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✨ Study generator for dev and test #607

Merged
merged 3 commits into from
Mar 31, 2021
Merged

✨ Study generator for dev and test #607

merged 3 commits into from
Mar 31, 2021

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znatty22
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@znatty22 znatty22 commented Mar 25, 2021 •
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Closes #604
Currently needed in #502 to generate data for unit tests

@znatty22 znatty22 added the feature New functionality label Mar 25, 2021
@znatty22 znatty22 self-assigned this Mar 25, 2021
@znatty22 znatty22 force-pushed the study-generator branch 3 times, most recently from d892dc1 to 60d45d7 Compare March 25, 2021 15:13
@znatty22 znatty22 changed the base branch from master to ingest-app March 25, 2021 15:15
@znatty22 znatty22 force-pushed the study-generator branch 3 times, most recently from 31c36ed to 8782649 Compare March 25, 2021 15:25
znatty22
znatty22 commented Mar 25, 2021
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creator/studies/data_generator/utils.py Outdated
logger = logging.getLogger(__name__)


def delete_kfids(host, endpoint, kfids):
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Both of these delete methods will be removed once kids-first/kf-utils-python#24 is released and imported from kf-utils-python

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This is complete

@znatty22 znatty22 force-pushed the study-generator branch 3 times, most recently from d0dbd80 to 05887f1 Compare March 25, 2021 15:43
@znatty22 znatty22 marked this pull request as ready for review March 25, 2021 15:45
@znatty22 znatty22 requested a review from dankolbman March 25, 2021 15:45
@gsantia gsantia force-pushed the ingest-app branch 2 times, most recently from 0411665 to 57827f6 Compare March 25, 2021 15:51
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codecov bot commented Mar 25, 2021 •
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Codecov Report

Merging #607 (1048f11) into ingest-app (ced6536) will decrease coverage by 1.31%.
The diff coverage is 74.71%.

❗ Current head 1048f11 differs from pull request most recent head 9a5cdb0. Consider uploading reports for the commit 9a5cdb0 to get more accurate results
Impacted file tree graph

@@              Coverage Diff               @@
##           ingest-app     #607      +/-   ##
==============================================
- Coverage       93.52%   92.21%   -1.32%     
==============================================
  Files             117      123       +6     
  Lines            5050     5317     +267     
==============================================
+ Hits             4723     4903     +180     
- Misses            327      414      +87
Impacted Files Coverage Δ
...enerator/ingest_package/extract_configs/biospec.py 0.00% <0.00%> (ø)
...enerator/ingest_package/extract_configs/genomic.py 0.00% <0.00%> (ø)
...ingest_package/extract_configs/s3_scrape_config.py 0.00% <0.00%> (ø)
..._generator/ingest_package/ingest_package_config.py 0.00% <0.00%> (ø)
.../data_generator/ingest_package/transform_module.py 0.00% <0.00%> (ø)
creator/studies/data_generator/study_generator.py 93.75% <93.75%> (ø)
creator/ingest_runs/tasks.py 73.46% <0.00%> (-24.21%) ⬇️
creator/ingest_runs/mutations.py 90.32% <0.00%> (-9.68%) ⬇️
creator/ingest_runs/models.py 93.33% <0.00%> (-6.67%) ⬇️
... and 5 more

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@gsantia gsantia self-requested a review March 26, 2021 19:58
@znatty22 znatty22 requested a review from dankolbman March 29, 2021 19:15
@znatty22 znatty22 force-pushed the study-generator branch 2 times, most recently from 96ff2c6 to 92ca6b4 Compare March 30, 2021 14:56
@znatty22 znatty22 requested review from gsantia and removed request for dankolbman March 30, 2021 14:59
@znatty22 znatty22 requested a review from dankolbman March 30, 2021 14:59
@znatty22 znatty22 requested a review from gsantia March 30, 2021 20:34
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dankolbman approved these changes Mar 31, 2021
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I need to install dev-requirements.txt again after installing requirements.txt because the ingest library seems to conflict with pytest versions. Using the pytest specified by ingest library breaks tests in the study creator.

It would be nice to clean up that dependency inside ingest library to avoid that conflict.

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znatty22 commented Mar 31, 2021 •
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I need to install dev-requirements.txt again after installing requirements.txt because the ingest library seems to conflict with pytest versions. Using the pytest specified by ingest library breaks tests in the study creator.

It would be nice to clean up that dependency inside ingest library to avoid that conflict.

@dankolbman Ok will try do that if no one uses the feature in ingest lib that uses pytest. kids-first/kf-lib-data-ingest#595. Going to merge this in for now

@znatty22 znatty22 merged commit 8f8ee36 into ingest-app Mar 31, 2021
@znatty22 znatty22 deleted the study-generator branch March 31, 2021 17:26
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@gsantia gsantia gsantia approved these changes

@dankolbman dankolbman dankolbman approved these changes

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Data Service study generator for testing
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@znatty22 @dankolbman @gsantia