#202: Deploy Data Builder at each GPC site
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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: |
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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=XXXXX
/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 INFO engine.url.URL(extract_password=...,
drivername=..., host=..., port=..., database=..., username=...,
password=...)
2015-01-15 02:04:12,761 INFO dataset DB:
sqlite:////home/databuilder/heron/BCS_for_GPC.db
2015-01-15 02:04:12,766 INFO exporting: 2 concepts from #2175 Breas-30
[-0440 @02:00:54 [1-15-2015] [databuilder] [PATIENTSET_2175]
2015-01-15 02:04:12,766 INFO initializing 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 INFO data summary:
Variable N. Patient N. Obs.
Language [607,674 facts; 303,837 patient 374 748
0390 Date of Diagnosis [8,654 facts; 8,1 374 424
0400 Primary Site [8,654 facts; 8,107 pa 374 848
0410 Laterality [8,654 facts; 8,107 pati 374 424
0440 Grade [8,653 facts; 8,106 patients] 374 424
0490 Diagnostic Confirmation [8,654 fact 374 424
0521 Morph--Type&Behav ICD-O-3 [7,691 fa 338 383
0820 Regional Nodes Positive [8,589 fact 374 424
0830 Regional Nodes Examined [8,589 fact 374 424
2850 CS Mets at DX [6,682 facts; 6,221 p 372 422
2860 CS Mets Eval [6,862 facts; 6,393 pa 372 422
<.... 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>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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