Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: dconnolly Type: task | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Comment (by finamore.joe): The URLs mentioned in comment 20 are correct. The situation is that we have moved past using the native PostgreSQL DB and are now pointing to our production SQL server database. We should be using the data_builder account created in the installation process, I presume, for this access instead of demo. When I look at the /var/log/data_builder/cdr2edc.log I see that it is trying to verify access to the i2b2 database for the demo account: 2015-01-16 10:14:28,615 INFO __main__ logging request parameters to: 2015-01-16T10:14:28.615923-demo.json 2015-01-16 10:14:28,616 INFO __main__ checking i2b2 password for: demo How can I move into production mode and specify the data_builder account instead for this access. Thanks. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:21 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site
--+---
Reporter: dconnolly | Owner: dconnolly
Type: task | Status: assigned
Priority: major | Milestone: bc-survey-cohort-def
Component: data-sharing | Resolution:
Keywords: breast-cancer-cohort | Blocked By:
Blocking:|
--+---
Comment (by dconnolly):
Replying to [comment:21 finamore.joe]:
... We should be using the data_builder account created in the
installation process, I presume, for this access instead of demo. When
I look at the /var/log/data_builder/cdr2edc.log I see that it is trying to
verify access to the i2b2 database for the demo account
The Error from back-end: incorrect credentials diagnostic indicates
failure to verify **i2b2 hive account** credentials with the i2b2 PM cell,
not database account credentials.
Does the `i2b2hive.py` integration test work?
{{{
Integration test usage::
$ python i2b2hive.py http:.../index.php http:.../PMService/ demo
demouser
}}}
--
Ticket URL:
http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:22
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Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: dconnolly Type: task | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Comment (by finamore.joe): I apologize to the group for spamming them, but it is important that I get this working. I executed the i2b2hive.py integration test and have attached the results to this. If anyone would be inclined to work with me directly, that would be fine (finamore@mcrf.mfldclin.edu). As near as I can tell, it got past the 'checked_access()' call but am not 100% sure. Thank you. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:23 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site
--+---
Reporter: dconnolly | Owner: dconnolly
Type: task | Status: assigned
Priority: major | Milestone: bc-survey-cohort-def
Component: data-sharing | Resolution:
Keywords: breast-cancer-cohort | Blocked By:
Blocking:|
--+---
Comment (by dconnolly):
Replying to [comment:19 lv]:
I get the following error:
Error from back-end: incorrect credentials
That diagnostic means that the javascript in the plug-in called the
`dfbuild.cgi` script, and that CGI script tried to confirm the credentials
with the i2b2 hive, but it got an error.
This can happen if either of the two URLs in the `dfbuild.cgi` script
don't point to the i2b2 hive correctly:
{{{
python -m cdr2edc.param_check \
deid \
http://localhost/webclient/index.php \
http://localhost:9090/i2b2/services/PMService/ \
/var/log/data_builder
}}}
Those URLs are known to work for `i2b2vmware-1703a.zip` (BuilderSaga#i2b2
-vm-dep), but perhaps your configuration is different?
--
Ticket URL:
http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:20
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Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site
--+---
Reporter: dconnolly | Owner: dconnolly
Type: task | Status: assigned
Priority: major | Milestone: bc-survey-cohort-def
Component: data-sharing | Resolution:
Keywords: breast-cancer-cohort | Blocked By:
Blocking:|
--+---
Comment (by huhickman):
I have it installed our i2b2 instance here at UNMC. The plugin duly
generate requests and if I process the request by hand:
{{{
rito-clar-deid cdr2edc # LOGNAME=databuilder extract_password=X
/usr/local/bin/python2.7 ./dfbuilder.py ../deploy/test.conf
/var/log/data_builder/queue/2015-01-15T02:03:46.655805-databuilder.json
/home/hhickman/run_bc.log
2015-01-15 02:04:12,702 INFOengine.url.URL(extract_password=...,
drivername=..., host=..., port=..., database=..., username=...,
password=...)
2015-01-15 02:04:12,761 INFOdataset DB:
sqlite:home/databuilder/heron/BCS_for_GPC.db
2015-01-15 02:04:12,766 INFOexporting: 2 concepts from #2175 Breas-30
[-0440 @02:00:54 [1-15-2015] [databuilder] [PATIENTSET_2175]
2015-01-15 02:04:12,766 INFOinitializing tables in
Engine(sqlite:home/databuilder/heron/BCS_for_GPC.db)
2015-01-15 02:04:12,783 DEBUG dest_star tables: ['observation_fact',
'modifier_dimension', 'visit_dimension', 'concept_dimension',
'patient_dimension']
MANY LINES LATER
2015-01-15 02:04:56,116 INFOdata summary:
Variable N. PatientN. Obs.
Language [607,674 facts; 303,837 patient374748
0390 Date of Diagnosis [8,654 facts; 8,1374424
0400 Primary Site [8,654 facts; 8,107 pa374848
0410 Laterality [8,654 facts; 8,107 pati374424
0440 Grade [8,653 facts; 8,106 patients]374424
0490 Diagnostic Confirmation [8,654 fact374424
0521 Morph--TypeBehav ICD-O-3 [7,691 fa338383
0820 Regional Nodes Positive [8,589 fact374424
0830 Regional Nodes Examined [8,589 fact374424
2850 CS Mets at DX [6,682 facts; 6,221 p372422
2860 CS Mets Eval [6,862 facts; 6,393 pa372422
more logging of the rest of the breast cancer elements
}}}
The end result is :
{{{
-rw--- 1 root root 6.7M Jan 15 02:04 BCS_for_GPC.db
}}}
I did install this with a Python 2.7 distribution (not wanting to mess
with the CentOS stock 2.6 on our server)
I still need to clean things up but we're operational enough to generate
files.
--
Ticket URL:
http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:18
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Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: dconnolly Type: task | Status: assigned Priority: minor | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Comment (by lv): Replying to [comment:15 dconnolly]: What browser are you using? Chrome, mainly. I have also tried I.E. 9. Can you check the javascript console for error messages? We had some problems with non-standard javascript that chrome rejected earlier. I am seeing the following errors: Uncaught ReferenceError:/webclient/js- i2b2/cells/plugins/fsm/DFBuilder/tool_widgets.js:175 backend is not defined http://i2b2prod5-lc/webclient/js- i2b2/cells/plugins/fsm/KaplanMeierStat/assets/icefish2.gif Failed to load resource: the server responded with a status of 404 (Not Found) -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:16 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
Check in the Apache error log as well. When I was having issues with permissions, the error was in there. Phillip Sent from my iPhone On Jan 14, 2015, at 2:58 PM, GPC Informatics d...@madmode.com wrote: #202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: dconnolly Type: task | Status: assigned Priority: minor | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Comment (by lv): Replying to [comment:15 dconnolly]: What browser are you using? Chrome, mainly. I have also tried I.E. 9. Can you check the javascript console for error messages? We had some problems with non-standard javascript that chrome rejected earlier. I am seeing the following errors: Uncaught ReferenceError:/webclient/js- i2b2/cells/plugins/fsm/DFBuilder/tool_widgets.js:175 backend is not defined http://i2b2prod5-lc/webclient/js- i2b2/cells/plugins/fsm/KaplanMeierStat/assets/icefish2.gif Failed to load resource: the server responded with a status of 404 (Not Found) -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:16 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev UT Southwestern Medical Center The future of medicine, today. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: dconnolly Type: task | Status: assigned Priority: minor | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Changes (by dconnolly): * owner: preeder = dconnolly Comment: Several DevTeams seem to have the data builder deployed for testing, if not production. Info on availability for 16 Jan target: - KUMC - yes - CMH - N/A - Dec 17 plan: mid to late March (comment:6) - UIOWA - ??? - Dec 9 plan: 2 - 3 weeks - Jan 6: not present at teleconference (#12) - WISC - yes? - Jan 8: success reported by email - was that production or just test? - MCW - not likely - Jan 6 plan: will be using something other than DataBuilder to get the 16 Jan results out - Dec 9 update: complete for test data - MCRF - not likely - 6 Jan update - UMN - not likely - Dec 9 estimate: Begin work in January; February completion. - UNMC - not likely - Jan 6 update: need an alternate method - UTHSCSA - yes - Jan 9 (comment:11) - UTSW - yes? - Jan 9 success report by email (test? prod?) -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:12 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: preeder Type: task | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Changes (by dconnolly): * owner: gkowalski = preeder -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:9 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: dconnolly Type: task | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Changes (by nateapathy): * owner: nateapathy = dconnolly -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:7 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: nateapathy Type: task | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Comment (by nateapathy): For CMH/Cerner, we are targeting a mid-to-late March install of this functionality, largely due to complications of not being able to plug-and- play the install script, and having to accommodate planned engineering roadmaps that were solidified before we were made aware of this requirement. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:6 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: nateapathy Type: task | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Comment (by dconnolly): In discussion with Brian M. @ UIOWA, I realized that if the data builder isn't ready at all sites when the BC survey needs it, we should be able to run it at just one site and use the resulting SQL query at all sites. Or hand-code some SQL or something. This fallback option is #205. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:5 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: lv Type: task | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Comment (by dconnolly): Nate, yes, the short-term need for the data builder is for the breast cancer survey. And yes, that's only the first of many planned uses of the technique; see DataSecurity#providing-data. So please do provide an estimate for deployment at CMH. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:3 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: lv Type: task | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Comment (by nateapathy): Hi all - I apologize for not being on the call to discuss this yesterday. I wasn't clear that this involved input from all sites. Rita and I followed up on this yesterday afternoon and confirmed that CMH won't have any breast cancer cohort data, being a pediatric site. In light of that, do we still need to install the R Databuilder? If there are other use cases for this tool down the line for other cohorts, we can certainly take on that project. Knowing that will help inform our work prioritization. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:2 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site
#202: Deploy Data Builder at each GPC site --+--- Reporter: dconnolly | Owner: lv Type: task | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking:| --+--- Changes (by dconnolly): * owner: dconnolly = lv * status: new = assigned Comment: Laurel, In tomorrow's teleconference, please poll sites for their guestimate of when they can have the data builder deployed for use in the breast cancer survey. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/202#comment:1 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
