Re: [gpc-informatics] #205: interim builder for breast cancer cohort summary
#205: interim builder for breast cancer cohort summary --+--- Reporter: dconnolly | Owner: prakashnadkarni Type: enhancement | Status: closed Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: fixed Keywords: breast-cancer-cohort | Blocked By: 32, 204 Blocking:| --+--- Changes (by dconnolly): * cc: tmcmahon, bchrischilles, bradley-mcdowell@… (removed) Comment: See also UTHSCSA scripts: ticket:217#comment:18 -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/205#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] #205: interim builder for breast cancer cohort summary
#205: interim builder for breast cancer cohort summary --+--- Reporter: dconnolly | Owner: huhickman Type: enhancement | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: 32, 204 Blocking:| --+--- Comment (by bokov): Replying to [comment:2 dconnolly]: I just wrote up BuilderSaga#builder-sql-guide, based on a log of a data builder run. It includes the exact schema of the sqlite output file: attachment:builder_output_schema.sql:wiki:BuilderSaga as well as each SQL statement that the data builder runs. If in ours, the `variable` and `job` tables are blank, will that interfere with your being able to extract our data for the purposes of the breast cancer cohort selection? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/205#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] #205: interim builder for breast cancer cohort summary
#205: interim builder for breast cancer cohort summary --+--- Reporter: dconnolly | Owner: huhickman Type: enhancement | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: 32, 204 Blocking:| --+--- Comment (by bos): Replying to [comment:10 dconnolly]: Replying to [comment:9 bokov]: If in ours, the `variable` and `job` tables are blank, will that interfere with your being able to extract our data for the purposes of the breast cancer cohort selection? I expect we can do without `job`, but we rely in `variable`. It's computable from the XML definition of your query. By design, everybody is using **exactly** the same query (#204), so we can just copy it from another data file. But it's reasonably important to be sure. If you do a timeline of your results, you can use `timeline_to_job.py` (from the databuilder code) to compute a JSON file with the relevant details. With a little tweaking to not look for a patient set id, it would probably work on an XML query definition. Then see `export_terms()` in `dfbuilder.py` for how we get the data into the variable table. It might be easier to just write your own 50 line script; or perhaps I could factor the relevant parts out. I think the relationship between the query definition and the variable table is pretty straightforward. If necessary, just give me the XML query definition that you ran and I'll compute it. [[BR]] We had some i2b2 issues, so we had to build run the query manually, then convert it to sqlite. Hence, hence our job and variable tables are empty. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/205#comment:11 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] #205: interim builder for breast cancer cohort summary at MCW, UMN (was: interim builder for breast cancer cohort summary)
#205: interim builder for breast cancer cohort summary at MCW, UMN --+--- Reporter: dconnolly | Owner: huhickman Type: enhancement | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: 32, 204 Blocking:| --+--- Comment (by dconnolly): re-scoping this a bit while closing #202. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/205#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] #205: interim builder for breast cancer cohort summary
#205: interim builder for breast cancer cohort summary --+--- Reporter: dconnolly | Owner: huhickman Type: enhancement | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: 32, 204 Blocking:| --+--- Comment (by huhickman): I've gotten the Data Builder installed and can generate sqlite files - so for UNMC, we won't be going to the interim route. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/205#comment:8 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] #205: interim builder for breast cancer cohort summary
#205: interim builder for breast cancer cohort summary --+--- Reporter: dconnolly | Owner: huhickman Type: enhancement | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: 32, 204 Blocking:| --+--- Comment (by tmcmahon): The REDCap survey link was sent to each institution's Honest Broker. You will upload the file to the survey. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/205#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] #205: interim builder for breast cancer cohort summary
#205: interim builder for breast cancer cohort summary --+--- Reporter: dconnolly | Owner: huhickman Type: enhancement | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: 32, 204 Blocking:| --+--- Comment (by jdale): I'm not clear on what the desired output is for breast cancer cohort. We can easily run the query in i2b2 and get our patient cohort, but I was thinking we would use that patient list and then go to our source table in the warehouse to grab each of the individual fields that are being requested. Is it possible to provide an example of the output? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/205#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] #205: interim builder for breast cancer cohort summary
#205: interim builder for breast cancer cohort summary --+--- Reporter: dconnolly | Owner: huhickman Type: enhancement | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: 32, 204 Blocking:| --+--- Changes (by dconnolly): * cc: rwaitman, sfennel, preeder, bokov (removed) * cc: gpc-dev@… (added) * owner: dconnolly = huhickman * status: new = assigned Comment: Hubert, Glenn, and everybody, I just wrote up BuilderSaga#builder-sql-guide, based on a log of a data builder run. It includes the exact schema of the sqlite output file: attachment:builder_output_schema.sql:wiki:BuilderSaga as well as each SQL statement that the data builder runs. Hubert, would you please review it to see if whatever method you had in mind can produce the same sort of output? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/205#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
