fractal-server 1.3.12a4__tar.gz → 1.3.13__tar.gz

{fractal_server-1.3.12a4 → fractal_server-1.3.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 1.3.12a4
+Version: 1.3.13
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -15,7 +15,6 @@ Classifier: Programming Language :: Python :: 3.11
 Provides-Extra: gunicorn
 Provides-Extra: postgres
 Provides-Extra: slurm
-Requires-Dist: SQLAlchemy-Utils (>=0.38.3,<0.39.0)
 Requires-Dist: aiosqlite (>=0.17.0,<0.18.0)
 Requires-Dist: alembic (>=1.9.1,<2.0.0)
 Requires-Dist: asyncpg (>=0.27.0,<0.28.0) ; extra == "postgres"
@@ -23,12 +22,11 @@ Requires-Dist: cloudpickle (>=2.2.1,<2.3.0) ; extra == "slurm"
 Requires-Dist: clusterfutures (>=0.5,<0.6) ; extra == "slurm"
 Requires-Dist: fastapi (>=0.103.0,<0.104.0)
 Requires-Dist: fastapi-users[oauth] (>=12.1.0,<13.0.0)
-Requires-Dist: greenlet
 Requires-Dist: gunicorn (>=20.1.0,<21.0.0) ; extra == "gunicorn"
 Requires-Dist: psycopg2 (>=2.9.5,<3.0.0) ; extra == "postgres"
 Requires-Dist: pydantic (>=1.10.8,<2)
 Requires-Dist: python-dotenv (>=0.20.0,<0.21.0)
-Requires-Dist: sqlalchemy (>=1.4,<2.0)
+Requires-Dist: sqlalchemy[asyncio] (>=1.4,<2.0)
 Requires-Dist: sqlmodel (>=0.0.8,<0.0.9)
 Requires-Dist: uvicorn (>=0.20.0,<0.21.0)
 Project-URL: Changelog, https://github.com/fractal-analytics-platform/fractal-server/blob/main/CHANGELOG.md

fractal_server-1.3.13/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "1.3.13"

{fractal_server-1.3.12a4 → fractal_server-1.3.13}/fractal_server/app/db/__init__.py

@@ -6,6 +6,7 @@ from typing import AsyncGenerator
 from typing import Generator
 
 from sqlalchemy import create_engine
+from sqlalchemy import event
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.ext.asyncio import create_async_engine
 from sqlalchemy.orm import Session as DBSyncSession
@@ -49,9 +50,9 @@ class DB:
 
         if settings.DB_ENGINE == "sqlite":
             logger.warning(
-                "SQLite is supported but discouraged in production. Given its "
-                "partial support for ForeignKey constraints, consistency of "
-                "the database cannot be guaranteed."
+                "SQLite is supported (for version >=3.37) but discouraged "
+                "in production. Given its partial support for ForeignKey "
+                "constraints, database consistency cannot be guaranteed."
             )
 
         # Set some sqlite-specific options
@@ -86,6 +87,13 @@ class DB:
             bind=cls._engine_sync, autocommit=False, autoflush=False
         )
 
+        @event.listens_for(cls._engine_sync, "connect")
+        def set_sqlite_pragma(dbapi_connection, connection_record):
+            if settings.DB_ENGINE == "sqlite":
+                cursor = dbapi_connection.cursor()
+                cursor.execute("PRAGMA journal_mode=WAL")
+                cursor.close()
+
     @classmethod
     async def get_db(cls) -> AsyncGenerator[AsyncSession, None]:
         """

{fractal_server-1.3.12a4 → fractal_server-1.3.13}/fractal_server/app/models/dataset.py

@@ -43,7 +43,9 @@ class Dataset(_DatasetBase, SQLModel, table=True):
         }
     )
     meta: dict[str, Any] = Field(sa_column=Column(JSON), default={})
-    history: list[dict[str, Any]] = Field(sa_column=Column(JSON), default=[])
+    history: list[dict[str, Any]] = Field(
+        sa_column=Column(JSON, server_default="[]", nullable=False)
+    )
 
     class Config:
         arbitrary_types_allowed = True

{fractal_server-1.3.12a4 → fractal_server-1.3.13}/fractal_server/app/runner/__init__.py

@@ -248,9 +248,8 @@ async def submit_workflow(
         )
         logger.debug(f'END workflow "{workflow.name}"')
 
-        # Replace output_dataset.meta with output_dataset_meta, while handling
-        # the history property in a special way (i.e. appending to and
-        # existing entry rather than replacing it)
+        # Replace output_dataset.meta and output_dataset.history with their
+        # up-to-date versions, obtained within process_workflow
         output_dataset.history = output_dataset_meta_hist.pop("history")
         output_dataset.meta = output_dataset_meta_hist.pop("metadata")
 

{fractal_server-1.3.12a4 → fractal_server-1.3.13}/fractal_server/config.py

@@ -419,4 +419,9 @@ class Settings(BaseSettings):
 
 
 def get_settings(settings=Settings()) -> Settings:
+    logging.debug("Fractal Settings:")
+    for key, value in settings.dict().items():
+        if any(s in key.upper() for s in ["PASSWORD", "SECRET"]):
+            value = "*****"
+        logging.debug(f"{key}: {value}")
     return settings

{fractal_server-1.3.12a4 → fractal_server-1.3.13}/fractal_server/migrations/script.py.mako

@@ -7,7 +7,6 @@ Create Date: ${create_date}
 """
 from alembic import op
 import sqlalchemy as sa
-import sqlalchemy_utils
 import sqlmodel
 ${imports if imports else ""}
 

fractal_server-1.3.13/fractal_server/migrations/versions/99ea79d9e5d2_add_dataset_history.py

@@ -0,0 +1,36 @@
+"""Add Dataset.history
+
+Revision ID: 99ea79d9e5d2
+Revises: 8f79bd162e35
+Create Date: 2023-10-16 09:45:15.132185
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "99ea79d9e5d2"
+down_revision = "8f79bd162e35"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("dataset", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "history", sa.JSON(), server_default="[]", nullable=False
+            )
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("dataset", schema=None) as batch_op:
+        batch_op.drop_column("history")
+
+    # ### end Alembic commands ###

{fractal_server-1.3.12a4 → fractal_server-1.3.13}/fractal_server/tasks/collection.py

@@ -83,7 +83,7 @@ def get_absolute_venv_path(venv_path: Path) -> Path:
         package_path = venv_path
     else:
         settings = Inject(get_settings)
-        package_path = settings.FRACTAL_TASKS_DIR / venv_path  # type: ignore
+        package_path = settings.FRACTAL_TASKS_DIR / venv_path
     return package_path
 
 
@@ -214,7 +214,7 @@ def create_package_dir_pip(
             "with `version=None`."
         )
     package_dir = f"{task_pkg.package}{task_pkg.package_version}"
-    venv_path = settings.FRACTAL_TASKS_DIR / user / package_dir  # type: ignore
+    venv_path = settings.FRACTAL_TASKS_DIR / user / package_dir
     if create:
         venv_path.mkdir(exist_ok=False, parents=True)
     return venv_path

{fractal_server-1.3.12a4 → fractal_server-1.3.13}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "1.3.12a4"
+version = "1.3.13"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Jacopo Nespolo <jacopo.nespolo@exact-lab.it>",
@@ -29,13 +29,11 @@ aiosqlite = "^0.17.0"
 fastapi-users = {extras = ["oauth"], version = "^12.1.0"}
 alembic = "^1.9.1"
 uvicorn = "^0.20.0"
-sqlalchemy = "^1.4"
-SQLAlchemy-Utils = "^0.38.3"
-greenlet = "*"
+sqlalchemy = {extras = ["asyncio"], version = "^1.4"}
 pydantic = ">=1.10.8,<2"
 
 clusterfutures = { version = "^0.5", optional = true}
-cloudpickle = {version = ">=2.2.1 <2.3.0", optional = true}
+cloudpickle = {version = ">=2.2.1,<2.3.0", optional = true}
 
 asyncpg = { version = "^0.27.0", optional = true }
 psycopg2 = { version = "^2.9.5", optional = true }
@@ -84,7 +82,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "1.3.12a4"
+current_version = "1.3.13"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true
@@ -109,5 +107,5 @@ relative_files = true
 omit = ["tests/*"]
 
 [[tool.mypy.overrides]]
-module = ["devtools", "uvicorn", "sqlalchemy_utils"]
+module = ["devtools", "uvicorn"]
 ignore_missing_imports = true

fractal_server-1.3.12a4/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "1.3.12a4"

fractal_server-1.3.12a4/fractal_server/migrations/versions/5c4ff7526508_add_dataset_history.py

@@ -1,35 +0,0 @@
-"""Add Dataset.history
-
-Revision ID: 5c4ff7526508
-Revises: 8f79bd162e35
-Create Date: 2023-10-13 14:26:07.955329
-
-"""
-import sqlalchemy as sa
-from alembic import op
-from sqlalchemy.sql import column
-from sqlalchemy.sql import table
-
-
-# revision identifiers, used by Alembic.
-revision = "5c4ff7526508"
-down_revision = "8f79bd162e35"
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    with op.batch_alter_table("dataset", schema=None) as batch_op:
-        batch_op.add_column(sa.Column("history", sa.JSON(), nullable=True))
-
-    with op.batch_alter_table("dataset", schema=None) as batch_op:
-        dataset = table("dataset", column("history"))
-        batch_op.execute(dataset.update().values(history=sa.JSON([])))
-
-    with op.batch_alter_table("dataset", schema=None) as batch_op:
-        batch_op.alter_column("dataset", nullable=False)
-
-
-def downgrade() -> None:
-    with op.batch_alter_table("dataset", schema=None) as batch_op:
-        batch_op.drop_column("history")