bin/pywps.cgi?/ExecuteProcess_ogrbuffer"
Content-Length: 1545
<?xml version="1.0" encoding="UTF-8"?><soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><soapenv:Body><ns1:ExecuteProcess_ogrbuffer xmlns:ns1="http://www.opengis.net/wps/1.0.0"><data xmlns=""><?xml version="1.0" encoding="UTF-8"?>
<ogr:FeatureCollection xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://ogr.maptools.org/ singlePoint.xsd" xmlns:ogr="http://ogr.maptools.org/" xmlns:gml="http://www.opengis.net/gml">
<gml:boundedBy>
<gml:Box>
<gml:coord><gml:X>348757.095296754</gml:X><gml:Y>239942.9447343307</gml:Y></gml:coord>
<gml:coord><gml:X>348757.095296754</gml:X><gml:Y>239942.9447343307</gml:Y></gml:coord>
</gml:Box>
</gml:boundedBy>
<gml:featureMember>
<ogr:singlePoint fid="F0">
<ogr:geometryProperty><gml:Point><gml:coordinates>348757.095296754036099,239942.944734330725623,741.989222523751437</gml:coordinates></gml:Point></ogr:geometryProperty>
<ogr:cat>1</ogr:cat>
</ogr:singlePoint>
</gml:featureMember>
</ogr:FeatureCollection></data><size xmlns="">10</size></ns1:ExecuteProcess_ogrbuffer></soapenv:Body></soapenv:Envelope>
DEBUG 2014-09-30 18:33:22,009 (org.apache.axis.transport.http.HTTPSender:627) - HTTP/1.1 500 Internal Server Error
DEBUG 2014-09-30 18:33:22,009 (org.apache.axis.transport.http.HTTPSender:627) - Date Tue, 30 Sep 2014 15:33:21 GMT
DEBUG 2014-09-30 18:33:22,009 (org.apache.axis.transport.http.HTTPSender:627) - Server Apache/2.2.25 (Win32)
DEBUG 2014-09-30 18:33:22,009 (org.apache.axis.transport.http.HTTPSender:627) - Content-Length 534
DEBUG 2014-09-30 18:33:22,009 (org.apache.axis.transport.http.HTTPSender:627) - Connection close
DEBUG 2014-09-30 18:33:22,009 (org.apache.axis.transport.http.HTTPSender:627) - Content-Type text/html; charset=iso-8859-1
DEBUG 2014-09-30 18:33:22,010 (org.apache.axis.transport.http.HTTPSender:146) - (500)Internal Server Error
ERROR 2014-09-30 18:33:22,010 (net.sf.taverna.t2.activities.wsdl.WSDLActivity:318) - Error invoking WSDL service ExecuteProcess_ogrbuffer
AxisFault
faultCode: {http://xml.apache.org/axis/}HTTP
faultSubcode:
faultString: (500)Internal Server Error
faultActor:
faultNode:
faultDetail:
{}:return code: 500
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>500 Internal Server Error</title>
</head><body>
<h1>Internal Server Error</h1>
<p>The server encountered an internal error or
misconfiguration and was unable to complete
your request.</p>
<p>Please contact the server administrator,
ad...@SE... and inform them of the time the error occurred,
and anything you might have done that may have
caused the error.</p>
<p>More information about this error may be available
in the server error log.</p>
</body></html>
{http://xml.apache.org/axis/}HttpErrorCode:500
(500)Internal Server Error
at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:744)
at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:144)
at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:1910)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invokeCall(WSDLSOAPInvoker.java:198)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invoke(WSDLSOAPInvoker.java:139)
at net.sf.taverna.t2.activities.wsdl.T2WSDLSOAPInvoker.invoke(T2WSDLSOAPInvoker.java:281)
at net.sf.taverna.t2.activities.wsdl.WSDLActivity$1.run(WSDLActivity.java:289)
at java.lang.Thread.run(Thread.java:724)
WARN 2014-09-30 18:33:22,010 (net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke:236) - Failed (INVOCATION) invoking net.sf.taverna.t2.activities.wsdl.WSDLActivity@42edf3a9 for job DispatchJobEvent facade8:Workflow1:ExecuteProcess_ogrbuffer[]: An error occurred invoking the WSDL service
AxisFault
faultCode: {http://xml.apache.org/axis/}HTTP
faultSubcode:
faultString: (500)Internal Server Error
faultActor:
faultNode:
faultDetail:
{}:return code: 500
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>500 Internal Server Error</title>
</head><body>
<h1>Internal Server Error</h1>
<p>The server encountered an internal error or
misconfiguration and was unable to complete
your request.</p>
<p>Please contact the server administrator,
ad...@SE... and inform them of the time the error occurred,
and anything you might have done that may have
caused the error.</p>
<p>More information about this error may be available
in the server error log.</p>
</body></html>
{http://xml.apache.org/axis/}HttpErrorCode:500
(500)Internal Server Error
at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:744)
at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:144)
at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:1910)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invokeCall(WSDLSOAPInvoker.java:198)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invoke(WSDLSOAPInvoker.java:139)
at net.sf.taverna.t2.activities.wsdl.T2WSDLSOAPInvoker.invoke(T2WSDLSOAPInvoker.java:281)
at net.sf.taverna.t2.activities.wsdl.WSDLActivity$1.run(WSDLActivity.java:289)
at java.lang.Thread.run(Thread.java:724)
INFO 2014-09-30 18:34:06,367 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 18:34:06,371 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 18:34:10,674 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 18:34:10,677 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 18:34:12,659 (net.sf.taverna.t2.workbench.helper.HelpCollator:214) - Attempting to register net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2014-09-30 18:34:12,659 (net.sf.taverna.t2.workbench.helper.HelpCollator:227) - Refused to register component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2014-09-30 18:34:14,834 (net.sf.taverna.t2.workbench.helper.HelpCollator:214) - Attempting to register net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2014-09-30 18:34:14,834 (net.sf.taverna.t2.workbench.helper.HelpCollator:227) - Refused to register component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2014-09-30 18:34:14,838 (net.sf.taverna.t2.reference.ui.CopyWorkflowSwingWorker:50) - CopyWorkflowSwingWorker: copying of the workflow started.
INFO 2014-09-30 18:34:14,952 (net.sf.taverna.t2.reference.ui.CopyWorkflowSwingWorker:52) - CopyWorkflowSwingWorker: copying of the workflow finished.
INFO 2014-09-30 18:34:16,956 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 18:34:16,958 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 18:34:17,086 (net.sf.taverna.t2.provenance.lineageservice.EventProcessor:204) - new workflow structure with ID 255d917c-f23f-498a-9634-c5dc8030a2d9
DEBUG 2014-09-30 18:34:17,370 (org.apache.axis.transport.http.HTTPSender:125) - Enter: HTTPSender::invoke
DEBUG 2014-09-30 18:34:17,372 (org.apache.axis.transport.http.HTTPSender:484) - XML sent:
DEBUG 2014-09-30 18:34:17,372 (org.apache.axis.transport.http.HTTPSender:485) - ---------------------------------------------------
DEBUG 2014-09-30 18:34:17,372 (org.apache.axis.transport.http.HTTPSender:519) - POST /cgi-bin/pywps.cgi? HTTP/1.0
Content-Type: text/xml; charset=utf-8
Accept: application/soap+xml, application/dime, multipart/related, text/*
User-Agent: Axis/1.4
Host: localhost
Cache-Control: no-cache
Pragma: no-cache
SOAPAction: "http://localhost/cgi-bin/pywps.cgi?/ExecuteProcess_ogrbuffer"
Content-Length: 1545
<?xml version="1.0" encoding="UTF-8"?><soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><soapenv:Body><ns1:ExecuteProcess_ogrbuffer xmlns:ns1="http://www.opengis.net/wps/1.0.0"><data xmlns=""><?xml version="1.0" encoding="UTF-8"?>
<ogr:FeatureCollection xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://ogr.maptools.org/ singlePoint.xsd" xmlns:ogr="http://ogr.maptools.org/" xmlns:gml="http://www.opengis.net/gml">
<gml:boundedBy>
<gml:Box>
<gml:coord><gml:X>348757.095296754</gml:X><gml:Y>239942.9447343307</gml:Y></gml:coord>
<gml:coord><gml:X>348757.095296754</gml:X><gml:Y>239942.9447343307</gml:Y></gml:coord>
</gml:Box>
</gml:boundedBy>
<gml:featureMember>
<ogr:singlePoint fid="F0">
<ogr:geometryProperty><gml:Point><gml:coordinates>348757.095296754036099,239942.944734330725623,741.989222523751437</gml:coordinates></gml:Point></ogr:geometryProperty>
<ogr:cat>1</ogr:cat>
</ogr:singlePoint>
</gml:featureMember>
</ogr:FeatureCollection></data><size xmlns="">10</size></ns1:ExecuteProcess_ogrbuffer></soapenv:Body></soapenv:Envelope>
DEBUG 2014-09-30 18:34:17,564 (org.apache.axis.transport.http.HTTPSender:627) - HTTP/1.1 500 Internal Server Error
DEBUG 2014-09-30 18:34:17,564 (org.apache.axis.transport.http.HTTPSender:627) - Date Tue, 30 Sep 2014 15:34:17 GMT
DEBUG 2014-09-30 18:34:17,564 (org.apache.axis.transport.http.HTTPSender:627) - Server Apache/2.2.25 (Win32)
DEBUG 2014-09-30 18:34:17,564 (org.apache.axis.transport.http.HTTPSender:627) - Content-Length 534
DEBUG 2014-09-30 18:34:17,564 (org.apache.axis.transport.http.HTTPSender:627) - Connection close
DEBUG 2014-09-30 18:34:17,564 (org.apache.axis.transport.http.HTTPSender:627) - Content-Type text/html; charset=iso-8859-1
DEBUG 2014-09-30 18:34:17,565 (org.apache.axis.transport.http.HTTPSender:146) - (500)Internal Server Error
ERROR 2014-09-30 18:34:17,565 (net.sf.taverna.t2.activities.wsdl.WSDLActivity:318) - Error invoking WSDL service ExecuteProcess_ogrbuffer
AxisFault
faultCode: {http://xml.apache.org/axis/}HTTP
faultSubcode:
faultString: (500)Internal Server Error
faultActor:
faultNode:
faultDetail:
{}:return code: 500
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>500 Internal Server Error</title>
</head><body>
<h1>Internal Server Error</h1>
<p>The server encountered an internal error or
misconfiguration and was unable to complete
your request.</p>
<p>Please contact the server administrator,
ad...@SE... and inform them of the time the error occurred,
and anything you might have done that may have
caused the error.</p>
<p>More information about this error may be available
in the server error log.</p>
</body></html>
{http://xml.apache.org/axis/}HttpErrorCode:500
(500)Internal Server Error
at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:744)
at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:144)
at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:1910)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invokeCall(WSDLSOAPInvoker.java:198)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invoke(WSDLSOAPInvoker.java:139)
at net.sf.taverna.t2.activities.wsdl.T2WSDLSOAPInvoker.invoke(T2WSDLSOAPInvoker.java:281)
at net.sf.taverna.t2.activities.wsdl.WSDLActivity$1.run(WSDLActivity.java:289)
at java.lang.Thread.run(Thread.java:724)
WARN 2014-09-30 18:34:17,566 (net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke:236) - Failed (INVOCATION) invoking net.sf.taverna.t2.activities.wsdl.WSDLActivity@5469a083 for job DispatchJobEvent facade9:Workflow1:ExecuteProcess_ogrbuffer[]: An error occurred invoking the WSDL service
AxisFault
faultCode: {http://xml.apache.org/axis/}HTTP
faultSubcode:
faultString: (500)Internal Server Error
faultActor:
faultNode:
faultDetail:
{}:return code: 500
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>500 Internal Server Error</title>
</head><body>
<h1>Internal Server Error</h1>
<p>The server encountered an internal error or
misconfiguration and was unable to complete
your request.</p>
<p>Please contact the server administrator,
ad...@SE... and inform them of the time the error occurred,
and anything you might have done that may have
caused the error.</p>
<p>More information about this error may be available
in the server error log.</p>
</body></html>
{http://xml.apache.org/axis/}HttpErrorCode:500
(500)Internal Server Error
at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:744)
at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:144)
at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:1910)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invokeCall(WSDLSOAPInvoker.java:198)
at net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invoke(WSDLSOAPInvoker.java:139)
at net.sf.taverna.t2.activities.wsdl.T2WSDLSOAPInvoker.invoke(T2WSDLSOAPInvoker.java:281)
at net.sf.taverna.t2.activities.wsdl.WSDLActivity$1.run(WSDLActivity.java:289)
at java.lang.Thread.run(Thread.java:724)
INFO 2014-09-30 18:35:33,550 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 18:35:33,552 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 18:35:33,565 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor XPath_Servicehas iteration setting 0
INFO 2014-09-30 18:35:33,718 (net.sf.taverna.t2.workbench.helper.HelpCollator:214) - Attempting to register net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2014-09-30 18:35:33,718 (net.sf.taverna.t2.workbench.helper.HelpCollator:227) - Refused to register component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2014-09-30 18:35:57,486 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 18:35:57,490 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 18:35:57,493 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor XPath_Servicehas iteration setting 0
INFO 2014-09-30 18:45:37,419 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 18:45:37,423 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 18:45:37,425 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor XPath_Servicehas iteration setting 0
INFO 2014-09-30 18:45:37,427 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 18:45:41,483 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 18:45:41,485 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 18:45:41,488 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor XPath_Servicehas iteration setting 0
INFO 2014-09-30 18:45:41,489 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 18:45:49,745 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 18:45:49,746 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 18:45:49,749 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor XPath_Servicehas iteration setting 0
INFO 2014-09-30 18:45:49,750 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 18:45:52,245 (net.sf.taverna.t2.workbench.helper.HelpCollator:214) - Attempting to register net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2014-09-30 18:45:52,245 (net.sf.taverna.t2.workbench.helper.HelpCollator:227) - Refused to register component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2014-09-30 18:45:57,055 (net.sf.taverna.t2.workbench.helper.HelpCollator:214) - Attempting to register net.sf.taverna.t2.workbench.ui.impl.Workbench-dialog
INFO 2014-09-30 18:45:57,055 (net.sf.taverna.t2.workbench.helper.HelpCollator:227) - Refused to register component as net.sf.taverna.t2.workbench.ui.impl.workbench-dialog - not in map
INFO 2014-09-30 18:45:57,058 (net.sf.taverna.t2.reference.ui.CopyWorkflowSwingWorker:50) - CopyWorkflowSwingWorker: copying of the workflow started.
INFO 2014-09-30 18:45:57,223 (net.sf.taverna.t2.reference.ui.CopyWorkflowSwingWorker:52) - CopyWorkflowSwingWorker: copying of the workflow finished.
INFO 2014-09-30 18:45:59,094 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbufferhas iteration setting 0
INFO 2014-09-30 18:45:59,096 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_DataInputshas iteration setting 0
INFO 2014-09-30 18:45:59,098 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor XPath_Servicehas iteration setting 0
INFO 2014-09-30 18:45:59,100 (net.sf.taverna.t2.workbench.models.graph.GraphController:1060) - processor ExecuteProcess_ogrbuffer_ProcessOutputshas iteration setting 0
INFO 2014-09-30 18:45:59,254 (net.sf.taverna.t2.provenance.lineageservice.EventProcessor:204) - new workflow structure with ID b039f6de-e587-4443-9352-5e06bd21d711
DEBUG 2014-09-30 18:45:59,552 (org.apache.axis.transport.http.HTTPSender:125) - Enter: HTTPSender::invoke
DEBUG 2014-09-30 18:45:59,553 (org.apache.axis.transport.http.HTTPSender:484) - XML sent:
DEBUG 2014-09-30 18:45:59,553 (org.apache.axis.transport.http.HTTPSender:485) - ---------------------------------------------------
DEBUG 2014-09-30 18:45:59,554 (org.apache.axis.transport.http.HTTPSender:519) - POST /cgi-bin/pywps.cgi? HTTP/1.0
Content-Type: text/xml; charset=utf-8
Accept: application/soap+xml, application/dime, multipart/related, text/*
User-Agent: Axis/1.4
Host: localhost
Cache-Control: no-cache
Pragma: no-cache
SOAPAction: "http://localhost/cgi-bin/pywps.cgi?/ExecuteProcess_ogrbuffer"
|
|
From: Deniz .. <dul...@ho...> - 2014-10-14 18:20:38
|
Hello again Alan, Thank you very much for your reply. Yes I changed the logging as suggested at http://dev.mygrid.org.uk/wiki/pages/viewpage.action?pageId=18974840 I attached some parts of generated 4 log files. Two of them are following. If you couldn`t get them, please inform me. Thank you! Deniz log 1: ERROR 2014-10-14 19:34:56,595 (System.err:139) - org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: java.net.SocketException: Permission denied: connect Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== ERROR 2014-10-14 19:34:56,595 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:257) ERROR 2014-10-14 19:34:56,596 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.getDataTypes(CentralDigestCachedImpl.java:785) ERROR 2014-10-14 19:34:56,596 (System.err:139) - at org.biomoby.shared.MobyDataType.getDataType(MobyDataType.java:122) ERROR 2014-10-14 19:34:56,596 (System.err:139) - at org.biomoby.shared.MobyDataType.getParent(MobyDataType.java:264) ERROR 2014-10-14 19:34:56,597 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.findDatatypeDescriptions(BiomobyQueryHelper.java:258) ERROR 2014-10-14 19:34:56,597 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.findServiceDescriptionsAsync(BiomobyQueryHelper.java:221) ERROR 2014-10-14 19:34:56,597 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider.findServiceDescriptionsAsync(BiomobyServiceProvider.java:60) ERROR 2014-10-14 19:34:56,598 (System.err:139) - at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670) ERROR 2014-10-14 19:34:56,598 (System.err:139) - Caused by: org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: java.net.SocketException: Permission denied: connect Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== ERROR 2014-10-14 19:34:56,599 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251) ERROR 2014-10-14 19:34:56,599 (System.err:139) - at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1807) ERROR 2014-10-14 19:34:56,599 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.getResourceURL(CentralDigestCachedImpl.java:438) ERROR 2014-10-14 19:34:56,600 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:140) ERROR 2014-10-14 19:34:56,600 (System.err:139) - ... 7 more ERROR 2014-10-14 19:34:56,601 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect ERROR 2014-10-14 19:34:56,601 (System.err:139) - at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) ERROR 2014-10-14 19:34:56,601 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154) ERROR 2014-10-14 19:34:56,602 (System.err:139) - at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) ERROR 2014-10-14 19:34:56,602 (System.err:139) - at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) ERROR 2014-10-14 19:34:56,602 (System.err:139) - at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) ERROR 2014-10-14 19:34:56,603 (System.err:139) - at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) ERROR 2014-10-14 19:34:56,603 (System.err:139) - at org.apache.axis.client.Call.invokeEngine(Call.java:2784) ERROR 2014-10-14 19:34:56,603 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2767) ERROR 2014-10-14 19:34:56,604 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2443) ERROR 2014-10-14 19:34:56,604 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2366) ERROR 2014-10-14 19:34:56,604 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247) ERROR 2014-10-14 19:34:56,605 (System.err:139) - ... 10 more ERROR 2014-10-14 19:34:56,605 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect ERROR 2014-10-14 19:34:56,606 (System.err:139) - at java.net.DualStackPlainSocketImpl.connect0(Native Method) ERROR 2014-10-14 19:34:56,606 (System.err:139) - at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:79) ERROR 2014-10-14 19:34:56,606 (System.err:139) - at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339) ERROR 2014-10-14 19:34:56,607 (System.err:139) - at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200) ERROR 2014-10-14 19:34:56,607 (System.err:139) - at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182) ERROR 2014-10-14 19:34:56,607 (System.err:139) - at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172) ERROR 2014-10-14 19:34:56,608 (System.err:139) - at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) ERROR 2014-10-14 19:34:56,608 (System.err:139) - at java.net.Socket.connect(Socket.java:579) ERROR 2014-10-14 19:34:56,608 (System.err:139) - at java.net.Socket.connect(Socket.java:528) ERROR 2014-10-14 19:34:56,609 (System.err:139) - at java.net.Socket.<init>(Socket.java:425) ERROR 2014-10-14 19:34:56,609 (System.err:139) - at java.net.Socket.<init>(Socket.java:208) ERROR 2014-10-14 19:34:56,609 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:149) ERROR 2014-10-14 19:34:56,610 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:120) ERROR 2014-10-14 19:34:56,610 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191) ERROR 2014-10-14 19:34:56,611 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404) ERROR 2014-10-14 19:34:56,611 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138) ERROR 2014-10-14 19:34:56,611 (System.err:139) - ... 19 more DEBUG 2014-10-14 19:34:56,619 (org.apache.axis.transport.http.HTTPSender:125) - Enter: HTTPSender::invoke DEBUG 2014-10-14 19:35:17,645 (org.apache.axis.transport.http.HTTPSender:146) - java.net.SocketException: Permission denied: connect ERROR 2014-10-14 19:35:17,648 (org.biomoby.shared.MobyException:86) - ; nested exception is: java.net.SocketException: Permission denied: connect ERROR 2014-10-14 19:35:17,649 (org.biomoby.shared.MobyException:86) - ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: java.net.SocketException: Permission denied: connect Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl log 2: <?xml version="1.0" encoding="UTF-8"?><soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><soapenv:Body><getAvailableAnalysesInCategory soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"><arg0 xsi:type="soapenc:string" xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/">utils</arg0></getAvailableAnalysesInCategory></soapenv:Body></soapenv:Envelope> DEBUG 2014-10-14 18:47:25,528 (org.apache.axis.transport.http.HTTPSender:627) - HTTP/1.1 200 OK DEBUG 2014-10-14 18:47:25,529 (org.apache.axis.transport.http.HTTPSender:627) - Date Tue, 14 Oct 2014 15:47:22 GMT DEBUG 2014-10-14 18:47:25,529 (org.apache.axis.transport.http.HTTPSender:627) - Server Apache DEBUG 2014-10-14 18:47:25,529 (org.apache.axis.transport.http.HTTPSender:627) - Content-Type text/xml;charset=utf-8 DEBUG 2014-10-14 18:47:25,530 (org.apache.axis.transport.http.HTTPSender:627) - Connection close DEBUG 2014-10-14 18:47:25,530 (org.apache.axis.transport.http.HTTPSender:791) - no Content-Length DEBUG 2014-10-14 18:47:25,530 (org.apache.axis.transport.http.HTTPSender:794) - XML received: DEBUG 2014-10-14 18:47:25,531 (org.apache.axis.transport.http.HTTPSender:795) - ----------------------------------------------- DEBUG 2014-10-14 18:47:25,533 (org.apache.axis.transport.http.HTTPSender:796) - <soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><soapenv:Body><getAvailableAnalysesInCategoryResponse soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"><getAvailableAnalysesInCategoryReturn soapenc:arrayType="xsd:string[2]" xsi:type="soapenc:Array" xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/"><getAvailableAnalysesInCategoryReturn xsi:type="xsd:string">utils.embossdata</getAvailableAnalysesInCategoryReturn><getAvailableAnalysesInCategoryReturn xsi:type="xsd:string">utils.embossversion</getAvailableAnalysesInCategoryReturn></getAvailableAnalysesInCategoryReturn></getAvailableAnalysesInCategoryResponse></soapenv:Body></soapenv:Envelope> DEBUG 2014-10-14 18:47:25,533 (org.apache.axis.transport.http.HTTPSender:157) - Exit: HTTPDispatchHandler::invoke DEBUG 2014-10-14 18:47:25,549 (org.apache.axis.transport.http.HTTPSender:125) - Enter: HTTPSender::invoke DEBUG 2014-10-14 18:47:25,579 (org.apache.axis.transport.http.HTTPSender:796) - <soap:Envelope xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/"><soap:Body><retrieveServiceNamesResponse><s-gensym3 xsi:type="xsd:string"><serviceNames> <serviceName name='fromFunCUTtoDASGFF' authURI='cnio.es' lsid='urn:lsid:biomoby.org:serviceinstance:cnio.es,fromFunCUTtoDASGFF:2001-09-21T16-00-00Z'/> <serviceName name='getEntryFromDSSP' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:org.inab.upc,getEntryFromDSSP:2001-09-21T16-00-00Z'/> <serviceName name='getEntryFromFSSP' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:org.inab.upc,getEntryFromFSSP:2001-09-21T16-00-00Z'/> <serviceName name='getEntryFromGenBank' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:org.inab.upc,getEntryFromGenBank:2001-09-21T16-00-00Z'/> <serviceName name='getEntryFromRefSeq' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:org.inab.upc,getEntryFromRefSeq:2001-09-21T16-00-00Z'/> <serviceName name='getEntryFromUniProt' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:org.inab.upc,getEntryFromUniProt:2001-09-21T16-00-00Z'/> <serviceName name='runNCut' authURI='cnio.es' lsid='urn:lsid:biomoby.org:serviceinstance:cnio.es,runNCut:2001-09-21T16-00-00Z'/> <serviceName name='runCreateTreeFromClustalw' authURI='www.bioinfo.uma.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.bioinfo.uma.es,runCreateTreeFromClustalw:2001-09-21T16-00-00Z'/> <serviceName name='translateGeneIDGFFPredictions' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,translateGeneIDGFFPredictions:2001-09-21T16-00-00Z'/> <serviceName name='runGeneIDGFF' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,runGeneIDGFF:2001-09-21T16-00-00Z'/> <serviceName name='runSGP2GFF' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,runSGP2GFF:2001-09-21T16-00-00Z'/> <serviceName name='fromMetaAlignmentsToScoreMatrix' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,fromMetaAlignmentsToScoreMatrix:2001-09-21T16-00-00Z'/> <serviceName name='fromGenericSequenceToFASTA' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,fromGenericSequenceToFASTA:2001-09-21T16-00-00Z'/> <serviceName name='fromGenericSequenceCollectionToFASTA' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,fromGenericSequenceCollectionToFASTA:2001-09-21T16-00-00Z'/> <serviceName name='runMemeText' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,runMemeText:2001-09-21T16-00-00Z'/> <serviceName name='parseMotifMatricesFromMEME' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,parseMotifMatricesFromMEME:2001-09-21T16-00-00Z'/> <serviceName name='runMatScanGFF' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,runMatScanGFF:2001-09-21T16-00-00Z'/> <serviceName name='runMatScanGFFCollection' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,runMatScanGFFCollection:2001-09-21T16-00-00Z'/> <serviceName name='runMetaAlignment' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,runMetaAlignment:2001-09-21T16-00-00Z'/> <serviceName name='runMemeHTML' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,runMemeHTML:2001-09-21T16-00-00Z'/> <serviceName name='runMatScanGFFCollectionVsInputMatrices' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,runMatScanGFFCollectionVsInputMatrices:2001-09-21T16-00-00Z'/> <serviceName name='runMetaAlignmentGFF' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,runMetaAlignmentGFF:2001-09-21T16-00-00Z'/> <serviceName name='runMultiPairwiseMetaAlignment' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,runMultiPairwiseMetaAlignment:2001-09-21T16-00-00Z'/> <serviceName name='runMultiPairwiseMetaAlignmentGFF' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,runMultiPairwiseMetaAlignmentGFF:2001-09-21T16-00-00Z'/> <serviceName name='fromFASTAToDNASequence' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,fromFASTAToDNASequence:2001-09-21T16-00-00Z'/> <serviceName name='fromFASTAToAminoAcidSequence' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,fromFASTAToAminoAcidSequence:2001-09-21T16-00-00Z'/> <serviceName name='fromFASTAToDNASequenceCollection' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,fromFASTAToDNASequenceCollection:2001-09-21T16-00-00Z'/> <serviceName name='fromFASTAToAminoAcidSequenceCollection' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,fromFASTAToAminoAcidSequenceCollection:2001-09-21T16-00-00Z'/> <serviceName name='fromMetaAlignmentsToTextScoreMatrix' authURI='genome.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:genome.imim.es,fromMetaAlignmentsToTextScoreMatrix:2001-09-21T16-00-00Z'/> <serviceName name='runISS' authURI='cnio.es' lsid='urn:lsid:biomoby.org:serviceinstance:cnio.es,runISS:2001-09-21T16-00-00Z'/> <serviceName name='runFunCUT' authURI='cnio.es' lsid='urn:lsid:biomoby.org:serviceinstance:cnio.es,runFunCUT:2001-09-21T16-00-00Z'/> <serviceName name='runOFunCUT' authURI='cnio.es' lsid='urn:lsid:biomoby.org:serviceinstance:cnio.es,runOFunCUT:2001-09-21T16-00-00Z'/> <serviceName name='parseGFFFromFeatureAASequence' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,parseGFFFromFeatureAASequence:2001-09-21T16-00-00Z'/> <serviceName name='getStructureFromPDB' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getStructureFromPDB:2001-09-21T16-00-00Z'/> <serviceName name='getHeaderFromPDB' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getHeaderFromPDB:2001-09-21T16-00-00Z'/> <serviceName name='getAminoAcidSequenceFromPDB' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getAminoAcidSequenceFromPDB:2001-09-21T16-00-00Z'/> <serviceName name='parseMultipleAlignFromBLASTText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,parseMultipleAlignFromBLASTText:2001-09-21T16-00-00Z'/> <serviceName name='parseAminoAcidSequenceFromPDBText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,parseAminoAcidSequenceFromPDBText:2001-09-21T16-00-00Z'/> <serviceName name='parseFeatureAASequenceFromFSOLVText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,parseFeatureAASequenceFromFSOLVText:2001-09-21T16-00-00Z'/> <serviceName name='parsePropertySequenceFromFSOLVText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,parsePropertySequenceFromFSOLVText:2001-09-21T16-00-00Z'/> <serviceName name='showFSOLVonStructure' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,showFSOLVonStructure:2001-09-21T16-00-00Z'/> <serviceName name='showPMUTonStructure' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,showPMUTonStructure:2001-09-21T16-00-00Z'/> <serviceName name='runPMUTHotSpotFromFASTA' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,runPMUTHotSpotFromFASTA:2001-09-21T16-00-00Z'/> <serviceName name='parseFeatureAASequenceFromPMUTText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,parseFeatureAASequenceFromPMUTText:2001-09-21T16-00-00Z'/> <serviceName name='parsePropertySequenceFromPMUTText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,parsePropertySequenceFromPMUTText:2001-09-21T16-00-00Z'/> <serviceName name='runPHDFromFASTA' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,runPHDFromFASTA:2001-09-21T16-00-00Z'/> <serviceName name='runPMUTHotSpotFromAminoAcidSequence' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,runPMUTHotSpotFromAminoAcidSequence:2001-09-21T16-00-00Z'/> <serviceName name='runPHDFromAminoAcidSequence' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,runPHDFromAminoAcidSequence:2001-09-21T16-00-00Z'/> <serviceName name='runPMUTHotSpotFromBLASTText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,runPMUTHotSpotFromBLASTText:2001-09-21T16-00-00Z'/> <serviceName name='runPHDFromBLASTText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,runPHDFromBLASTText:2001-09-21T16-00-00Z'/> <serviceName name='plotFeatureAASequence' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,plotFeatureAASequence:2001-09-21T16-00-00Z'/> <serviceName name='runPSIBlastpFromFASTA' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,runPSIBlastpFromFASTA:2001-09-21T16-00-00Z'/> <serviceName name='runPSIBlastpFromAminoAcidSequence' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,runPSIBlastpFromAminoAcidSequence:2001-09-21T16-00-00Z'/> <serviceName name='getInteractionMethodDesc' authURI='pdg.cnb.uam.es' lsid='urn:lsid:biomoby.org:serviceinstance:pdg.cnb.uam.es,getInteractionMethodDesc:2001-09-21T16-00-00Z'/> <serviceName name='getInteractingMethods' authURI='pdg.cnb.uam.es' lsid='urn:lsid:biomoby.org:serviceinstance:pdg.cnb.uam.es,getInteractingMethods:2001-09-21T16-00-00Z'/> <serviceName name='getInteractionsXML' authURI='pdg.cnb.uam.es' lsid='urn:lsid:biomoby.org:serviceinstance:pdg.cnb.uam.es,getInteractionsXML:2001-09-21T16-00-00Z'/> <serviceName name='getInteractions' authURI='pdg.cnb.uam.es' lsid='urn:lsid:biomoby.org:serviceinstance:pdg.cnb.uam.es,getInteractions:2001-09-21T16-00-00Z'/> <serviceName name='parseFromIntAct' authURI='pdg.cnb.uam.es' lsid='urn:lsid:biomoby.org:serviceinstance:pdg.cnb.uam.es,parseFromIntAct:2001-09-21T16-00-00Z'/> <serviceName name='runISSComplete' authURI='cnio.es' lsid='urn:lsid:biomoby.org:serviceinstance:cnio.es,runISSComplete:2007-07-20T15-39-43Z'/> <serviceName name='runNCBIBlastx' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runNCBIBlastx:2007-11-13T15-56-47Z'/> <serviceName name='runNCBITBlastn' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runNCBITBlastn:2007-11-13T15-56-49Z'/> <serviceName name='runNCBITBlastx' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runNCBITBlastx:2007-11-13T15-56-51Z'/> <serviceName name='runHMMBuild' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runHMMBuild:2007-11-14T14-28-23Z'/> <serviceName name='runClustalwFast' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runClustalwFast:2007-11-16T13-32-51Z'/> <serviceName name='runClustalwFull' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runClustalwFull:2007-11-16T13-32-53Z'/> <serviceName name='runEmbossAntigenicFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossAntigenicFromSequence:2007-11-16T13-32-54Z'/> <serviceName name='runEmbossChargeFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossChargeFromSequence:2007-11-16T13-32-56Z'/> <serviceName name='runEmbossCodcmpFromTables' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossCodcmpFromTables:2007-11-16T13-32-57Z'/> <serviceName name='runEmbossConsFromAlignment' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossConsFromAlignment:2007-11-16T13-32-59Z'/> <serviceName name='runEmbossCuspFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossCuspFromSequence:2007-11-16T13-33-02Z'/> <serviceName name='runEmbossEmowse' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossEmowse:2007-11-16T13-33-05Z'/> <serviceName name='runEmbossEquicktandemFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossEquicktandemFromSequence:2007-11-16T13-33-06Z'/> <serviceName name='runEmbossFindkm' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossFindkm:2007-11-16T13-33-08Z'/> <serviceName name='runEmbossGetorfFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossGetorfFromSequence:2007-11-16T13-33-09Z'/> <serviceName name='runEmbossNeedleFromSequences' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossNeedleFromSequences:2007-11-16T13-33-12Z'/> <serviceName name='runEmbossPatmatdb' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossPatmatdb:2007-11-16T13-33-15Z'/> <serviceName name='runEmbossPatmatdbFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossPatmatdbFromSequence:2007-11-16T13-33-17Z'/> <serviceName name='runEmbossPatmatmotifsFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossPatmatmotifsFromSequence:2007-11-16T13-33-18Z'/> <serviceName name='runEmbossPepcoilFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossPepcoilFromSequence:2007-11-16T13-33-20Z'/> <serviceName name='runEmbossPepinfoFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossPepinfoFromSequence:2007-11-16T13-33-21Z'/> <serviceName name='runEmbossPepstatsFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossPepstatsFromSequence:2007-11-16T13-33-23Z'/> <serviceName name='runEmbossPepwindowFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossPepwindowFromSequence:2007-11-16T13-33-25Z'/> <serviceName name='runEmbossPepwindowallFromSequences' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossPepwindowallFromSequences:2007-11-16T13-33-26Z'/> <serviceName name='runEmbossRestrictFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossRestrictFromSequence:2007-11-16T13-33-28Z'/> <serviceName name='runEmbossSigcleaveFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossSigcleaveFromSequence:2007-11-16T13-33-30Z'/> <serviceName name='runEmbossTmapFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossTmapFromSequence:2007-11-16T13-33-32Z'/> <serviceName name='runEmbossTranseqFromSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossTranseqFromSequence:2007-11-16T13-33-34Z'/> <serviceName name='runEmbossWaterFromSequences' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runEmbossWaterFromSequences:2007-11-16T13-33-35Z'/> <serviceName name='runFastaForAminoAcids' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runFastaForAminoAcids:2007-11-16T13-33-37Z'/> <serviceName name='runFastaForNucleotides' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runFastaForNucleotides:2007-11-16T13-33-38Z'/> <serviceName name='runFastx' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runFastx:2007-11-16T13-33-40Z'/> <serviceName name='runFasty' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runFasty:2007-11-16T13-33-42Z'/> <serviceName name='runHMMPfam' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runHMMPfam:2007-11-16T13-33-46Z'/> <serviceName name='runHMMSearchAgainstDB' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runHMMSearchAgainstDB:2007-11-16T13-33-47Z'/> <serviceName name='runHMMSearchAgainstSeqs' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runHMMSearchAgainstSeqs:2007-11-16T13-33-49Z'/> <serviceName name='runMuscleFromSequences' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runMuscleFromSequences:2007-11-16T13-33-50Z'/> <serviceName name='runNCBIBlastAgainstDB' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runNCBIBlastAgainstDB:2007-11-16T13-33-52Z'/> <serviceName name='runNCBIBlastnXML' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runNCBIBlastnXML:2007-11-16T13-33-55Z'/> <serviceName name='runNCBIBlastpXML' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runNCBIBlastpXML:2007-11-16T13-33-58Z'/> <serviceName name='runNCBIBlastxXML' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runNCBIBlastxXML:2007-11-16T13-34-02Z'/> <serviceName name='runNCBITBlastnXML' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runNCBITBlastnXML:2007-11-16T13-34-06Z'/> <serviceName name='runNCBITBlastxXML' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runNCBITBlastxXML:2007-11-16T13-34-10Z'/> <serviceName name='runPhylipDnadist' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runPhylipDnadist:2007-11-16T13-34-12Z'/> <serviceName name='runPhylipDnaml' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runPhylipDnaml:2007-11-16T13-34-14Z'/> <serviceName name='runPhylipDnamlk' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runPhylipDnamlk:2007-11-16T13-34-15Z'/> <serviceName name='runPhylipDnapars' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runPhylipDnapars:2007-11-16T13-34-17Z'/> <serviceName name='runPhylipDnapenny' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runPhylipDnapenny:2007-11-16T13-34-19Z'/> <serviceName name='runPhylipFitch' authURI='inb.bsc.es' 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lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,parseBlastIDs:2008-05-13T13-20-55Z'/> <serviceName name='getCrossReferencesSQL' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,getCrossReferencesSQL:2008-05-20T23-27-27Z'/> <serviceName name='getPDBIdsFromProteinID' authURI='cgl.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:cgl.imim.es,getPDBIdsFromProteinID:2008-06-16T10-02-56Z'/> <serviceName name='getIDsFromBlast' authURI='cgl.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:cgl.imim.es,getIDsFromBlast:2008-06-16T10-03-30Z'/> <serviceName name='getUniProtIdsFromProteinID' authURI='cgl.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:cgl.imim.es,getUniProtIdsFromProteinID:2008-06-26T08-18-39Z'/> <serviceName name='runSIAM' authURI='cnio.es' lsid='urn:lsid:biomoby.org:serviceinstance:cnio.es,runSIAM:2008-07-04T13-01-59Z'/> <serviceName name='getAAFromWeightedObject' authURI='cgl.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:cgl.imim.es,getAAFromWeightedObject:2008-07-07T16-11-38Z'/> <serviceName name='getIdNameValueFromBlast' authURI='cgl.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:cgl.imim.es,getIdNameValueFromBlast:2008-07-09T15-56-44Z'/> <serviceName name='runBlastXP' authURI='cgl.imim.es' lsid='urn:lsid:biomoby.org:serviceinstance:cgl.imim.es,runBlastXP:2008-07-10T10-38-23Z'/> <serviceName name='getEntryFromPDB' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,getEntryFromPDB:2008-08-05T15-30-11Z'/> <serviceName name='optimizeStructureFromNAMD_Structure' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,optimizeStructureFromNAMD_Structure:2009-02-17T10-32-28Z'/> <serviceName name='WhichNameSpaceForID' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,WhichNameSpaceForID:2009-04-21T21-06-50Z'/> <serviceName name='getEntryFromEMBL' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,getEntryFromEMBL:2009-04-29T11-44-32Z'/> <serviceName name='parseAnatomicalStructures' authURI='www.cnb.csic.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.cnb.csic.es,parseAnatomicalStructures:2009-05-13T14-50-08Z'/> <serviceName name='getExpressionStatistics' authURI='www.cnb.csic.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.cnb.csic.es,getExpressionStatistics:2009-05-13T14-51-52Z'/> <serviceName name='parseExpressedGenes' authURI='www.cnb.csic.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.cnb.csic.es,parseExpressedGenes:2009-05-13T14-55-30Z'/> <serviceName name='parseExpressionStatistics' authURI='www.cnb.csic.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.cnb.csic.es,parseExpressionStatistics:2009-05-20T13-43-46Z'/> <serviceName name='getEntryFromOMIM' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,getEntryFromOMIM:2009-05-26T11-49-25Z'/> <serviceName name='fromMGIToEMBL' authURI='www.cnb.csic.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.cnb.csic.es,fromMGIToEMBL:2009-06-18T10-06-02Z'/> <serviceName name='fromEMBLToMGI' authURI='www.cnb.csic.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.cnb.csic.es,fromEMBLToMGI:2009-06-18T10-06-11Z'/> <serviceName name='fromEMBLToMGI' authURI='www.cnb.uam.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.cnb.uam.es,fromEMBLToMGI:2009-06-22T12-31-01Z'/> <serviceName name='fromClustalwToPhylip' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,fromClustalwToPhylip:2009-06-25T17-09-53Z'/> <serviceName name='getmmCifFileFromPDBID' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,getmmCifFileFromPDBID:2009-07-15T10-34-11Z'/> <serviceName name='fromMGIToRefSeq' authURI='www.cnb.csic.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.cnb.csic.es,fromMGIToRefSeq:2009-07-21T15-42-58Z'/> <serviceName name='parsePDBIntoChains' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,parsePDBIntoChains:2009-07-22T11-28-01Z'/> <serviceName name='parsePDBIntoSeqs' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,parsePDBIntoSeqs:2009-07-23T11-47-42Z'/> <serviceName name='parseSwissIntoPDBids' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,parseSwissIntoPDBids:2009-07-24T10-29-03Z'/> <serviceName name='runClustalwFast' authURI='www.cnb.uam.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.cnb.uam.es,runClustalwFast:2009-07-30T12-22-01Z'/> <serviceName name='runPhylipDnaml' authURI='www.cnb.uam.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.cnb.uam.es,runPhylipDnaml:2009-07-30T12-22-20Z'/> <serviceName name='runPreprocessing' authURI='bioinfo.cipf.es' lsid='urn:lsid:biomoby.org:serviceinstance:bioinfo.cipf.es,runPreprocessing:2009-09-08T09-28-11Z'/> <serviceName name='displayClustering' authURI='bioinfo.cipf.es' lsid='urn:lsid:biomoby.org:serviceinstance:bioinfo.cipf.es,displayClustering:2009-09-08T09-36-26Z'/> <serviceName name='runDifferentialExpressionTest' authURI='bioinfo.cipf.es' lsid='urn:lsid:biomoby.org:serviceinstance:bioinfo.cipf.es,runDifferentialExpressionTest:2009-09-08T10-04-23Z'/> <serviceName name='runPredictorTraining' authURI='bioinfo.cipf.es' lsid='urn:lsid:biomoby.org:serviceinstance:bioinfo.cipf.es,runPredictorTraining:2009-09-08T10-18-46Z'/> <serviceName name='runClustering' authURI='bioinfo.cipf.es' lsid='urn:lsid:biomoby.org:serviceinstance:bioinfo.cipf.es,runClustering:2009-09-08T15-32-55Z'/> <serviceName name='runFatiGO' authURI='bioinfo.cipf.es' lsid='urn:lsid:biomoby.org:serviceinstance:bioinfo.cipf.es,runFatiGO:2009-09-09T13-17-17Z'/> <serviceName name='runFatiScan' authURI='bioinfo.cipf.es' lsid='urn:lsid:biomoby.org:serviceinstance:bioinfo.cipf.es,runFatiScan:2009-09-14T12-36-16Z'/> <serviceName name='runFasts' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runFasts:2009-10-26T15-26-46Z'/> <serviceName name='getAminoAcidSequenceUMA' authURI='chirimoyo.ac.uma.es' lsid='urn:lsid:biomoby.org:serviceinstance:chirimoyo.ac.uma.es,getAminoAcidSequenceUMA:2010-01-12T08-58-07Z'/> <serviceName name='runNCBIBlastp1' authURI='chirimoyo.ac.uma.es' lsid='urn:lsid:biomoby.org:serviceinstance:chirimoyo.ac.uma.es,runNCBIBlastp1:2010-01-12T08-59-58Z'/> <serviceName name='runClustalwFastUMA' authURI='chirimoyo.ac.uma.es' lsid='urn:lsid:biomoby.org:serviceinstance:chirimoyo.ac.uma.es,runClustalwFastUMA:2010-01-12T09-07-33Z'/> <serviceName name='getAminoAcidSequenceCollection' authURI='www.bioinfo.uma.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.bioinfo.uma.es,getAminoAcidSequenceCollection:2010-01-12T17-08-23Z'/> <serviceName name='getBestHitsFromBlast' authURI='www.bioinfo.uma.es' lsid='urn:lsid:biomoby.org:serviceinstance:www.bioinfo.uma.es,getBestHitsFromBlast:2010-02-01T11-57-56Z'/> <serviceName name='getNucleotideSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,getNucleotideSequence:2010-10-23T18-38-47Z'/> <serviceName name='getEntryFromSCOPPath' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,getEntryFromSCOPPath:2011-02-01T12-31-19Z'/> <serviceName name='getURLfromId' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,getURLfromId:2011-02-02T13-29-44Z'/> <serviceName name='getEntryFromSCOPwithPDBID' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,getEntryFromSCOPwithPDBID:2011-02-04T10-24-37Z'/> <serviceName name='overlappingFromBL2G' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,overlappingFromBL2G:2011-05-12T13-01-01Z'/> <serviceName name='runBlast2gene' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runBlast2gene:2011-05-12T13-01-03Z'/> <serviceName name='runGenewise' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,runGenewise:2011-05-12T13-01-04Z'/> <serviceName name='getAminoAcidSequence' authURI='inb.bsc.es' lsid='urn:lsid:biomoby.org:serviceinstance:inb.bsc.es,getAminoAcidSequence:2011-06-23T10-57-24Z'/> <serviceName name='addDisulphideBondsFromPDBText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,addDisulphideBondsFromPDBText:2011-08-30T15-15-19Z'/> <serviceName name='addHydrogensFromPDBText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,addHydrogensFromPDBText:2011-08-30T15-31-45Z'/> <serviceName name='addLigandToGROMACS_MD_Structure' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,addLigandToGROMACS_MD_Structure:2011-08-30T15-33-10Z'/> <serviceName name='build3DstructureFromNucleotideSequence' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,build3DstructureFromNucleotideSequence:2011-08-30T15-34-36Z'/> <serviceName name='build3DstructureWithHelicalParametersFromNucleotideSequence' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,build3DstructureWithHelicalParametersFromNucleotideSequence:2011-08-30T15-35-30Z'/> <serviceName name='cleanStructureFromPDBText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,cleanStructureFromPDBText:2011-08-30T15-36-22Z'/> <serviceName name='fromMD_TrajectoryToMD_TrajectoryBINPOS' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,fromMD_TrajectoryToMD_TrajectoryBINPOS:2011-08-30T15-38-17Z'/> <serviceName name='fromMD_TrajectoryToMD_TrajectoryCRD' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,fromMD_TrajectoryToMD_TrajectoryCRD:2011-08-30T15-38-34Z'/> <serviceName name='fromMD_TrajectoryToMD_TrajectoryDCD' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,fromMD_TrajectoryToMD_TrajectoryDCD:2011-08-30T15-38-48Z'/> <serviceName name='fromMD_TrajectoryToMD_TrajectoryNetCDF' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,fromMD_TrajectoryToMD_TrajectoryNetCDF:2011-08-30T15-39-02Z'/> <serviceName name='fromMD_TrajectoryToPDB_Collection' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,fromMD_TrajectoryToPDB_Collection:2011-08-30T15-39-16Z'/> <serviceName name='fromPDB_CollectionToMD_TrajectoryNetCDF' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,fromPDB_CollectionToMD_TrajectoryNetCDF:2011-08-30T15-39-29Z'/> <serviceName name='getAverageStructure' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getAverageStructure:2011-08-30T15-44-30Z'/> <serviceName name='getAverageStructureFromMD_Trajectory' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getAverageStructureFromMD_Trajectory:2011-08-30T15-45-10Z'/> <serviceName name='getDryTrajectoryFromMD_Trajectory' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getDryTrajectoryFromMD_Trajectory:2011-08-30T15-48-36Z'/> <serviceName name='getGROMACS_ConfFromMD_TrajectoryXTC' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getGROMACS_ConfFromMD_TrajectoryXTC:2011-08-30T15-52-34Z'/> <serviceName name='getGROMACS_ConfFromGROMACS_MD_Structure' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getGROMACS_ConfFromGROMACS_MD_Structure:2011-08-30T15-52-47Z'/> <serviceName name='getGROMACS_MD_StructureFromPDBText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getGROMACS_MD_StructureFromPDBText:2011-08-30T15-53-44Z'/> <serviceName name='getMaskTrajectoryFromMD_Trajectory' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getMaskTrajectoryFromMD_Trajectory:2011-08-30T15-54-58Z'/> <serviceName name='getNAMD_ConfFromNAMD_MD_Structure' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getNAMD_ConfFromNAMD_MD_Structure:2011-08-30T15-56-46Z'/> <serviceName name='getNAMD_ConfFromMD_TrajectoryDCD' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getNAMD_ConfFromMD_TrajectoryDCD:2011-08-30T15-57-08Z'/> <serviceName name='getNAMD_MD_StructureFromPDBText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getNAMD_MD_StructureFromPDBText:2011-08-30T15-58-07Z'/> <serviceName name='getPersistentFile' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getPersistentFile:2011-08-30T16-02-11Z'/> <serviceName name='getSliceFromMD_Trajectory' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getSliceFromMD_Trajectory:2011-08-30T16-06-28Z'/> <serviceName name='getSnapshotFromMD_Trajectory' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getSnapshotFromMD_Trajectory:2011-08-30T16-06-52Z'/> <serviceName name='getTrajectoryBfactorPerResidue' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getTrajectoryBfactorPerResidue:2011-08-30T16-09-13Z'/> <serviceName name='getTrajectoryBfactorPerResidueFromMD_Trajectory' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getTrajectoryBfactorPerResidueFromMD_Trajectory:2011-08-30T16-09-27Z'/> <serviceName name='getTrajectoryRadiusOfGyrationFromMD_Trajectory' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getTrajectoryRadiusOfGyrationFromMD_Trajectory:2011-08-30T16-09-42Z'/> <serviceName name='getTrajectoryRms' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getTrajectoryRms:2011-08-30T16-09-58Z'/> <serviceName name='getTrajectoryRmsFromMD_Trajectory' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getTrajectoryRmsFromMD_Trajectory:2011-08-30T16-10-14Z'/> <serviceName name='getTrajectoryRmsPerResidue' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getTrajectoryRmsPerResidue:2011-08-30T16-10-29Z'/> <serviceName name='getTrajectoryRmsPerResidueFromMD_Trajectory' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,getTrajectoryRmsPerResidueFromMD_Trajectory:2011-08-30T16-10-40Z'/> <serviceName name='loadPersistentFile' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,loadPersistentFile:2011-08-30T16-15-02Z'/> <serviceName name='mutateResidueFromPDBText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,mutateResidueFromPDBText:2011-08-30T16-16-11Z'/> <serviceName name='optimizeStructureFromNAMD_MD_Structure' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,optimizeStructureFromNAMD_MD_Structure:2011-08-30T16-16-49Z'/> <serviceName name='optimizeStructureFromGROMACS_MD_Structure' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,optimizeStructureFromGROMACS_MD_Structure:2011-08-30T16-17-00Z'/> <serviceName name='protonateHistidinesFromPDBText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,protonateHistidinesFromPDBText:2011-08-30T16-24-16Z'/> <serviceName name='protonateIonizableResiduesFromPDBText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,protonateIonizableResiduesFromPDBText:2011-08-30T16-24-35Z'/> <serviceName name='titrateStructureFromPDBText' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub.es,titrateStructureFromPDBText:2011-08-30T16-24-44Z'/> <serviceName name='protonateHistidinesFromMD_Structure' authURI='mmb.pcb.ub.es' lsid='urn:lsid:biomoby.org:serviceinstance:mmb.pcb.ub... [truncated message content] |
|
From: Alan R W. <ala...@ma...> - 2014-10-14 10:38:29
|
On 13/10/2014 18:37, Deniz .. wrote: > Hi All, Hello Deniz, > Thank you very much for your replies Alan and Jorge. > I still couldn`t solve the problem. > Yes I found the log messages and attached the Taverna 2.5.0 log file > (some part) Did you change the logging as suggested at http://dev.mygrid.org.uk/wiki/pages/viewpage.action?pageId=18974840 ? You need to do that so that we can see what is being sent by Taverna "on the wire". Alan |
|
From: Deniz .. <dul...@ho...> - 2014-09-30 19:13:22
|
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:38:04,198 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
ERROR 2014-09-30 21:38:04,199 (System.err:139) - at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1807)
ERROR 2014-09-30 21:38:04,199 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.getResourceURL(CentralDigestCachedImpl.java:438)
ERROR 2014-09-30 21:38:04,199 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:140)
ERROR 2014-09-30 21:38:04,200 (System.err:139) - ... 7 more
ERROR 2014-09-30 21:38:04,200 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:38:04,201 (System.err:139) - at org.apache.axis.AxisFault.makeFault(AxisFault.java:101)
ERROR 2014-09-30 21:38:04,201 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154)
ERROR 2014-09-30 21:38:04,201 (System.err:139) - at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
ERROR 2014-09-30 21:38:04,202 (System.err:139) - at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
ERROR 2014-09-30 21:38:04,202 (System.err:139) - at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
ERROR 2014-09-30 21:38:04,203 (System.err:139) - at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
ERROR 2014-09-30 21:38:04,203 (System.err:139) - at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
ERROR 2014-09-30 21:38:04,203 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2767)
ERROR 2014-09-30 21:38:04,204 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2443)
ERROR 2014-09-30 21:38:04,204 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2366)
ERROR 2014-09-30 21:38:04,204 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247)
ERROR 2014-09-30 21:38:04,205 (System.err:139) - ... 10 more
ERROR 2014-09-30 21:38:04,205 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:38:04,205 (System.err:139) - at java.net.DualStackPlainSocketImpl.connect0(Native Method)
ERROR 2014-09-30 21:38:04,206 (System.err:139) - at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:79)
ERROR 2014-09-30 21:38:04,206 (System.err:139) - at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
ERROR 2014-09-30 21:38:04,206 (System.err:139) - at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
ERROR 2014-09-30 21:38:04,207 (System.err:139) - at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
ERROR 2014-09-30 21:38:04,207 (System.err:139) - at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
ERROR 2014-09-30 21:38:04,208 (System.err:139) - at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
ERROR 2014-09-30 21:38:04,208 (System.err:139) - at java.net.Socket.connect(Socket.java:579)
ERROR 2014-09-30 21:38:04,209 (System.err:139) - at java.net.Socket.connect(Socket.java:528)
ERROR 2014-09-30 21:38:04,209 (System.err:139) - at java.net.Socket.<init>(Socket.java:425)
ERROR 2014-09-30 21:38:04,209 (System.err:139) - at java.net.Socket.<init>(Socket.java:208)
ERROR 2014-09-30 21:38:04,210 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:149)
ERROR 2014-09-30 21:38:04,210 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:120)
ERROR 2014-09-30 21:38:04,211 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191)
ERROR 2014-09-30 21:38:04,211 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404)
ERROR 2014-09-30 21:38:04,211 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138)
ERROR 2014-09-30 21:38:04,212 (System.err:139) - ... 19 more
DEBUG 2014-09-30 21:38:04,225 (org.apache.axis.transport.http.HTTPSender:125) - Enter: HTTPSender::invoke
DEBUG 2014-09-30 21:38:25,223 (org.apache.axis.transport.http.HTTPSender:146) - java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:38:25,226 (org.biomoby.shared.MobyException:86) - ; nested exception is:
java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:38:25,226 (org.biomoby.shared.MobyException:86) - ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
WARN 2014-09-30 21:38:25,227 (org.biomoby.shared.MobyDataType:129) - Cannot parse MOBY Datatype Ontology: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:38:25,227 (System.err:139) - org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:38:25,228 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:257)
ERROR 2014-09-30 21:38:25,228 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.getDataTypes(CentralDigestCachedImpl.java:785)
ERROR 2014-09-30 21:38:25,229 (System.err:139) - at org.biomoby.shared.MobyDataType.getDataType(MobyDataType.java:122)
ERROR 2014-09-30 21:38:25,229 (System.err:139) - at org.biomoby.shared.MobyDataType.getParent(MobyDataType.java:264)
ERROR 2014-09-30 21:38:25,230 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.findDatatypeDescriptions(BiomobyQueryHelper.java:258)
ERROR 2014-09-30 21:38:25,230 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.findServiceDescriptionsAsync(BiomobyQueryHelper.java:221)
ERROR 2014-09-30 21:38:25,231 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider.findServiceDescriptionsAsync(BiomobyServiceProvider.java:60)
ERROR 2014-09-30 21:38:25,232 (System.err:139) - at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
ERROR 2014-09-30 21:38:25,232 (System.err:139) - Caused by: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:38:25,233 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
ERROR 2014-09-30 21:38:25,233 (System.err:139) - at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1807)
ERROR 2014-09-30 21:38:25,234 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.getResourceURL(CentralDigestCachedImpl.java:438)
ERROR 2014-09-30 21:38:25,234 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:140)
ERROR 2014-09-30 21:38:25,234 (System.err:139) - ... 7 more
ERROR 2014-09-30 21:38:25,235 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:38:25,235 (System.err:139) - at org.apache.axis.AxisFault.makeFault(AxisFault.java:101)
ERROR 2014-09-30 21:38:25,236 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154)
ERROR 2014-09-30 21:38:25,236 (System.err:139) - at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
ERROR 2014-09-30 21:38:25,236 (System.err:139) - at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
ERROR 2014-09-30 21:38:25,237 (System.err:139) - at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
ERROR 2014-09-30 21:38:25,237 (System.err:139) - at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
ERROR 2014-09-30 21:38:25,237 (System.err:139) - at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
ERROR 2014-09-30 21:38:25,238 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2767)
ERROR 2014-09-30 21:38:25,238 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2443)
ERROR 2014-09-30 21:38:25,238 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2366)
ERROR 2014-09-30 21:38:25,239 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247)
ERROR 2014-09-30 21:38:25,239 (System.err:139) - ... 10 more
ERROR 2014-09-30 21:38:25,240 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:38:25,240 (System.err:139) - at java.net.DualStackPlainSocketImpl.connect0(Native Method)
ERROR 2014-09-30 21:38:25,240 (System.err:139) - at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:79)
ERROR 2014-09-30 21:38:25,241 (System.err:139) - at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
ERROR 2014-09-30 21:38:25,241 (System.err:139) - at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
ERROR 2014-09-30 21:38:25,241 (System.err:139) - at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
ERROR 2014-09-30 21:38:25,243 (System.err:139) - at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
ERROR 2014-09-30 21:38:25,243 (System.err:139) - at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
ERROR 2014-09-30 21:38:25,244 (System.err:139) - at java.net.Socket.connect(Socket.java:579)
ERROR 2014-09-30 21:38:25,244 (System.err:139) - at java.net.Socket.connect(Socket.java:528)
ERROR 2014-09-30 21:38:25,244 (System.err:139) - at java.net.Socket.<init>(Socket.java:425)
ERROR 2014-09-30 21:38:25,245 (System.err:139) - at java.net.Socket.<init>(Socket.java:208)
ERROR 2014-09-30 21:38:25,245 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:149)
ERROR 2014-09-30 21:38:25,246 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:120)
ERROR 2014-09-30 21:38:25,246 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191)
ERROR 2014-09-30 21:38:25,246 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404)
ERROR 2014-09-30 21:38:25,247 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138)
ERROR 2014-09-30 21:38:25,247 (System.err:139) - ... 19 more
DEBUG 2014-09-30 21:38:25,258 (org.apache.axis.transport.http.HTTPSender:125) - Enter: HTTPSender::invoke
DEBUG 2014-09-30 21:38:46,264 (org.apache.axis.transport.http.HTTPSender:146) - java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:38:46,265 (org.biomoby.shared.MobyException:86) - ; nested exception is:
java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:38:46,265 (org.biomoby.shared.MobyException:86) - ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
WARN 2014-09-30 21:38:46,265 (org.biomoby.shared.MobyDataType:129) - Cannot parse MOBY Datatype Ontology: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:38:46,266 (System.err:139) - org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:38:46,266 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:257)
ERROR 2014-09-30 21:38:46,266 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.getDataTypes(CentralDigestCachedImpl.java:785)
ERROR 2014-09-30 21:38:46,266 (System.err:139) - at org.biomoby.shared.MobyDataType.getDataType(MobyDataType.java:122)
ERROR 2014-09-30 21:38:46,266 (System.err:139) - at org.biomoby.shared.MobyDataType.getParent(MobyDataType.java:264)
ERROR 2014-09-30 21:38:46,266 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.findDatatypeDescriptions(BiomobyQueryHelper.java:258)
ERROR 2014-09-30 21:38:46,267 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.findServiceDescriptionsAsync(BiomobyQueryHelper.java:221)
ERROR 2014-09-30 21:38:46,267 (System.err:139) - at net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider.findServiceDescriptionsAsync(BiomobyServiceProvider.java:60)
ERROR 2014-09-30 21:38:46,267 (System.err:139) - at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
ERROR 2014-09-30 21:38:46,267 (System.err:139) - Caused by: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Permission denied: connect
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2014-09-30 21:38:46,267 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
ERROR 2014-09-30 21:38:46,267 (System.err:139) - at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1807)
ERROR 2014-09-30 21:38:46,267 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.getResourceURL(CentralDigestCachedImpl.java:438)
ERROR 2014-09-30 21:38:46,267 (System.err:139) - at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:140)
ERROR 2014-09-30 21:38:46,268 (System.err:139) - ... 7 more
ERROR 2014-09-30 21:38:46,268 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:38:46,268 (System.err:139) - at org.apache.axis.AxisFault.makeFault(AxisFault.java:101)
ERROR 2014-09-30 21:38:46,268 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154)
ERROR 2014-09-30 21:38:46,268 (System.err:139) - at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
ERROR 2014-09-30 21:38:46,268 (System.err:139) - at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
ERROR 2014-09-30 21:38:46,268 (System.err:139) - at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
ERROR 2014-09-30 21:38:46,268 (System.err:139) - at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
ERROR 2014-09-30 21:38:46,268 (System.err:139) - at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
ERROR 2014-09-30 21:38:46,269 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2767)
ERROR 2014-09-30 21:38:46,269 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2443)
ERROR 2014-09-30 21:38:46,269 (System.err:139) - at org.apache.axis.client.Call.invoke(Call.java:2366)
ERROR 2014-09-30 21:38:46,269 (System.err:139) - at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247)
ERROR 2014-09-30 21:38:46,269 (System.err:139) - ... 10 more
ERROR 2014-09-30 21:38:46,269 (System.err:139) - Caused by: java.net.SocketException: Permission denied: connect
ERROR 2014-09-30 21:38:46,269 (System.err:139) - at java.net.DualStackPlainSocketImpl.connect0(Native Method)
ERROR 2014-09-30 21:38:46,270 (System.err:139) - at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:79)
ERROR 2014-09-30 21:38:46,270 (System.err:139) - at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
ERROR 2014-09-30 21:38:46,270 (System.err:139) - at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
ERROR 2014-09-30 21:38:46,270 (System.err:139) - at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
ERROR 2014-09-30 21:38:46,270 (System.err:139) - at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
ERROR 2014-09-30 21:38:46,270 (System.err:139) - at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
ERROR 2014-09-30 21:38:46,270 (System.err:139) - at java.net.Socket.connect(Socket.java:579)
ERROR 2014-09-30 21:38:46,270 (System.err:139) - at java.net.Socket.connect(Socket.java:528)
ERROR 2014-09-30 21:38:46,271 (System.err:139) - at java.net.Socket.<init>(Socket.java:425)
ERROR 2014-09-30 21:38:46,271 (System.err:139) - at java.net.Socket.<init>(Socket.java:208)
ERROR 2014-09-30 21:38:46,271 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:149)
ERROR 2014-09-30 21:38:46,271 (System.err:139) - at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:120)
ERROR 2014-09-30 21:38:46,271 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191)
ERROR 2014-09-30 21:38:46,271 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404)
ERROR 2014-09-30 21:38:46,271 (System.err:139) - at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138)
ERROR 2014-09-30 21:38:46,271 (System.err:139) - ... 19 more
DEBUG 2014-09-30 21:38:46,277 (org.apache.axis.transport.http.HTTPSender:125) - Enter: HTTPSender::invoke
|
|
From: Jorge S. M. de J. <jor...@wu...> - 2014-09-29 14:30:47
|
Hi to all Deniz, have you checked the explanation on how to work with XML?? http://wiki.rsg.pml.ac.uk/pywps/XMLIO Could you run the workflows and with the providence activated so that Taverna keeps information on the request sent and returned??? I think the WSDL is correct, is just a problem understanding how things work. Cheers Jorge On 28-09-14 20:16, Alan R Williams wrote: > Hello, > > Can you enable logging of the SOAP messages? See > http://dev.mygrid.org.uk/wiki/pages/viewpage.action?pageId=18974840 > > Try to call the 'ExecuteProcess_ogrbuffer' service. > > You can find the logs in the logs subfolder of the folder opened under > Advanced -> Show logs and data folder. Can you then send > taverna-*-2.5.0.log to su...@my... ? * is probably enterprise > for you. > > Alan > > ------------------------------------------------------------------------------ > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk > _______________________________________________ > taverna-users mailing list > tav...@li... > tav...@li... > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/about/contact-us/ -- ISRIC - World Soil Information Post: PO box 353, 6700 AJ, Wageningen, The Netherlands Visiting Address: Droevendaalsesteeg 3, 6708 PB Wageningen (Bdg. 101), Office: C.013 Office Phone: +31 (0) 317 4 83715 Mobile Phone: +31 (0) 613 9 06950 OpenPGPKey: 0xA3D0065A |
|
From: Alan R W. <ala...@ma...> - 2014-09-28 18:16:22
|
Hello, Can you enable logging of the SOAP messages? See http://dev.mygrid.org.uk/wiki/pages/viewpage.action?pageId=18974840 Try to call the 'ExecuteProcess_ogrbuffer' service. You can find the logs in the logs subfolder of the folder opened under Advanced -> Show logs and data folder. Can you then send taverna-*-2.5.0.log to su...@my... ? * is probably enterprise for you. Alan |
|
From: Alan R W. <ala...@ma...> - 2014-09-27 09:43:09
|
On 25-Sep-14 16:08, Deniz .. wrote: > Hello everyone, Hello > I`m new to Taverna. I`m using 'Taverna workbench enterprise 2.5.0' in > windows 8 environment. I have loaded some WSDL services to use in my > workflow. But I couldn`t load XML input files to my services. When you say "my services" - are they services that your machine is hosting or are they somewhere else? > As an > input, text files and single values are ok, but I couldn`t succeed to > run services with XML files neither from 'set file location' nor from > 'Set URL'. > > It gives following errors: > > Processor 'ExecuteProcess_returner' - Port 'ProcessOutputs': An error > occurred invoking the WSDL service > (500)Internal Server Error Internal Server Error is returned by the machine that has the WSDL service on it. See http://en.wikipedia.org/wiki/List_of_HTTP_status_codes#5xx_Server_Error What service are you trying to call? If you send more information I can check that it still happens with, for example, SoapUI. [snip] > I tried similar solutions from mailing list but I`m still getting the > same error. > If anyone could help me, I`ll be pleased. > Thank you very much, > > Phd student Alan |
|
From: Deniz .. <dul...@ho...> - 2014-09-25 15:09:00
|
Hello everyone, I`m new to Taverna. I`m using 'Taverna workbench enterprise 2.5.0' in windows 8 environment. I have loaded some WSDL services to use in my workflow. But I couldn`t load XML input files to my services. As an input, text files and single values are ok, but I couldn`t succeed to run services with XML files neither from 'set file location' nor from 'Set URL'. It gives following errors: Processor 'ExecuteProcess_returner' - Port 'ProcessOutputs': An error occurred invoking the WSDL service (500)Internal Server Error org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:744) org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:144) org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) org.apache.axis.client.Call.invokeEngine(Call.java:2784) org.apache.axis.client.Call.invoke(Call.java:2767) org.apache.axis.client.Call.invoke(Call.java:1910) net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invokeCall(WSDLSOAPInvoker.java:198) net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invoke(WSDLSOAPInvoker.java:139) net.sf.taverna.t2.activities.wsdl.T2WSDLSOAPInvoker.invoke(T2WSDLSOAPInvoker.java:281) net.sf.taverna.t2.activities.wsdl.WSDLActivity$1.run(WSDLActivity.java:289) java.lang.Thread.run(Thread.java:724) I tried similar solutions from mailing list but I`m still getting the same error. If anyone could help me, I`ll be pleased. Thank you very much, Phd student |
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