Merge pull request #65 from bcgsc/feat/DEVSU-2701-update-and-test-pori-demo

Feat/devsu 2701 update and test pori demo

Author: elewis2

.github/workflows/compose-test.yml

@@ -11,7 +11,7 @@ jobs:
       - uses: actions/checkout@v2
       - run: mkdir -p databases/{postgres,orientdb}/{backup,data}
       - run: mkdir keys
-      - run: docker-compose -f "docker-compose.dev.yml" up -d --build
+      - run: docker compose -f "docker-compose.dev.yml" up -d --build
       - run: bash tests/test-docker-compose.sh
-      - run: docker-compose -f "docker-compose.dev.yml" down
+      - run: docker compose -f "docker-compose.dev.yml" down
         if: always()

README.md

@@ -27,7 +27,7 @@ will be updated on merge to the master branch of this repository.
 First, set up a virtual environment (Optional but recommended)
 
 ```bash
-python3 -m venv venv
+python3.8 -m venv venv
 source venv/bin/activate
 pip install -U setuptools pip
 ```

demo/Dockerfile.auth

@@ -1,4 +1,4 @@
-FROM jboss/keycloak:16.1.1
+FROM quay.io/keycloak/keycloak:16.1.1
 USER root
 RUN mkdir -p /tmp/realm_data/
 COPY demo/kc_setup_keyfile.sh /scripts/kc_setup_keyfile.sh

docker-compose.dev.yml

@@ -36,12 +36,8 @@ services:
     networks:
       - app-network
     volumes:
-      - source: ./databases/orientdb/data
-        target: /orientdb/databases
-        type: bind
-      - source: ./databases/orientdb/backup
-        target: /orientdb/backup
-        type: bind
+      - orientdb_data:/orientdb/databases
+      - orientdb_backup:/orientdb/backup
   graphkb_api:
     image: bcgsc/pori-graphkb-api:latest
     ports:
@@ -139,7 +135,7 @@ services:
     image: bcgsc/pori-ipr-api:latest
     command: npm start
     ports:
-      - 8081:8080
+      - 8082:8080
     environment:
       IPR_DATABASE_HOSTNAME: ipr_db
       IPR_DATABASE_NAME: ipr_demo
@@ -176,7 +172,7 @@ services:
     environment:
       KEYCLOAK_REALM: PORI
       # customize settings below
-      API_BASE_URL: http://localhost:8081/api
+      API_BASE_URL: http://localhost:8082/api
       GRAPHKB_URL: http://localhost:5000
       KEYCLOAK_URL: http://localhost:8888/auth
       PUBLIC_PATH: /
@@ -190,3 +186,6 @@ services:
 networks:
   app-network:
     driver: bridge
+volumes:
+  orientdb_data:
+  orientdb_backup:

docker-compose.prod.yml

@@ -18,7 +18,7 @@ services:
         target: /orientdb/backup
         type: bind
   graphkb_api:
-    image: bcgsc/pori-graphkb-api:v3.13.3
+    image: bcgsc/pori-graphkb-api:v3.15.2
     ports:
       - 8080:8080
     environment:
@@ -48,7 +48,7 @@ services:
       timeout: 10s
       retries: 5
   graphkb_client:
-    image: bcgsc/pori-graphkb-client:v4.2.2
+    image: bcgsc/pori-graphkb-client:v4.3.2
     environment:
       KEYCLOAK_REALM: PORI
       KEYCLOAK_CLIENT_ID: GraphKB
@@ -65,7 +65,7 @@ services:
       - app-network
     restart: always
   ipr_db:
-    image: bcgsc/pori-ipr-demodb:v7.2.1
+    image: bcgsc/pori-ipr-demodb:v8.2.0
     restart: always
     environment:
       DATABASE_NAME: ipr_demo
@@ -107,7 +107,7 @@ services:
       - app-network
     restart: always
   ipr_api:
-    image: bcgsc/pori-ipr-api:v7.2.1
+    image: bcgsc/pori-ipr-api:v8.2.0
     ports:
       - 8081:8080
     environment:
@@ -141,7 +141,7 @@ services:
       timeout: 10s
       retries: 5
   ipr_client:
-    image: bcgsc/pori-ipr-client:v6.6.3
+    image: bcgsc/pori-ipr-client:v7.1.0
     environment:
       KEYCLOAK_REALM: PORI
       # customize settings below

docs/build_external.sh

@@ -4,28 +4,15 @@
 # clone the IPR python adapter if it does not exist, otherwise update
 if ! [ -d docs/_pori_ipr_python ];
 then
-    git clone https://github.com/bcgsc/pori_ipr_python.git docs/_pori_ipr_python
-    echo "hide: true" > docs/_pori_ipr_python/.pages
+    git clone https://github.com/bcgsc/pori_python.git docs/_pori_python
+    echo "hide: true" > docs/_pori_python/.pages
 else
-    cd docs/_pori_ipr_python
+    cd docs/_pori_python
     git checkout master
     git pull
     cd ../..
 fi
 
-# clone the GraphKB Python adapter if it does not exist, otherwise update
-if ! [ -d docs/_pori_graphkb_python ];
-then
-    git clone https://github.com/bcgsc/pori_graphkb_python.git docs/_pori_graphkb_python
-    echo "hide: true" > docs/_pori_graphkb_python/.pages
-else
-    cd docs/_pori_graphkb_python
-    git checkout master
-    git pull
-    cd ../..
-fi
-
-
 # clone the loaders repo if it does not exist, otherwise update
 if ! [ -d docs/graphkb/_pori_graphkb_loader ];
 then
@@ -40,8 +27,8 @@ fi
 
 # now build the reference python module API files
 markdown_refdocs \
-    docs/_pori_graphkb_python/graphkb \
-    docs/_pori_ipr_python/ipr  \
+    docs/_pori_python/pori_python/graphkb \
+    docs/_pori_python/pori_python/ipr  \
     -o docs/developer_reference \
     --link
 

docs/index.md

@@ -5,7 +5,6 @@ software designed to support scalable precision oncology. The platform has two m
 a graph knowledge base ([GraphKB](./graphkb)) and an integrated pipeline reporting application ([IPR](./ipr)). This site
 contains central documentation for the platform as well as setup and installation instructions.
 
-Click on the menu icon (:material-menu:) to see a full table of contents for this site.
 
 ![pori server stack](./images/pori-server-stack.png)
 

docs/install.md

@@ -9,7 +9,7 @@ Most of the servers are auto-started together with docker-compose but the keyclo
 
     If this is not your first time setting up or running these instructions see the [update instructions](#updating-an-existing-demo-install) instead
 
-Start by cloning this repository which contains the default docker compose configs (`docker-compose.yml` and `docker-compose.dev.yml`)
+Start by cloning this repository which contains the default docker compose configs (`docker-compose.dev.yml`)
 
 ```bash
 git clone https://github.com/bcgsc/pori.git
@@ -53,7 +53,7 @@ mkdir keys
 Next, use docker-compose to start the DB, API, and client servers. The paths/URLs in the docker-compose.yml file should be adjusted to match your deployment. In our demo deployment we have a proxy pass set up from the configured ports to handle the https layer
 
 ```bash
-docker-compose -f docker-compose.dev.yml up -d --build --remove-orphans
+docker compose -f docker-compose.dev.yml up -d --build --remove-orphans
 ```
 
 This will start the following services

docs/ipr_spec_tables.py

@@ -79,7 +79,7 @@ def spec_to_md(spec, optional_only=False, ignore_nested=False):
     return result
 
 
-specfile = os.path.join(os.path.dirname(__file__), '_pori_ipr_python/ipr/content.spec.json')
+specfile = os.path.join(os.path.dirname(__file__), '_pori_python/pori_python/ipr/content.spec.json')
 with open(specfile, 'r') as fh:
     spec = json.load(fh)
 

docs/repos.md

@@ -76,17 +76,9 @@ A developer reference for these packages including the function signatures and p
 
 <div class='projects' markdown='1'>
 
-- ### [GraphKB Python Adapter](https://github.com/bcgsc/pori_graphkb_python)
+- ### [Pori Python Adapter](https://github.com/bcgsc/pori_python)
 
-    ![graphkb python](./images/graph-icon_outline.svg)
-
-    Python adapter package for querying the GraphKB API. See the related
-    [user manual](../graphkb/python/docs) for instructions on incorporating
-    this into custom scripts.
-
-- ### [IPR Python Adapter](https://github.com/bcgsc/pori_ipr_python)
-
-    ![ipr python](./images/wrench.svg)
+    ![pori python](./images/wrench.svg)
 
     Python adapter for generating reports uploaded to the IPR API. This python tool takes in variant inputs as tab-delimited files and annotates them using GraphKB. The resulting output is uploaded to IPR as a report. Additional report content such as images and metadata can be passed to be included in the report upload.