Bump urllib3 from 1.24.1 to 1.24.2 in /greent

README.md

@@ -3,17 +3,13 @@
 
 ### Tools Available:
 
-## UberOnto API
-### version h-bar/2
-
-```
-updates to follow
-```
-
 ## Onto API
-### To edit/execute Onto API locally:
+Onto is a facility which aggregates lookup services that provide generic facts about ontologies. It leverages the Uberongraph RDB (a SPARQL-queried Uberongraph available at https://stars-app.renci.org/uberongraph/#query) for data.
+
+### To edit/execute/test Onto API locally:
 
 ```
+- TO EDIT:
 $git clone [email protected]:NCATS-Translator/reasoner-tools
 
 - make a virtual env and activate it, recommended as follows:
@@ -22,21 +18,41 @@ $source YOUR_ENV_NAME/bin/activate
 
 $cd reasoner-tools
 
+Make functionality changes in greent/services/ontology.py
+Make front-end changes in greent/api/onto_gunicorn.py
+The above two files should be considered in tandem.
+
+Add unit test cases to greent/test/test_ontology.py
+
+
+- TO RUN:
 $pip install -r greent/requirements.txt
 $export greent_conf=greent/greent.conf
 
-- TO RUN:
 $gunicorn onto_gunicorn:app --workers 1 --pythonpath=$PWD/greent/api
-navigate to http://127.0.0.1:8000/apidocs
+Navigate in your browser to http://127.0.0.1:8000/apidocs.
+
 
-make functionality changes in greent/services/ontology.py
-make front-end changes in greent/api/onto.py
-the above two files should be considered in tandem
+- TO TEST:
+$cd reasoner-tools
+
+- To run all unit tests:
+pytest greent/test/test_ontology.py
+
+- Remove warnings and get more information as tests run:
+pytest -p no:warnings -vv greent/test/test_ontology.py
+
+- Run a single unit test:
+pytest greent/test/test_ontology.py -k <test_name>
+pytest greent/test/test_ontology.py -k test_label
 ```
 
 ## BioNames API
+BioNames is a generic facility which aggregates bio-ontology lookup services.  It retrieve names from IDs or IDs based on Natural Language names.
+### To edit/execute/test BioNames API locally:
 
 ```
+- TO EDIT:
 $git clone [email protected]:NCATS-Translator/reasoner-tools
 
 - make a virtual env and activate it, recommended as follows:
@@ -45,13 +61,30 @@ $source YOUR_ENV_NAME/bin/activate
 
 $cd reasoner-tools
 
+Make functionality changes in greent/services/bionames.py
+Make front-end changes in builder/api/naming.py
+The above two files should be considered in tandem.
+
+Add unit test cases to greent/test/test_bionames.py
+
+
+- TO RUN:
 $pip install -r greent/requirements.txt
 
-- TO RUN VIA PYTHON:
 $PYTHONPATH=$PWD python3 builder/api/naming.py
--navigate to localhost:5000/apidocs
+- Navigate in your browser to localhost:5000/apidocs.
 
-make functionality changes in greent/services/bionames.py
-make front-end changes in builder/api/naming.py
-the above two files should be considered in tandem
+
+- TO TEST:
+$cd reasoner-tools
+
+- To run all unit tests:
+pytest greent/test/test_bionames.py
+
+- Remove warnings and get more information as tests run:
+pytest -p no:warnings -vv greent/test/test_bionames.py
+
+- Run a single unit test:
+pytest greent/test/test_bionames.py -k <test_name>
+pytest greent/test/test_bionames.py -k test_lookup_router
 ```

builder/api/naming.py

@@ -15,7 +15,7 @@
   "swagger": "2.0",
   "info": {
     "title": "BioNames API",
-    "description": "Generic facility aggregating bio-ontology lookup services to retrieve names from IDs or IDs based on Natural Language names.",
+    "description": "Bionames is a generic facility which aggregates bio-ontology lookup services to retrieve names from IDs or IDs based on Natural Language names.",
     "contact": {
       "responsibleOrganization": "renci.org",
       "responsibleDeveloper": "[email protected]",
@@ -125,7 +125,7 @@ def ID_to_label (ID):
    return jsonify(result)
 
 if __name__ == "__main__":
-   parser = argparse.ArgumentParser(description='Rosetta Server')
+   parser = argparse.ArgumentParser(description='BioNames Server')
    parser.add_argument('-p', '--port',  type=int, help='Port to run service on.', default=5000)
    parser.add_argument('-d', '--debug', help="Debug.", default=False)
    parser.add_argument('-c', '--conf',  help='GreenT config file to use.', default="greent.conf")
@@ -135,4 +135,4 @@ def ID_to_label (ID):
        'config' : args.conf,
        'debug'  : args.debug
    }
-   app.run(host='0.0.0.0', port=args.port, debug=True, threaded=True)
+   app.run(host='0.0.0.0', port=args.port, debug=True, threaded=True)

greent/api/onto_gunicorn.py

@@ -14,7 +14,7 @@
   "swagger": "2.0",
   "info": {
     "title": "Generic Ontology API",
-    "description": "Generic facts about ontologies (Flask/Gunicorn). This interface utilizes flat file .obo files as well as leveraging the Uberongraph RDB (a SPARQL-queried Uberongraph available at https://stars-app.renci.org/uberongraph/#query)",
+    "description": "Onto is a facility which aggregates lookup services that provide generic facts about ontologies. It leverages the Uberongraph RDB (a SPARQL-queried Uberongraph available at https://stars-app.renci.org/uberongraph/#query) for data.",
     "contact": {
       "responsibleOrganization": "renci.org",
       "responsibleDeveloper": "[email protected]",
@@ -466,10 +466,6 @@ def all_properties (curie):
    ont = get_ontology_service() 
    return jsonify({"all_properties" : ont.all_properties(curie_normalize(curie))})
 
-##################
-# start of sparkle based access to the Uberongraph RDB
-##################
-
 @app.route('/descendants/<curie>')
 def descendants(curie):
   """ Get all cascading 'is_a' descendants of an input CURIE term.
@@ -565,7 +561,7 @@ def label(curie):
 
 @app.route('/uri/<curie>')
 def uri_from_curie(curie):
-   """ Exapnds a curie to uri.
+   """ Expands a curie to uri.
    ---
    parameters:
      - name: curie
@@ -602,11 +598,10 @@ def get_curie_uri_map():
 
 
 if __name__ == "__main__":
-   parser = argparse.ArgumentParser(description='Rosetta Server')
+   parser = argparse.ArgumentParser(description='Onto Server')
    parser.add_argument('-p', '--port',  type=int, help='Port to run service on.', default=5000)
    parser.add_argument('-d', '--debug', help="Debug.", default=False)
-   parser.add_argument('-t', '--data',  help="Ontology data source.", default="c:/Users/powen/PycharmProjects/Reasoner/reasoner-tools/")
-  #  parser.add_argument('-t', '--data',  help="Ontology data source.", default="/projects/stars/reasoner/var/ontologies/")
+   parser.add_argument('-t', '--data',  help="Ontology data source.", default="/projects/stars/reasoner/var/ontologies/")
    parser.add_argument('-c', '--conf',  help='GreenT config file to use.', default="greent.conf")
    args = parser.parse_args ()
    app.config['SWAGGER']['greent_conf'] = args.greent_conf = args.conf

greent/api/onto_wsgi.py

@@ -0,0 +1,5 @@
+# usage: gunicorn --workers=3 --timeout=120 --bind=0.0.0.0:5000 --pythonpath '../../' onto_wsgi:app
+from onto_gunicorn import app
+
+if __name__ == "__main__":
+    app.run()

greent/requirements.txt

@@ -32,5 +32,5 @@ rdflib==4.2.2
 requests==2.21.0
 six==1.12.0
 SPARQLWrapper==1.8.2
-urllib3==1.24.1
+urllib3==1.24.2
 Werkzeug==0.15.1

greent/services/bionames.py

@@ -96,7 +96,8 @@ def _search_onto(self, q, concept=None):
         try:
             result = self.context.core.onto.search (q, is_regex=True, full=True)
             if concept:
-                result = [r for r in result if r['type'] == concept]
+                # Added fix for KeyException when there's no 'type' key in dict r
+                result = [r for r in result if 'type' in r and r['type'] == concept]
         except:
             traceback.print_exc ()
         return result

greent/services/ontology.py

@@ -51,7 +51,7 @@ def query_sparql(self, query_template, inputs, outputs):
 
 
     def label(self,identifier):
-        """Return the exitlabel for an identifier"""       
+        """Return the label for an identifier"""
         query_text = f"""
         PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
             SELECT DISTINCT ?labels