Remove unused endpoints

.github/workflows/run_tests.yaml

@@ -0,0 +1,23 @@
+name: Run-tests
+on: [push]
+jobs:
+  run-pr-test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          ref: ${{ github.head_ref }}
+      - uses: actions/setup-python@v2
+        name: setup python
+        with:
+          python-version: 3.7
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+      - name: Run Tests
+        run: |
+          export PYTHONPATH=.:$PYTHONPATH
+          python ./biolink/app.py &
+          sleep 15
+          cd tests && behave -f plain

Dockerfile

@@ -0,0 +1,40 @@
+FROM python:3.7-slim
+
+WORKDIR /biolink-api
+
+VOLUME /config
+
+RUN apt-get -y update && apt-get install -y git curl
+
+COPY requirements.txt ./
+COPY wsgi.py ./
+COPY logging.conf ./
+
+COPY biolink ./biolink
+COPY biomodel ./biomodel
+COPY biowikidata ./biowikidata
+COPY causalmodels ./causalmodels
+COPY conf ./conf
+COPY scigraph ./scigraph
+COPY tests ./tests
+COPY .git ./.git
+
+RUN mkdir /biolink-api/scripts
+# COPY docker ./scripts
+
+ENV PYTHONPATH "${PYTHONPATH}:/biolink-api"
+
+ENV PATH="/biolink-api/scripts/:$PATH"
+
+RUN pip install -r requirements.txt
+
+ENTRYPOINT ["python"]
+CMD ["biolink/app.py"]
+
+EXPOSE 8888
+
+
+# docker build -t name_of_image folder_containing_dockerfile (names image and stores it)
+# docker run -d --name sierra_test -p 8888:8888 go_api  (expose ports and name the container)
+# docker rm sierra_test (removes image)
+# docker port sierra_test (see the port mapping)

README.md

@@ -4,7 +4,8 @@ The Gene Ontology API instance is accessible here:
 
 https://api.geneontology.org/api/
 
-Is is an implementation of both the [BioLink Model](https://github.com/biolink/biolink-model) and [BioLink Implementation](https://github.com/biolink/biolink-api) which rely on [Ontobio](https://github.com/biolink/ontobio)
+It is an implementation of both the [BioLink Model](https://github.com/biolink/biolink-model) 
+and [BioLink Implementation](https://github.com/biolink/biolink-api) which rely on [Ontobio](https://github.com/biolink/ontobio)
 
 ## Running the server
 
@@ -14,16 +15,16 @@ After checking out this repo:
 ./start-server.sh
 ```
 
-This uses gunicorn and starts a server on 8888 by default. pyvenv is
+This uses gunicorn and starts a server on 5000 by default. pyvenv is
 activated automatically.
 
 Then look at:
 
-http://localhost:8888/api/
+http://localhost:5000/api/
 
 For the swagger docs
 
-To run in development mode:
+To run locally in development mode:
 
 ```
 pyvenv venv
@@ -33,5 +34,7 @@ export PYTHONPATH=.:$PYTHONPATH
 python biolink/app.py
 ```
 
+Production AWS environment details
+ [Production AWS Details](docs/prod.md).
 
 

biolink/api/bio/association_counts.py

@@ -265,6 +265,7 @@ def parse_taxon_pivot(taxon_pivot, key):
         counts_map[taxon] = counts
     return counts_map
 
+
 def merge_counts(d1, d2):
     d = {}
     d1_key_set = set(x for x in d1.keys())

biolink/api/bio/closure_bins.py

@@ -27,6 +27,7 @@
     'CL:0000000PHENOTYPE': 'Cellular'
 }
 
+
 def create_closure_bin(fcmap={}):
     """
     Given a facet count dict from golr_query (i.e. map of class ID to count)
@@ -42,7 +43,7 @@ def create_closure_bin(fcmap={}):
     for curie, label in closure_map.items():
         lmap[label] = 0
         idmap[curie] = 0
-    for k,v in fcmap.items():
+    for k, v in fcmap.items():
         if k in closure_map:
             label = closure_map[k]