fractal-server 2.7.0a11__tar.gz → 2.7.1__tar.gz

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/PKG-INFO

@@ -1,35 +1,29 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.7.0a11
+Version: 2.7.1
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
 Author: Tommaso Comparin
 Author-email: tommaso.comparin@exact-lab.it
-Requires-Python: >=3.9,<4.0
+Requires-Python: >=3.10,<4.0
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Provides-Extra: gunicorn
-Provides-Extra: postgres
-Provides-Extra: postgres-psycopg-binary
 Requires-Dist: aiosqlite (>=0.19.0,<0.20.0)
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
-Requires-Dist: asyncpg (>=0.29.0,<0.30.0) ; extra == "postgres"
 Requires-Dist: bcrypt (==4.0.1)
 Requires-Dist: cloudpickle (>=3.0.0,<3.1.0)
 Requires-Dist: clusterfutures (>=0.5,<0.6)
 Requires-Dist: fabric (>=3.2.2,<4.0.0)
 Requires-Dist: fastapi (>=0.115.0,<0.116.0)
 Requires-Dist: fastapi-users[oauth] (>=12.1.0,<13.0.0)
-Requires-Dist: gunicorn (>=21.2,<23.0) ; extra == "gunicorn"
+Requires-Dist: gunicorn (>=21.2,<23.0)
 Requires-Dist: packaging (>=23.2,<24.0)
 Requires-Dist: psutil (>=5.9.8,<6.0.0)
-Requires-Dist: psycopg2 (>=2.9.5,<3.0.0) ; extra == "postgres"
-Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0) ; extra == "postgres-psycopg-binary"
+Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0)
 Requires-Dist: pydantic (>=1.10.8,<2)
 Requires-Dist: python-dotenv (>=1.0.0,<2.0.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)

fractal_server-2.7.1/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.7.1"

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/fractal_server/app/models/v2/task.py

@@ -29,7 +29,6 @@ class TaskV2(SQLModel, table=True):
         sa_column=Column(JSON, server_default="{}", default={}, nullable=False)
     )
 
-    owner: Optional[str] = None
     version: Optional[str] = None
     args_schema_non_parallel: Optional[dict[str, Any]] = Field(
         sa_column=Column(JSON), default=None
@@ -44,7 +43,7 @@ class TaskV2(SQLModel, table=True):
     input_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
     output_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
 
-    taskgroupv2_id: Optional[int] = Field(foreign_key="taskgroupv2.id")
+    taskgroupv2_id: int = Field(foreign_key="taskgroupv2.id")
 
     category: Optional[str] = None
     modality: Optional[str] = None

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/fractal_server/app/routes/admin/v2/task_group.py

@@ -21,6 +21,7 @@ from fractal_server.app.routes.auth._aux_auth import (
 )
 from fractal_server.app.schemas.v2 import TaskGroupReadV2
 from fractal_server.app.schemas.v2 import TaskGroupUpdateV2
+from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.logger import set_logger
 
 router = APIRouter()
@@ -50,6 +51,8 @@ async def query_task_group_list(
     user_group_id: Optional[int] = None,
     private: Optional[bool] = None,
     active: Optional[bool] = None,
+    pkg_name: Optional[str] = None,
+    origin: Optional[TaskGroupV2OriginEnum] = None,
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskGroupReadV2]:
@@ -75,6 +78,10 @@ async def query_task_group_list(
             stm = stm.where(is_(TaskGroupV2.active, True))
         else:
             stm = stm.where(is_(TaskGroupV2.active, False))
+    if origin is not None:
+        stm = stm.where(TaskGroupV2.origin == origin)
+    if pkg_name is not None:
+        stm = stm.where(TaskGroupV2.pkg_name.icontains(pkg_name))
 
     res = await db.execute(stm)
     task_groups_list = res.scalars().all()

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/fractal_server/app/routes/api/v2/task.py

@@ -24,6 +24,7 @@ from fractal_server.app.models.v2 import TaskV2
 from fractal_server.app.routes.auth import current_active_user
 from fractal_server.app.routes.auth import current_active_verified_user
 from fractal_server.app.schemas.v2 import TaskCreateV2
+from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.app.schemas.v2 import TaskReadV2
 from fractal_server.app.schemas.v2 import TaskUpdateV2
 from fractal_server.logger import set_logger
@@ -200,7 +201,7 @@ async def create_task(
         user_group_id=user_group_id,
         active=True,
         task_list=[db_task],
-        origin="other",
+        origin=TaskGroupV2OriginEnum.OTHER,
         version=db_task.version,
         pkg_name=pkg_name,
     )

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/fractal_server/app/routes/api/v2/task_collection.py

@@ -30,6 +30,7 @@ from ._aux_functions_tasks import _verify_non_duplication_user_constraint
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.auth import current_active_user
 from fractal_server.app.routes.auth import current_active_verified_user
+from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.tasks.utils import _normalize_package_name
 from fractal_server.tasks.utils import get_collection_log_v2
 from fractal_server.tasks.v2.background_operations import (
@@ -121,11 +122,11 @@ async def collect_tasks_pip(
             wheel_info["distribution"]
         )
         task_group_attrs["version"] = wheel_info["version"]
-        task_group_attrs["origin"] = "wheel-file"
+        task_group_attrs["origin"] = TaskGroupV2OriginEnum.WHEELFILE
     else:
         pkg_name = task_collect.package
         task_group_attrs["pkg_name"] = _normalize_package_name(pkg_name)
-        task_group_attrs["origin"] = "pypi"
+        task_group_attrs["origin"] = TaskGroupV2OriginEnum.PYPI
         latest_version = await get_package_version_from_pypi(
             task_collect.package,
             task_collect.package_version,

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/fractal_server/app/routes/api/v2/task_collection_custom.py

@@ -21,6 +21,7 @@ from fractal_server.app.routes.auth import current_active_verified_user
 from fractal_server.app.schemas.v2 import TaskCollectCustomV2
 from fractal_server.app.schemas.v2 import TaskCreateV2
 from fractal_server.app.schemas.v2 import TaskGroupCreateV2
+from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.app.schemas.v2 import TaskReadV2
 from fractal_server.config import get_settings
 from fractal_server.logger import set_logger
@@ -140,7 +141,7 @@ async def collect_task_custom(
 
     # Prepare task-group attributes
     task_group_attrs = dict(
-        origin="other",
+        origin=TaskGroupV2OriginEnum.OTHER,
         pkg_name=task_collect.label,
         user_id=user.id,
         user_group_id=user_group_id,

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/fractal_server/app/schemas/v2/__init__.py

@@ -30,6 +30,7 @@ from .task_collection import TaskCollectPipV2  # noqa F401
 from .task_group import TaskGroupCreateV2  # noqa F401
 from .task_group import TaskGroupReadV2  # noqa F401
 from .task_group import TaskGroupUpdateV2  # noqa F401
+from .task_group import TaskGroupV2OriginEnum  # noqa F401
 from .workflow import WorkflowCreateV2  # noqa F401
 from .workflow import WorkflowExportV2  # noqa F401
 from .workflow import WorkflowImportV2  # noqa F401

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/fractal_server/app/schemas/v2/task_group.py

@@ -1,4 +1,5 @@
 from datetime import datetime
+from enum import Enum
 from typing import Literal
 from typing import Optional
 
@@ -13,11 +14,17 @@ from .._validators import valstr
 from .task import TaskReadV2
 
 
+class TaskGroupV2OriginEnum(str, Enum):
+    PYPI = "pypi"
+    WHEELFILE = "wheel-file"
+    OTHER = "other"
+
+
 class TaskGroupCreateV2(BaseModel, extra=Extra.forbid):
     user_id: int
     user_group_id: Optional[int] = None
     active: bool = True
-    origin: Literal["pypi", "wheel-file", "other"]
+    origin: TaskGroupV2OriginEnum
     pkg_name: str
     version: Optional[str] = None
     python_version: Optional[str] = None

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/fractal_server/app/security/__init__.py

@@ -315,13 +315,20 @@ async def _create_first_user(
 
 
 def _create_first_group():
+    """
+    Create a `UserGroup` with `name=FRACTAL_DEFAULT_GROUP_NAME`, if missing.
+    """
     function_logger = set_logger("fractal_server.create_first_group")
 
     function_logger.info(
         f"START _create_first_group, with name '{FRACTAL_DEFAULT_GROUP_NAME}'"
     )
     with next(get_sync_db()) as db:
-        group_all = db.execute(select(UserGroup))
+        group_all = db.execute(
+            select(UserGroup).where(
+                UserGroup.name == FRACTAL_DEFAULT_GROUP_NAME
+            )
+        )
         if group_all.scalars().one_or_none() is None:
             first_group = UserGroup(name=FRACTAL_DEFAULT_GROUP_NAME)
             db.add(first_group)

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/fractal_server/config.py

@@ -167,9 +167,9 @@ class Settings(BaseSettings):
     ###########################################################################
     # DATABASE
     ###########################################################################
-    DB_ENGINE: Literal["sqlite", "postgres", "postgres-psycopg"] = "sqlite"
+    DB_ENGINE: Literal["sqlite", "postgres-psycopg"] = "sqlite"
     """
-    Select which database engine to use (supported: `sqlite` and `postgres`).
+    Database engine to use (supported: `sqlite`, `postgres-psycopg`).
     """
     DB_ECHO: bool = False
     """
@@ -203,16 +203,7 @@ class Settings(BaseSettings):
 
     @property
     def DATABASE_ASYNC_URL(self) -> URL:
-        if self.DB_ENGINE == "postgres":
-            url = URL.create(
-                drivername="postgresql+asyncpg",
-                username=self.POSTGRES_USER,
-                password=self.POSTGRES_PASSWORD,
-                host=self.POSTGRES_HOST,
-                port=self.POSTGRES_PORT,
-                database=self.POSTGRES_DB,
-            )
-        elif self.DB_ENGINE == "postgres-psycopg":
+        if self.DB_ENGINE == "postgres-psycopg":
             url = URL.create(
                 drivername="postgresql+psycopg",
                 username=self.POSTGRES_USER,
@@ -235,11 +226,7 @@ class Settings(BaseSettings):
 
     @property
     def DATABASE_SYNC_URL(self):
-        if self.DB_ENGINE == "postgres":
-            return self.DATABASE_ASYNC_URL.set(
-                drivername="postgresql+psycopg2"
-            )
-        elif self.DB_ENGINE == "postgres-psycopg":
+        if self.DB_ENGINE == "postgres-psycopg":
             return self.DATABASE_ASYNC_URL.set(drivername="postgresql+psycopg")
         else:
             if not self.SQLITE_PATH:
@@ -546,20 +533,13 @@ class Settings(BaseSettings):
         """
         Checks that db environment variables are properly set.
         """
-        if self.DB_ENGINE == "postgres":
+        if self.DB_ENGINE == "postgres-psycopg":
             if not self.POSTGRES_DB:
                 raise FractalConfigurationError(
-                    "POSTGRES_DB cannot be None when DB_ENGINE=postgres."
-                )
-            try:
-                import psycopg2  # noqa: F401
-                import asyncpg  # noqa: F401
-            except ModuleNotFoundError:
-                raise FractalConfigurationError(
-                    "DB engine is `postgres` but `psycopg2` or `asyncpg` "
-                    "are not available"
+                    "POSTGRES_DB cannot be None when DB_ENGINE="
+                    "postgres-psycopg."
                 )
-        elif self.DB_ENGINE == "postgres-psycopg":
+
             try:
                 import psycopg  # noqa: F401
             except ModuleNotFoundError:

fractal_server-2.7.1/fractal_server/migrations/versions/8e8f227a3e36_update_taskv2_post_2_7_0.py

@@ -0,0 +1,42 @@
+"""Update TaskV2 post 2.7.0
+
+Revision ID: 8e8f227a3e36
+Revises: 034a469ec2eb
+Create Date: 2024-10-29 09:01:33.075251
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "8e8f227a3e36"
+down_revision = "034a469ec2eb"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("taskv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "taskgroupv2_id", existing_type=sa.INTEGER(), nullable=False
+        )
+        batch_op.drop_column("owner")
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("taskv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "owner", sa.VARCHAR(), autoincrement=False, nullable=True
+            )
+        )
+        batch_op.alter_column(
+            "taskgroupv2_id", existing_type=sa.INTEGER(), nullable=True
+        )
+
+    # ### end Alembic commands ###

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/fractal_server/tasks/v2/_venv_pip.py

@@ -73,6 +73,11 @@ async def _pip_install(
         ),
         logger_name=logger_name,
     )
+    await execute_command(
+        cwd=Path(task_group.venv_path),
+        command=f"{python_bin} -m pip install setuptools",
+        logger_name=logger_name,
+    )
     await execute_command(
         cwd=Path(task_group.venv_path),
         command=f"{python_bin} -m pip install {pip_install_str}",

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/fractal_server/tasks/v2/background_operations_ssh.py

@@ -205,7 +205,7 @@ def background_collect_pip_ssh(
                 remove_venv_folder_upon_failure = True
 
                 stdout = _customize_and_run_template(
-                    script_filename="_2_upgrade_pip.sh",
+                    script_filename="_2_preliminary_pip_operations.sh",
                     **common_args,
                 )
                 stdout = _customize_and_run_template(

fractal_server-2.7.0a11/fractal_server/tasks/v2/templates/_2_upgrade_pip.sh → fractal_server-2.7.1/fractal_server/tasks/v2/templates/_2_preliminary_pip_operations.sh

@@ -15,6 +15,7 @@ VENVPYTHON=${PACKAGE_ENV_DIR}/bin/python
 # Upgrade pip
 write_log "START upgrade pip"
 "$VENVPYTHON" -m pip install "pip<=__FRACTAL_MAX_PIP_VERSION__" --upgrade
+"$VENVPYTHON" -m pip install setuptools
 write_log "END   upgrade pip"
 echo
 

{fractal_server-2.7.0a11 → fractal_server-2.7.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.7.0a11"
+version = "2.7.1"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Tommaso Comparin <tommaso.comparin@exact-lab.it>",
@@ -24,7 +24,7 @@ exclude = [
 
 
 [tool.poetry.dependencies]
-python = "^3.9"
+python = "^3.10"
 python-dotenv = "^1.0.0"
 fastapi = "^0.115.0"
 sqlmodel = "^0.0.21"
@@ -40,17 +40,12 @@ clusterfutures = "^0.5"
 cloudpickle = ">=3.0.0,<3.1.0"
 fabric = "^3.2.2"
 
-asyncpg = { version = "^0.29.0", optional = true }
-gunicorn = { version = ">=21.2,<23.0", optional = true }
-psycopg = { version = "^3.1.0", extras=["binary"], optional=true }
-psycopg2 = { version = "^2.9.5", optional = true }
+gunicorn = { version = ">=21.2,<23.0" }
+psycopg = { version = "^3.1.0", extras=["binary"] }
 psutil = "^5.9.8"
 uvicorn-worker = "^0.2.0"
 
 [tool.poetry.extras]
-postgres = ["asyncpg", "psycopg2"]
-gunicorn = ["gunicorn"]
-postgres-psycopg-binary = ["psycopg"]
 
 [tool.poetry.group.dev.dependencies]
 asgi-lifespan = "^2"
@@ -92,7 +87,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.7.0a11"
+current_version = "2.7.1"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.7.0a11/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.7.0a11"