Fix epi orm exports #982
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Fix epi orm exports #982
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rabstejnek
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Jul 2, 2024
* Epi export rewrite (#911) * preliminary epi rewrite * changes * changes * changes * fix * added back something accidentally deleted * moved code * fix test * remove old stuff * cleanup: * use vectorized timestamp conversion * minor formatting --------- Co-authored-by: Andy Shapiro <shapiromatron@gmail.com> * rewrite riskofbias exports (#921) * preliminary epi rewrite * changes * changes * changes * fix * added back something accidentally deleted * moved code * fix test * remove old stuff * cleanup: * rewrite riskofbias exports * update naming for domain and metric --------- Co-authored-by: Daniel Rabstejnek <rabstejnek@gmail.com> * Epimeta export rewrite (#922) * preliminary epi rewrite * changes * changes * changes * fix * added back something accidentally deleted * moved code * fix test * remove old stuff * cleanup: * epimeta export rewrite * remove obsolete code * changes * merge fix * update admin site to browse data pivot by evidence type --------- Co-authored-by: Andy Shapiro <shapiromatron@gmail.com> * Invitro export rewrite (#958) * Convert invitro exports * Fix exporter datetime converter when datetime is None * Fix exports where there's no data * DTXSID in export should be None instead of useless dict if missing * add endpoint categories * Remove bloated dsstox dict from exports in favor of dtxsid --------- Co-authored-by: Andy Shapiro <shapiromatron@gmail.com> * Animal export rewrite (#961) * Made animal model exports, began configuring exporters * first export largely done, second export mostly done * Some cleanups, finished fourth animal exporter * Changes after more testing * Fix tests * Remove remaining flat_complete_* methods * Cleanup * Update sql_display to accept dict * Add TODO to comment to easily find it * Rename exporters to match the flat file exporter class names * Add safeguard for qs accessing and fix groupby side effects (#982) * two updates * move to correct place * exports-v2 - Updates from image review (#1058) * remove duplicate rename calls * add ci calculation * update treatment period calculation * add back space; fix caused too many false positives in comparison * properly handle a 500 response from the server in a data pivot * fix epi logic from plot review * fix invitro export when category id is null; remove category id from export * add unique rob columns * use same method for categories * refactor into a reusable method * remove pytest warning "Marks applied to fixtures have no effect" * refactor; write tests * add tests * rewrite animal export test using same pattern * add udf to openapi * remove extra whitespace (will change visuals; known change) --------- Co-authored-by: Daniel Rabstejnek <rabstejnek@gmail.com>
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There are two issues in the epi exports that are addressed in this PR:
groupbyresults in no groups thenapplycalls would just return an empty dataframe with all the original columns; this behavior was interfering with laterjoincalls in one of the exporters.