Reference Data Update Type Equality Check #789
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bpblanken
changed the title
bpblanken
changed the title
bpblanken
commented
May 23, 2024
| ) | ||
| return cls(paths, versions, enums, selects) | ||
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| def validate_selects_types( |
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The idea here is to just ensure that any fields shared between the existing table and an "update" are identically typed.
imo we're getting very close to needing a statically defined schema for these, but trying to squeeze that in was much messier.
bpblanken
commented
May 23, 2024
| @@ -45,7 +45,7 @@ | |||
| hl.tstruct( | |||
| locus=hl.tlocus('GRCh38'), | |||
| alleles=hl.tarray(hl.tstr), | |||
| PHRED=hl.tint32, | |||
| PHRED=hl.tfloat32, | |||
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we had a few types in our tests/mock data that weren't right and doing this work caught them 🤩 !
hanars
approved these changes
May 23, 2024
| @@ -183,11 +194,12 @@ def test_from_rdc_or_annotations_ht(self): | |||
| self.assertTrue( | |||
| rdc_globals.enums == {'screen': {'region_type': ['C', 'D']}}, | |||
| ) | |||
| print(rdc_globals.selects) | |||
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I assume this is left in by mistake?
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yep 🤦 I'm going to add a lint rule for this...
bpblanken
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May 28, 2024
* Miscellaneous VEP tweaks * Benb/validate with allele type (#785) * Bump requirements * add validation * format * Fix syntax (#787) * Bump requirements * add validation * format * Fix syntax * allele registry (#759) * add allele registry step in update vat with samples task * shh * existing tests pass * fix test deps * test * annotation_dependencies * ruff * take out the zero check * fix requirements new task name * move vep into new variants task * only annotate lookup from callset_ht * clean up mocks * r * working * working? * not that * minor changes and test cases * most recent script * working version * fix the test * implement ht chunking * fix patches * fix patches * register now yields id map of returned caids * r * fix some tests * return a hail table instead * use __str__ * log to track variants we can't map back * move to gcs with flag * union ar_ht instead of a bunch of left joins to prevent CAID, CAID_1, CAID_2... * cleaner * it is all coming together now ' * gnomad ids for 37' * use genomicalleles and gnomad ids * secrets * secret * move stuff out of environment file * add more logging * fix test * fix the other test * ruff * test * comments * o * Reference Data Update Type Equality Check (#789) * Finish validity check test * ruff * update dbnsfp field * More types * more types * ugh * twiddle it back * update type * more tweaks * lint * fix floats * decompose * ruff formatg * Update compare_globals_test.py * print lint rule (#791) * tiny ar bug (#792) --------- Co-authored-by: Benjamin Blankenmeister <bblanken@broadinstitute.org> Co-authored-by: Benjamin Blankenmeister <b.p.blankenmeister@gmail.com>
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