Merge branch 'master' into issue387-empty-categories

.github/workflows/test.yml

@@ -33,7 +33,10 @@ jobs:
 
       - name: install dependencies
         run: |
-          pip install -r requirements.txt
+          pip install -r requirements.txt > /dev/null
+          SITE_PACKAGES=$( python -c 'import site; print(site.getsitepackages()[0])' )
+          cp ./resources/biolink-config.yaml ./conf/config.yaml
+          cp ./resources/ontobio-config.yaml ${SITE_PACKAGES}/ontobio/config.yaml
 
       - name: run behave tests
         run: |

Dockerfile

@@ -26,4 +26,7 @@ ENV PATH="/biolink-api/scripts/:$PATH"
 
 RUN pip install -r requirements.txt
 
+COPY ./resources/biolink-config.yaml /biolink-api/conf/config.yaml
+COPY ./resources/ontobio-config.yaml /usr/local/lib/python3.8/site-packages/ontobio/config.yaml
+
 EXPOSE 5000

README.md

@@ -72,7 +72,7 @@ For testing purposes these can be copied from the defaults, eg
 ```
 mkdir config
 cp conf/config.yaml config/biolink-config.yaml
-cp venv/lib/python3.7/site-packages/ontobio/config.yaml config/ontobio-config.yaml
+cp venv/lib/python3.8/site-packages/ontobio/config.yaml config/ontobio-config.yaml
 ```
 
 ```

docker/start-server

@@ -1,6 +1,6 @@
 #!/bin/sh
 
 cp /config/biolink-config.yaml /biolink-api/conf/config.yaml
-cp /config/ontobio-config.yaml /usr/local/lib/python3.7/site-packages/ontobio/config.yaml
+cp /config/ontobio-config.yaml /usr/local/lib/python3.8/site-packages/ontobio/config.yaml
 
 gunicorn "$@"

requirements.txt

@@ -1,10 +1,10 @@
 prefixcommons>=0.0
 # ontobio>=2.7.14
-git+https://github.com/falquaddoomi/ontobio.git@7894361056bf87a69cacb8cefcf10ac4f51f2924#egg=ontobio
+git+https://github.com/monarch-initiative/ontobio.git@baf3b5a7344fe6dda9c3980c8d472655431cb5df#egg=ontobio
 pip>=9.0.1
 wheel>0.25.0
-itsdangerous==2.0.1
-Flask==1.1.2
+markupsafe==2.0.1
+Flask==1.1.4
 flask-restplus>=0.10.1
 Flask-SQLAlchemy>=2.1
 flask-cors>=0.0

resources/biolink-config.yaml

@@ -0,0 +1,32 @@
+solr_assocs:
+  url: "http://solr.monarchinitiative.org/solr/golr"
+  timeout: 60
+amigo_solr_assocs:
+  url: "http://golr.berkeleybop.org"
+  timeout: 4
+solr_search:
+  url: "http://solr.monarchinitiative.org/solr/search"
+  timeout: 60
+amigo_solr_search:
+  url: "http://golr.berkeleybop.org"
+  timeout: 2
+sparql:
+  url: "http://sparql.hegroup.org/sparql"
+  timeout: 2
+scigraph_ontology:
+  url: "http://scigraph-ontology.monarchinitiative.org/scigraph/"
+  timeout: 60
+scigraph_data:
+  url: "http://scigraph-data.monarchinitiative.org/scigraph/"
+  timeout: 60
+use_amigo_for:
+  - function
+identifier_converter: biolink.identifier_converter.SciGraphIdentifierConverter
+ontologies:
+  - id: go
+    handle: go
+    pre_load: false
+  - id: hp
+    handle: hp
+    pre_load: false
+

resources/ontobio-config.yaml

@@ -0,0 +1,36 @@
+solr_assocs:
+  url: "http://solr.monarchinitiative.org/solr/golr"
+  timeout: 60
+amigo_solr_assocs:
+  url: "http://golr-aux.geneontology.io/solr"
+  timeout: 4
+solr_search:
+  url: "http://solr.monarchinitiative.org/solr/search"
+  timeout: 60
+lay_person_search:
+  url: "http://solr.monarchinitiative.org/solr/hpo-pl"
+  timeout: 60
+amigo_solr_search:
+  url: "http://golr-aux.geneontology.io/solr"
+  timeout: 2
+sparql:
+  url: "http://sparql.hegroup.org/sparql"
+  timeout: 2
+scigraph_ontology:
+  url: "http://scigraph-ontology.monarchinitiative.org/scigraph"
+  timeout: 60
+scigraph_data:
+  url: "http://scigraph-data.monarchinitiative.org/scigraph"
+  timeout: 60
+owlsim2:
+  url: "http://owlsim.monarchinitiative.org/"
+  timeout: 60
+owlsim3:
+  url: "http://owlsim3.monarchinitiative.org/api/"
+  timeout: 5
+use_amigo_for:
+  - function
+ontologies:
+  - id: magic1234
+    handle: pato
+    pre_load: true