fractal-server 2.12.0a1__tar.gz → 2.13.0__tar.gz

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.12.0a1
+Version: 2.13.0
 Summary: Backend component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -13,22 +13,21 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
-Requires-Dist: cloudpickle (>=3.0.0,<3.1.0)
-Requires-Dist: clusterfutures (==0.5)
-Requires-Dist: cryptography (>=44.0.0,<44.1.0)
+Requires-Dist: cloudpickle (>=3.1.0,<3.2.0)
+Requires-Dist: cryptography (>=44.0.1,<44.1.0)
 Requires-Dist: fabric (>=3.2.2,<3.3.0)
 Requires-Dist: fastapi (>=0.115.0,<0.116.0)
 Requires-Dist: fastapi-users[oauth] (>=14,<15)
-Requires-Dist: gunicorn (>=21.2,<23.0)
-Requires-Dist: packaging (>=23.2.0,<24.0.0)
-Requires-Dist: psutil (==5.9.8)
+Requires-Dist: gunicorn (>=23.0,<24.0)
+Requires-Dist: packaging (>=24.0.0,<25.0.0)
 Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0)
-Requires-Dist: pydantic (>=1.10.8,<2)
+Requires-Dist: pydantic (>=2.10.0,<2.11.0)
+Requires-Dist: pydantic-settings (>=2.7.0)
 Requires-Dist: python-dotenv (>=1.0.0,<1.1.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)
-Requires-Dist: sqlmodel (==0.0.21)
-Requires-Dist: uvicorn (==0.29.0)
-Requires-Dist: uvicorn-worker (==0.2.0)
+Requires-Dist: sqlmodel (==0.0.22)
+Requires-Dist: uvicorn (>=0.29.0,<0.35.0)
+Requires-Dist: uvicorn-worker (==0.3.0)
 Project-URL: Documentation, https://fractal-analytics-platform.github.io/fractal-server
 Project-URL: Repository, https://github.com/fractal-analytics-platform/fractal-server
 Project-URL: changelog, https://github.com/fractal-analytics-platform/fractal-server/blob/main/CHANGELOG.md

fractal_server-2.13.0/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.13.0"

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/__main__.py

@@ -63,45 +63,18 @@ update_db_data_parser = subparsers.add_parser(
     description="Apply data-migration script to an existing database.",
 )
 
-# fractalctl email-settings
-email_settings_parser = subparsers.add_parser(
-    "email-settings",
+# fractalctl encrypt-email-password
+encrypt_email_password_parser = subparsers.add_parser(
+    "encrypt-email-password",
     description=(
         "Generate valid values for environment variables "
-        "`FRACTAL_EMAIL_SETTINGS` and `FRACTAL_EMAIL_SETTINGS_KEY`."
+        "FRACTAL_EMAIL_PASSWORD and FRACTAL_EMAIL_PASSWORD_KEY."
     ),
 )
-email_settings_parser.add_argument(
-    "sender",
-    type=str,
-    help="Email of the sender",
-)
-email_settings_parser.add_argument(
-    "server",
-    type=str,
-    help="SMPT server used to send emails",
-)
-email_settings_parser.add_argument(
-    "port",
-    type=int,
-    help="Port of the SMPT server",
-)
-email_settings_parser.add_argument(
-    "instance",
-    type=str,
-    help="Name of the Fractal instance sending emails",
-)
-email_settings_parser.add_argument(
-    "--skip-starttls",
-    action="store_true",
-    default=False,
-    help="If set, skip the execution of `starttls` when sending emails",
-)
 
 
 def save_openapi(dest="openapi.json"):
     from fractal_server.main import start_application
-    import json
 
     app = start_application()
     openapi_schema = app.openapi()
@@ -129,6 +102,11 @@ def set_db(skip_init_data: bool = False):
     from pathlib import Path
     import fractal_server
 
+    # Check settings
+    settings = Inject(get_settings)
+    settings.check_db()
+
+    # Perform migrations
     alembic_ini = Path(fractal_server.__file__).parent / "alembic.ini"
     alembic_args = ["-c", alembic_ini.as_posix(), "upgrade", "head"]
     print(f"START: Run alembic.config, with argv={alembic_args}")
@@ -138,12 +116,10 @@ def set_db(skip_init_data: bool = False):
     if skip_init_data:
         return
 
-    # Insert default group
+    # Create default group and user
     print()
     _create_first_group()
     print()
-    # NOTE: It will be fixed with #1739
-    settings = Inject(get_settings)
     asyncio.run(
         _create_first_user(
             email=settings.FRACTAL_DEFAULT_ADMIN_EMAIL,
@@ -224,31 +200,15 @@ def update_db_data():
     current_update_db_data_module.fix_db()
 
 
-def print_mail_settings(
-    sender: str,
-    server: str,
-    port: int,
-    instance: str,
-    skip_starttls: bool,
-):
+def print_encrypted_password():
     from cryptography.fernet import Fernet
 
-    password = input(f"Insert email password for sender '{sender}': ")
+    password = input("Insert email password: ").encode("utf-8")
     key = Fernet.generate_key().decode("utf-8")
-    fractal_mail_settings = json.dumps(
-        dict(
-            sender=sender,
-            password=password,
-            smtp_server=server,
-            port=port,
-            instance_name=instance,
-            use_starttls=(not skip_starttls),
-        )
-    ).encode("utf-8")
-    email_settings = Fernet(key).encrypt(fractal_mail_settings).decode("utf-8")
+    encrypted_password = Fernet(key).encrypt(password).decode("utf-8")
 
-    print(f"\nFRACTAL_EMAIL_SETTINGS: {email_settings}")
-    print(f"FRACTAL_EMAIL_SETTINGS_KEY: {key}")
+    print(f"\nFRACTAL_EMAIL_PASSWORD={encrypted_password}")
+    print(f"FRACTAL_EMAIL_PASSWORD_KEY={key}")
 
 
 def run():
@@ -267,14 +227,8 @@ def run():
             port=args.port,
             reload=args.reload,
         )
-    elif args.cmd == "email-settings":
-        print_mail_settings(
-            sender=args.sender,
-            server=args.server,
-            port=args.port,
-            instance=args.instance,
-            skip_starttls=args.skip_starttls,
-        )
+    elif args.cmd == "encrypt-email-password":
+        print_encrypted_password()
     else:
         sys.exit(f"Error: invalid command '{args.cmd}'.")
 

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/models/security.py

@@ -12,6 +12,7 @@
 from datetime import datetime
 from typing import Optional
 
+from pydantic import ConfigDict
 from pydantic import EmailStr
 from sqlalchemy import Column
 from sqlalchemy.types import DateTime
@@ -50,13 +51,11 @@ class OAuthAccount(SQLModel, table=True):
     user: Optional["UserOAuth"] = Relationship(back_populates="oauth_accounts")
     oauth_name: str = Field(index=True, nullable=False)
     access_token: str = Field(nullable=False)
-    expires_at: Optional[int] = Field(nullable=True)
-    refresh_token: Optional[str] = Field(nullable=True)
+    expires_at: Optional[int] = Field(nullable=True, default=None)
+    refresh_token: Optional[str] = Field(nullable=True, default=None)
     account_id: str = Field(index=True, nullable=False)
     account_email: str = Field(nullable=False)
-
-    class Config:
-        orm_mode = True
+    model_config = ConfigDict(from_attributes=True)
 
 
 class UserOAuth(SQLModel, table=True):
@@ -88,11 +87,11 @@ class UserOAuth(SQLModel, table=True):
         sa_column_kwargs={"unique": True, "index": True}, nullable=False
     )
     hashed_password: str
-    is_active: bool = Field(True, nullable=False)
-    is_superuser: bool = Field(False, nullable=False)
-    is_verified: bool = Field(False, nullable=False)
+    is_active: bool = Field(default=True, nullable=False)
+    is_superuser: bool = Field(default=False, nullable=False)
+    is_verified: bool = Field(default=False, nullable=False)
 
-    username: Optional[str]
+    username: Optional[str] = None
 
     oauth_accounts: list["OAuthAccount"] = Relationship(
         back_populates="user",
@@ -105,9 +104,7 @@ class UserOAuth(SQLModel, table=True):
     settings: Optional[UserSettings] = Relationship(
         sa_relationship_kwargs=dict(lazy="selectin", cascade="all, delete")
     )
-
-    class Config:
-        orm_mode = True
+    model_config = ConfigDict(from_attributes=True)
 
 
 class UserGroup(SQLModel, table=True):

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/models/v2/dataset.py

@@ -2,6 +2,7 @@ from datetime import datetime
 from typing import Any
 from typing import Optional
 
+from pydantic import ConfigDict
 from sqlalchemy import Column
 from sqlalchemy.types import DateTime
 from sqlalchemy.types import JSON
@@ -14,8 +15,7 @@ from fractal_server.images.models import AttributeFiltersType
 
 
 class DatasetV2(SQLModel, table=True):
-    class Config:
-        arbitrary_types_allowed = True
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
     id: Optional[int] = Field(default=None, primary_key=True)
     name: str

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/models/v2/job.py

@@ -2,6 +2,7 @@ from datetime import datetime
 from typing import Any
 from typing import Optional
 
+from pydantic import ConfigDict
 from sqlalchemy import Column
 from sqlalchemy.types import DateTime
 from sqlalchemy.types import JSON
@@ -14,16 +15,17 @@ from fractal_server.images.models import AttributeFiltersType
 
 
 class JobV2(SQLModel, table=True):
-    class Config:
-        arbitrary_types_allowed = True
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
     id: Optional[int] = Field(default=None, primary_key=True)
-    project_id: Optional[int] = Field(foreign_key="projectv2.id")
-    workflow_id: Optional[int] = Field(foreign_key="workflowv2.id")
-    dataset_id: Optional[int] = Field(foreign_key="datasetv2.id")
+    project_id: Optional[int] = Field(foreign_key="projectv2.id", default=None)
+    workflow_id: Optional[int] = Field(
+        foreign_key="workflowv2.id", default=None
+    )
+    dataset_id: Optional[int] = Field(foreign_key="datasetv2.id", default=None)
 
     user_email: str = Field(nullable=False)
-    slurm_account: Optional[str]
+    slurm_account: Optional[str] = None
 
     dataset_dump: dict[str, Any] = Field(
         sa_column=Column(JSON, nullable=False)
@@ -35,9 +37,9 @@ class JobV2(SQLModel, table=True):
         sa_column=Column(JSON, nullable=False)
     )
 
-    worker_init: Optional[str]
-    working_dir: Optional[str]
-    working_dir_user: Optional[str]
+    worker_init: Optional[str] = None
+    working_dir: Optional[str] = None
+    working_dir_user: Optional[str] = None
     first_task_index: int
     last_task_index: int
 

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/models/v2/task.py

@@ -1,7 +1,6 @@
 from typing import Any
 from typing import Optional
 
-from pydantic import HttpUrl
 from sqlalchemy import Column
 from sqlalchemy.types import JSON
 from sqlmodel import Field
@@ -31,9 +30,9 @@ class TaskV2(SQLModel, table=True):
     args_schema_parallel: Optional[dict[str, Any]] = Field(
         sa_column=Column(JSON), default=None
     )
-    args_schema_version: Optional[str]
+    args_schema_version: Optional[str] = None
     docs_info: Optional[str] = None
-    docs_link: Optional[HttpUrl] = None
+    docs_link: Optional[str] = None
 
     input_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
     output_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/models/v2/task_group.py

@@ -22,7 +22,9 @@ class TaskGroupV2(SQLModel, table=True):
     )
 
     user_id: int = Field(foreign_key="user_oauth.id")
-    user_group_id: Optional[int] = Field(foreign_key="usergroup.id")
+    user_group_id: Optional[int] = Field(
+        foreign_key="usergroup.id", default=None
+    )
 
     origin: str
     pkg_name: str
@@ -97,7 +99,9 @@ class TaskGroupActivityV2(SQLModel, table=True):
 
     id: Optional[int] = Field(default=None, primary_key=True)
     user_id: int = Field(foreign_key="user_oauth.id")
-    taskgroupv2_id: Optional[int] = Field(foreign_key="taskgroupv2.id")
+    taskgroupv2_id: Optional[int] = Field(
+        default=None, foreign_key="taskgroupv2.id"
+    )
     timestamp_started: datetime = Field(
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/models/v2/workflowtask.py

@@ -1,6 +1,7 @@
 from typing import Any
 from typing import Optional
 
+from pydantic import ConfigDict
 from sqlalchemy import Column
 from sqlalchemy.types import JSON
 from sqlmodel import Field
@@ -11,18 +12,24 @@ from .task import TaskV2
 
 
 class WorkflowTaskV2(SQLModel, table=True):
-    class Config:
-        arbitrary_types_allowed = True
-        fields = {"parent": {"exclude": True}}
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
     id: Optional[int] = Field(default=None, primary_key=True)
 
     workflow_id: int = Field(foreign_key="workflowv2.id")
-    order: Optional[int]
-    meta_parallel: Optional[dict[str, Any]] = Field(sa_column=Column(JSON))
-    meta_non_parallel: Optional[dict[str, Any]] = Field(sa_column=Column(JSON))
-    args_parallel: Optional[dict[str, Any]] = Field(sa_column=Column(JSON))
-    args_non_parallel: Optional[dict[str, Any]] = Field(sa_column=Column(JSON))
+    order: Optional[int] = None
+    meta_parallel: Optional[dict[str, Any]] = Field(
+        sa_column=Column(JSON), default=None
+    )
+    meta_non_parallel: Optional[dict[str, Any]] = Field(
+        sa_column=Column(JSON), default=None
+    )
+    args_parallel: Optional[dict[str, Any]] = Field(
+        sa_column=Column(JSON), default=None
+    )
+    args_non_parallel: Optional[dict[str, Any]] = Field(
+        sa_column=Column(JSON), default=None
+    )
 
     type_filters: dict[str, bool] = Field(
         sa_column=Column(JSON, nullable=False, server_default="{}")

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/routes/admin/v2/task.py

@@ -28,7 +28,7 @@ class TaskV2Minimal(BaseModel):
     type: str
     taskgroupv2_id: int
     command_non_parallel: Optional[str] = None
-    command_parallel: Optional[str]
+    command_parallel: Optional[str] = None
     source: Optional[str] = None
     version: Optional[str] = None
 

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/routes/admin/v2/task_group.py

@@ -163,7 +163,7 @@ async def patch_task_group(
             detail=f"TaskGroupV2 {task_group_id} not found",
         )
 
-    for key, value in task_group_update.dict(exclude_unset=True).items():
+    for key, value in task_group_update.model_dump(exclude_unset=True).items():
         if (key == "user_group_id") and (value is not None):
             await _verify_user_belongs_to_group(
                 user_id=user.id, user_group_id=value, db=db

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/routes/api/v2/dataset.py

@@ -60,7 +60,7 @@ async def create_dataset(
         db_dataset = DatasetV2(
             project_id=project_id,
             zarr_dir="__PLACEHOLDER__",
-            **dataset.dict(exclude={"zarr_dir"}),
+            **dataset.model_dump(exclude={"zarr_dir"}),
         )
         db.add(db_dataset)
         await db.commit()
@@ -77,7 +77,7 @@ async def create_dataset(
         await db.commit()
         await db.refresh(db_dataset)
     else:
-        db_dataset = DatasetV2(project_id=project_id, **dataset.dict())
+        db_dataset = DatasetV2(project_id=project_id, **dataset.model_dump())
         db.add(db_dataset)
         await db.commit()
         await db.refresh(db_dataset)
@@ -172,7 +172,7 @@ async def update_dataset(
             ),
         )
 
-    for key, value in dataset_update.dict(exclude_unset=True).items():
+    for key, value in dataset_update.model_dump(exclude_unset=True).items():
         setattr(db_dataset, key, value)
 
     await db.commit()
@@ -316,7 +316,7 @@ async def import_dataset(
     # Create new Dataset
     db_dataset = DatasetV2(
         project_id=project_id,
-        **dataset.dict(exclude_none=True),
+        **dataset.model_dump(exclude_none=True),
     )
     db.add(db_dataset)
     await db.commit()

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/routes/api/v2/images.py

@@ -8,8 +8,8 @@ from fastapi import Response
 from fastapi import status
 from pydantic import BaseModel
 from pydantic import Field
-from pydantic import root_validator
-from pydantic import validator
+from pydantic import field_validator
+from pydantic import model_validator
 from sqlalchemy.orm.attributes import flag_modified
 
 from ._aux_functions import _get_dataset_check_owner
@@ -44,18 +44,18 @@ class ImagePage(BaseModel):
 
 
 class ImageQuery(BaseModel):
-    zarr_url: Optional[str]
+    zarr_url: Optional[str] = None
     type_filters: dict[str, bool] = Field(default_factory=dict)
     attribute_filters: AttributeFiltersType = Field(default_factory=dict)
 
-    _dict_keys = root_validator(pre=True, allow_reuse=True)(
-        root_validate_dict_keys
+    _dict_keys = model_validator(mode="before")(
+        classmethod(root_validate_dict_keys)
     )
-    _type_filters = validator("type_filters", allow_reuse=True)(
-        validate_type_filters
+    _type_filters = field_validator("type_filters")(
+        classmethod(validate_type_filters)
     )
-    _attribute_filters = validator("attribute_filters", allow_reuse=True)(
-        validate_attribute_filters
+    _attribute_filters = field_validator("attribute_filters")(
+        classmethod(validate_attribute_filters)
     )
 
 
@@ -102,7 +102,7 @@ async def post_new_image(
             ),
         )
 
-    dataset.images.append(new_image.dict())
+    dataset.images.append(new_image.model_dump())
     flag_modified(dataset, "images")
 
     await db.commit()
@@ -118,7 +118,6 @@ async def post_new_image(
 async def query_dataset_images(
     project_id: int,
     dataset_id: int,
-    use_dataset_filters: bool = False,  # query param
     page: int = 1,  # query param
     page_size: Optional[int] = None,  # query param
     query: Optional[ImageQuery] = None,  # body
@@ -138,17 +137,6 @@ async def query_dataset_images(
     dataset = output["dataset"]
     images = dataset.images
 
-    if use_dataset_filters is True:
-        images = [
-            image
-            for image in images
-            if match_filter(
-                image=image,
-                type_filters=dataset.type_filters,
-                attribute_filters=dataset.attribute_filters,
-            )
-        ]
-
     attributes = {}
     for image in images:
         for k, v in image["attributes"].items():
@@ -290,7 +278,7 @@ async def patch_dataset_image(
         )
     index = ret["index"]
 
-    for key, value in image_update.dict(
+    for key, value in image_update.model_dump(
         exclude_none=True, exclude={"zarr_url"}
     ).items():
         db_dataset.images[index][key] = value

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/routes/api/v2/project.py

@@ -62,7 +62,7 @@ async def create_project(
         project_name=project.name, user_id=user.id, db=db
     )
 
-    db_project = ProjectV2(**project.dict())
+    db_project = ProjectV2(**project.model_dump())
     db_project.user_list.append(user)
 
     db.add(db_project)
@@ -106,7 +106,7 @@ async def update_project(
             project_name=project_update.name, user_id=user.id, db=db
         )
 
-    for key, value in project_update.dict(exclude_unset=True).items():
+    for key, value in project_update.model_dump(exclude_unset=True).items():
         setattr(project, key, value)
 
     await db.commit()

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/routes/api/v2/status.py

@@ -154,7 +154,7 @@ async def get_workflowtask_status(
         if wf_task_status is None:
             # If a wftask ID was not found, ignore it and continue
             continue
-        clean_workflow_tasks_status_dict[wf_task.id] = wf_task_status
+        clean_workflow_tasks_status_dict[str(wf_task.id)] = wf_task_status
         if wf_task_status == WorkflowTaskStatusTypeV2.FAILED:
             # Starting from the beginning of `workflow.task_list`, stop the
             # first time that you hit a failed job

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/routes/api/v2/submit.py

@@ -165,11 +165,15 @@ async def apply_workflow(
         # The 'filters' field is not supported any more but still exists as a
         # database column, therefore we manually exclude it from dumps.
         dataset_dump=json.loads(
-            dataset.json(exclude={"images", "history", "filters"})
+            dataset.model_dump_json(exclude={"images", "history", "filters"})
         ),
-        workflow_dump=json.loads(workflow.json(exclude={"task_list"})),
-        project_dump=json.loads(project.json(exclude={"user_list"})),
-        **job_create.dict(),
+        workflow_dump=json.loads(
+            workflow.model_dump_json(exclude={"task_list"})
+        ),
+        project_dump=json.loads(
+            project.model_dump_json(exclude={"user_list"})
+        ),
+        **job_create.model_dump(),
     )
 
     db.add(job)
@@ -202,8 +206,6 @@ async def apply_workflow(
     # Define user-side job directory
     if FRACTAL_RUNNER_BACKEND == "local":
         WORKFLOW_DIR_REMOTE = WORKFLOW_DIR_LOCAL
-    elif FRACTAL_RUNNER_BACKEND == "local_experimental":
-        WORKFLOW_DIR_REMOTE = WORKFLOW_DIR_LOCAL
     elif FRACTAL_RUNNER_BACKEND == "slurm":
         WORKFLOW_DIR_REMOTE = cache_dir / WORKFLOW_DIR_LOCAL.name
     elif FRACTAL_RUNNER_BACKEND == "slurm_ssh":

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/routes/api/v2/task.py

@@ -107,7 +107,7 @@ async def patch_task(
     db_task = await _get_task_full_access(
         task_id=task_id, user_id=user.id, db=db
     )
-    update = task_update.dict(exclude_unset=True)
+    update = task_update.model_dump(exclude_unset=True)
 
     # Forbid changes that set a previously unset command
     if db_task.type == "non_parallel" and "command_parallel" in update:
@@ -182,7 +182,8 @@ async def create_task(
         )
 
     # Add task
-    db_task = TaskV2(**task.dict(), type=task_type)
+
+    db_task = TaskV2(**task.model_dump(exclude_unset=True), type=task_type)
     pkg_name = db_task.name
     await _verify_non_duplication_user_constraint(
         db=db, pkg_name=pkg_name, user_id=user.id, version=db_task.version
@@ -206,6 +207,7 @@ async def create_task(
     await db.commit()
     await db.refresh(db_task)
     await db.close()
+
     return db_task
 
 

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/routes/api/v2/task_collection.py

@@ -13,7 +13,7 @@ from fastapi import Response
 from fastapi import status
 from fastapi import UploadFile
 from pydantic import BaseModel
-from pydantic import root_validator
+from pydantic import model_validator
 from pydantic import ValidationError
 from sqlmodel import select
 
@@ -68,7 +68,8 @@ class CollectionRequestData(BaseModel):
     file: Optional[UploadFile] = None
     origin: TaskGroupV2OriginEnum
 
-    @root_validator(pre=True)
+    @model_validator(mode="before")
+    @classmethod
     def validate_data(cls, values):
         file = values.get("file")
         package = values.get("task_collect").package

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/routes/api/v2/task_group.py

@@ -223,7 +223,7 @@ async def patch_task_group(
         db=db,
     )
     if (
-        "user_group_id" in task_group_update.dict(exclude_unset=True)
+        "user_group_id" in task_group_update.model_dump(exclude_unset=True)
         and task_group_update.user_group_id != task_group.user_group_id
     ):
         await _verify_non_duplication_group_constraint(
@@ -232,7 +232,7 @@ async def patch_task_group(
             version=task_group.version,
             user_group_id=task_group_update.user_group_id,
         )
-    for key, value in task_group_update.dict(exclude_unset=True).items():
+    for key, value in task_group_update.model_dump(exclude_unset=True).items():
         if (key == "user_group_id") and (value is not None):
             await _verify_user_belongs_to_group(
                 user_id=user.id, user_group_id=value, db=db

{fractal_server-2.12.0a1 → fractal_server-2.13.0}/fractal_server/app/routes/api/v2/workflow.py

@@ -82,7 +82,7 @@ async def create_workflow(
         name=workflow.name, project_id=project_id, db=db
     )
 
-    db_workflow = WorkflowV2(project_id=project_id, **workflow.dict())
+    db_workflow = WorkflowV2(project_id=project_id, **workflow.model_dump())
     db.add(db_workflow)
     await db.commit()
     await db.refresh(db_workflow)
@@ -149,7 +149,7 @@ async def update_workflow(
             name=patch.name, project_id=project_id, db=db
         )
 
-    for key, value in patch.dict(exclude_unset=True).items():
+    for key, value in patch.model_dump(exclude_unset=True).items():
         if key == "reordered_workflowtask_ids":
             current_workflowtask_ids = [
                 wftask.id for wftask in workflow.task_list
@@ -262,7 +262,7 @@ async def export_worfklow(
     wf_task_list = []
     for wftask in workflow.task_list:
         task_group = await db.get(TaskGroupV2, wftask.task.taskgroupv2_id)
-        wf_task_list.append(wftask.dict())
+        wf_task_list.append(wftask.model_dump())
         wf_task_list[-1]["task"] = dict(
             pkg_name=task_group.pkg_name,
             version=task_group.version,