Dockerizing (#199)

* Fix Bulk Publish function

Changes to be committed:
	modified:   api/scripts/method_specific/POST_api_objects_publish.py
	modified:   api/scripts/utilities/JsonUtils.py

* Changed for Dockerizing
Changes to be committed:
	modified:   Dockerfile
	modified:   README.md
	modified:   authentication/apis.py
	modified:   search/selectors.py
	modified:   server.conf

* Update platform in `docker-compose.yml`

* updates for FDA deployment

Changes to be committed:
	modified:   Dockerfile
	modified:   docker-compose.yml

Author: HadleyKing

Dockerfile

@@ -2,6 +2,10 @@ FROM ubuntu:22.04
 LABEL org.opencontainers.image.source https://github.com/biocompute-objects/bco_api
 ENV DEBIAN_FRONTEND=noninteractive
 
+LABEL org.opencontainers.image.source=https://github.com/octocat/my-repo
+LABEL org.opencontainers.image.description="My container image"
+LABEL org.opencontainers.image.licenses=MIT
+
 # Note that this is just for debug / test purposes; should not be set via the setup for production
 # ENV DJANGO_SUPERUSER_PASSWORD="BioCompute123"
 # ENV DJANGO_SUPERUSER_USERNAME="BioComputeSuperUser"
@@ -17,12 +21,12 @@ COPY requirements.txt .
 
 RUN python3 -m pip install -r requirements.txt
 
-COPY bco_api ./bco_api
+COPY . ./
 
-WORKDIR /biocompute_api/bco_api
+WORKDIR /biocompute_api/
 
-RUN python3 manage.py migrate
-RUN python3 manage.py createsuperuser --no-input
+# RUN python3 manage.py migrate
+# RUN python3 manage.py createsuperuser --no-input
 
 EXPOSE 8000
 #CMD ["bash"]

README.md

@@ -61,10 +61,14 @@ This will build a container named `bco_api` with the tag `latest`.
 
 ### Running the container via Docker
 
-The BCO Api container can be run via docker on the command line by running:
+The BCO Api container can be run via docker on the command line in linux by running:
 
 `docker run --rm --network host -it bco_api:latest`
 
+The BCO Api container can be run via docker on the command line in MacOS by running:
+
+`docker run --rm -p 8000:8000 -it bco_api:latest`
+
 This will expose the server at `http://127.0.0.1:8000`.
 
 #### Overriding the port
@@ -73,6 +77,7 @@ It is possible to override the port 8000 to whatever port is desired.  This is d
 
 `docker run --rm --network host -it bco_api:latest 0.0.0.0:8080`
 
+
 NOTE: The ip address of 0.0.0.0 is to allow the web serer to properly associate with 127.0.0.1 - if given 127.0.0.1 it will not allow communications outside of the container!
 
 With 8080 representing the desired port.  You can also give it a specific network created with `docker network create` if you wanted to give assigned IP addresses.

authentication/apis.py

@@ -223,12 +223,12 @@ def post(self, request):
         """"""
 
         result = validate_auth_service(request.data)
+        
         if result != 1:
             return Response(
                 status=status.HTTP_403_FORBIDDEN,
                 data=result
             )
-
         try:
             auth_object = Authentication.objects.get(username=request.user.username)
         except Authentication.DoesNotExist:

docker-compose.yml

@@ -4,12 +4,13 @@ version: '3.4'
 
 services:
   bco-api:
+    platform: linux/amd64
     build: .
-    # image: ghcr.io/biocompute-objects/bco_api:latest
+    image: ghcr.io/biocompute-objects/bco_api:23.07
     container_name: bco-api
     volumes:
-       - /Users/hadleyking/GitHub/biocompute-objects/dev/data/db.sqlite3:/biocompute_api/bco_api/db.sqlite3
-       - /Users/hadleyking/GitHub/biocompute-objects/dev/data/server.conf:/biocompute_api/bco_api/server.conf
+       - ./data/db.sqlite3:/biocompute_api/db.sqlite3
+       - ./data/server.conf:/biocompute_api/server.conf
     environment:
       TZ: 'America/New_York'
       ENV DJANGO_SUPERUSER_PASSWORD: "BioCompute123"

search/selectors.py

@@ -45,7 +45,7 @@ def controled_list(user: User) -> QuerySet:
     raw_prefixes = UserUtils().prefix_perms_for_user(user_object=user)
     for prefix in raw_prefixes :
         pre = prefix.split("_")[1]
-        if pre not in prefix_list and pre is not "prefix":
+        if pre not in prefix_list and pre != "prefix":
             prefix_list.append(pre)
 
     for prefix in prefix_list: