Merge Private Dashboards into Staging

.env.example

@@ -1,7 +1,12 @@
 FAIRHUB_DATABASE_URL="postgresql://admin:root@localhost:5432/fairhub_local"
 FAIRHUB_SECRET="AddAny32+CharacterCountWordHereAsYourSecret"
-
 FAIRHUB_AZURE_READ_SAS_TOKEN=
 FAIRHUB_AZURE_STORAGE_ACCOUNT_NAME=
-
-FAIRHUB_GROWTHBOOK_CLIENT_KEY=
+FAIRHUB_GROWTHBOOK_CLIENT_KEY=
+FAIRHUB_CACHE_DEFAULT_TIMEOUT=86400
+FAIRHUB_CACHE_KEY_PREFIX=fairhub-io#
+FAIRHUB_CACHE_HOST=localhost
+FAIRHUB_CACHE_PORT=6379
+FAIRHUB_CACHE_TYPE=RedisCache
+FAIRHUB_CACHE_DB=0
+FAIRHUB_CACHE_URL=redis://127.0.0.1:6379

.github/workflows/deploy-app-to-main-slot.yml

@@ -0,0 +1,67 @@
+# Docs for the Azure Web Apps Deploy action: https://github.com/Azure/webapps-deploy
+# More GitHub Actions for Azure: https://github.com/Azure/actions
+# More info on Python, GitHub Actions, and Azure App Service: https://aka.ms/python-webapps-actions
+
+name: Build and deploy Python app to Azure Web App - api-fairhub-io
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types: [opened, synchronize, reopened, closed]
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python version
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.10"
+
+      - name: Create and start virtual environment
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+
+      - name: Install dependencies
+        run: pip install poetry==1.3.2 && poetry install
+
+      # Optional: Add step to run tests here (PyTest, Django test suites, etc.)
+
+      - name: Upload artifact for deployment jobs
+        uses: actions/upload-artifact@v2
+        with:
+          name: python-app
+          path: |
+            . 
+            !venv/
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+    environment:
+      name: "main"
+      url: ${{ steps.deploy-to-webapp.outputs.webapp-url }}
+
+    steps:
+      - name: Download artifact from build job
+        uses: actions/download-artifact@v2
+        with:
+          name: python-app
+          path: .
+
+      - name: "Deploy to Azure Web App"
+        uses: azure/webapps-deploy@v2
+        id: deploy-to-webapp
+        with:
+          app-name: "api-fairhub-io"
+          slot-name: "main"
+          publish-profile: ${{ secrets.AZUREAPPSERVICE_PUBLISHPROFILE_6C6B1227CD464BFDBC9173E57CDEEC65 }}

.github/workflows/deploy-app-to-staging-slot.yml

@@ -0,0 +1,67 @@
+# Docs for the Azure Web Apps Deploy action: https://github.com/Azure/webapps-deploy
+# More GitHub Actions for Azure: https://github.com/Azure/actions
+# More info on Python, GitHub Actions, and Azure App Service: https://aka.ms/python-webapps-actions
+
+name: Build and deploy Python app to Azure Web App - api-fairhub-io
+
+on:
+  push:
+    branches:
+      - staging
+  pull_request:
+    types: [opened, synchronize, reopened, closed]
+    branches:
+      - staging
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python version
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.10"
+
+      - name: Create and start virtual environment
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+
+      - name: Install dependencies
+        run: pip install poetry==1.3.2 && poetry install
+
+      # Optional: Add step to run tests here (PyTest, Django test suites, etc.)
+
+      - name: Upload artifact for deployment jobs
+        uses: actions/upload-artifact@v2
+        with:
+          name: python-app
+          path: |
+            . 
+            !venv/
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+    environment:
+      name: "staging"
+      url: ${{ steps.deploy-to-webapp.outputs.webapp-url }}
+
+    steps:
+      - name: Download artifact from build job
+        uses: actions/download-artifact@v2
+        with:
+          name: python-app
+          path: .
+
+      - name: "Deploy to Azure Web App"
+        uses: azure/webapps-deploy@v2
+        id: deploy-to-webapp
+        with:
+          app-name: "api-fairhub-io"
+          slot-name: "staging"
+          publish-profile: ${{ secrets.AZUREAPPSERVICE_PUBLISHPROFILE_STAGING }}

.gitignore

@@ -33,6 +33,7 @@ coverage
 
 # Environment variables
 .env
+.venv
 
 # Virutal Environments
 .venv

.pylint.ini

@@ -410,4 +410,4 @@ known-third-party=enchant
 # Exceptions that will emit a warning when being caught. Defaults to
 # "Exception"
 overgeneral-exceptions=builtins.BaseException,
-                       builtins.Exception
+                       builtins.Exception

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.8-alpine
+FROM python:3.10-alpine
 
 EXPOSE 5000
 

README.md

@@ -98,6 +98,20 @@ Close the database with:
 docker-compose -f ./db-docker-compose.yaml down -v
 ```
 
+## Running
+
+For developer mode:
+
+```bash
+flask run --debug
+```
+
+For production mode:
+
+```bash
+python3 app.py --host $HOST --port $PORT
+```
+
 ## License
 
 This work is licensed under

alembic/versions/0defbfc71c59_add_identifier_to_version.py

@@ -5,6 +5,7 @@
 Create Date: 2024-01-05 13:25:15.547450
 
 """
+
 from typing import Sequence, Union
 
 from alembic import op

alembic/versions/29e42ce4be3f_adding_license_text.py

@@ -5,6 +5,7 @@
 Create Date: 2023-12-21 13:34:26.478808
 
 """
+
 from typing import Sequence, Union
 
 from alembic import op

alembic/versions/72ac2b020c7c_delete_dataset_readme_table.py

@@ -5,6 +5,7 @@
 Create Date: 2023-11-08 15:47:00.205940
 
 """
+
 from typing import Sequence, Union
 
 import alembic

apis/__init__.py

@@ -1,11 +1,13 @@
 """Initialize the api system for the backend"""
+
 from flask_restx import Api, Resource
 
 from apis.dataset_metadata_namespace import api as dataset_metadata_namespace
 from apis.study_metadata_namespace import api as study_metadata_namespace
 
 from .authentication import api as authentication
 from .contributor import api as contributors_api
+from .dashboard import api as dashboard
 from .dataset import api as dataset_api
 from .dataset_metadata.dataset_access import api as access
 from .dataset_metadata.dataset_alternate_identifier import api as alternate_identifier
@@ -23,6 +25,7 @@
 from .dataset_metadata.dataset_title import api as title
 from .file import api as file_api
 from .participant import api as participants_api
+from .redcap import api as redcap
 from .study import api as study_api
 from .study_metadata.study_arm import api as arm
 from .study_metadata.study_available_ipd import api as available_ipd
@@ -89,6 +92,8 @@
     "identification",
     "study_description",
     "dataset_contributor",
+    "redcap",
+    "dashboard",
     "utils",
 ]
 
@@ -117,3 +122,5 @@ def get(self):
 api.add_namespace(contributors_api)
 api.add_namespace(user)
 api.add_namespace(utils)
+api.add_namespace(redcap)
+api.add_namespace(dashboard)

apis/authentication.py

@@ -1,6 +1,7 @@
 """This module is used to authenticate users to the system and
 handle few authentication errors. Also, it sets token for logged user
 along with expiration date"""
+
 import datetime
 import importlib
 import os
@@ -322,6 +323,12 @@ def is_granted(permission: str, study=None):
             "participant",
             "study_metadata",
             "dataset_metadata",
+            "add_redcap",
+            "update_redcap",
+            "delete_redcap",
+            "add_dashboard",
+            "update_dashboard",
+            "delete_dashboard",
             "make_owner",
         ],
         "admin": [
@@ -341,6 +348,12 @@ def is_granted(permission: str, study=None):
             "participant",
             "study_metadata",
             "dataset_metadata",
+            "add_redcap",
+            "update_redcap",
+            "delete_redcap",
+            "add_dashboard",
+            "update_dashboard",
+            "delete_delete",
         ],
         "editor": [
             "editor",