enhancements for organs and dataset-types

.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>hs-ontology-api</name>
+	<comment></comment>
+	<projects>
+		<project>ubkg-api</project>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.python.pydev.pythonNature</nature>
+	</natures>
+</projectDescription>

.pydevproject

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+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?eclipse-pydev version="1.0"?><pydev_project>
+
+    <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python interpreter</pydev_property>
+
+    <pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
+
+    <pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
+        <path>/${PROJECT_DIR_NAME}/src</path>
+        <path>/${PROJECT_DIR_NAME}/dev</path>
+    </pydev_pathproperty>
+
+</pydev_project>

dev/.gitignore

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+#config file
+instance/app.cfg

dev/Dockerfile

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+FROM hubmap/api-base-image:1.0.0
+
+LABEL description="DEV Server for Assayclasses"
+
+WORKDIR /usr/src/app
+
+COPY . .
+
+RUN pip install --upgrade pip -r requirements.txt
+
+EXPOSE 8181
+
+CMD [ "python", "-m" , "app"]

dev/README.md

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+## Development AssayClasses RESTful service
+
+The service contained within this directory exposes two endpoints:
+  - /assayclasses?application_context=HUBMAP
+  - assayclasses/<assay-code>?application_context=HUBMAP
+
+To run this service, in this directory:
+  - copy instance/app.cfg.example to instance/app.cfg
+  - create a python virtual environment with the contents of requirements.txt imported into the environment
+  - source/activage the virtual environment
+  - execute `python app.py`
+The service will be available on port 8181.
+
+Both endpoints require the `application_context=HUBMAP` parameter.  (A future version will allow SENNET context as well, which will read results from a different file).
+
+The `/assayclasses` endpoint simply returns the contents of the file https://raw.githubusercontent.com/x-atlas-consortia/hs-ontology-api/dev-integrate/dev/assayclasses.json as a json response.
+
+The `/assayclasses/<assay-code>` endpoint searches the same [assayclasses.json file](https://raw.githubusercontent.com/x-atlas-consortia/hs-ontology-api/dev-integrate/dev/assayclasses.json) 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.  For example if `/assayclasses/C200001?application_context=HUBMAP` is called the return value is:
+
+```
+{
+  "rule_description": {
+    "application_context": "HUBMAP",
+    "code": "C200150",
+    "name": "non-DCWG primary IMC2D"
+  },
+  "value": {
+    "active_status": "active",
+    "assaytype": "IMC2D",
+    "dataset_type": {
+      "PDR_category": "MxNF",
+      "dataset_type": "2D Imaging Mass Cytometry",
+      "fig2": {
+        "aggregated_assaytype": "LC-MS",
+        "category": "bulk",
+        "modality": "Proteomics"
+      }
+    },
+    "description": "2D Imaging Mass Cytometry",
+    "dir_schema": "imc-v0",
+    "is_multiassay": false,
+    "measurement_assay": {
+      "codes": [
+        {
+          "code": "SENNET:C006901",
+          "term": "Imaging Mass Cytometry Measurement Assay"
+        },
+        {
+          "code": "HUBMAP:C006901",
+          "term": "Imaging Mass Cytometry Measurement Assay"
+        },
+        {
+          "code": "OBI:0003096",
+          "term": "imaging mass cytometry assay"
+        }
+      ],
+      "contains_full_genetic_sequences": false
+    },
+    "must_contain": [],
+    "pipeline_shorthand": null,
+    "process_state": "primary",
+    "provider": "IEC",
+    "tbl_schema": "imc-v",
+    "vitessce_hints": []
+  }
+}
+```
+
+## Docker Deployment on DEV VM
+
+First build a new docker image
+
+```
+docker compose build
+```
+
+Then spin up the container
+
+```
+docker compose up -d
+```
+
+Once the container is up running correctly, you can access at `http://gateway.dev.hubmapconsortium.org:8181/assayclasses`

dev/app.py

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+import os
+import json
+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()
+
+
+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 is None or application_context.upper() != "HUBMAP":
+        abort(Response(json.dumps({"message": "A query parameter of application_context=HUBMAP must be specified"}),
+                       400,
+                       mimetype='application/json'))
+
+
+@app.route('/', methods=['GET'])
+def index():
+    return "Hello! This is the DEV AssayClass service :)"
+
+
+@app.route('/assayclasses/<code>', methods=['GET'])
+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')
+
+
+@app.route('/assayclasses', methods=['GET'])
+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(assayclasses_list), 200, mimetype='application/json')
+
+
+# For development/testing only
+if __name__ == '__main__':
+    try:
+        port = 8181
+        app.run(port=port, host='0.0.0.0')
+    finally:
+        pass