Dear all,
My problem deals with the execution of the protocol check / validate pipeline.
I precise that the DicomToNifti pipeline works fine so a few things are well set up I guess.
The configuration I use is:
- NeuroDebian 6.0.6 (64 bit)
- Xnat Release 1.6.1
- java version 1.7.0_25
- Apache Tomcat/
6.0.35.0- PostgreSQL 8.4.17
My Protocol Check pipeline stops at 20% and then I receive a confirmation email of the failure which copies what's in the log file:
-----------
Pipeline:
/usr/local/xnat/pipeline/catalog/validation_tools/Validate.xml
Cause:
org.nrg.pipeline.exception.PipelineEngineException: Unable to complete pipeline Execution of
/usr/local/xnat/pipeline/xnat-tools/XNATRestClient -u ff0f1a06-568e-4816-9cd3-8fbd2534d9d5 -p ######## -host
http://127.0.0.1:8080/xnat/ -remote "/REST/projects/MIBRAIN_GL/resources/validation_xnat_mrSessionData/files/" -m GET > /Library/XNAT/build/MIBRAIN_GL/20130823_122415/WE021_MR1/VALIDATION/ at Step[id= 0b:]
was unsuccesfull Execution of /usr/local/xnat/pipeline/xnat-tools/XNATRestClient -u ff0f1a06-568e-4816-9cd3-8fbd2534d9d5 -p ######## -host
http://127.0.0.1:8080/xnat/ -remote "/REST/projects/MIBRAIN_GL/resources/validation_xnat_mrSessionData/files/" -m GET > /Library/XNAT/build/MIBRAIN_GL/20130823_122415/WE021_MR1/VALIDATION/ at Step[id= 0b:]
was unsuccesfull at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:226) at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:193) at org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:65)
at org.nrg.pipeline.client.XNATPipelineLauncher.run(XNATPipelineLauncher.java:231) at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:221)
--------------
and the long log file in the xnat_home/pipeline/log folder looks like that:
----------------------
[...]
FATAL main org.nrg.pipeline.client.XNATPipelineLauncher - Couldnt search for queued workflows
java.io.FileNotFoundException: /usr/share/tomcat6/32.xml (Permission denied)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(Unknown Source)
at java.io.FileOutputStream.<init>(Unknown Source)
at org.nrg.xnattools.xml.XMLSearch.execute(XMLSearch.java:248)
at org.nrg.xnattools.xml.XMLSearch.searchAll(XMLSearch.java:109)
at org.nrg.pipeline.client.XNATPipelineLauncher.isPipelineQueuedOrAwaitingOrOnHold(XNATPipelineLauncher.java:281)
at org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:63)
at org.nrg.pipeline.client.XNATPipelineLauncher.run(XNATPipelineLauncher.java:231)
at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:221)
DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre /usr/local/xnat/pipeline/catalog/validation_tools/resources/svrl/nrg_iso_svrl_for_xslt2.xsl [/usr/local/xnat/pipeline/catalog/validation_tools/resources/svrl/nrg_iso_svrl_for_xslt2.xsl]
DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^concat('validation_',translate(/Pipeline/parameters/parameter[name='sessionType']/values/unique/text(),':','_'))^ [validation_xnat_mrSessionData]
DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^concat(translate(/Pipeline/parameters/parameter[name='builddir']/values/unique/text(),'/',fileUtils:GetFileSeparator()),fileUtils:GetFileSeparator(),/Pipeline/parameters/parameter[name='sessionLabel']/values/unique/text())^ [/Library/XNAT/build/MIBRAIN_GL/20130823_122415/WE021_MR1]
DEBUG main httpclient.wire.header - >> "GET /xnat/REST/projects/MIBRAIN_GL/files?format=json HTTP/1.1[\r][\n]"
DEBUG main httpclient.wire.header - >> "User-Agent: Noelios-Restlet-Engine/1.1.rc1[\r][\n]"
DEBUG main httpclient.wire.header - >> "Cookie: JSESSIONID=9465AD3FD95DC676BB342C64AA74A9FE[\r][\n]"
DEBUG main httpclient.wire.header - >> "Accept: */*[\r][\n]"
DEBUG main httpclient.wire.header - >> "Host: 127.0.0.1:8080[\r][\n]"
DEBUG main httpclient.wire.header - >> "[\r][\n]"
DEBUG main httpclient.wire.header - << "HTTP/1.1 200 OK[\r][\n]"
DEBUG main httpclient.wire.header - << "HTTP/1.1 200 OK[\r][\n]"
DEBUG main httpclient.wire.header - << "Set-Cookie: SESSION_EXPIRATION_TIME="0,900000"; Version=1; Path=/[\r][\n]"
DEBUG main httpclient.wire.header - << "Date: Fri, 23 Aug 2013 10:24:18 GMT[\r][\n]"
DEBUG main httpclient.wire.header - << "Vary: Accept-Charset, Accept-Encoding, Accept-Language, Accept[\r][\n]"
DEBUG main httpclient.wire.header - << "Accept-Ranges: bytes[\r][\n]"
DEBUG main httpclient.wire.header - << "Server: Noelios-Restlet-Engine/1.1.6[\r][\n]"
DEBUG main httpclient.wire.header - << "Content-Type: application/json[\r][\n]"
DEBUG main httpclient.wire.header - << "Transfer-Encoding: chunked[\r][\n]"
DEBUG main httpclient.wire.header - << "[\r][\n]"
DEBUG main httpclient.wire.content - << "1"
DEBUG main httpclient.wire.content - << "3"
DEBUG main httpclient.wire.content - << "e"
DEBUG main httpclient.wire.content - << "[\r]"
DEBUG main httpclient.wire.content - << "[\n]"
DEBUG main httpclient.wire.content - << "{"
DEBUG main httpclient.wire.content - << ""ResultSet":{"Columns":[{"key":"URI","serverRoot":"/xnat"}],"Result":[{"Name":"mrsession_rules.sch","file_content":"","cat_ID":"16","collection":"validation_xnat_mrSessionData","file_format":"","file_tags":"","URI":"/data/projects/MIBRAIN_GL/resources/16/files/mrsession_rules.sch","Size":"6136"}], "title": "Files"}}"
DEBUG main httpclient.wire.content - << "[\r]"
DEBUG main httpclient.wire.content - << "[\n]"
DEBUG main httpclient.wire.content - << "0"
DEBUG main httpclient.wire.content - << "[\r]"
DEBUG main httpclient.wire.content - << "[\n]"
DEBUG main httpclient.wire.content - << "[\r]"
DEBUG main httpclient.wire.content - << "[\n]"
DEBUG main httpclient.wire.header - << "[\r][\n]"
[...]
----------------------
I'm afraid I can't move on in the debug of the pipeline so if someone has suggestions, they are welcome.
Thank you.
Gaelle.