Create PFB-based verbatim manifest format for AnVIL (#6040) #6115

nadove-ucsc · 2024-04-02T02:28:48Z

Connected issues: #6040

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Shorthand for review comments

L line is too long
W line wrapping is wrong
Q bad quotes
F other formatting problem

codecov · 2024-04-02T03:00:38Z

Codecov Report

Attention: Patch coverage is 88.34356% with 19 lines in your changes are missing coverage. Please review.

Project coverage is 85.39%. Comparing base (9149d91) to head (8cb87e9).

Files	Patch %	Lines
test/integration_test.py	0.00%	16 Missing ⚠️
src/azul/service/avro_pfb.py	95.65%	3 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #6115      +/-   ##
===========================================
+ Coverage    85.36%   85.39%   +0.03%     
===========================================
  Files          154      154              
  Lines        20170    20290     +120     
===========================================
+ Hits         17218    17327     +109     
- Misses        2952     2963      +11

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

coveralls · 2024-04-04T13:08:57Z

Changes unknown
when pulling 8cb87e9 on issues/nadove-ucsc/6040-pfb-verbatim-manifest
into ** on develop**.

nadove-ucsc · 2024-04-12T11:51:39Z

Integration tests pass on personal deployments colocated with dev, anvildev, and anvilprod.
Tested successful handover of verbatim PFB manifest on personal deployment colocated with anvildev (workspace link and anvilprod (workspace link).
Generation of unfiltered manifest fails on personal deployment colocated with dev due to an inconsistency in the shape of the contents.contributors.project_role field for project replicas. Some projects use the form:

"project_role" : {
    "ontology_label" : "experimental scientist",
    "text" : "experimental scientist",
    "ontology" : "EFO:0009741"
}

But others have

"project_role" : "experimental scientist"

To fix this, we could make the schema parsing more flexible by just using a union whenever we encounter a polymorphic field like this.

hannes-ucsc · 2024-04-12T23:30:59Z

test/indexer/__init__.py

@@ -89,6 +90,10 @@ class CannedFileTestCase(AzulUnitTestCase):
    expected outputs.
    """

+    @classmethod
+    def _data_path(cls, module: Literal['service', 'indexer'], path: str) -> str | bytes:


L and I prefer using Path instances over raw strings to represent file paths

hannes-ucsc · 2024-04-12T23:32:30Z

test/service/test_manifest.py

+        response = self._get_manifest(ManifestFormat.verbatim_jsonl, filters={})
+        self.assertEqual(200, response.status_code)
+        manifest = [
+            json.loads(row)['contents']


This should assert the entire row, i.e., the type and contents properties.

src/azul/service/avro_pfb.py

hannes-ucsc

Please update CL to match template.

https://ucsc-gi.slack.com/archives/C705Y6G9Z/p1713751938125189

hannes-ucsc · 2024-04-24T18:18:20Z

Security design review

nadove-ucsc added API API change affecting callers chained [process] PR needs to based of develop before merging labels Apr 2, 2024

github-actions bot added the orange [process] Done by the Azul team label Apr 2, 2024

nadove-ucsc force-pushed the issues/nadove-ucsc/6040-pfb-verbatim-manifest branch 2 times, most recently from 2c2b945 to a6aafd1 Compare April 2, 2024 02:39

dsotirho-ucsc changed the base branch from issues/nadove-ucsc/6028-create-verbatim-jsonl to develop April 2, 2024 19:56

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nadove-ucsc force-pushed the issues/nadove-ucsc/6040-pfb-verbatim-manifest branch 9 times, most recently from 76fd8a6 to 0a78b85 Compare April 12, 2024 01:59

nadove-ucsc force-pushed the issues/nadove-ucsc/6040-pfb-verbatim-manifest branch 2 times, most recently from ae149dc to 8495197 Compare April 12, 2024 20:24

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nadove-ucsc force-pushed the issues/nadove-ucsc/6040-pfb-verbatim-manifest branch from 3ca0110 to 8495197 Compare April 12, 2024 23:40

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nadove-ucsc force-pushed the issues/nadove-ucsc/6040-pfb-verbatim-manifest branch from 8495197 to 309aa17 Compare April 13, 2024 00:25

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nadove-ucsc force-pushed the issues/nadove-ucsc/6040-pfb-verbatim-manifest branch from 5c6fe2a to 5199c21 Compare April 22, 2024 08:22

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hannes-ucsc approved these changes Apr 22, 2024

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nadove-ucsc and others added 11 commits April 24, 2024 10:25

Change row sorting in JSONL manifest test

5552252

Refactor JSONL manifest test

46f5df7

Add unit test for AnVIL JSONL manifest (#6140)

54eb44e

Refactor canned file loading

7ef15e4

Refactor HCA supported manifest formats to match AnVIL

d3bfa68

Refactor avro_pfb.py

7bd2fc0

Extract ABC from verbatim manifest generator

cd113dc

Include replica_type in JSONL manifest

cef2223

[a] Create PFB-based verbatim manifest format for AnVIL (#6040)

85fdaeb

Add FIXME (#6139)

827d610

Refactor and document PFB integration test

8cb87e9

hannes-ucsc force-pushed the issues/nadove-ucsc/6040-pfb-verbatim-manifest branch from 99ce91e to 8cb87e9 Compare April 24, 2024 18:16

hannes-ucsc assigned achave11-ucsc and unassigned hannes-ucsc Apr 24, 2024

achave11-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Apr 24, 2024

achave11-ucsc merged commit 1794c26 into develop Apr 24, 2024
11 checks passed

achave11-ucsc removed the base [process] Another PR needs to be rebased before merging this one label Apr 24, 2024

achave11-ucsc deleted the issues/nadove-ucsc/6040-pfb-verbatim-manifest branch April 24, 2024 23:13

achave11-ucsc removed their assignment Apr 24, 2024

achave11-ucsc restored the issues/nadove-ucsc/6040-pfb-verbatim-manifest branch April 24, 2024 23:17

achave11-ucsc deleted the issues/nadove-ucsc/6040-pfb-verbatim-manifest branch April 24, 2024 23:18

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Create PFB-based verbatim manifest format for AnVIL (#6040) #6115

Create PFB-based verbatim manifest format for AnVIL (#6040) #6115

nadove-ucsc commented Apr 2, 2024 •

edited by achave11-ucsc

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hannes-ucsc commented Apr 24, 2024

Create PFB-based verbatim manifest format for AnVIL (#6040) #6115

Create PFB-based verbatim manifest format for AnVIL (#6040) #6115

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nadove-ucsc commented Apr 2, 2024 • edited by achave11-ucsc Loading

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hannes-ucsc commented Apr 24, 2024

Security design review

nadove-ucsc commented Apr 2, 2024 •

edited by achave11-ucsc

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