Merge branch 'main' of https://github.com/x-atlas-consortia/ubkg-api …

…into dev-integrate

README.md

@@ -54,6 +54,12 @@ If you are working with a local Docker distribution based on from [ubkg-neo4j](h
    - USERNAME=neo4j
    - PASSWORD= the value of _neo4j_password_ from the common **container.cfg** file.
 
+## Using API keys
+Some deployments based on the UBKG API may require that calls to endpoints include an API key in the header.
+Because this involves integration with authorization architecture (e.g., API gateways and authorization specific to a 
+network resource), the configuration of API keys is beyond the scope of the UBKG API. 
+
+
 ### Starting your neo4j instance
 If you are using a local instance of the UBKG, the instance should be running. 
 In particular, if you installed a local Docker instance of UBKG, be sure that Docker Desktop is running. 

VERSION

@@ -1 +1 @@
-2.1.4
+2.1.5

dd-api-spec.yaml

@@ -13,7 +13,7 @@ servers:
   - url: https://datadistillery.api.sennetconsortium.org/
     description: Production server
 security:
-  - api_key: []
+  - umls_key: []
 paths:
   /codes/{code_id}/codes:
     get:
@@ -166,12 +166,12 @@ paths:
           description: No Definitions associated with the Concept _query_concept_id_.
         '5XX':
           description: Unknown error
-  /concepts/{identifier}/nodeobjects:
+  /concepts/{concept_id}/nodeobjects:
     get:
       operationId: concepts_identifier_nodes_get
       summary: Returns a set of "Concept Node objects" that "match" an identifier. [A Concept node in the UBKG is the origin of a subgraph that links the Concept node to a set of Code, Term, Definition, and Semantic Type nodes. A "Concept Node object" represents this subgraph as a set of Concept properties--i.e., all of the Concept's linked Codes, terms, definitions, and semantic types. A "match" is an exact match between an identifier and a text-based property in a Concept Node object. Because an identifier may match properties in more than one Concept Node object, the endpoint can return multiple Concept Node objects.]
       parameters:
-        - name: identifier
+        - name: concept_id
           in: path
           required: true
           description: The string to match against properties related to Concepts. Related properties include the preferred term for the Concept; the CUI for the Concept; the CodeID for a Code linked to the Concept; and terms for a Code linked to a Concept.
@@ -887,9 +887,10 @@ paths:
           description: Unknown error
 components:
   securitySchemes:
-    api_key:
+    umls_key:
       type: apiKey
-      name: X-API-KEY
+      description: API key for a UMLS licensee account, prefixed with "UMLS-Key "--e.g., "UMLS-Key <my-umls-key>"
+      name: Authorization
       in: header
   schemas:
     CodesCodesObj: # Schema name

pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ubkg_api"
-version = "2.1.4"
+version = "2.1.5"
 authors = [
   { name="HuBMAP Consortium", email="[email protected]" },
 ]

tests/python_client_test.py

@@ -1,20 +1,20 @@
 # coding: utf-8
 
-# Simple Python script that demonstrates how to use the API key stored in a file named api.key
+# Simple Python script that demonstrates how to use the API key stored in a file named umls.key
 # in the application directory to execute an endpoint.
 
 import requests
 import os
 
 # Read the API key.
 fpath = os.path.dirname(os.getcwd())
-fpath = os.path.join(fpath, 'tests', 'api.key')
+fpath = os.path.join(fpath, 'tests', 'umls.key')
 f = open(fpath, 'r')
 apikey = f.read()
 f.close()
 
 # Add the API key to authorization for the URL.
-headers = {'X-API-KEY': f'{apikey}'}
+headers = {'Authorization': f'UMLS-Key {apikey}'}
 
 # Execute the endpoint.