Can not create new program in Browser Tab
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Gang Liu
Apr 20, 2017, 12:38:44 PM4/20/17
to transmart-discuss
Hi all,
After I installed transmart 16.2 new release on ubuntu 14.04, I run into similar problem as this post https://groups.google.com/forum/#!msg/transmart-discuss/_p3Tuu1_h24/DOIykx_ZAwAJ;context-place=forum/transmart-discuss. I can not create a program in Browser Tab since therapeutic domain is required but it can not auto fill a value. Can anyone help on this?
Thanks,
Gang
Ward Weistra
Apr 21, 2017, 4:25:55 AM4/21/17
to transmart-discuss, Peter Rice
To be sure I'll copy the answer here that Peter Rice gave on the Hipchat support room to the same question:
[10:12 AM] Peter Rice: Hi @GangLiuGuest the therapeutic domains should be set up when you installed transmart.
[10:15 AM] Peter Rice: Two possibilities... some bug stopping it from finding the domains (check the /var/log/tomcat7/transmart.log file for any stacktrace messages) or something went wrong with the database loading - check table biomart.bio_concept_code where code_type_name = 'THERAPEUTIC_DOMAIN' that is where the Browse tab looks for them.
Gang Liu
Apr 21, 2017, 10:09:01 AM4/21/17
to transmar...@googlegroups.com, Peter Rice
Thank you for your quick response. Based on your instructions, i first checked the databases loaded in transmart and found that the table biomart.bio_concept_code was loaded properly. "THERAPEUTIC_DOMAIN" was found and the table looked fine. Then I went to see the log file. I did find a lot of warning messages and error messages as well. Please see these messages as below.
------------------------------------------------------------------------
20-04-2017 09:36:26,623 WARN GrailsUtil - [WARNING] Property [id] of domain class blend4j.plugin.StatusOfExport has type [int] and doesn't support constraint [nullable]. This constraint will not be checked during validation.
20-04-2017 09:36:26,726 WARN GrailsUtil - [WARNING] Property [id] of domain class blend4j.plugin.GalaxyUserDetails has type [int] and doesn't support constraint [nullable]. This constraint will not be checked during validation.
20-04-2017 09:36:38,832 WARN DefaultGrailsApplicationAttributes - ApplicationContext not found in org.codehaus.groovy.grails.APPLICATION_CONTEXT attribute of servlet context.
20-04-2017 09:36:39,732 WARN ModuleDeclarationsFactory - 'grails.resources.modules' in config does not define any modules
20-04-2017 09:36:42,795 WARN GrailsUtil - [WARNING] Property [id] of domain class blend4j.plugin.StatusOfExport has type [int] and doesn't support constraint [nullable]. This constraint will not be checked during validation.
20-04-2017 09:36:42,809 WARN GrailsUtil - [WARNING] Property [id] of domain class blend4j.plugin.GalaxyUserDetails has type [int] and doesn't support constraint [nullable]. This constraint will not be checked during validation.
20-04-2017 09:42:16,474 ERROR FmFolderController - Unable to save program
20-04-2017 09:42:16,490 ERROR FmFolderController - <ul><li>Therapeutic domain field requires a value.</li></ul>
20-04-2017 09:55:56,140 ERROR ResourceMeta - While processing /css/genesignature.css, a resource was required but not found: /images/skin/info.png
20-04-2017 09:55:56,143 WARN ResourceMetaStore - Cannot locate resource [/images/skin/info.png]
20-04-2017 09:55:56,143 WARN cssrewriter - Cannot resolve CSS resource, leaving link as is: resource:/images/skin/info.png
20-04-2017 10:16:41,728 ERROR GrailsExceptionResolver - IllegalArgumentException occurred when processing request: [POST] /transmart/ontology/showConceptDefinition
Concept key must start with \\. Stacktrace follows:
java.lang.IllegalArgumentException: Concept key must start with \\
at org.transmartproject.core.concept.ConceptKey.<init>(ConceptKey.groovy:42)
at org.transmartproject.db.ontology.AcrossTrialsConceptsResourceDecorator.getByKey(AcrossTrialsConceptsResourceDecorator.groovy:43)
at OntologyController$_closure7.doCall(OntologyController.groovy:89)
at grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:198)
at grails.plugin.cache.web.filter.AbstractFilter.doFilter(AbstractFilter.java:63)
at grails.plugin.springsecurity.web.filter.GrailsAnonymousAuthenticationFilter.doFilter(GrailsAnonymousAuthenticationFilter.java:53)
at grails.plugin.springsecurity.web.authentication.RequestHolderAuthenticationFilter.doFilter(RequestHolderAuthenticationFilter.java:53)
at grails.plugin.springsecurity.web.authentication.logout.MutableLogoutFilter.doFilter(MutableLogoutFilter.java:62)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
20-04-2017 10:22:36,081 ERROR FmFolderController - Unable to save program
20-04-2017 10:22:36,083 ERROR FmFolderController - <ul><li>Name field requires a value.</li><li>Description field requires a value.</li><li>Program target/pathway/phenotype field requires a value.</li><li>Therapeutic domain field requires a value.</li></ul>
------------------------------------------------------------------------
Can you instruct how to correct these errors?
Thank you!
Gang
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Peter Rice
Apr 21, 2017, 11:28:05 AM4/21/17
to Gang Liu, transmar...@googlegroups.com
Hi Gang,
I wonder why it used the AcrossTrials code. But that was after.
I see the failure to define the program, but no other message from the
program definition except to say it had no therapeutic domain.
Do you see anything when you try to type the first letter of the
therapeutic domain? It should offer you a list of choices, or write an
rror message to the log file
One possibility is to edit your
~tomcat7/.grails/transmartConfig/Config.groovy file and change the log4j
definition from "warn" to "info" to see if any more messages help.
Also, you could look for any browser error messages (e.g. with Firebug
for firefox, or whetever Crhome or other browsers use).
Hope that helps.
Peter
> <https://wiki.transmartfoundation.org/display/transmartwiki/Getting+Support>
> <mailto:transmart-disc...@googlegroups.com>.
> <https://groups.google.com/d/optout>.
>
>
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I wonder why it used the AcrossTrials code. But that was after.
I see the failure to define the program, but no other message from the
program definition except to say it had no therapeutic domain.
Do you see anything when you try to type the first letter of the
therapeutic domain? It should offer you a list of choices, or write an
rror message to the log file
One possibility is to edit your
~tomcat7/.grails/transmartConfig/Config.groovy file and change the log4j
definition from "warn" to "info" to see if any more messages help.
Also, you could look for any browser error messages (e.g. with Firebug
for firefox, or whetever Crhome or other browsers use).
Hope that helps.
Peter
> to the same question:
>
> [10:12 AM] Peter Rice: Hi @GangLiuGuest the therapeutic domains
> should be set up when you installed transmart.
> [10:15 AM] Peter Rice: Two possibilities... some bug stopping it
> from finding the domains (check the /var/log/tomcat7/transmart.log
> file for any stacktrace messages) or something went wrong with the
> database loading - check table biomart.bio_concept_code where
> code_type_name = 'THERAPEUTIC_DOMAIN' that is where the Browse tab
> looks for them.
>
> On Thursday, April 20, 2017 at 6:38:44 PM UTC+2, Gang Liu wrote:
>
> Hi all,
>
> After I installed transmart 16.2 new release on ubuntu 14.04, I
> run into similar problem as this post
> https://groups.google.com/forum/#!msg/transmart-discuss/_p3Tuu1_h24/DOIykx_ZAwAJ;context-place=forum/transmart-discuss
> <https://groups.google.com/forum/#!msg/transmart-discuss/_p3Tuu1_h24/DOIykx_ZAwAJ;context-place=forum/transmart-discuss>.
>
> [10:12 AM] Peter Rice: Hi @GangLiuGuest the therapeutic domains
> should be set up when you installed transmart.
> [10:15 AM] Peter Rice: Two possibilities... some bug stopping it
> from finding the domains (check the /var/log/tomcat7/transmart.log
> file for any stacktrace messages) or something went wrong with the
> database loading - check table biomart.bio_concept_code where
> code_type_name = 'THERAPEUTIC_DOMAIN' that is where the Browse tab
> looks for them.
>
> On Thursday, April 20, 2017 at 6:38:44 PM UTC+2, Gang Liu wrote:
>
> Hi all,
>
> After I installed transmart 16.2 new release on ubuntu 14.04, I
> run into similar problem as this post
> https://groups.google.com/forum/#!msg/transmart-discuss/_p3Tuu1_h24/DOIykx_ZAwAJ;context-place=forum/transmart-discuss
> I can not create a program in Browser Tab since therapeutic
> domain is required but it can not auto fill a value. Can anyone
> help on this?
>
> Thanks,
> Gang
>
> --
> For more ways to get in contact with the tranSMART community visit
> https://wiki.transmartfoundation.org/display/transmartwiki/Getting+Support
> <https://wiki.transmartfoundation.org/display/transmartwiki/Getting+Support>
> ---
> You received this message because you are subscribed to a topic in
> the Google Groups "transmart-discuss" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/transmart-discuss/YS_5v4cmyZU/unsubscribe
> <https://groups.google.com/d/topic/transmart-discuss/YS_5v4cmyZU/unsubscribe>.
> domain is required but it can not auto fill a value. Can anyone
> help on this?
>
> Thanks,
> Gang
>
> --
> For more ways to get in contact with the tranSMART community visit
> https://wiki.transmartfoundation.org/display/transmartwiki/Getting+Support
> <https://wiki.transmartfoundation.org/display/transmartwiki/Getting+Support>
> ---
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> https://groups.google.com/d/msgid/transmart-discuss/47872bc8-823f-416b-9adb-3e781555aab8%40googlegroups.com
> <https://groups.google.com/d/optout>.
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>
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Gang Liu
Apr 21, 2017, 2:58:05 PM4/21/17
to Peter Rice, transmar...@googlegroups.com
Hi Peter,
I followed your instruction to get the detailed error messages. Tying the letter like "D" or "E" did lead to several hits in the database but no hits were shown in the IE and the new program was not created. Any idea about what went wrong?
--------------------------------
21-04-2017 14:38:47,491 INFO MetaDataController - EXT SEARCH called
21-04-2017 14:38:47,491 INFO MetaDataController - [term:C, codeTypeName:THERAPEUTIC_DOMAIN, _:1492799968921, action:extSearch, controller:metaData]
21-04-2017 14:38:47,493 INFO MetaDataController - There are 2 THERAPEUTIC_DOMAIN records found in ConceptCode
21-04-2017 14:38:49,145 INFO FmFolderController - saveProgram called
21-04-2017 14:38:49,145 INFO FmFolderController - [id:, description:TEST, amTagItem_31:DIS:D000388, folderName:TEST, folderType:PROGRAM, action:saveProgram, controller:fmFolder]
21-04-2017 14:38:49,157 ERROR FmFolderController - Unable to save program
21-04-2017 14:38:49,158 ERROR FmFolderController - <ul><li>Therapeutic domain field requires a value.</li></ul>
21-04-2017 14:38:50,459 INFO FmFolderController - saveProgram called
21-04-2017 14:38:50,459 INFO FmFolderController - [id:, description:TEST, amTagItem_31:DIS:D000388, folderName:TEST, folderType:PROGRAM, action:saveProgram, controller:fmFolder]
21-04-2017 14:38:50,470 ERROR FmFolderController - Unable to save program
21-04-2017 14:38:50,471 ERROR FmFolderController - <ul><li>Therapeutic domain field requires a value.</li></ul>
21-04-2017 14:40:00,002 INFO FmFolderService - importFiles() called
21-04-2017 14:45:00,002 INFO FmFolderService - importFiles() called
21-04-2017 14:49:41,304 INFO MetaDataController - EXT SEARCH called
21-04-2017 14:49:41,304 INFO MetaDataController - [term:D, codeTypeName:THERAPEUTIC_DOMAIN, _:1492800622741, action:extSearch, controller:metaData]
21-04-2017 14:49:41,306 INFO MetaDataController - There are 2 THERAPEUTIC_DOMAIN records found in ConceptCode
21-04-2017 14:49:43,680 INFO MetaDataController - EXT SEARCH called
21-04-2017 14:49:43,681 INFO MetaDataController - [term:, codeTypeName:THERAPEUTIC_DOMAIN, _:1492800625142, action:extSearch, controller:metaData]
21-04-2017 14:49:43,684 INFO MetaDataController - There are 10 THERAPEUTIC_DOMAIN records found in ConceptCode
21-04-2017 14:49:44,296 INFO MetaDataController - EXT SEARCH called
21-04-2017 14:49:44,296 INFO MetaDataController - [term:D, codeTypeName:THERAPEUTIC_DOMAIN, _:1492800625758, action:extSearch, controller:metaData]
21-04-2017 14:49:44,298 INFO MetaDataController - There are 2 THERAPEUTIC_DOMAIN records found in ConceptCode
21-04-2017 14:49:45,058 INFO MetaDataController - EXT SEARCH called
21-04-2017 14:49:45,058 INFO MetaDataController - [term:, codeTypeName:THERAPEUTIC_DOMAIN, _:1492800626518, action:extSearch, controller:metaData]
21-04-2017 14:49:45,061 INFO MetaDataController - There are 10 THERAPEUTIC_DOMAIN records found in ConceptCode
21-04-2017 14:49:45,419 INFO MetaDataController - EXT SEARCH called
21-04-2017 14:49:45,419 INFO MetaDataController - [term:E, codeTypeName:THERAPEUTIC_DOMAIN, _:1492800626880, action:extSearch, controller:metaData]
21-04-2017 14:49:45,421 INFO MetaDataController - There are 2 THERAPEUTIC_DOMAIN records found in ConceptCode
21-04-2017 14:49:46,402 INFO MetaDataController - EXT SEARCH called
21-04-2017 14:49:46,402 INFO MetaDataController - [term:, codeTypeName:THERAPEUTIC_DOMAIN, _:1492800627862, action:extSearch, controller:metaData]
21-04-2017 14:49:46,405 INFO MetaDataController - There are 10 THERAPEUTIC_DOMAIN records found in ConceptCode
21-04-2017 14:49:46,780 INFO MetaDataController - EXT SEARCH called
21-04-2017 14:49:46,780 INFO MetaDataController - [term:E, codeTypeName:THERAPEUTIC_DOMAIN, _:1492800628241, action:extSearch, controller:metaData]
21-04-2017 14:49:46,782 INFO MetaDataController - There are 2 THERAPEUTIC_DOMAIN records found in ConceptCode
21-04-2017 14:50:00,002 INFO FmFolderService - importFiles() called
--------------------------------
Best,
Gang
To view this discussion on the web visit
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Peter Rice
Apr 24, 2017, 7:37:53 AM4/24/17
to Gang Liu, transmar...@googlegroups.com
Hi Gang,
That looks good. It should find two therapeutic domains for both D and E
as the first letter.
Do you see any error message in your browser diagnostics?
What browser (and which version) are you using?
regards,
Peter
> <mailto:wa...@thehyve.nl> <mailto:wa...@thehyve.nl
> transmart-disc...@googlegroups.com
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>
> <mailto:transmart-disc...@googlegroups.com
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>>.
That looks good. It should find two therapeutic domains for both D and E
as the first letter.
Do you see any error message in your browser diagnostics?
What browser (and which version) are you using?
regards,
Peter
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>
> <mailto:transmart-disc...@googlegroups.com
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/transmart-discuss/47872bc8-823f-416b-9adb-3e781555aab8%40googlegroups.com
> <https://groups.google.com/d/msgid/transmart-discuss/47872bc8-823f-416b-9adb-3e781555aab8%40googlegroups.com>
>
> <https://groups.google.com/d/msgid/transmart-discuss/47872bc8-823f-416b-9adb-3e781555aab8%40googlegroups.com?utm_medium=email&utm_source=footer
> https://groups.google.com/d/msgid/transmart-discuss/47872bc8-823f-416b-9adb-3e781555aab8%40googlegroups.com
> <https://groups.google.com/d/msgid/transmart-discuss/47872bc8-823f-416b-9adb-3e781555aab8%40googlegroups.com>
>
Gang Liu
Apr 24, 2017, 10:43:30 AM4/24/17
to Peter Rice, transmar...@googlegroups.com
Hi Peter,
Thanks for the follow-up. I did try IE, Chrome, and Firfox. All of them showed no http error messages in console window after trying to save the program. In Firefox, the console windows are as below:
There are some error message in "filter" window.
"Expected ‘none’, URL, or filter function but found ‘Alpha(’. Error in parsing value for ‘filter’. Declaration
dropped."
Is this related?
Thanks,
Gang
Peter Rice
Apr 24, 2017, 11:01:49 AM4/24/17
to Gang Liu, transmar...@googlegroups.com
Hi Gang,
I do not think this is a problem, but I see the alpha line in sanofi.css
on line 615 for 16.2.
I can see from the second screenshot it is passing a disease DIS:012723,
plus 'aa' as the program name and description, but there is no
therapeutic domain.
It seems to be missing the display of the two therapeutic domains
starting with 'D' or 'E' so you were unable to pick one. That is the
step where we need to find a diagnostic message somewhere.
regards,
Peter
On 24/04/2017 15:43, Gang Liu wrote:
> Hi Peter,
>
> parsing value for ‘filter’. Declaration*
> *dropped."
> *
> FmFolderController - saveProgram called
> 21-04-2017 14 <tel:21-04-2017%2014>:38:49,145 INFO
> FmFolderController - saveProgram called
> 21-04-2017 14 <tel:21-04-2017%2014>:38:50,459 INFO
> FmFolderService - importFiles() called
> 21-04-2017 14 <tel:21-04-2017%2014>:45:00,002 INFO
> FmFolderService - importFiles() called
> 21-04-2017 14 <tel:21-04-2017%2014>:49:41,304 INFO
> <mailto:peter...@transmartfoundation.org>
> <mailto:peter...@transmartfoundation.org
> transmart-disc...@googlegroups.com
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>
>
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com
> <mailto:transmart-discuss%252Buns...@googlegroups.com>>
>
> <mailto:transmart-disc...@googlegroups.com
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>
>
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com
> <mailto:transmart-discuss%252Buns...@googlegroups.com>>>.
I do not think this is a problem, but I see the alpha line in sanofi.css
on line 615 for 16.2.
I can see from the second screenshot it is passing a disease DIS:012723,
plus 'aa' as the program name and description, but there is no
therapeutic domain.
It seems to be missing the display of the two therapeutic domains
starting with 'D' or 'E' so you were unable to pick one. That is the
step where we need to find a diagnostic message somewhere.
regards,
Peter
On 24/04/2017 15:43, Gang Liu wrote:
> Hi Peter,
>
> Thanks for the follow-up. I did try IE, Chrome, and Firfox. All of them
> showed no http error messages in console window after trying to save the
> program. In Firefox, the console windows are as below:
>
> Inline image 1
> showed no http error messages in console window after trying to save the
> program. In Firefox, the console windows are as below:
>
>
> Inline image 2
>
> There are some error message in "filter" window.
>
> *"Expected ‘none’, URL, or filter function but found ‘Alpha(’. Error in
> Inline image 2
>
> There are some error message in "filter" window.
>
> parsing value for ‘filter’. Declaration*
> *dropped."
> *
>
> Is this related?
>
> Thanks,
> Gang
>
>
> On Mon, Apr 24, 2017 at 11:37 AM, Peter Rice
> <peter...@transmartfoundation.org
> Is this related?
>
> Thanks,
> Gang
>
>
> On Mon, Apr 24, 2017 at 11:37 AM, Peter Rice
> <peter...@transmartfoundation.org
> <mailto:peter...@transmartfoundation.org>> wrote:
>
> Hi Gang,
>
> That looks good. It should find two therapeutic domains for both D
> and E as the first letter.
>
> Do you see any error message in your browser diagnostics?
>
> What browser (and which version) are you using?
>
> regards,
>
> Peter
>
>
>
> On 21/04/2017 19:57, Gang Liu wrote:
>
> Hi Peter,
>
> I followed your instruction to get the detailed error messages.
> Tying the letter like "D" or "E" did lead to several hits in the
> database but no hits were shown in the IE and the new program
> was not created. Any idea about what went wrong?
>
> --------------------------------
> 21-04-2017 14 <tel:21-04-2017%2014>:38:47,491 INFO
>
> Hi Gang,
>
> That looks good. It should find two therapeutic domains for both D
> and E as the first letter.
>
> Do you see any error message in your browser diagnostics?
>
> What browser (and which version) are you using?
>
> regards,
>
> Peter
>
>
>
> On 21/04/2017 19:57, Gang Liu wrote:
>
> Hi Peter,
>
> I followed your instruction to get the detailed error messages.
> Tying the letter like "D" or "E" did lead to several hits in the
> database but no hits were shown in the IE and the new program
> was not created. Any idea about what went wrong?
>
> --------------------------------
> MetaDataController - EXT SEARCH called
> 21-04-2017 14 <tel:21-04-2017%2014>:38:47,491 INFO
> MetaDataController - [term:C, codeTypeName:THERAPEUTIC_DOMAIN,
> _:1492799968921, action:extSearch, controller:metaData]
> 21-04-2017 14 <tel:21-04-2017%2014>:38:47,493 INFO
> _:1492799968921, action:extSearch, controller:metaData]
> MetaDataController - There are 2 THERAPEUTIC_DOMAIN records
> found in ConceptCode
> 21-04-2017 14 <tel:21-04-2017%2014>:38:49,145 INFO
> found in ConceptCode
> FmFolderController - saveProgram called
> 21-04-2017 14 <tel:21-04-2017%2014>:38:49,145 INFO
> FmFolderController - [id:, description:TEST,
> amTagItem_31:DIS:D000388, folderName:TEST, folderType:PROGRAM,
> action:saveProgram, controller:fmFolder]
> 21-04-2017 14 <tel:21-04-2017%2014>:38:49,157 ERROR
> amTagItem_31:DIS:D000388, folderName:TEST, folderType:PROGRAM,
> action:saveProgram, controller:fmFolder]
> FmFolderController - Unable to save program
> 21-04-2017 14 <tel:21-04-2017%2014>:38:49,158 ERROR
> FmFolderController - <ul><li>Therapeutic domain field requires a
> value.</li></ul>
> 21-04-2017 14 <tel:21-04-2017%2014>:38:50,459 INFO
> value.</li></ul>
> FmFolderController - saveProgram called
> 21-04-2017 14 <tel:21-04-2017%2014>:38:50,459 INFO
> FmFolderController - [id:, description:TEST,
> amTagItem_31:DIS:D000388, folderName:TEST, folderType:PROGRAM,
> action:saveProgram, controller:fmFolder]
> 21-04-2017 14 <tel:21-04-2017%2014>:38:50,470 ERROR
> amTagItem_31:DIS:D000388, folderName:TEST, folderType:PROGRAM,
> action:saveProgram, controller:fmFolder]
> FmFolderController - Unable to save program
> 21-04-2017 14 <tel:21-04-2017%2014>:38:50,471 ERROR
> FmFolderController - <ul><li>Therapeutic domain field requires a
> value.</li></ul>
> 21-04-2017 14 <tel:21-04-2017%2014>:40:00,002 INFO
> value.</li></ul>
> FmFolderService - importFiles() called
> 21-04-2017 14 <tel:21-04-2017%2014>:45:00,002 INFO
> FmFolderService - importFiles() called
> 21-04-2017 14 <tel:21-04-2017%2014>:49:41,304 INFO
> MetaDataController - EXT SEARCH called
> 21-04-2017 14 <tel:21-04-2017%2014>:49:41,304 INFO
> MetaDataController - [term:D, codeTypeName:THERAPEUTIC_DOMAIN,
> _:1492800622741, action:extSearch, controller:metaData]
> 21-04-2017 14 <tel:21-04-2017%2014>:49:41,306 INFO
> _:1492800622741, action:extSearch, controller:metaData]
> MetaDataController - There are 2 THERAPEUTIC_DOMAIN records
> found in ConceptCode
> 21-04-2017 14 <tel:21-04-2017%2014>:49:43,680 INFO
> found in ConceptCode
> MetaDataController - EXT SEARCH called
> 21-04-2017 14 <tel:21-04-2017%2014>:49:43,681 INFO
> MetaDataController - [term:, codeTypeName:THERAPEUTIC_DOMAIN,
> _:1492800625142, action:extSearch, controller:metaData]
> 21-04-2017 14 <tel:21-04-2017%2014>:49:43,684 INFO
> _:1492800625142, action:extSearch, controller:metaData]
> MetaDataController - There are 10 THERAPEUTIC_DOMAIN records
> found in ConceptCode
> 21-04-2017 14 <tel:21-04-2017%2014>:49:44,296 INFO
> found in ConceptCode
> MetaDataController - EXT SEARCH called
> 21-04-2017 14 <tel:21-04-2017%2014>:49:44,296 INFO
> MetaDataController - [term:D, codeTypeName:THERAPEUTIC_DOMAIN,
> _:1492800625758, action:extSearch, controller:metaData]
> 21-04-2017 14 <tel:21-04-2017%2014>:49:44,298 INFO
> _:1492800625758, action:extSearch, controller:metaData]
> MetaDataController - There are 2 THERAPEUTIC_DOMAIN records
> found in ConceptCode
> 21-04-2017 14 <tel:21-04-2017%2014>:49:45,058 INFO
> found in ConceptCode
> MetaDataController - EXT SEARCH called
> 21-04-2017 14 <tel:21-04-2017%2014>:49:45,058 INFO
> MetaDataController - [term:, codeTypeName:THERAPEUTIC_DOMAIN,
> _:1492800626518, action:extSearch, controller:metaData]
> 21-04-2017 14 <tel:21-04-2017%2014>:49:45,061 INFO
> _:1492800626518, action:extSearch, controller:metaData]
> MetaDataController - There are 10 THERAPEUTIC_DOMAIN records
> found in ConceptCode
> 21-04-2017 14 <tel:21-04-2017%2014>:49:45,419 INFO
> found in ConceptCode
> MetaDataController - EXT SEARCH called
> 21-04-2017 14 <tel:21-04-2017%2014>:49:45,419 INFO
> MetaDataController - [term:E, codeTypeName:THERAPEUTIC_DOMAIN,
> _:1492800626880, action:extSearch, controller:metaData]
> 21-04-2017 14 <tel:21-04-2017%2014>:49:45,421 INFO
> _:1492800626880, action:extSearch, controller:metaData]
> MetaDataController - There are 2 THERAPEUTIC_DOMAIN records
> found in ConceptCode
> 21-04-2017 14 <tel:21-04-2017%2014>:49:46,402 INFO
> found in ConceptCode
> MetaDataController - EXT SEARCH called
> 21-04-2017 14 <tel:21-04-2017%2014>:49:46,402 INFO
> MetaDataController - [term:, codeTypeName:THERAPEUTIC_DOMAIN,
> _:1492800627862, action:extSearch, controller:metaData]
> 21-04-2017 14 <tel:21-04-2017%2014>:49:46,405 INFO
> _:1492800627862, action:extSearch, controller:metaData]
> MetaDataController - There are 10 THERAPEUTIC_DOMAIN records
> found in ConceptCode
> 21-04-2017 14 <tel:21-04-2017%2014>:49:46,780 INFO
> found in ConceptCode
> MetaDataController - EXT SEARCH called
> 21-04-2017 14 <tel:21-04-2017%2014>:49:46,780 INFO
> MetaDataController - [term:E, codeTypeName:THERAPEUTIC_DOMAIN,
> _:1492800628241, action:extSearch, controller:metaData]
> 21-04-2017 14 <tel:21-04-2017%2014>:49:46,782 INFO
> _:1492800628241, action:extSearch, controller:metaData]
> MetaDataController - There are 2 THERAPEUTIC_DOMAIN records
> found in ConceptCode
> 21-04-2017 14 <tel:21-04-2017%2014>:50:00,002 INFO
> found in ConceptCode
> FmFolderService - importFiles() called
> --------------------------------
>
> Best,
> Gang
>
> On Fri, Apr 21, 2017 at 11:27 AM, Peter Rice
> <peter...@transmartfoundation.org
> --------------------------------
>
> Best,
> Gang
>
> On Fri, Apr 21, 2017 at 11:27 AM, Peter Rice
> <mailto:peter...@transmartfoundation.org>
> <mailto:peter...@transmartfoundation.org
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>
>
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com
> <mailto:transmart-discuss%252Buns...@googlegroups.com>>
>
> <mailto:transmart-disc...@googlegroups.com
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>
>
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com
> <mailto:transmart-discuss%252Buns...@googlegroups.com>>>.
Gang Liu
Apr 24, 2017, 11:20:29 AM4/24/17
to Peter Rice, transmar...@googlegroups.com
How can we debug to identify the problem?
Thanks,
Gang
On Mon, Apr 24, 2017 at 3:01 PM, Peter Rice <peter...@transmartfoundation.org> wrote:
Hi Gang,
<mailto:transmart-discuss%2Bunsubs...@googlegroups.com
<mailto:transmart-discuss%252Bunsub...@googlegroups.com>>
<mailto:transmart-discuss+unsubsc...@googlegroups.com
<mailto:transmart-discuss%2Bunsubs...@googlegroups.com>
<mailto:transmart-discuss%2Bunsubs...@googlegroups.com
<mailto:transmart-discuss%252Bunsub...@googlegroups.com>>>.
Peter Rice
Apr 24, 2017, 11:31:07 AM4/24/17
to Gang Liu, transmar...@googlegroups.com
Hi Gang,
Which version of transmart are you running - what was the size or date
of the transmart.war file you downloaded?
regards,
Peter
On 24/04/2017 16:20, Gang Liu wrote:
> How can we debug to identify the problem?
>
> Thanks,
> Gang
>
> On Mon, Apr 24, 2017 at 3:01 PM, Peter Rice
> <peter...@transmartfoundation.org
> <mailto:transmart-discuss%252Buns...@googlegroups.com>
>
> <mailto:transmart-discuss%252Buns...@googlegroups.com
> <mailto:transmart-discuss%25252Bun...@googlegroups.com>>>
> <mailto:transmart-discuss%25252Bun...@googlegroups.com>>>>.
Which version of transmart are you running - what was the size or date
of the transmart.war file you downloaded?
regards,
Peter
On 24/04/2017 16:20, Gang Liu wrote:
> How can we debug to identify the problem?
>
> Thanks,
> Gang
>
> On Mon, Apr 24, 2017 at 3:01 PM, Peter Rice
> <peter...@transmartfoundation.org
> <peter...@transmartfoundation.org
> <mailto:peter...@transmartfoundation.org>
> <mailto:peter...@transmartfoundation.org
> <mailto:peter...@transmartfoundation.org>
> <mailto:peter...@transmartfoundation.org
> <peter...@transmartfoundation.org
> <mailto:peter...@transmartfoundation.org>
> <mailto:peter...@transmartfoundation.org
> <mailto:peter...@transmartfoundation.org>>
> <mailto:peter...@transmartfoundation.org
> <mailto:peter...@transmartfoundation.org>
>
> <mailto:peter...@transmartfoundation.org
> <mailto:peter...@transmartfoundation.org>
> <mailto:peter...@transmartfoundation.org
> <mailto:peter...@transmartfoundation.org>>
> <mailto:peter...@transmartfoundation.org
> <mailto:peter...@transmartfoundation.org>
>
> <mailto:peter...@transmartfoundation.org
> transmart-disc...@googlegroups.com
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>
>
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com
> <mailto:transmart-discuss%252Buns...@googlegroups.com>>
>
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>
>
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com
> <mailto:transmart-discuss%252Buns...@googlegroups.com>>
>
> <mailto:transmart-discuss%252Buns...@googlegroups.com>
>
> <mailto:transmart-discuss%252Buns...@googlegroups.com
> <mailto:transmart-discuss%25252Bun...@googlegroups.com>>>
>
> <mailto:transmart-disc...@googlegroups.com
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>
>
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com
> <mailto:transmart-discuss%252Buns...@googlegroups.com>>
>
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com
> <mailto:transmart-discuss%252Buns...@googlegroups.com>
>
> <mailto:transmart-discuss%252Buns...@googlegroups.com
> <mailto:transmart-disc...@googlegroups.com
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com>
>
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com
> <mailto:transmart-discuss%252Buns...@googlegroups.com>>
>
> <mailto:transmart-discuss%2Bunsu...@googlegroups.com
> <mailto:transmart-discuss%252Buns...@googlegroups.com>
>
> <mailto:transmart-discuss%25252Bun...@googlegroups.com>>>>.
Gang Liu
Apr 24, 2017, 11:43:28 AM4/24/17
to Peter Rice, transmar...@googlegroups.com
16.2 release and the size is 196496971. I used All-in-one script to install the transmart.
Thanks,
Gang
On Mon, Apr 24, 2017 at 3:31 PM, Peter Rice <peter...@transmartfoundation.org> wrote:
Hi Gang,
Which version of transmart are you running - what was the size or date of the transmart.war file you downloaded?
regards,
Peter
On 24/04/2017 16:20, Gang Liu wrote:
How can we debug to identify the problem?
Thanks,
Gang
<mailto:transmart-discuss+unsubsc...@googlegroups.com
<mailto:transmart-discuss%2Bunsubs...@googlegroups.com>
<mailto:transmart-discuss%2Bunsubs...@googlegroups.com
<mailto:transmart-discuss%252Bunsub...@googlegroups.com>>
<mailto:transmart-discuss%2Bunsubs...@googlegroups.com
<mailto:transmart-discuss%252Bunsub...@googlegroups.com>
Paula
Aug 17, 2017, 9:34:27 AM8/17/17
to transmart-discuss, peter...@transmartfoundation.org
Hi Gang,
Did you solve the issue with creating a program in the end? If so, can you share how?
It appears that I have the same issue. I checked that I get hits on the therapeutic domain when looking in the transmart.log, but nothing comes up in the dropdown.
Thanks,
Paula
On Monday, April 24, 2017 at 5:43:28 PM UTC+2, Gang Liu wrote:
16.2 release and the size is 196496971. I used All-in-one script to install the transmart.Thanks,Gang
On Mon, Apr 24, 2017 at 3:31 PM, Peter Rice <peter...@transmartfoundation.org> wrote:
Hi Gang,
Which version of transmart are you running - what was the size or date of the transmart.war file you downloaded?
regards,
Peter
On 24/04/2017 16:20, Gang Liu wrote:
How can we debug to identify the problem?
Thanks,
Gang
<peter...@transmartfoundation.org
<mailto:peter...@transmartfoundation.org>
<mailto:peter...@transmartfoundation.org
<mailto:peter...@transmartfoundation.org>>
<mailto:peter...@transmartfoundation.org
<mailto:peter...@transmartfoundation.org>
<mailto:peter...@transmartfoundation.org
<mailto:transmart-discuss%2Bunsu...@googlegroups.com
<mailto:transmart-discuss%252Bunsubscribe@googlegroups.com>
<mailto:transmart-discuss%252Bunsubscribe@googlegroups.com
<mailto:transmart-discuss%25252Bunsubscribe@googlegroups.com>>>
<mailto:transmart-discuss+unsub...@googlegroups.com
<mailto:transmart-discuss%2Bunsu...@googlegroups.com>
<mailto:transmart-discuss%2Bunsu...@googlegroups.com
<mailto:transmart-discuss%252Bunsubscribe@googlegroups.com>>
<mailto:transmart-discuss%2Bunsu...@googlegroups.com
<mailto:transmart-discuss%252Bunsubscribe@googlegroups.com>
<mailto:transmart-discuss%252Bunsubscribe@googlegroups.com
<mailto:transmart-discuss%25252Bunsubscribe@googlegroups.com>>>>.
Patrick Doherty
Sep 8, 2017, 7:44:12 AM9/8/17
to transmart-discuss
Hi all,
I've got exactly the same problem. Anyone know what the fix is?
Thanks
Patrick
Paula
Sep 8, 2017, 8:00:24 AM9/8/17
to transmart-discuss
Hi Patrick,
We managed to solve the issue of creating programs by updating the biomart.bio_data_uid table.
For some reason, release 16.2 appears to be missing some concepts (see concepts from release 16.2 branch: https://github.com/tranSMART-Foundation/transmart-data/blob/release-16.2/data/common/biomart/bio_data_uid.tsv vs the master branch: https://github.com/tranSMART-Foundation/transmart-data/blob/master/data/common/biomart/bio_data_uid.tsv), like THERAPEUTIC_DOMAIN, which is needed when creating a new program. This is something we discovered by looking at the source code, so I have no info on the reason for the difference.
There are several other concepts than THERAPEUTIC_DOMAIN that are missing from the bio_data_uid table, so if you want, I can share the SQL commands we used to insert the missing rows.
Kind regards,
Paula
Patrick Doherty
Sep 8, 2017, 8:40:39 AM9/8/17
to transmart-discuss
Hi Paula,
thanks for the reply - if you could share the sql that would be great!
Many thanks
Patrick
On Thursday, 20 April 2017 17:38:44 UTC+1, Gang Liu wrote:
On Thursday, 20 April 2017 17:38:44 UTC+1, Gang Liu wrote:
Paula
Sep 8, 2017, 10:25:03 AM9/8/17
to transmart-discuss
Hi Patrick,
Kind regards,
Paula
Patrick Doherty
Sep 11, 2017, 4:14:58 AM9/11/17
to transmart-discuss
Hi Paula,
that worked for me.
Many thanks for your help.
Patrick
On Thursday, 20 April 2017 17:38:44 UTC+1, Gang Liu wrote:
On Thursday, 20 April 2017 17:38:44 UTC+1, Gang Liu wrote:
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