Add medical action association table to UI (plus fixture & enum regen) #937

kevinschaper · 2025-01-09T00:38:54Z

Adds a medical action table showing the MaXO term, predicate, phenotype and disease. For simplicity sake, the section is labeled as "Medical Action" on both MaXO pages and phenotype pages.

Creating as a draft, because I realized that it needs to show up on disease pages as well, which means that the API request will need to change so that when "entity=" comes into the api request, disease_context_qualifier is searched, and I think we'll also want to make sure we're searching disease_context_qualifier_closure as well (which is hopefully already getting generated!

Closes #919
Closes #935

netlify · 2025-01-09T00:40:05Z

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…counts & association table searches

… queries, update fixtures, format

…into path

codecov · 2025-01-09T21:49:07Z

Codecov Report

Attention: Patch coverage is 95.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 70.77%. Comparing base (da511ba) to head (b898670).

Files with missing lines	Patch %	Lines
...rc/monarch_py/implementations/solr/solr_parsers.py	33.33%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #937      +/-   ##
==========================================
- Coverage   71.26%   70.77%   -0.49%     
==========================================
  Files          91       91              
  Lines        3149     3100      -49     
==========================================
- Hits         2244     2194      -50     
- Misses        905      906       +1

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kevinschaper · 2025-01-09T21:52:26Z

backend/src/monarch_py/implementations/spacy/spacy_implementation.py

-                self.nlp = spacy.load(str(str(model_archive.parent / model_subdir.name / inner_model_dir.name / model_subdir.name)))
+                self.nlp = spacy.load(
+                    str(str(model_archive.parent / model_subdir.name / inner_model_dir.name / model_subdir.name))
+                )



Everything in this file is just formatting changes that got picked up

Check, I'm ignoring it then.

kevinschaper · 2025-01-09T21:52:58Z

.github/workflows/test-backend.yaml

@@ -4,6 +4,9 @@ on:
  pull_request:
  workflow_dispatch:

+env:
+  PYTHONPATH: ${{ github.workspace }}/backend
+


fix for #935

kevinschaper · 2025-01-09T22:00:11Z

@amc-corey-cox @ptgolden The more straightforward part of this is the specific handling for MaXO associations in the UI. The weird part is that by default, we want disease pages to return these MaXO associations in the association-counts part of the entity response, and be able to fetch an association table for MaXO associations where the ID of the page that we're on is a MONDO ID which is in the disease_context_qualifier or disease_context_qualifier_closure field. I handled that by expanding what is matched in the API endpoint for the entity param, since we intend that to return associations involving that entity, and this is the first situation we have where we want the association to show up on a page based on the ID appearing in a qualifier field. I don't know if it's a 100% perfect solution, but I talked myself into the idea that it's a pretty reasonable one.

amc-corey-cox

I didn't review the big diffs in tests/ or frontend/fixtures but I don't see anything that jumps out as concerning to me. I flagged a couple of things just to make sure you noticed them and that they were done on purpose.
There doesn't appear to be a deploy preview. Would you like me to review the frontend view?

amc-corey-cox · 2025-01-10T15:44:10Z

backend/src/monarch_py/datamodels/category_enums.py

-    WEB_PAGE = "biolink:WebPage"
-    ZYGOSITY = "biolink:Zygosity"
+    MOLECULAR_ENTITY = "biolink:MolecularEntity"
+    LIFE_STAGE = "biolink:LifeStage"


I'm going to presume that all of these deletions and additions make sense, although I admit I didn't check to make sure we don't need these.

amc-corey-cox · 2025-01-10T15:45:26Z

backend/src/monarch_py/datamodels/category_enums.py

+    CHEMICAL_OR_DRUG_OR_TREATMENT_TO_DISEASE_OR_PHENOTYPIC_FEATURE_ASSOCIATION = (
+        "biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"
+    )
+    VARIANT_TO_PHENOTYPIC_FEATURE_ASSOCIATION = "biolink:VariantToPhenotypicFeatureAssociation"


Again, I'll presume your reorganization is for improving readability or logical consistency.

amc-corey-cox · 2025-01-10T15:47:40Z

backend/src/monarch_py/implementations/solr/solr_parsers.py

+    ):
+        # This is a special case for disease_context_qualifier, if an association between two other entities
+        # only occurs within the context of a disease, we can treat it like an incoming association
+        direction = AssociationDirectionEnum.incoming


Codecov is complaining that 261 and 267 aren't covered by tests. It seems reasonable to ignore this but if it's easy to make a test here it would be nice to cover these edge cases.

amc-corey-cox · 2025-01-10T15:49:34Z

backend/src/monarch_py/implementations/spacy/spacy_implementation.py

-                self.nlp = spacy.load(str(str(model_archive.parent / model_subdir.name / inner_model_dir.name / model_subdir.name)))
+                self.nlp = spacy.load(
+                    str(str(model_archive.parent / model_subdir.name / inner_model_dir.name / model_subdir.name))
+                )



Check, I'm ignoring it then.

… expansion fields

…ble, add some unfortunate hardcoding for external CHEBI links when we don't have the CHEBI node

…D is in the disease_context_qualifier slot

Add medical action association tables (plus fixture & enum regen)

f315267

kevinschaper added 7 commits January 9, 2025 10:37

Add querying for disease_context_qualifier (+closure) to association …

3982104

…counts & association table searches

update multiple entity query test to expect disease_context_qualifier…

9c66192

… queries, update fixtures, format

try setting the PYTHONPATH before running tests to get backend/tests …

5e08d73

…into path

try setting PYTHONPATH another way

e0307f3

try setting PYTHONPATH another way

90fa0eb

trying a working dir change?

61bf967

keep going with the working dir change

b898670

kevinschaper mentioned this pull request Jan 9, 2025

Pytest seems to be failing in certain environments #935

Open

kevinschaper requested a review from amc-corey-cox January 9, 2025 21:51

kevinschaper assigned ptgolden Jan 9, 2025

kevinschaper commented Jan 9, 2025

View reviewed changes

kevinschaper marked this pull request as ready for review January 9, 2025 21:54

kevinschaper assigned kevinschaper and unassigned ptgolden Jan 9, 2025

kevinschaper requested a review from ptgolden January 9, 2025 21:54

amc-corey-cox approved these changes Jan 10, 2025

View reviewed changes

add subject & object specialization qualifiers to model, plus closure…

8a046f2

… expansion fields

glass-ships mentioned this pull request Jan 13, 2025

Update to eslint.config.js #890

Open

kevinschaper added 4 commits January 13, 2025 09:36

add original predicate to model

07d9acb

use original_predicate for maxo_relation column in medical actions ta…

efccb45

…ble, add some unfortunate hardcoding for external CHEBI links when we don't have the CHEBI node

update fixtures with new kg

a716bdd

update association entity test to handle the case where the matched I…

9ee736d

…D is in the disease_context_qualifier slot

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Add medical action association table to UI (plus fixture & enum regen) #937

Add medical action association table to UI (plus fixture & enum regen) #937

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Add medical action association table to UI (plus fixture & enum regen) #937

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kevinschaper commented Jan 9, 2025 •

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