Merge pull request #885 from hubmapconsortium/karlburke/AssayTypeCleanup

Initial commit to clean up after Assay Type deprecations.
hubmapconsortium · Oct 3, 2024 · decdc48 · decdc48
2 parents c4a74c7 + ac51d2a
commit decdc48
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Showing 9 changed files with 4 additions and 1,275 deletions.
diff --git a/search-api-spec.yaml b/search-api-spec.yaml
@@ -410,7 +410,7 @@ components:
             - TR
             - UR
             - UT
-          description: "Organ code specifier, only set if sample_category == organ.  Valid values found in: [organ types](https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/organ_types.yaml)"
+          description: "Organ code specifier, only set if sample_category == organ.  Valid values found using [the Ontology API](https://ontology.api.hubmapconsortium.org/organs?application_context=HUBMAP)"
         direct_ancestor_uuid:
           type: string
           writeOnly: true

diff --git a/src/libs/assay_type.py b/src/libs/assay_type.py
diff --git a/src/libs/assay_type_schema.yml b/src/libs/assay_type_schema.yml
diff --git a/src/libs/hubmap_endpoints.py b/src/libs/hubmap_endpoints.py
diff --git a/src/libs/test.sh b/src/libs/test.sh
diff --git a/src/main.py b/src/main.py
@@ -6,7 +6,6 @@
 from yaml import safe_load
 
 sys.path.append("search-adaptor/src")
-import libs.hubmap_endpoints
 search_adaptor_module = importlib.import_module("app", "search-adaptor/src")
 
 config = {}
@@ -39,12 +38,9 @@
 
 translator_module = importlib.import_module("hubmap_translator")
 
-sys.path.append("libs")
-
-hubmap_blueprint = libs.hubmap_endpoints.hubmap_blueprint
-
 # This `app` will be imported by wsgi.py when deployed with uWSGI server
-app = search_adaptor_module.SearchAPI(config, translator_module, hubmap_blueprint).app
+app = search_adaptor_module.SearchAPI(  config=config
+                                        , translator_module=translator_module).app
 
 # For local standalone (non-docker) development/testing
 if __name__ == "__main__":