Merge branch 'master' into filepicker-bug

.github/workflows/ci-testing-deploy.yml

@@ -1379,7 +1379,6 @@ jobs:
         run: ./ci/github/unit-testing/postgres-database.bash install
       - name: typecheck
         run: ./ci/github/unit-testing/postgres-database.bash typecheck
-        continue-on-error: true
       - name: test
         if: always()
         run: ./ci/github/unit-testing/postgres-database.bash test

packages/postgres-database/requirements/_test.in

@@ -20,3 +20,5 @@ pytest-instafail
 pytest-runner
 pyyaml
 sqlalchemy[mypy] # adds Mypy / Pep-484 Support for ORM Mappings SEE https://docs.sqlalchemy.org/en/20/orm/extensions/mypy.html
+types-docker
+types-psycopg2

packages/postgres-database/requirements/_test.txt

@@ -75,9 +75,21 @@ tomli==2.0.1
     #   coverage
     #   mypy
     #   pytest
+types-docker==7.1.0.20240806
+    # via -r requirements/_test.in
+types-psycopg2==2.9.21.20240417
+    # via -r requirements/_test.in
+types-requests==2.32.0.20240712
+    # via types-docker
 typing-extensions==4.12.2
     # via
     #   -c requirements/_base.txt
     #   -c requirements/_migration.txt
     #   mypy
     #   sqlalchemy2-stubs
+urllib3==2.2.2
+    # via
+    #   -c requirements/../../../requirements/constraints.txt
+    #   -c requirements/_migration.txt
+    #   types-docker
+    #   types-requests

packages/postgres-database/setup.cfg

@@ -13,3 +13,8 @@ addopts = -W error::sqlalchemy.exc.SAWarning
 markers =
 	acceptance_test: "marks tests as 'acceptance tests' i.e. does the system do what the user expects? Typically those are workflows."
 	testit: "marks test to run during development"
+
+[mypy]
+plugins =
+	pydantic.mypy
+	sqlalchemy.ext.mypy.plugin

packages/postgres-database/src/simcore_postgres_database/cli.py

@@ -1,6 +1,7 @@
 """ command line interface for migration
 
 """
+
 # pylint: disable=wildcard-import
 # pylint: disable=unused-wildcard-import
 
@@ -159,14 +160,16 @@ def clean():
 @main.command()
 def upgrade_and_close():
     """Used in migration service program to discover, upgrade and close"""
-
+    assert discover.callback  # nosec
     for attempt in Retrying(wait=wait_fixed(5), after=after_log(log, logging.ERROR)):
         with attempt:
             if not discover.callback():
                 raise PostgresNotFoundError
 
     try:
+        assert info.callback  # nosec
         info.callback()
+        assert upgrade.callback  # nosec
         upgrade.callback(revision="head")
         info.callback()
     except Exception:  # pylint: disable=broad-except

packages/postgres-database/src/simcore_postgres_database/migration/env.py

@@ -1,9 +1,8 @@
 from logging.config import fileConfig
 
 from alembic import context
-from sqlalchemy import engine_from_config, pool
-
 from simcore_postgres_database.settings import target_metadatas
+from sqlalchemy import engine_from_config, pool
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
@@ -15,6 +14,7 @@
 if __name__ == "__main__":
     # swallows up all log messages from tests
     # only enable it during cli invocation
+    assert config.config_file_name is not None  # nosec
     fileConfig(config.config_file_name)
 
 # add your model's MetaData object here

packages/postgres-database/src/simcore_postgres_database/migration/versions/009c81406676_add_project_running_state.py

@@ -5,6 +5,7 @@
 Create Date: 2020-10-12 08:38:40.807576+00:00
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 from sqlalchemy.dialects import postgresql
@@ -87,7 +88,7 @@ def upgrade():
         FAILED: "FAILED",
     }
     [
-        op.execute(
+        op.execute(  # type: ignore[func-returns-value] # no reason to change now
             sa.DDL(
                 f"""
 UPDATE comp_pipeline
@@ -99,7 +100,7 @@ def upgrade():
         for old, new in migration_map.items()
     ]
     [
-        op.execute(
+        op.execute(  # type: ignore[func-returns-value] # no reason to change now
             sa.DDL(
                 f"""
 UPDATE comp_tasks
@@ -146,7 +147,7 @@ def downgrade():
         "FAILED": FAILED,
     }
     [
-        op.execute(
+        op.execute(  # type: ignore[func-returns-value] # no reason to change now
             sa.DDL(
                 f"""
 UPDATE comp_pipeline
@@ -158,7 +159,7 @@ def downgrade():
         for old, new in migration_map.items()
     ]
     [
-        op.execute(
+        op.execute(  # type: ignore[func-returns-value] # no reason to change now
             sa.DDL(
                 f"""
 UPDATE comp_tasks

packages/postgres-database/src/simcore_postgres_database/migration/versions/10b293fdcd56_alters_product_login_settings.py

@@ -5,6 +5,7 @@
 Create Date: 2023-01-14 21:12:56.182870+00:00
 
 """
+
 import json
 
 import sqlalchemy as sa
@@ -40,7 +41,7 @@ def upgrade():
         "products",
         "login_settings",
         server_default=sa.text("'{}'::jsonb"),
-        existing_server_default=sa.text("'{\"two_factor_enabled\": false}'::jsonb"),
+        existing_server_default=sa.text("'{\"two_factor_enabled\": false}'::jsonb"),  # type: ignore[arg-type]
     )
 
 
@@ -67,6 +68,6 @@ def downgrade():
         "products",
         "login_settings",
         existing_type=postgresql.JSONB(astext_type=sa.Text()),
-        existing_server_default=sa.text("'{}'::jsonb"),
+        existing_server_default=sa.text("'{}'::jsonb"),  # type: ignore[arg-type]
         server_default=sa.text("'{\"two_factor_enabled\": false}'::jsonb"),
     )

packages/postgres-database/src/simcore_postgres_database/migration/versions/a8f0bacbbaef_product_issue_cols_nullable.py

@@ -5,6 +5,7 @@
 Create Date: 2022-08-24 13:33:30.104287+00:00
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 
@@ -22,7 +23,7 @@ def upgrade():
         "issues_login_url",
         existing_type=sa.VARCHAR(),
         nullable=True,
-        existing_server_default=sa.text(
+        existing_server_default=sa.text(  # type: ignore[arg-type]
             "'https://github.com/ITISFoundation/osparc-simcore/issues'::character varying"
         ),
     )
@@ -31,7 +32,7 @@ def upgrade():
         "issues_new_url",
         existing_type=sa.VARCHAR(),
         nullable=True,
-        existing_server_default=sa.text(
+        existing_server_default=sa.text(  # type: ignore[arg-type]
             "'https://github.com/ITISFoundation/osparc-simcore/issues/new'::character varying"
         ),
     )
@@ -45,7 +46,7 @@ def downgrade():
         "issues_new_url",
         existing_type=sa.VARCHAR(),
         nullable=False,
-        existing_server_default=sa.text(
+        existing_server_default=sa.text(  # type: ignore[arg-type]
             "'https://github.com/ITISFoundation/osparc-simcore/issues/new'::character varying"
         ),
     )
@@ -54,7 +55,7 @@ def downgrade():
         "issues_login_url",
         existing_type=sa.VARCHAR(),
         nullable=False,
-        existing_server_default=sa.text(
+        existing_server_default=sa.text(  # type: ignore[arg-type]
             "'https://github.com/ITISFoundation/osparc-simcore/issues'::character varying"
         ),
     )

packages/postgres-database/src/simcore_postgres_database/models/base.py

@@ -3,10 +3,14 @@
     - Collects all table's schemas
     - Metadata object needed to explicitly define table schemas
 """
+
+from typing import cast
+
 import sqlalchemy.orm
+from sqlalchemy.ext.declarative import DeclarativeMeta
 
 #  DO NOT inheriting from _base. Use instead explicit table definitions
 #  See https://docs.sqlalchemy.org/en/latest/orm/mapping_styles.html#classical-mappings
-Base = sqlalchemy.orm.declarative_base()
+Base = cast(DeclarativeMeta, sqlalchemy.orm.declarative_base())
 
 metadata = Base.metadata

packages/postgres-database/src/simcore_postgres_database/utils_aiopg_orm.py

@@ -6,11 +6,12 @@
         - the new async sqlalchemy ORM https://docs.sqlalchemy.org/en/14/orm/
         - https://piccolo-orm.readthedocs.io/en/latest/index.html
 """
+
 # pylint: disable=no-value-for-parameter
 
 import functools
 import operator
-from typing import Any, Generic, TypeVar
+from typing import Any, Generic, TypeVar, cast
 
 import sqlalchemy as sa
 from aiopg.sa.connection import SAConnection
@@ -246,7 +247,7 @@ async def update(
 
         query, is_scalar = self._append_returning(returning_cols, query)
         if is_scalar:
-            return await self._conn.scalar(query)
+            return cast(RowUId, await self._conn.scalar(query))
 
         result: ResultProxy = await self._conn.execute(query)
         row: RowProxy | None = await result.first()
@@ -261,7 +262,7 @@ async def insert(
 
         query, is_scalar = self._append_returning(returning_cols, query)
         if is_scalar:
-            return await self._conn.scalar(query)
+            return cast(RowUId, await self._conn.scalar(query))
 
         result: ResultProxy = await self._conn.execute(query)
         row: RowProxy | None = await result.first()

packages/postgres-database/src/simcore_postgres_database/utils_payments.py

@@ -88,7 +88,7 @@ async def update_payment_transaction_state(
         msg = f"cannot update state with {completion_state=} since it is already initiated"
         raise ValueError(msg)
 
-    optional = {}
+    optional: dict[str, str | None] = {}
     if state_message:
         optional["state_message"] = state_message
 
@@ -132,7 +132,7 @@ async def update_payment_transaction_state(
         )
         row = await result.first()
         assert row, "execute above should have caught this"  # nosec
-
+        assert isinstance(row, RowProxy)  # nosec
         return row
 
 

packages/postgres-database/src/simcore_postgres_database/utils_users.py

@@ -2,7 +2,6 @@
     i.e. models.users main table and all its relations
 """
 
-
 import re
 import secrets
 import string
@@ -152,7 +151,8 @@ async def get_billing_details(conn: SAConnection, user_id: int) -> RowProxy | No
             )
             .where(users.c.id == user_id)
         )
-        return await result.fetchone()
+        value: RowProxy | None = await result.fetchone()
+        return value
 
     @staticmethod
     async def get_role(conn: SAConnection, user_id: int) -> UserRole: