fractal-server 2.19.0a0__tar.gz → 2.19.0a2__tar.gz

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.19.0a0
+Version: 2.19.0a2
 Summary: Backend component of the Fractal analytics platform
 Author: Tommaso Comparin, Marco Franzon, Yuri Chiucconi, Jacopo Nespolo
 Author-email: Tommaso Comparin <tommaso.comparin@exact-lab.it>, Marco Franzon <marco.franzon@exact-lab.it>, Yuri Chiucconi <yuri.chiucconi@exact-lab.it>, Jacopo Nespolo <jacopo.nespolo@exact-lab.it>
@@ -17,7 +17,7 @@ Requires-Dist: pydantic>=2.12.0,<2.13.0
 Requires-Dist: pydantic-settings==2.12.0
 Requires-Dist: packaging>=25.0.0,<26.0.0
 Requires-Dist: fabric>=3.2.2,<3.3.0
-Requires-Dist: gunicorn>=23.0,<24.0
+Requires-Dist: gunicorn>=24.1,<25
 Requires-Dist: psycopg[binary]>=3.1.0,<4.0.0
 Requires-Dist: tomli-w>=1.2.0,<1.3.0
 Requires-Python: >=3.12, <3.15

fractal_server-2.19.0a2/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.19.0a2"

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/models/v2/task.py

@@ -14,7 +14,6 @@ class TaskV2(SQLModel, table=True):
     type: str
     command_non_parallel: str | None = None
     command_parallel: str | None = None
-    source: str | None = None
 
     meta_non_parallel: dict[str, Any] = Field(
         sa_column=Column(JSON, server_default="{}", default={}, nullable=False)

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/models/v2/workflow.py

@@ -32,3 +32,5 @@ class WorkflowV2(SQLModel, table=True):
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),
     )
+
+    description: str | None = Field(default=None, nullable=True)

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/models/v2/workflowtask.py

@@ -39,3 +39,6 @@ class WorkflowTaskV2(SQLModel, table=True):
     task_type: str
     task_id: int = Field(foreign_key="taskv2.id")
     task: TaskV2 = Relationship(sa_relationship_kwargs=dict(lazy="selectin"))
+
+    alias: str | None = Field(default=None, nullable=True)
+    description: str | None = Field(default=None, nullable=True)

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/routes/admin/v2/task.py

@@ -30,7 +30,6 @@ class TaskMinimal(BaseModel):
     taskgroupv2_id: int
     command_non_parallel: str | None = None
     command_parallel: str | None = None
-    source: str | None = None
     version: str | None = None
 
 
@@ -55,7 +54,6 @@ class TaskInfo(BaseModel):
 @router.get("/", response_model=PaginationResponse[TaskInfo])
 async def query_tasks(
     id: int | None = None,
-    source: str | None = None,
     version: str | None = None,
     name: str | None = None,
     task_type: TaskType | None = None,
@@ -81,9 +79,6 @@ async def query_tasks(
     if id is not None:
         stm = stm.where(TaskV2.id == id)
         stm_count = stm_count.where(TaskV2.id == id)
-    if source is not None:
-        stm = stm.where(TaskV2.source.icontains(source))
-        stm_count = stm_count.where(TaskV2.source.icontains(source))
     if version is not None:
         stm = stm.where(TaskV2.version == version)
         stm_count = stm_count.where(TaskV2.version == version)

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/routes/api/v2/_aux_functions_task_lifecycle.py

@@ -2,8 +2,6 @@ from fastapi import HTTPException
 from fastapi import status
 from httpx import AsyncClient
 from httpx import TimeoutException
-from packaging.version import InvalidVersion
-from packaging.version import Version
 from sqlmodel import func
 from sqlmodel import select
 
@@ -14,6 +12,7 @@ from fractal_server.app.models.v2 import TaskGroupV2
 from fractal_server.app.models.v2 import TaskV2
 from fractal_server.app.models.v2 import WorkflowTaskV2
 from fractal_server.app.models.v2 import WorkflowV2
+from fractal_server.app.routes.aux._versions import _find_latest_version_or_422
 from fractal_server.app.schemas.v2 import JobStatusType
 from fractal_server.app.schemas.v2 import TaskGroupActivityStatus
 from fractal_server.logger import set_logger
@@ -26,24 +25,6 @@ PYPI_JSON_HEADERS = {"Accept": "application/vnd.pypi.simple.v1+json"}
 logger = set_logger(__name__)
 
 
-def _find_latest_version_or_422(versions: list[str]) -> str:
-    """
-    > For PEP 440 versions, this is easy enough for the client to do (using
-    > the `packaging` library [...]. For non-standard versions, there is no
-    > well-defined ordering, and clients will need to decide on what rule is
-    > appropriate for their needs.
-    (https://peps.python.org/pep-0700/#why-not-provide-a-latest-version-value)
-    """
-    try:
-        latest = max(versions, key=lambda v_str: Version(v_str))
-        return latest
-    except InvalidVersion as e:
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
-            detail=f"Cannot find latest version (original error: {str(e)}).",
-        )
-
-
 async def get_package_version_from_pypi(
     name: str,
     version: str | None = None,

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/routes/api/v2/submit.py

@@ -216,7 +216,7 @@ async def submit_job(
             dataset.model_dump_json(exclude={"images", "history"})
         ),
         workflow_dump=json.loads(
-            workflow.model_dump_json(exclude={"task_list"})
+            workflow.model_dump_json(exclude={"task_list", "description"})
         ),
         project_dump=json.loads(
             project.model_dump_json(exclude={"resource_id"})

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/routes/api/v2/task_group.py

@@ -4,9 +4,6 @@ from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
 from fastapi import status
-from packaging.version import InvalidVersion
-from packaging.version import Version
-from packaging.version import parse
 from pydantic.types import AwareDatetime
 from sqlmodel import or_
 from sqlmodel import select
@@ -25,6 +22,7 @@ from fractal_server.app.routes.auth._aux_auth import (
 from fractal_server.app.routes.auth._aux_auth import (
     _verify_user_belongs_to_group,
 )
+from fractal_server.app.routes.aux._versions import _version_sort_key
 from fractal_server.app.schemas.v2 import TaskGroupActivityAction
 from fractal_server.app.schemas.v2 import TaskGroupActivityRead
 from fractal_server.app.schemas.v2 import TaskGroupActivityStatus
@@ -43,26 +41,6 @@ router = APIRouter()
 logger = set_logger(__name__)
 
 
-def _version_sort_key(
-    task_group: TaskGroupV2,
-) -> tuple[int, Version | str | None]:
-    """
-    Returns a tuple used as (reverse) ordering key for TaskGroups in
-    `get_task_group_list`.
-    The TaskGroups with a parsable versions are the first in order,
-    sorted according to the sorting rules of packaging.version.Version.
-    Next in order we have the TaskGroups with non-null non-parsable versions,
-    sorted alphabetically.
-    Last we have the TaskGroups with null version.
-    """
-    if task_group.version is None:
-        return (0, task_group.version)
-    try:
-        return (2, parse(task_group.version))
-    except InvalidVersion:
-        return (1, task_group.version)
-
-
 @router.get("/activity/", response_model=list[TaskGroupActivityRead])
 async def get_task_group_activity_list(
     task_group_activity_id: int | None = None,
@@ -176,7 +154,7 @@ async def get_task_group_list(
                 await remove_duplicate_task_groups(
                     task_groups=sorted(
                         list(groups),
-                        key=_version_sort_key,
+                        key=lambda group: _version_sort_key(group.version),
                         reverse=True,
                     ),
                     user_id=user.id,

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/routes/api/v2/workflow.py

@@ -149,7 +149,7 @@ async def update_workflow(
         db=db,
     )
 
-    if patch.name:
+    if patch.name and patch.name != workflow.name:
         await _check_workflow_exists(
             name=patch.name, project_id=project_id, db=db
         )

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/routes/api/v2/workflow_import.py

@@ -19,8 +19,8 @@ from fractal_server.app.routes.auth import get_api_user
 from fractal_server.app.routes.auth._aux_auth import (
     _get_default_usergroup_id_or_none,
 )
+from fractal_server.app.routes.aux._versions import _version_sort_key
 from fractal_server.app.schemas.v2 import TaskImport
-from fractal_server.app.schemas.v2 import TaskImportLegacy
 from fractal_server.app.schemas.v2 import WorkflowImport
 from fractal_server.app.schemas.v2 import WorkflowReadWithWarnings
 from fractal_server.app.schemas.v2 import WorkflowTaskCreate
@@ -73,32 +73,6 @@ async def _get_user_accessible_taskgroups(
     return accessible_task_groups
 
 
-async def _get_task_by_source(
-    source: str,
-    task_groups_list: list[TaskGroupV2],
-) -> int | None:
-    """
-    Find task with a given source.
-
-    Args:
-        source: `source` of the task to be imported.
-        task_groups_list: Current list of valid task groups.
-
-    Return:
-        `id` of the matching task, or `None`.
-    """
-    task_id = next(
-        iter(
-            task.id
-            for task_group in task_groups_list
-            for task in task_group.task_list
-            if task.source == source
-        ),
-        None,
-    )
-    return task_id
-
-
 async def _get_task_by_taskimport(
     *,
     task_import: TaskImport,
@@ -141,14 +115,15 @@ async def _get_task_by_taskimport(
         return None
 
     # Determine target `version`
-    # Note that task_import.version cannot be "", due to a validator
     if task_import.version is None:
         logger.debug(
             "[_get_task_by_taskimport] "
             "No version requested, looking for latest."
         )
-        latest_task = max(matching_task_groups, key=lambda tg: tg.version or "")
-        version = latest_task.version
+        version = max(
+            [tg.version for tg in matching_task_groups],
+            key=_version_sort_key,
+        )
         logger.debug(
             f"[_get_task_by_taskimport] Latest version set to {version}."
         )
@@ -246,19 +221,13 @@ async def import_workflow(
     list_task_ids = []
     for wf_task in workflow_import.task_list:
         task_import = wf_task.task
-        if isinstance(task_import, TaskImportLegacy):
-            task_id = await _get_task_by_source(
-                source=task_import.source,
-                task_groups_list=task_group_list,
-            )
-        else:
-            task_id = await _get_task_by_taskimport(
-                task_import=task_import,
-                user_id=user.id,
-                default_group_id=default_group_id,
-                task_groups_list=task_group_list,
-                db=db,
-            )
+        task_id = await _get_task_by_taskimport(
+            task_import=task_import,
+            user_id=user.id,
+            default_group_id=default_group_id,
+            task_groups_list=task_group_list,
+            db=db,
+        )
         if task_id is None:
             raise HTTPException(
                 status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/routes/api/v2/workflowtask.py

@@ -193,13 +193,8 @@ async def update_workflowtask(
             if not actual_args:
                 actual_args = None
             setattr(db_wf_task, key, actual_args)
-        elif key in ["meta_parallel", "meta_non_parallel", "type_filters"]:
-            setattr(db_wf_task, key, value)
         else:
-            raise HTTPException(
-                status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
-                detail=f"patch_workflow_task endpoint cannot set {key=}",
-            )
+            setattr(db_wf_task, key, value)
 
     await db.commit()
     await db.refresh(db_wf_task)

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/routes/auth/current_user.py

@@ -4,6 +4,8 @@ Definition of `/auth/current-user/` endpoints
 
 from fastapi import APIRouter
 from fastapi import Depends
+from fastapi import HTTPException
+from fastapi import status
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlmodel import select
 
@@ -52,6 +54,12 @@ async def patch_current_user(
     Note: a user cannot patch their own password (as enforced within the
     `UserUpdateStrict` schema).
     """
+    if current_user.is_guest:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN,
+            detail="This feature is not available for guest users.",
+        )
+
     update = UserUpdate(**user_update.model_dump(exclude_unset=True))
 
     # NOTE: here it would be relevant to catch an `InvalidPasswordException`

fractal_server-2.19.0a2/fractal_server/app/routes/aux/_versions.py

@@ -0,0 +1,42 @@
+from fastapi import HTTPException
+from fastapi import status
+from packaging.version import InvalidVersion
+from packaging.version import Version
+
+
+def _version_sort_key(version: str | None) -> tuple[int, Version | str | None]:
+    """
+    Returns a tuple used as (reverse) ordering key for TaskGroups in
+    `get_task_group_list`.
+    The parsable versions are the first in order, sorted according to the
+    sorting rules of packaging.version.Version.
+    Next in order we have the non-null non-parsable versions, sorted
+    alphabetically.
+    """
+    if version is None:
+        return (0, None)
+    try:
+        return (2, Version(version))
+    except InvalidVersion:
+        return (1, version)
+
+
+def _find_latest_version_or_422(versions: list[str]) -> str:
+    """
+    > For PEP 440 versions, this is easy enough for the client to do (using
+    > the `packaging` library [...]. For non-standard versions, there is no
+    > well-defined ordering, and clients will need to decide on what rule is
+    > appropriate for their needs.
+    (https://peps.python.org/pep-0700/#why-not-provide-a-latest-version-value)
+
+    The `versions` array is coming from the PyPI API, and its elements are
+    assumed parsable.
+    """
+    try:
+        latest = max(versions, key=lambda v_str: Version(v_str))
+        return latest
+    except InvalidVersion as e:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
+            detail=f"Cannot find latest version (original error: {str(e)}).",
+        )

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/schemas/v2/__init__.py

@@ -47,7 +47,6 @@ from .status_legacy import WorkflowTaskStatusType  # noqa F401
 from .task import TaskCreate  # noqa F401
 from .task import TaskExport  # noqa F401
 from .task import TaskImport  # noqa F401
-from .task import TaskImportLegacy  # noqa F401
 from .task import TaskRead  # noqa F401
 from .task import TaskType  # noqa F401
 from .task import TaskUpdate  # noqa F401

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/schemas/v2/dumps.py

@@ -30,7 +30,6 @@ class TaskDump(BaseModel):
 
     command_non_parallel: str | None = None
     command_parallel: str | None = None
-    source: str | None = None
     version: str | None = None
 
     input_types: dict[str, bool]

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/schemas/v2/task.py

@@ -94,7 +94,6 @@ class TaskRead(BaseModel):
     id: int
     name: str
     type: TaskType
-    source: str | None = None
     version: str | None = None
 
     command_non_parallel: str | None = None
@@ -139,10 +138,6 @@ class TaskImport(BaseModel):
     name: NonEmptyStr
 
 
-class TaskImportLegacy(BaseModel):
-    source: NonEmptyStr
-
-
 class TaskExport(BaseModel):
     pkg_name: NonEmptyStr
     version: NonEmptyStr | None = None

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/schemas/v2/workflow.py

@@ -29,6 +29,7 @@ class WorkflowRead(BaseModel):
     task_list: list[WorkflowTaskRead]
     project: ProjectRead
     timestamp_created: AwareDatetime
+    description: str | None
 
     @field_serializer("timestamp_created")
     def serialize_datetime(v: datetime) -> str:
@@ -44,6 +45,7 @@ class WorkflowUpdate(BaseModel):
 
     name: NonEmptyStr = None
     reordered_workflowtask_ids: ListUniqueNonNegativeInt | None = None
+    description: str | None = None
 
 
 class WorkflowImport(BaseModel):

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/schemas/v2/workflowtask.py

@@ -11,7 +11,6 @@ from fractal_server.types import WorkflowTaskArgument
 
 from .task import TaskExport
 from .task import TaskImport
-from .task import TaskImportLegacy
 from .task import TaskRead
 from .task import TaskType
 
@@ -50,6 +49,9 @@ class WorkflowTaskRead(BaseModel):
     task_id: int
     task: TaskRead
 
+    alias: str | None = None
+    description: str | None = None
+
 
 class WorkflowTaskReadWithWarning(WorkflowTaskRead):
     warning: str | None = None
@@ -63,6 +65,8 @@ class WorkflowTaskUpdate(BaseModel):
     args_non_parallel: WorkflowTaskArgument | None = None
     args_parallel: WorkflowTaskArgument | None = None
     type_filters: TypeFilters = None
+    description: str | None = None
+    alias: str | None = None
 
 
 class WorkflowTaskImport(BaseModel):
@@ -75,7 +79,7 @@ class WorkflowTaskImport(BaseModel):
     type_filters: TypeFilters | None = None
     input_filters: dict[str, Any] | None = None
 
-    task: TaskImport | TaskImportLegacy
+    task: TaskImport
 
     @model_validator(mode="before")
     @classmethod

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/fractal_server/app/security/__init__.py

@@ -21,6 +21,7 @@ from collections.abc import AsyncGenerator
 from typing import Any
 from typing import Generic
 from typing import Self
+from typing import override
 
 from fastapi import Depends
 from fastapi import Request
@@ -188,19 +189,22 @@ class UserManager(IntegerIDMixin, BaseUserManager[UserOAuth, int]):
             password_helper=password_helper,
         )
 
+    @override
     async def validate_password(self, password: str, user: UserOAuth) -> None:
         # check password length
         min_length = 4
-        max_length = 100
+        max_length = 72
         if len(password) < min_length:
             raise InvalidPasswordException(
                 f"The password is too short (minimum length: {min_length})."
             )
-        elif len(password) > max_length:
+        if len(password.encode("utf-8")) > max_length:
             raise InvalidPasswordException(
-                f"The password is too long (maximum length: {min_length})."
+                "The password is too long "
+                f"(maximum length: {max_length} bytes)."
             )
 
+    @override
     async def oauth_callback(
         self: Self,
         oauth_name: str,
@@ -324,6 +328,7 @@ class UserManager(IntegerIDMixin, BaseUserManager[UserOAuth, int]):
 
         return user
 
+    @override
     async def on_after_register(
         self, user: UserOAuth, request: Request | None = None
     ):

fractal_server-2.19.0a2/fractal_server/migrations/versions/1bf8785755f9_add_description_to_workflow_and_.py

@@ -0,0 +1,53 @@
+"""Add description to workflow and description and alias to workflow task
+
+Revision ID: 1bf8785755f9
+Revises: 5fb08bf05b14
+Create Date: 2026-01-26 09:03:18.396841
+
+"""
+
+import sqlalchemy as sa
+import sqlmodel
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "1bf8785755f9"
+down_revision = "5fb08bf05b14"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "alias", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "description", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+            )
+        )
+
+    with op.batch_alter_table("workflowv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "description", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+            )
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("workflowv2", schema=None) as batch_op:
+        batch_op.drop_column("description")
+
+    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+        batch_op.drop_column("description")
+        batch_op.drop_column("alias")
+
+    # ### end Alembic commands ###

fractal_server-2.19.0a2/fractal_server/migrations/versions/5fb08bf05b14_drop_taskv2_source.py

@@ -0,0 +1,36 @@
+"""drop TaskV2.source
+
+Revision ID: 5fb08bf05b14
+Revises: e53dc51fdf93
+Create Date: 2026-01-21 12:50:39.072816
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "5fb08bf05b14"
+down_revision = "e53dc51fdf93"
+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.drop_column("source")
+
+    # ### 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(
+                "source", sa.VARCHAR(), autoincrement=False, nullable=True
+            )
+        )
+
+    # ### end Alembic commands ###

{fractal_server-2.19.0a0 → fractal_server-2.19.0a2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.19.0a0"
+version = "2.19.0a2"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -25,7 +25,7 @@ dependencies = [
     "pydantic-settings ==2.12.0",
     "packaging >= 25.0.0, <26.0.0",
     "fabric >= 3.2.2, <3.3.0",
-    "gunicorn >=23.0,<24.0",
+    "gunicorn >=24.1,<25",
     "psycopg[binary] >= 3.1.0, <4.0.0",
     "tomli_w >=1.2.0, <1.3.0 "
 ]
@@ -48,7 +48,6 @@ dev = [
     "devtools ==0.12",
     "pytest-asyncio >= 1.2.0,<1.3.0",
     "bumpver >=2024.0",
-    "pre-commit ==4.2.0",
     "coverage>=7.12.0,<7.13.0",
     "pytest-docker >=3.2.0,<3.3.0",
     "pytest-subprocess >=1.5.0,<1.6.0",
@@ -93,7 +92,7 @@ filterwarnings = [
 markers = ["container", "ssh", "fails_on_macos", "oauth"]
 
 [tool.bumpver]
-current_version = "2.19.0a0"
+current_version = "2.19.0a2"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.19.0a0/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.19.0a0"