Handle special HLAType format in crossmatch API #1188

abragtim · 2023-04-12T09:12:59Z

Closes #1139

abragtim · 2023-04-12T09:15:47Z

PR Checklist

Update swagger and approve with @kubantjan .
Change crossmatch API
Create tests
Update dataclasses and their methods

txmatching/web/swagger/swagger.json

kubantjan

nevidim ten display code? Ten uz se posilal i predtim? Pokud jo tak to napis, ze to v issue bylo redundantne

kubantjan · 2023-04-13T07:20:35Z

To summary ma mit domplet informace (tzn i hla kod) jen proste ne list protilatek ale jen jednu. Tzn ted to neni dobre jak to tam mas.

abragtim · 2023-04-13T08:19:15Z

To summary ma mit domplet informace (tzn i hla kod) jen proste ne list protilatek ale jen jednu. Tzn ted to neni dobre jak to tam mas.

@kubantjan
Podle mě v tom summary je jen jedna HLAAntibody, ne? Žádný list tam není

kubantjan

Jo takhle dobre, jdu to poslat do ikemu :)

txmatching/utils/hla_system/hla_crossmatch.py

jakubmonhart

Vypadá to dobře, jenom pár poznámek.

txmatching/utils/hla_system/hla_crossmatch.py

txmatching/web/api/crossmatch_api.py

kubantjan

privedlo me to review na jeden pripad: pokud pacient ma typizaci a pro ni nejsou protilatky ani ve splitu tak co ted delas? mam pocit ze to prevedes na split a nechas to tak, je to tak? To mi prijde ok

pridej urcite test

txmatching/data_transfer_objects/hla/hla_swagger.py

txmatching/utils/hla_system/hla_crossmatch.py

tests/web/test_do_crossmatch_api.py

Co-authored-by: Jakub Monhart <monhart.jakub@gmail.com>

…d_in_low_res.

Fix some tests.

Replace example for crossmatch API on correct one.

…toring.

…nings. Describe new terms in comments.

+ small fix.

txmatching/web/api/crossmatch_api.py

kubantjan

jen ten jeden malej komentar jinak ok

kubantjan

jen ten jeden malej komentar jinak ok

txmatching/web/api/crossmatch_api.py

abragtim linked an issue Apr 12, 2023 that may be closed by this pull request

Umet si poradit i se spesl formatem hla type pri pocitani crossmatche #1139

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abragtim requested a review from kubantjan April 12, 2023 09:16

kubantjan requested changes Apr 13, 2023

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abragtim requested a review from kubantjan April 13, 2023 08:50

kubantjan reviewed Apr 14, 2023

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abragtim force-pushed the 1139-umet-si-poradit-i-se-spesl-formatem-hla-type-pri-pocitani-crossmatche branch 2 times, most recently from d4029a2 to 30d0b71 Compare April 20, 2023 14:31

abragtim changed the base branch from master to 1168_add_support_for_theoretical_and_double_antibodies_ April 20, 2023 14:31

abragtim commented Apr 20, 2023

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abragtim marked this pull request as ready for review April 24, 2023 05:35

abragtim requested review from jakubmonhart and kristinagalik April 24, 2023 05:35

jakubmonhart reviewed Apr 26, 2023

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abragtim force-pushed the 1139-umet-si-poradit-i-se-spesl-formatem-hla-type-pri-pocitani-crossmatche branch 2 times, most recently from 2530f73 to d6ff793 Compare April 26, 2023 21:02

abragtim added the DO NOT MERGE Do not merge the PR label Apr 26, 2023

abragtim removed the request for review from kristinagalik April 26, 2023 21:18

abragtim force-pushed the 1139-umet-si-poradit-i-se-spesl-formatem-hla-type-pri-pocitani-crossmatche branch from d6ff793 to d0df02b Compare April 26, 2023 21:21

abragtim requested a review from jakubmonhart April 26, 2023 21:30

jakubmonhart previously approved these changes Apr 27, 2023

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abragtim requested a review from kubantjan April 27, 2023 06:54

kubantjan force-pushed the 1168_add_support_for_theoretical_and_double_antibodies_ branch from 46daae2 to 74adb2d Compare May 3, 2023 15:22

Base automatically changed from 1168_add_support_for_theoretical_and_double_antibodies_ to master May 3, 2023 15:23

kubantjan dismissed jakubmonhart’s stale review via e2a359e May 3, 2023 15:23

kubantjan removed the DO NOT MERGE Do not merge the PR label May 3, 2023

kubantjan requested changes May 3, 2023

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abragtim and others added 20 commits May 25, 2023 00:01

Don't convert in low res just in distribution.

f11a83a

Refactor __is_hla_type_in_high_res

df5125b

Co-authored-by: Jakub Monhart <monhart.jakub@gmail.com>

Fix true/false -> True/False.

24c03cb

Rename: is_hla_type_assumed_in_low_res -> is_hla_type_uniquely_define…

29770ba

…d_in_low_res.

Small fix for test.

89ac580

Add comment for fancy approach to get unique list.

d44d493

Add test for crossmatch with ultra high res codes.

01bfd0c

Rename hla_type -> hla_types.

d4fa579

Fix bug: undecidable instead high res.

11b2983

Update tests (comments and more cases).

2740804

Fix some tests.

Replace example for crossmatch API on correct one.

cbf205a

Replace example for crossmatch API on correct one.

Allow non unique matches in the list.

4d15965

Add TODO for the new issue 1204.

f4bb0c5

Stop mute AntibodyMatchForHLAType, so compute and then create + refac…

4e96826

…toring.

Add typing.

df9ee5a

Use just assumed hla type and potential hla type in two different mea…

acaa563

…nings. Describe new terms in comments.

Add test for assumed HLA type from supportive antibodies.

75f7a73

Add assumed HLA type from supportive antibodies.

44520f0

Solve potential HLA typing for all antibodies, not just crossmatched.

c9582e4

+ small fix.

Add some CS fixes.

fd3b76a

kubantjan force-pushed the 1139-umet-si-poradit-i-se-spesl-formatem-hla-type-pri-pocitani-crossmatche branch from 7c901ea to fd3b76a Compare May 24, 2023 22:01

kubantjan approved these changes May 24, 2023

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kristinagalik and others added 2 commits May 25, 2023 10:54

make pull request

61b5630

Refactor: don't use solve potential phrase.

829e478

abragtim requested a review from kubantjan May 25, 2023 08:57

kubantjan merged commit cba7852 into master May 25, 2023

kubantjan deleted the 1139-umet-si-poradit-i-se-spesl-formatem-hla-type-pri-pocitani-crossmatche branch May 25, 2023 10:40

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Handle special HLAType format in crossmatch API #1188

Handle special HLAType format in crossmatch API #1188

abragtim commented Apr 12, 2023

abragtim commented Apr 12, 2023 •

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Handle special HLAType format in crossmatch API #1188

Handle special HLAType format in crossmatch API #1188

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abragtim commented Apr 12, 2023

abragtim commented Apr 12, 2023 • edited Loading

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abragtim commented Apr 12, 2023 •

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