Add README edits for env vars, add configs bind mount

README.md

@@ -66,6 +66,15 @@ Then run:
 Upon initial install, an example administrator user, example dataset, concept database, vocab and project are setup. 
 The next session provides further details.
 
+4\. (Optional), Environment variables are used to configure the app:
+
+|Parameter|Description|
+|---------|-----------|
+|MEDCAT_CONFIG_FILE|MedCAT config file as described [here](https://github.com/CogStack/MedCAT/blob/master/medcat/config.py)|
+|BEHIND_RP| If you're running MedCATtrainer, use 1, othewise this defaults to 0 i.e. False|
+
+
+
 <a name="admin-setup"></a>
 # Administrator Setup
 

docker-compose.yml

@@ -7,6 +7,7 @@ services:
     restart: always
     image: cogstacksystems/medcat-trainer:latest
     volumes:
+      - ./configs:/home/configs
       - api-media:/home/api/media
       - api-static:/home/api/static
       - api-db:/home/api/db

envs/env

@@ -1,2 +1 @@
-medcat_config_file=/home/configs/base.txt
-behind_rp=0
+MEDCAT_CONFIG_FILE=/home/configs/base.txt

webapp/api/api/utils.py

@@ -270,7 +270,7 @@ def get_medcat(CDB_MAP, VOCAB_MAP, CAT_MAP, project):
         else:
             cdb_path = project.concept_db.cdb_file.path
             cdb = CDB.load(cdb_path)
-            cdb.config.parse_config_file(path=os.getenv("medcat_config_file"))
+            cdb.config.parse_config_file(path=os.getenv("MEDCAT_CONFIG_FILE"))
             CDB_MAP[cdb_id] = cdb
 
         if vocab_id in VOCAB_MAP:

webapp/api/api/views.py

@@ -619,4 +619,4 @@ def download_deployment(request):
 
 @api_view(http_method_names=['GET'])
 def behind_reverse_proxy(request):
-    return Response(bool(int(os.environ.get('behind_rp', False))))
+    return Response(bool(int(os.environ.get('BEHIND_RP', False))))