parameterized obo ontologies

docker-compose.yml

@@ -9,6 +9,7 @@ services:
       - REMOTE_URL=${REMOTE_URL}
       - REMOTE_USER=${REMOTE_USER}
       - REMOTE_PASSWORD=${REMOTE_PASSWORD}
+      - OBO_ONTOLOGIES=${OBO_ONTOLOGIES}
     volumes:
       - type: bind
         source: ${DOWNLOAD_PATH}

main.py

+import json
+import logging
 import os
-import py2neo
 from time import sleep
-import logging
-from py2neo.wiring import WireError
-import json
-from datetime import datetime
-from multiprocessing import Pool
 
-from graphpipeline.parser import ParserSet
+import py2neo
 from biomedgraph.datasources import OboFoundry, GeneOntology
 from biomedgraph.parser import OboFoundryParser, GeneOntologyAssociationParser
+from graphpipeline.parser import ParserSet
+from py2neo.wiring import WireError
 
 logging.basicConfig(level=logging.INFO)
 logging.getLogger('biomedgraph').setLevel(level=logging.DEBUG)
@@ -20,18 +18,19 @@ log.setLevel(level=logging.DEBUG)
 
 ROOT_DIR = os.getenv('ROOT_DIR', '/download')
 RUN_MODE = os.getenv('RUN_MODE', 'test')
+OBO_ONTOLOGIES = os.getenv('OBO_ONTOLOGIES')
 # TODO replace with ENV vars and change pipeline file
 REMOTE_URL = "ftp://u261019-sub1.your-storagebox.de/download"
 REMOTE_USER = "u261019-sub1"
 REMOTE_PASSWORD = "YMnBAIPBer09jJJN"
 
+
 log.info([REMOTE_URL, REMOTE_USER, REMOTE_PASSWORD])
+log.info(OBO_ONTOLOGIES)
 
 NEO4J_CONFIG_STRING = os.getenv("NEO4J")
-
 log.info(NEO4J_CONFIG_STRING)
 NEO4J_CONFIG_DICT = json.loads(NEO4J_CONFIG_STRING)
-
 log.info(f'dict {NEO4J_CONFIG_DICT}')
 
 if __name__ == '__main__':
@@ -63,11 +62,12 @@ if __name__ == '__main__':
     geneontology_local = geneontology.latest_local_instance(taxids=['9606', '10090'])
 
     parserset = ParserSet()
-
-    for ontology_abbreviation in ['go', 'doid', 'mp', 'pato']:
+    log.info("Add Ontology Parsers")
+    for obo_abbreviation in OBO_ONTOLOGIES.split(','):
+        log.info(f"Add {obo_abbreviation}")
         go_parser = OboFoundryParser()
         go_parser.datasource_instances.append(obofoundry_local)
-        go_parser.ontology_name = ontology_abbreviation
+        go_parser.ontology_name = obo_abbreviation
         parserset.add(go_parser)
 
     for taxid in ['9606', '10090']: