Merge pull request #275 from VariantEffect/release-2024.3.0

Release 2024.3.0

Author: bencap

.github/workflows/run-tests-on-push.yml

@@ -2,6 +2,9 @@ name: Run Tests (On Push)
 on:
   push:
 
+env:
+  LOG_CONFIG: test
+
 jobs:
   run-tests-3_9:
     runs-on: ubuntu-20.04
@@ -15,7 +18,7 @@ jobs:
     - run: pip install --upgrade pip
     - run: pip install poetry
     - run: poetry install --with dev --extras server
-    - run: poetry run pytest tests/
+    - run: poetry run pytest tests/ --show-capture=stdout
 
   run-tests-3_10:
     runs-on: ubuntu-latest
@@ -29,7 +32,7 @@ jobs:
     - run: pip install --upgrade pip
     - run: pip install poetry
     - run: poetry install --with dev --extras server
-    - run: poetry run pytest tests/
+    - run: poetry run pytest tests/ --show-capture=stdout
 
   run-tests-3_11:
     runs-on: ubuntu-latest
@@ -43,7 +46,7 @@ jobs:
     - run: pip install --upgrade pip
     - run: pip install poetry
     - run: poetry install --with dev --extras server
-    - run: poetry run pytest tests/
+    - run: poetry run pytest tests/ --show-capture=stdout
 
   run-mypy-3_10:
     runs-on: ubuntu-latest

Dockerfile.test

@@ -37,6 +37,8 @@ COPY src ./src
 COPY tests/ ./tests/
 COPY mypy_stubs ./mypy_stubs/
 
+ENV LOG_CONFIG=test
+
 RUN useradd testuser -d /code
 USER testuser
 RUN --network=none poetry run pytest

alembic/versions/44a45d616036_make_index_on_users_unique.py

@@ -0,0 +1,29 @@
+"""Make Index on Users Unique
+
+Revision ID: 44a45d616036
+Revises: ec5d2787bec9
+Create Date: 2024-08-16 13:25:14.980820
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision = "44a45d616036"
+down_revision = "ec5d2787bec9"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index("ix_users_username", table_name="users")
+    op.create_index(op.f("ix_users_username"), "users", ["username"], unique=True)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f("ix_users_username"), table_name="users")
+    op.create_index("ix_users_username", "users", ["username"], unique=False)
+    # ### end Alembic commands ###

alembic/versions/76e1e55bc5c1_add_contributors.py

@@ -0,0 +1,56 @@
+"""Add contributors
+
+Revision ID: 76e1e55bc5c1
+Revises: 9702d32bacb3
+Create Date: 2024-08-22 06:17:03.265438
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '76e1e55bc5c1'
+down_revision = '9702d32bacb3'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.create_table('contributors',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('orcid_id', sa.String(), nullable=False),
+    sa.Column('given_name', sa.String(), nullable=True),
+    sa.Column('family_name', sa.String(), nullable=True),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_contributors_orcid_id'), 'contributors', ['orcid_id'], unique=False)
+    op.create_table('experiment_set_contributors',
+    sa.Column('experiment_set_id', sa.Integer(), nullable=False),
+    sa.Column('contributor_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['contributor_id'], ['contributors.id'], ),
+    sa.ForeignKeyConstraint(['experiment_set_id'], ['experiment_sets.id'], ),
+    sa.PrimaryKeyConstraint('experiment_set_id', 'contributor_id')
+    )
+    op.create_table('experiment_contributors',
+    sa.Column('experiment_id', sa.Integer(), nullable=False),
+    sa.Column('contributor_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['contributor_id'], ['contributors.id'], ),
+    sa.ForeignKeyConstraint(['experiment_id'], ['experiments.id'], ),
+    sa.PrimaryKeyConstraint('experiment_id', 'contributor_id')
+    )
+    op.create_table('scoreset_contributors',
+    sa.Column('scoreset_id', sa.Integer(), nullable=False),
+    sa.Column('contributor_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['contributor_id'], ['contributors.id'], ),
+    sa.ForeignKeyConstraint(['scoreset_id'], ['scoresets.id'], ),
+    sa.PrimaryKeyConstraint('scoreset_id', 'contributor_id')
+    )
+
+
+def downgrade():
+    op.drop_table('scoreset_contributors')
+    op.drop_table('experiment_contributors')
+    op.drop_table('experiment_set_contributors')
+    op.drop_index(op.f('ix_contributors_orcid_id'), table_name='contributors')
+    op.drop_table('contributors')

alembic/versions/9702d32bacb3_controlled_keyword.py

@@ -18,6 +18,7 @@ services:
       REDIS_IP: redis
       REDIS_PORT: 6379
       REDIS_SSL: "false"
+      LOG_CONFIG: dev
     ports:
       - "8002:8000"
     volumes:
@@ -37,6 +38,7 @@ services:
       REDIS_IP: redis
       REDIS_PORT: 6379
       REDIS_SSL: "false"
+      LOG_CONFIG: dev
     volumes:
       - .:/code
     depends_on:

docker-compose-dev.yml

@@ -15,6 +15,10 @@ services:
     environment:
       DB_HOST: db
       DB_PORT: 5432
+      REDIS_IP: redis
+      REDIS_PORT: 6379
+      REDIS_SSL: False
+      LOG_CONFIG: dev
     ports:
       - "8444:8000"
     restart: unless-stopped
@@ -33,6 +37,7 @@ services:
       REDIS_IP: redis
       REDIS_PORT: 6379
       REDIS_SSL: False
+      LOG_CONFIG: dev
     depends_on:
       - db
       - redis

docker-compose-local.yml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "mavedb"
-version = "2024.2.2"
+version = "2024.3.0"
 description = "API for MaveDB, the database of Multiplexed Assays of Variant Effect."
 license = "AGPL-3.0-only"
 readme = "README.md"
@@ -37,7 +37,10 @@ httpx = "~0.26.0"
 pandas = "~1.4.1"
 pydantic = "~1.10"
 python-dotenv = "~0.20.0"
+python-json-logger = "~2.0.7"
 SQLAlchemy = "~2.0.0"
+starlette = "~0.27.0"
+starlette-context = "^0.3.6"
 
 # Optional dependencies for running this application as a server
 alembic = { version = "~1.7.6", optional = true }
@@ -53,7 +56,6 @@ python-jose = { extras = ["cryptography"], version = "~3.3.0", optional = true }
 python-multipart = { version = "~0.0.5", optional = true }
 requests = { version = "~2.31.0", optional = true }
 slack-sdk = { version = "~3.21.3", optional = true }
-starlette = { version = "~0.27.0", optional = true }
 uvicorn = { extras = ["standard"], version = "*", optional = true }
 watchtower = { version = "~3.2.0", optional = true }
 
@@ -64,7 +66,7 @@ optional = true
 black = "*"
 boto3-stubs = "~1.34.97"
 flake8 = "*"
-mypy = "*"
+mypy = "~1.10.0"
 pre-commit = "*"
 jsonschema = "*"
 fakeredis = "~2.21.1"
@@ -75,13 +77,14 @@ pytest-socket = "~0.6.0"
 pandas-stubs = "~2.1.4"
 types-requests = "~2.31.0"
 types-python-jose = "~3.3.4"
+types-PyYAML = "~6.0.12.20240808"
 redis = "~5.0.2"
 requests-mock = "~1.11.0"
 SQLAlchemy = { extras = ["mypy"], version = "~2.0.0" }
 
 
 [tool.poetry.extras]
-server = ["alembic", "arq", "authlib", "boto3", "cryptography", "fastapi", "email-validator", "orcid", "psycopg2", "python-jose", "python-multipart", "requests", "slack-sdk", "starlette", "uvicorn", "watchtower"]
+server = ["alembic", "arq", "authlib", "boto3", "cryptography", "fastapi", "email-validator", "orcid", "psycopg2", "python-jose", "python-multipart", "requests", "slack-sdk", "uvicorn", "watchtower"]
 
 
 [tool.black]

poetry.lock

@@ -1,2 +1,11 @@
+import logging as module_logging
+
+import mavedb.logging as application_logging
+
+application_logging.configure()
+logger = module_logging.getLogger(__name__)
+
 __project__ = "mavedb-api"
-__version__ = "2024.2.2"
+__version__ = "2024.3.0"
+
+logger.info(f"MaveDB {__version__}")