Merge pull request #32 from CanDIG/daisieh/integration

Dockerfile

@@ -17,7 +17,7 @@ RUN apk add --no-cache \
 
 COPY ./ /app/
 
-RUN pip install --no-cache-dir -r app/tests/requirements.txt
+RUN pip install --no-cache-dir -r /app/requirements.txt
 
 RUN touch initial_setup
 ENTRYPOINT ["bash", "/app/entrypoint.sh"]

README.md

@@ -1,60 +1,5 @@
 # Open Policy Agent for CanDIGv2
 
-This is the implementation of [OPA](https://www.openpolicyagent.org/) for CanDIGv2. The OPA service provides a unified policy engine across CanDIG services.  
+This is the implementation of [OPA](https://www.openpolicyagent.org/) for CanDIGv2. The OPA service provides a unified policy engine across CanDIG services.
 
-## Testing with katsu
-
-
-This script creates 6 datasets *name_i*(open1, open2, registered3, controlled4, controlled5, controlled6) with one phenopacket with id *pheno_i* in each one.
-
-Capture tokens by running: 
-```
-TOKEN1=$( python3 ./tests/capture_token.py user1 pass1 oidc1 )
-TOKEN2=$( python3 ./tests/capture_token.py user2 pass2 oidc1 )
-```
-
-then you can query katsu and see what datasets you get back:
-
-```
-curl --insecure -XGET -H "X-CANDIG-LOCAL-OIDC: \"$TOKEN1\"" 'localhost:8001/api/phenopackets'|jq '.results'|jq '[.[] | {id: .id}]'
-curl --insecure -XGET -H "X-CANDIG-LOCAL-OIDC: \"$TOKEN2\"" 'localhost:8001/api/phenopackets'|jq '.results'|jq '[.[] | {id: .id}]'
-```
-User1 should have access to 4 datasets, open1, open2, registered3 and controlled4. 
-User2 should have access to 3 datasets, open1, open2, and controlled5. 
-
-
-What's happening here is as described below
-
-```mermaid
-sequenceDiagram
-    participant user2
-    participant keycloak
-    participant katsu
-    participant opa
-
-    user2->>keycloak: Get ID token (would normally go via _e.g._ Tyk)
-    keycloak-->>user2: ID token for user2
-    user2->>+katsu: Request data with ID token
-    katsu->>opa: What datasets are allowed for user2 on this reququest?
-    opa->>katsu: open1, open2, dataset_3, testdset3, controlled5
-    katsu->>-user2: Here's the data from allowed datases
-```
-
-
-You can also query OPA directly with a script provided:
-
-```
-python3 ./tests/lookup_permissions.py ${TOKEN2}
-```
-
-And you should get the result:
-```
-{"result":["open1","open2","dataset_3","testdset3","controlled5"]}
-```
-
-From here you can run the tests to make sure everything works:
-
-```
-pytest tests/test_authx.py
-pytest tests/katsu_tests/
-```
+Opa can be tested as part of the CanDIGv2 stack: from the CanDIGv2 repo directory, run `pytest etc/tests`.