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Scope of genes call set to UBKG; proposed endpoints for proteins and genes #48
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AlanSimmons
commented
Oct 31, 2023
- With the removal of calls to data from Cells API, the genes endpoint now has scope of UBKG--i.e., it returns all genes in UBKG, not just those relevant to HuBMAP.
- The SmartAPI specification YAML describes proposed endpoints for:
- proteins
- protein/{id}
- celltypes
- celltype/{id}
…ypes.yaml, field_entities.yaml, field_assays.yaml, and field_schemas.yaml in ingest-validation-tools.
…names of routes--i.e., genes and genes-info.
… Moved loadquerystring function into neo4j_logic.py.
…nd celltypes-info/celltypes endpoints. Updated YAML for new pagination object in *-info endpoints.
return make_response(f'There are no genes with HGNC symbols that start with \'{starts_with}\'.', 404) | ||
genecount = genelist_count_get_logic(neo4j_instance, startswith) | ||
if genecount == 0: | ||
return make_response(f'There are no genes with HGNC symbols that start with \'{startswith}\'.', 404) |
Check warning
Code scanning / CodeQL
Reflected server-side cross-site scripting
Updated change log:
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@AlanSimmons two things to change:
- since you use underscore-separated fields (
approved_name
,approved_symbol
...) in the response json payload, we should also do the same with the pagination fields for consistency. Add underscore as a separator for the following fields:
"itemcount": 43143,
"itemsperpage": 10,
"startswith": "",
"totalpages": 4315
- To merge this PR, we'll also need to resolve the merge conflicts caused by
hs-ontology-api-spec.yaml
.
….g. starts_with instead of startswith).
I changed all references everywhere (parameters, returns, etc.) to use underscores--e.g., starts_with instead of startswith. |
Merge conflicts resolved in YAML file. |
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field-descriptions field-types field-entities field-assays field-schemas Also changed underscores to dashes in route summary fields to reflect the names of the legacy YAML files.