moved ontologies download to Dockerfile

Author: Thomas Hanke

Dockerfile

@@ -6,5 +6,8 @@ RUN apt-get -y upgrade
 ADD . /src
 RUN pip install --no-cache-dir -r /src/requirements.txt
 WORKDIR /src
+# get ontologies
+RUN curl https://raw.githubusercontent.com/Mat-O-Lab/MSEO/main/MSEO_mid.ttl > ./ontologies/mseo.ttl
+RUN curl https://raw.githubusercontent.com/CommonCoreOntology/CommonCoreOntologies/master/cco-merged/MergedAllCoreOntology-v1.3-2021-03-01.ttl > ./ontologies/cco.ttl
 
 CMD ["gunicorn", "-b", "0.0.0.0:5000", "wsgi:app", "--workers=3"]

docker-compose.yml

@@ -7,8 +7,8 @@ services:
       container_name: maptomethod
       ports:
         - ${APP_PORT}:5000
-      # volumes:
-      #  - .:/src
+      volumes:
+       - .:/src
       restart: always
       networks:
         maptomethod_net:

maptomethod.py

@@ -34,16 +34,20 @@ def dict_constructor(loader, node):
 
 # MSEO_URL='https://purl.matolab.org/mseo/mid'
 OBO = Namespace('http://purl.obolibrary.org/obo/')
-MSEO_URL = 'https://raw.githubusercontent.com/Mat-O-Lab/MSEO/main/MSEO_mid.owl'
-CCO_URL = 'https://github.com/CommonCoreOntology/CommonCoreOntologies/raw/master/cco-merged/MergedAllCoreOntology-v1.3-2021-03-01.ttl'
-MSEO = Namespace(MSEO_URL)
+MSEO_NAMESPACE = 'https://raw.githubusercontent.com/Mat-O-Lab/MSEO/main/MSEO_mid.owl'
+#CCO_URL = 'https://github.com/CommonCoreOntology/CommonCoreOntologies/raw/master/cco-merged/MergedAllCoreOntology-v1.3-2021-03-01.ttl'
+MSEO_URL = './ontologies/mseo.ttl'
+CCO_URL = './ontologies/cco.ttl'
+
+
+MSEO = Namespace(MSEO_NAMESPACE)
 CCO = Namespace('http://www.ontologyrepository.com/CommonCoreOntologies/')
 CSVW = Namespace('http://www.w3.org/ns/csvw#')
 OA = Namespace('http://www.w3.org/ns/oa#')
 
 mseo_graph = Graph()
 mseo_graph.parse(CCO_URL, format='turtle')
-mseo_graph.parse(str(MSEO), format='xml')
+mseo_graph.parse(MSEO_URL, format='turtle')
 
 InformtionContentEntity = CCO.InformationContentEntity
 TemporalRegionClass = OBO.BFO_0000008