#205: interim builder for breast cancer cohort summary
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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: |
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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
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