Updated and tested as per issue 116.

dev/app.py

@@ -1,34 +1,117 @@
 import os
 import json
-from flask import Flask, Response
+from flask import Flask, request, Response, abort
+from urllib.request import urlopen
+from urllib.error import HTTPError
+import logging
+
+#
+# This is a RESTful service that exposes two endpoints:
+#     /assayclasses?application_context=HUBMAP
+#     /assayclasses/<assay-code>?application_context=HUBMAP
+#
+# Both endpoints require the application_context=HUBMAP parameter to be included, otherwise they return a 400.
+#
+# This service is intended to be for development purposes only, so a developer can easily control the output by
+# changing the [assayclasses.json file in GitHub], specified in the ASSAYCLASSES_JSON_URL app.conf parameter.
+#
+# It is intended to mimic the services:
+#     https://ontology-api.dev.hubmapconsortium.org/assayclasses?application_context=HUBMAP
+#     https://ontology-api.dev.hubmapconsortium.org/assayclasses/C200150?application_context=HUBMAP
+#
+# Please see Issue: https://github.com/orgs/hubmapconsortium/projects/40/views/1?filterQuery=kollar&visibleFields=%5B%22Title%22%2C%22Assignees%22%2C%22Status%22%2C%22Labels%22%2C117184707%5D&pane=issue&itemId=74945308
+
+
+logging.basicConfig(format='[%(asctime)s] %(levelname)s in %(module)s: %(message)s',
+                    level=logging.DEBUG,
+                    datefmt='%Y-%m-%d %H:%M:%S'
+                    )
+logger = logging.getLogger()
+
 
-# Specify the absolute path of the instance folder and use the config file relative to the instance path
 app = Flask(__name__,
             instance_path=os.path.join(os.path.abspath(os.path.dirname(__file__)), 'instance'),
             instance_relative_config=True)
 app.config.from_pyfile('app.cfg')
 
+
+def get_assayclasses() -> dict:
+    """
+    Download the assayclasses information and return it as a dict.
+    Since this is done at startup time, on error it will log an error and exit as the app cannot recover from this.
+    """
+    if "ASSAYCLASSES_JSON_URL" not in app.config:
+        logger.error("app.cfg must contain ASSAYCLASSES_JSON_URL")
+        exit(1)
+    assayclasses_json_url: str = app.config["ASSAYCLASSES_JSON_URL"]
+    try:
+        response = urlopen(assayclasses_json_url)
+        data: str = response.read().decode("utf-8")
+    except HTTPError as he:
+        logger.error(f"Could not read ASSAYCLASSES_JSON_URL: {assayclasses_json_url}, error: {he}")
+        exit(1)
+    try:
+        json_dict: dict = json.loads(data)
+    except json.JSONDecodeError as jde:
+        logger.error(f"Invalid JSON syntax: {jde}")
+        exit(1)
+    logger.info(f"successfully downloaded app.cfg:ASSAYCLASSES_JSON_URL={assayclasses_json_url} json as dict")
+    return json_dict
+
+
+assayclasses_list: dict = get_assayclasses()
+
+
+def find_assayclass_with_rule_description_code(code: str):
+    """
+    Find the assayclass corresponding the rule_description code given or return None.
+    """
+    for ad in assayclasses_list:
+        if "rule_description" in ad and "code" in ad["rule_description"] and ad["rule_description"]["code"] == code:
+            return ad
+    return None
+
+
+def check_for_valid_application_context() -> None:
+    """
+    Check for a valid auery parameter application_context, and if not found abort with a 400.
+    """
+    application_context = request.args.get('application_context')
+    if application_context != "HUBMAP":
+        abort(400, "A query parameter of application_context=HUBMAP must be specified")
+
+
 @app.route('/', methods=['GET'])
 def index():
     return "Hello! This is the DEV AssayClass service :)"
 
+
 @app.route('/assayclasses/<code>', methods=['GET'])
-def assayclasses(code):
-    response_code = 200
-    response_data = {
-        'message': f'This endpoint not yet implemented code: {code}'
-    }
+def assayclasses_by_code(code):
+    """
+    This endpoint searches the same assayclasses.json file for an assayclass item matching
+    rule_description.code and returns the full matching assayclass item as a json response.
+    If the code is not found a 404 is returned.
+    """
+    check_for_valid_application_context()
+
+    assayclass_dict = find_assayclass_with_rule_description_code(code)
+
+    if assayclass_dict is not None:
+        return Response(json.dumps(assayclass_dict), 200, mimetype='application/json')
+
+    return Response(json.dumps({"message": f"No assayclass corresponding the rule_description code:{code} was found"}),
+                    404, mimetype='application/json')
 
-    return Response(json.dumps(response_data), response_code, mimetype='application/json')
 
 @app.route('/assayclasses', methods=['GET'])
-def assayclass_by_code():
-    response_code = 200
-    response_data = {
-        'message': 'This endpoint not yet implemented'
-    }
+def assayclass():
+    """
+    This endpoint returns the contents of the ASSAYCLASSES_JSON_URL as a json response.
+    """
+    check_for_valid_application_context()
 
-    return Response(json.dumps(response_data), response_code, mimetype='application/json')
+    return Response(json.dumps(assayclasses_list), 200, mimetype='application/json')
 
 
 # For development/testing only

dev/test_api.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+set -e
+set -u
+
+ASSAYCLASS_URL_LOCAL=http://localhost:8181
+ASSAYCLASS_URL=$ASSAYCLASS_URL_LOCAL
+
+
+curl --request GET \
+ --url "${ASSAYCLASS_URL}"
+echo
+
+
+# Both endpoints require the application_context=HUBMAP parameter to be included, otherwise return a 400.
+curl --request GET \
+ --url "${ASSAYCLASS_URL}/assayclasses" \
+ --header "Accept: application/json"
+echo
+
+curl --request GET \
+ --url "${ASSAYCLASS_URL}/assayclasses?application_context=HUBMAP" \
+ --header "Accept: application/json"
+echo
+
+
+curl --request GET \
+ --url "${ASSAYCLASS_URL}/assayclasses/C200010" \
+ --header "Accept: application/json"
+echo
+
+curl --request GET \
+ --url "${ASSAYCLASS_URL}/assayclasses/xyzzy?application_context=HUBMAP" \
+ --header "Accept: application/json"
+echo
+
+curl --request GET \
+ --url "${ASSAYCLASS_URL}/assayclasses/C200010?application_context=HUBMAP" \
+ --header "Accept: application/json"
+echo