merge: staging into main

.github/workflows/build-and-deploy-to-main.yml

@@ -3,6 +3,9 @@
 name: (main) Build and push api image to Azure Container Registry
 
 on:
+  push:
+    branches:
+      - main
   pull_request:
     types: [closed]
     branches:

.github/workflows/lint.yml

@@ -21,9 +21,9 @@ jobs:
       - uses: Gr1N/setup-poetry@v8
 
       - name: Install dependencies
-        run: poetry install
+        run: poetry install --no-root
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: .venv
           key: ${{ runner.os }}-poetry-${{ hashFiles('poetry.lock') }}

.github/workflows/staging-build-and-deploy.yml

@@ -1,48 +1,48 @@
-on: 
-  push:
-    branches:
-      - staging
-  pull_request:
-    types: [opened, synchronize, reopened, closed]
-    branches:
-      - staging
+on:
+  # push:
+  #   branches:
+  #     - staging
+  # pull_request:
+  #   types: [opened, synchronize, reopened, closed]
+  #   branches:
+  #     - staging
   workflow_dispatch:
-  
+
 name: Staging_Container_Workflow
 
 jobs:
-    build-and-deploy:
-        runs-on: ubuntu-latest
-        steps:
-        # checkout the repo
-        - name: 'Checkout GitHub Action'
-          uses: actions/checkout@v4
-          with:
-            ref: staging
-          
-        - name: 'Login via Azure CLI'
-          uses: azure/login@v1
-          with:
-            creds: ${{ secrets.AZURE_CREDENTIALS }}
-        
-        - name: 'Build and push image'
-          uses: azure/docker-login@v1
-          with:
-            login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
-            username: ${{ secrets.REGISTRY_USERNAME }}
-            password: ${{ secrets.REGISTRY_PASSWORD }}
-        - run: |
-            docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/fairhub-flask-api:staging${{ github.sha }}
-            docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/fairhub-flask-api:staging${{ github.sha }}
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      # checkout the repo
+      - name: "Checkout GitHub Action"
+        uses: actions/checkout@v4
+        with:
+          ref: staging
+
+      - name: "Login via Azure CLI"
+        uses: azure/login@v1
+        with:
+          creds: ${{ secrets.AZURE_CREDENTIALS }}
+
+      - name: "Build and push image"
+        uses: azure/docker-login@v1
+        with:
+          login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
+          username: ${{ secrets.REGISTRY_USERNAME }}
+          password: ${{ secrets.REGISTRY_PASSWORD }}
+      - run: |
+          docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/fairhub-flask-api:staging${{ github.sha }}
+          docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/fairhub-flask-api:staging${{ github.sha }}
 
-        - name: 'Deploy to Azure Container Instances'
-          uses: 'azure/aci-deploy@v1'
-          with:
-            resource-group: ${{ secrets.RESOURCE_GROUP }}
-            dns-name-label: ${{ secrets.RESOURCE_GROUP }}${{ github.run_number }}
-            image: ${{ secrets.REGISTRY_LOGIN_SERVER }}/sampleapp:${{ github.sha }}
-            registry-login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
-            registry-username: ${{ secrets.REGISTRY_USERNAME }}
-            registry-password: ${{ secrets.REGISTRY_PASSWORD }}
-            name: fairhub-flask-api-staging
-            location: 'west us'
+      - name: "Deploy to Azure Container Instances"
+        uses: "azure/aci-deploy@v1"
+        with:
+          resource-group: ${{ secrets.RESOURCE_GROUP }}
+          dns-name-label: ${{ secrets.RESOURCE_GROUP }}${{ github.run_number }}
+          image: ${{ secrets.REGISTRY_LOGIN_SERVER }}/sampleapp:${{ github.sha }}
+          registry-login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
+          registry-username: ${{ secrets.REGISTRY_USERNAME }}
+          registry-password: ${{ secrets.REGISTRY_PASSWORD }}
+          name: fairhub-flask-api-staging
+          location: "west us"

.github/workflows/test.yml

@@ -29,9 +29,9 @@ jobs:
       - uses: Gr1N/setup-poetry@v8
 
       - name: Install dependencies
-        run: poetry install
+        run: poetry install --no-root
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: .venv
           key: ${{ runner.os }}-poetry-${{ hashFiles('poetry.lock') }}

Dockerfile

@@ -1,34 +1,47 @@
-FROM python:3.10-alpine
+# Use official slim Python image
+FROM python:3.10-slim
 
+# Expose the port your app will run on
 EXPOSE 5000
 
+# Set working directory
 WORKDIR /app
 
+# Environment
 ENV POETRY_VERSION=1.3.2
-
-RUN apk update
-RUN apk add --no-cache gcc libffi-dev musl-dev postgresql-dev
-
+# Note: Force pip to use pre-built wheels
+ENV PIP_ONLY_BINARY=:all:
+
+# Install system dependencies for building Python packages
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    gcc \
+    build-essential \
+    libffi-dev \
+    libpq-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Poetry
 RUN pip install "poetry==$POETRY_VERSION"
 
-COPY poetry.lock pyproject.toml ./
-
+# Install Python dependencies
+COPY pyproject.toml poetry.lock ./
 RUN poetry config virtualenvs.create false
-RUN poetry install
+RUN poetry install --no-root
 
+# Copy source code and config
 COPY apis ./apis
 COPY model ./model
 COPY core ./core
 COPY modules ./modules
-COPY app.py .
-COPY config.py .
-COPY caching.py .
-
+COPY app.py config.py caching.py ./
+# Copy database/migration setup
 COPY alembic ./alembic
 COPY alembic.ini .
-
+# Copy runtime entrypoint
 COPY entrypoint.sh .
+COPY alembic alembic.ini ./
+COPY entrypoint.sh ./
 
+# Setup Entrypoint
 RUN chmod +x entrypoint.sh
-
-ENTRYPOINT ["./entrypoint.sh"]
+ENTRYPOINT ["./entrypoint.sh"]

alembic/versions/0ff53a655198_update_email_verification.py

@@ -0,0 +1,36 @@
+"""update_email_verification
+
+Revision ID: 0ff53a655198
+Revises: 3ffefbd9c03b
+Create Date: 2025-02-18 13:50:48.808176
+
+"""
+from typing import Sequence, Union
+import sqlalchemy as sa
+import datetime
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision: str = '0ff53a655198'
+down_revision: Union[str, None] = '5c1257547eb8'
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+created_at = int(datetime.datetime.now(datetime.timezone.utc).timestamp())
+
+
+def upgrade() -> None:
+    op.alter_column("email_verification", "token", type_=sa.String)
+    op.alter_column("email_verification", "user_id", type_=sa.CHAR(36))
+
+    op.drop_column("email_verification", "created_at")
+
+    op.add_column(
+        "email_verification", sa.Column("created_at", sa.BIGINT(), nullable=True)
+    )
+
+    op.execute(f"UPDATE \"email_verification\" SET created_at ='{created_at}'")
+
+    op.alter_column("email_verification", "created_at", nullable=False)

alembic/versions/3ffefbd9c03b_email_verified_type.py

@@ -0,0 +1,33 @@
+"""email verified type
+
+Revision ID: 3ffefbd9c03b
+Revises: 9698369d7a8c
+Create Date: 2024-07-01 12:28:02.596192
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = '3ffefbd9c03b'
+down_revision: Union[str, None] = '9698369d7a8c'
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    with op.batch_alter_table("user") as batch_op:
+        batch_op.alter_column(
+            "email_verified",
+            type_=sa.Boolean(),
+            postgresql_using="email_verified::boolean",
+        )
+
+
+
+
+
+

alembic/versions/5c1257547eb8_update_study_acronym.py

@@ -0,0 +1,28 @@
+"""update_study_acronym
+
+Revision ID: 5c1257547eb8
+Revises: 3ffefbd9c03b
+Create Date: 2025-02-19 16:25:24.597207
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = '5c1257547eb8'
+down_revision: Union[str, None] = '3ffefbd9c03b'
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    with op.batch_alter_table("study") as batch_op:
+        batch_op.alter_column(
+            "acronym",
+            new_column_name="short_description",
+            type_=sa.String(300),
+            nullable=False
+        )

alembic/versions/9698369d7a8c_create_session_table.py

@@ -0,0 +1,27 @@
+"""create session table
+
+Revision ID: 9698369d7a8c
+Revises: 
+Create Date: 2024-06-13 09:59:17.605666
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = '9698369d7a8c'
+down_revision: Union[str, None] = None
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        'session',
+        sa.Column('id', sa.CHAR(36), primary_key=True),
+        sa.Column('user_id', sa.CHAR(36), sa.ForeignKey("user.id"), nullable=False),
+        sa.Column('expires_at', sa.BigInteger, nullable=False)
+    )
+

alembic/versions/df71df391cdb_add_token_to_user.py

@@ -0,0 +1,26 @@
+"""add token to user
+
+Revision ID: df71df391cdb
+Revises: 3ffefbd9c03b
+Create Date: 2024-07-03 10:15:49.657807
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+import uuid
+
+
+# revision identifiers, used by Alembic.
+revision: str = 'df71df391cdb'
+down_revision: Union[str, None] = '0ff53a655198'
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+password_reset_token = str(uuid.uuid4())
+
+def upgrade() -> None:
+    op.add_column(
+        "user", sa.Column("password_reset_token", sa.String, nullable=True)
+    )

alembic/versions_backup/6173282aef08_remove_invite_info.py

@@ -0,0 +1,24 @@
+"""remove_invite_info
+
+Revision ID: 6173282aef08
+Revises: f150341d2741
+Create Date: 2023-12-19 00:32:08.157538
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "6173282aef08"
+down_revision: Union[str, None] = "f150341d2741"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.drop_column("invite", "info")
+    with op.batch_alter_table("notification") as batch_op:
+        batch_op.alter_column("target", nullable=True)