fractal-server 2.0.4__py3-none-any.whl → 2.0.6__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.0.4"
+__VERSION__ = "2.0.6"

fractal_server/app/models/__init__.py

@@ -1,7 +1,3 @@
-"""
-`models` module
-"""
-from .security import *  # noqa: F401, F403
 from .v1 import Project  # noqa: F401
 from .v2 import ProjectV2  # noqa: F401
 

fractal_server/app/models/security.py

@@ -18,9 +18,6 @@ from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
-from .linkuserproject import LinkUserProject
-from .linkuserproject import LinkUserProjectV2
-
 
 class OAuthAccount(SQLModel, table=True):
     """
@@ -103,16 +100,6 @@ class UserOAuth(SQLModel, table=True):
         back_populates="user",
         sa_relationship_kwargs={"lazy": "joined", "cascade": "all, delete"},
     )
-    project_list: list["Project"] = Relationship(  # noqa
-        back_populates="user_list",
-        link_model=LinkUserProject,
-        sa_relationship_kwargs={"lazy": "selectin"},
-    )
-    project_list_v2: list["ProjectV2"] = Relationship(  # noqa
-        back_populates="user_list",
-        link_model=LinkUserProjectV2,
-        sa_relationship_kwargs={"lazy": "selectin"},
-    )
 
     class Config:
         orm_mode = True

fractal_server/app/models/v1/__init__.py

@@ -1,12 +1,13 @@
 """
 `models` module
 """
-from .dataset import Dataset  # noqa: F401
-from .dataset import Resource  # noqa: F401
-from .job import ApplyWorkflow  # noqa: F403, F401
-from .job import JobStatusTypeV1  # noqa: F401, F403
-from .project import Project  # noqa: F403, F401
-from .state import State  # noqa: F403, F401
-from .task import Task  # noqa: F403, F401
-from .workflow import Workflow  # noqa: F401, F403
-from .workflow import WorkflowTask  # noqa: F401, F403
+from ..linkuserproject import LinkUserProject  # noqa F401
+from .dataset import Dataset  # noqa F401
+from .dataset import Resource  # noqa F401
+from .job import ApplyWorkflow  # noqa F401
+from .job import JobStatusTypeV1  # noqa F401
+from .project import Project  # noqa F401
+from .state import State  # noqa F401
+from .task import Task  # noqa F401
+from .workflow import Workflow  # noqa F401
+from .workflow import WorkflowTask  # noqa F401

fractal_server/app/models/v1/project.py

@@ -7,9 +7,9 @@ from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
+from . import LinkUserProject
 from ....utils import get_timestamp
 from ...schemas.v1.project import _ProjectBaseV1
-from ..linkuserproject import LinkUserProject
 from ..security import UserOAuth
 
 
@@ -23,7 +23,6 @@ class Project(_ProjectBaseV1, SQLModel, table=True):
 
     user_list: list[UserOAuth] = Relationship(
         link_model=LinkUserProject,
-        back_populates="project_list",
         sa_relationship_kwargs={
             "lazy": "selectin",
         },

fractal_server/app/models/v2/project.py

@@ -7,8 +7,8 @@ from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
+from . import LinkUserProjectV2
 from ....utils import get_timestamp
-from ..linkuserproject import LinkUserProjectV2
 from ..security import UserOAuth
 
 
@@ -23,7 +23,6 @@ class ProjectV2(SQLModel, table=True):
 
     user_list: list[UserOAuth] = Relationship(
         link_model=LinkUserProjectV2,
-        back_populates="project_list_v2",
         sa_relationship_kwargs={
             "lazy": "selectin",
         },

fractal_server/app/routes/admin/v2.py

@@ -4,6 +4,7 @@ Definition of `/admin` routes.
 from datetime import datetime
 from datetime import timezone
 from pathlib import Path
+from typing import Literal
 from typing import Optional
 
 from fastapi import APIRouter
@@ -13,6 +14,8 @@ from fastapi import Response
 from fastapi import status
 from fastapi.responses import StreamingResponse
 from pydantic import BaseModel
+from pydantic import EmailStr
+from pydantic import Field
 from sqlmodel import select
 
 from ....config import get_settings
@@ -24,6 +27,9 @@ from ...models.security import UserOAuth as User
 from ...models.v1 import Task
 from ...models.v2 import JobV2
 from ...models.v2 import ProjectV2
+from ...models.v2 import TaskV2
+from ...models.v2 import WorkflowTaskV2
+from ...models.v2 import WorkflowV2
 from ...runner.filenames import WORKFLOW_LOG_FILENAME
 from ...schemas.v2 import JobReadV2
 from ...schemas.v2 import JobStatusTypeV2
@@ -307,3 +313,128 @@ async def flag_task_v1_as_v2_compatible(
     await db.close()
 
     return Response(status_code=status.HTTP_200_OK)
+
+
+class TaskV2Minimal(BaseModel):
+
+    id: int
+    name: str
+    type: str
+    command_non_parallel: Optional[str]
+    command_parallel: Optional[str]
+    source: str
+    owner: Optional[str]
+    version: Optional[str]
+
+
+class ProjectUser(BaseModel):
+
+    id: int
+    email: EmailStr
+
+
+class TaskV2Relationship(BaseModel):
+
+    workflow_id: int
+    workflow_name: str
+    project_id: int
+    project_name: str
+    project_users: list[ProjectUser] = Field(default_factory=list)
+
+
+class TaskV2Info(BaseModel):
+
+    task: TaskV2Minimal
+    relationships: list[TaskV2Relationship]
+
+
+@router_admin_v2.get("/task/", response_model=list[TaskV2Info])
+async def query_tasks(
+    id: Optional[int] = None,
+    source: Optional[str] = None,
+    version: Optional[str] = None,
+    name: Optional[str] = None,
+    owner: Optional[str] = None,
+    kind: Optional[Literal["common", "users"]] = None,
+    max_number_of_results: int = 25,
+    user: User = Depends(current_active_superuser),
+    db: AsyncSession = Depends(get_async_db),
+) -> list[TaskV2Info]:
+    """
+    Query `TaskV2` table and get informations about related items
+    (WorkflowV2s and ProjectV2s)
+
+    Args:
+        id: If not `None`, query for matching `task.id`.
+        source: If not `None`, query for contained case insensitive
+            `task.source`.
+        version: If not `None`, query for matching `task.version`.
+        name: If not `None`, query for contained case insensitive `task.name`.
+        owner: If not `None`, query for matching `task.owner`.
+        kind: If not `None`, query for TaskV2s that have (`users`) or don't
+            have (`common`) a `task.owner`.
+        max_number_of_results: The maximum length of the response.
+    """
+
+    stm = select(TaskV2)
+
+    if id is not None:
+        stm = stm.where(TaskV2.id == id)
+    if source is not None:
+        stm = stm.where(TaskV2.source.icontains(source))
+    if version is not None:
+        stm = stm.where(TaskV2.version == version)
+    if name is not None:
+        stm = stm.where(TaskV2.name.icontains(name))
+    if owner is not None:
+        stm = stm.where(TaskV2.owner == owner)
+
+    if kind == "common":
+        stm = stm.where(TaskV2.owner == None)  # noqa E711
+    elif kind == "users":
+        stm = stm.where(TaskV2.owner != None)  # noqa E711
+
+    res = await db.execute(stm)
+    task_list = res.scalars().all()
+    if len(task_list) > max_number_of_results:
+        await db.close()
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                f"Too many Tasks ({len(task_list)} > {max_number_of_results})."
+                " Please add more query filters."
+            ),
+        )
+
+    task_info_list = []
+
+    for task in task_list:
+        stm = (
+            select(WorkflowV2)
+            .join(WorkflowTaskV2)
+            .where(WorkflowTaskV2.workflow_id == WorkflowV2.id)
+            .where(WorkflowTaskV2.task_id == task.id)
+        )
+        res = await db.execute(stm)
+        wf_list = res.scalars().all()
+
+        task_info_list.append(
+            dict(
+                task=task.model_dump(),
+                relationships=[
+                    dict(
+                        workflow_id=workflow.id,
+                        workflow_name=workflow.name,
+                        project_id=workflow.project.id,
+                        project_name=workflow.project.name,
+                        project_users=[
+                            dict(id=user.id, email=user.email)
+                            for user in workflow.project.user_list
+                        ],
+                    )
+                    for workflow in wf_list
+                ],
+            )
+        )
+
+    return task_info_list

fractal_server/app/routes/api/v1/_aux_functions.py

@@ -12,9 +12,9 @@ from sqlmodel import select
 from sqlmodel.sql.expression import SelectOfScalar
 
 from ....db import AsyncSession
-from ....models import LinkUserProject
 from ....models.v1 import ApplyWorkflow
 from ....models.v1 import Dataset
+from ....models.v1 import LinkUserProject
 from ....models.v1 import Project
 from ....models.v1 import Task
 from ....models.v1 import Workflow

fractal_server/app/routes/api/v1/project.py

@@ -18,9 +18,9 @@ from .....logger import set_logger
 from .....syringe import Inject
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models import LinkUserProject
 from ....models.v1 import ApplyWorkflow
 from ....models.v1 import Dataset
+from ....models.v1 import LinkUserProject
 from ....models.v1 import Project
 from ....models.v1 import Workflow
 from ....runner.set_start_and_last_task_index import (

fractal_server/app/routes/api/v2/submit.py

@@ -1,6 +1,7 @@
 from datetime import datetime
 from datetime import timedelta
 from datetime import timezone
+from pathlib import Path
 from typing import Optional
 
 from fastapi import APIRouter
@@ -12,6 +13,7 @@ from sqlmodel import select
 
 from .....config import get_settings
 from .....syringe import Inject
+from .....utils import get_timestamp
 from ....db import AsyncSession
 from ....db import get_async_db
 from ....models.v2 import JobV2
@@ -91,23 +93,17 @@ async def apply_workflow(
 
     # If backend is SLURM, check that the user has required attributes
     settings = Inject(get_settings)
-    backend = settings.FRACTAL_RUNNER_BACKEND
-    if backend == "slurm":
+    FRACTAL_RUNNER_BACKEND = settings.FRACTAL_RUNNER_BACKEND
+    if FRACTAL_RUNNER_BACKEND == "slurm":
         if not user.slurm_user:
             raise HTTPException(
                 status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                detail=(
-                    f"FRACTAL_RUNNER_BACKEND={backend}, "
-                    f"but {user.slurm_user=}."
-                ),
+                detail=f"{FRACTAL_RUNNER_BACKEND=}, but {user.slurm_user=}.",
             )
         if not user.cache_dir:
             raise HTTPException(
                 status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                detail=(
-                    f"FRACTAL_RUNNER_BACKEND={backend}, "
-                    f"but {user.cache_dir=}."
-                ),
+                detail=f"{FRACTAL_RUNNER_BACKEND=}, but {user.cache_dir=}.",
             )
 
     # Check that no other job with the same dataset_id is SUBMITTED
@@ -197,6 +193,30 @@ async def apply_workflow(
     await db.commit()
     await db.refresh(job)
 
+    # Define server-side job directory
+    timestamp_string = get_timestamp().strftime("%Y%m%d_%H%M%S")
+    WORKFLOW_DIR = (
+        settings.FRACTAL_RUNNER_WORKING_BASE_DIR
+        / (
+            f"proj_v2_{project_id:07d}_wf_{workflow_id:07d}_job_{job.id:07d}"
+            f"_{timestamp_string}"
+        )
+    ).resolve()
+
+    # Define user-side job directory
+    if FRACTAL_RUNNER_BACKEND == "local":
+        WORKFLOW_DIR_USER = WORKFLOW_DIR
+    elif FRACTAL_RUNNER_BACKEND == "slurm":
+        WORKFLOW_DIR_USER = (
+            Path(user.cache_dir) / f"{WORKFLOW_DIR.name}"
+        ).resolve()
+
+    # Update job folders in the db
+    job.working_dir = WORKFLOW_DIR.as_posix()
+    job.working_dir_user = WORKFLOW_DIR_USER.as_posix()
+    await db.merge(job)
+    await db.commit()
+
     background_tasks.add_task(
         submit_workflow,
         workflow_id=workflow.id,
@@ -208,5 +228,4 @@ async def apply_workflow(
     )
 
     await db.close()
-
     return job

fractal_server/app/routes/api/v2/task.py

@@ -14,6 +14,7 @@ from ....db import get_async_db
 from ....models.v1 import Task as TaskV1
 from ....models.v2 import TaskV2
 from ....models.v2 import WorkflowTaskV2
+from ....models.v2 import WorkflowV2
 from ....schemas.v2 import TaskCreateV2
 from ....schemas.v2 import TaskReadV2
 from ....schemas.v2 import TaskUpdateV2
@@ -204,16 +205,45 @@ async def delete_task(
     # Check that the TaskV2 is not in relationship with some WorkflowTaskV2
     stm = select(WorkflowTaskV2).filter(WorkflowTaskV2.task_id == task_id)
     res = await db.execute(stm)
-    workflowtask_list = res.scalars().all()
-    if workflowtask_list:
+    workflow_tasks = res.scalars().all()
+
+    if workflow_tasks:
+        # Find IDs of all affected workflows
+        workflow_ids = set(wftask.workflow_id for wftask in workflow_tasks)
+        # Fetch all affected workflows from DB
+        stm = select(WorkflowV2).where(WorkflowV2.id.in_(workflow_ids))
+        res = await db.execute(stm)
+        workflows = res.scalars().all()
+
+        # Find which workflows are associated to the current user
+        workflows_current_user = [
+            wf for wf in workflows if user in wf.project.user_list
+        ]
+        if workflows_current_user:
+            current_user_msg = (
+                "For the current-user workflows (listed below),"
+                " you can update the task or remove the workflows.\n"
+            )
+            current_user_msg += "\n".join(
+                [
+                    f"* '{wf.name}' (id={wf.id})"
+                    for wf in workflows_current_user
+                ]
+            )
+        else:
+            current_user_msg = ""
+
+        # Count workflows of current users or other users
+        num_workflows_current_user = len(workflows_current_user)
+        num_workflows_other_users = len(workflows) - num_workflows_current_user
+
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
             detail=(
-                f"Cannot remove TaskV2 {task_id} because it is currently "
-                "imported in WorkflowsV2 "
-                f"{[x.workflow_id for x in workflowtask_list]}. "
-                "If you want to remove this task, then you should first remove"
-                " the workflows.",
+                f"Cannot remove Task with id={task_id}: it is currently in "
+                f"use in {num_workflows_current_user} current-user workflows "
+                f"and in {num_workflows_other_users} other-users workflows.\n"
+                f"{current_user_msg}"
             ),
         )
 

fractal_server/app/runner/executors/slurm/_subprocess_run_as_user.py

@@ -141,7 +141,7 @@ def _glob_as_user_strict(
     new_output = []
     known_filenames = [
         f"{startswith}{suffix}"
-        for suffix in [".args.json", ".metadiff.json", ".err", ".out"]
+        for suffix in [".args.json", ".metadiff.json", ".err", ".out", ".log"]
     ]
     for filename in output:
         if filename in known_filenames:

fractal_server/app/runner/v2/__init__.py

@@ -108,18 +108,15 @@ async def submit_workflow(
             return
 
         # Define and create server-side working folder
-        project_id = workflow.project_id
-        timestamp_string = get_timestamp().strftime("%Y%m%d_%H%M%S")
-        WORKFLOW_DIR = (
-            settings.FRACTAL_RUNNER_WORKING_BASE_DIR
-            / (
-                f"proj_{project_id:07d}_wf_{workflow_id:07d}_job_{job_id:07d}"
-                f"_{timestamp_string}"
-            )
-        ).resolve()
-
+        WORKFLOW_DIR = Path(job.working_dir)
         if WORKFLOW_DIR.exists():
-            raise RuntimeError(f"Workflow dir {WORKFLOW_DIR} already exists.")
+            job.status = JobStatusTypeV2.FAILED
+            job.end_timestamp = get_timestamp()
+            job.log = f"Workflow dir {WORKFLOW_DIR} already exists."
+            db_sync.merge(job)
+            db_sync.commit()
+            db_sync.close()
+            return
 
         # Create WORKFLOW_DIR with 755 permissions
         original_umask = os.umask(0)
@@ -127,26 +124,13 @@ async def submit_workflow(
         os.umask(original_umask)
 
         # Define and create user-side working folder, if needed
-        if FRACTAL_RUNNER_BACKEND == "local":
-            WORKFLOW_DIR_USER = WORKFLOW_DIR
-        elif FRACTAL_RUNNER_BACKEND == "slurm":
-
+        WORKFLOW_DIR_USER = Path(job.working_dir_user)
+        if FRACTAL_RUNNER_BACKEND == "slurm":
             from ..executors.slurm._subprocess_run_as_user import (
                 _mkdir_as_user,
             )
 
-            WORKFLOW_DIR_USER = (
-                Path(user_cache_dir) / f"{WORKFLOW_DIR.name}"
-            ).resolve()
             _mkdir_as_user(folder=str(WORKFLOW_DIR_USER), user=slurm_user)
-        else:
-            raise ValueError(f"{FRACTAL_RUNNER_BACKEND=} not supported")
-
-        # Update db
-        job.working_dir = WORKFLOW_DIR.as_posix()
-        job.working_dir_user = WORKFLOW_DIR_USER.as_posix()
-        db_sync.merge(job)
-        db_sync.commit()
 
         # After Session.commit() is called, either explicitly or when using a
         # context manager, all objects associated with the Session are expired.

fractal_server/config.py

@@ -361,6 +361,11 @@ class Settings(BaseSettings):
     attribute in their input-arguments JSON file.
     """
 
+    FRACTAL_API_V1_MODE: Literal["include", "exclude"] = "include"
+    """
+    Whether to include the v1 API.
+    """
+
     ###########################################################################
     # BUSINESS LOGIC
     ###########################################################################

fractal_server/{logger.py → logger/__init__.py}

@@ -17,8 +17,8 @@ from pathlib import Path
 from typing import Optional
 from typing import Union
 
-from .config import get_settings
-from .syringe import Inject
+from ..config import get_settings
+from ..syringe import Inject
 
 
 LOG_FORMAT = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
@@ -136,3 +136,29 @@ def reset_logger_handlers(logger: logging.Logger) -> None:
     """
     close_logger(logger)
     logger.handlers.clear()
+
+
+def config_uvicorn_loggers():
+    """
+    Change the formatter for the uvicorn access/error loggers.
+
+    This is similar to https://stackoverflow.com/a/68864979/19085332. See also
+    https://github.com/tiangolo/fastapi/issues/1508.
+
+    This function is meant to work in two scenarios:
+
+    1. The most relevant case is for a `gunicorn` startup command, with
+       `--access-logfile` and `--error-logfile` options set.
+    2. The case of `fractalctl start` (directly calling `uvicorn`).
+
+    Because of the second use case, we need to check whether uvicorn loggers
+    already have a handler. If not, we skip the formatting.
+    """
+
+    access_logger = logging.getLogger("uvicorn.access")
+    if len(access_logger.handlers) > 0:
+        access_logger.handlers[0].setFormatter(LOG_FORMATTER)
+
+    error_logger = logging.getLogger("uvicorn.error")
+    if len(error_logger.handlers) > 0:
+        error_logger.handlers[0].setFormatter(LOG_FORMATTER)

fractal_server/logger/gunicorn_logger.py

@@ -0,0 +1,19 @@
+"""
+This module (which is only executed if `gunicorn` can be imported) subclasses
+the gunicorn `Logger` class in order to slightly change its log formats.
+
+This class can be used by including this `gunicorn` command-line option:
+```
+--logger-class fractal_server.logger.gunicorn_logger.FractalGunicornLogger
+```
+"""
+
+try:
+    from gunicorn.glogging import Logger as GunicornLogger
+
+    class FractalGunicornLogger(GunicornLogger):
+        error_fmt = r"%(asctime)s   - gunicorn.error - %(levelname)s - [pid %(process)d] - %(message)s"  # noqa: E501
+        datefmt = r"%Y-%m-%d %H:%M:%S,%u"
+
+except (ModuleNotFoundError, ImportError):
+    pass

fractal_server/main.py

@@ -19,6 +19,7 @@ from fastapi import FastAPI
 
 from .app.security import _create_first_user
 from .config import get_settings
+from .logger import config_uvicorn_loggers
 from .logger import reset_logger_handlers
 from .logger import set_logger
 from .syringe import Inject
@@ -39,12 +40,15 @@ def collect_routers(app: FastAPI) -> None:
     from .app.routes.admin.v2 import router_admin_v2
     from .app.routes.auth import router_auth
 
+    settings = Inject(get_settings)
+
     app.include_router(router_api, prefix="/api")
-    app.include_router(router_api_v1, prefix="/api/v1")
+    if settings.FRACTAL_API_V1_MODE == "include":
+        app.include_router(router_api_v1, prefix="/api/v1")
+        app.include_router(
+            router_admin_v1, prefix="/admin/v1", tags=["V1 Admin area"]
+        )
     app.include_router(router_api_v2, prefix="/api/v2")
-    app.include_router(
-        router_admin_v1, prefix="/admin/v1", tags=["V1 Admin area"]
-    )
     app.include_router(
         router_admin_v2, prefix="/admin/v2", tags=["V2 Admin area"]
     )
@@ -81,6 +85,7 @@ async def __on_startup() -> None:
     callable.
     """
     check_settings()
+    config_uvicorn_loggers()
 
 
 def start_application() -> FastAPI:

{fractal_server-2.0.4.dist-info → fractal_server-2.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.0.4
+Version: 2.0.6
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

{fractal_server-2.0.4.dist-info → fractal_server-2.0.6.dist-info}/RECORD

@@ -1,15 +1,15 @@
-fractal_server/__init__.py,sha256=dHp8YqTkoz9qO-fmbD43kqbzj_u4UgsCauJnWEM4z0k,22
+fractal_server/__init__.py,sha256=S5hrGn9zHoCPoN-w6jqLkqipFDSl7JkGHq3amd7eoVE,22
 fractal_server/__main__.py,sha256=CocbzZooX1UtGqPi55GcHGNxnrJXFg5tUU5b3wyFCyo,4958
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/db/__init__.py,sha256=WZEVfdJAX7ZyBM1ngfEGeqWWcjK_NygtCbawpmbwGpU,4042
-fractal_server/app/models/__init__.py,sha256=FRRDJkx7LgPaUqSp8IV7qevu_VE2dt0-fQtQruHFaVo,267
+fractal_server/app/models/__init__.py,sha256=QGRjxBgk6GzHyyXh_7RuHvpLoe5PTl1g5KLkGqhFYMQ,199
 fractal_server/app/models/linkuserproject.py,sha256=eQaourbGRshvlMVlKzLYJKHEjfsW1CbWws9yW4eHXhA,567
-fractal_server/app/models/security.py,sha256=UG9wCVA5GRSyHrYEFhH8lIF1hXykxsr9LSi8_dFToMY,3378
-fractal_server/app/models/v1/__init__.py,sha256=qUlUGnWFaIm3aBXfUuLdhcW9f_s1VzAEuypr31zvHGo,458
+fractal_server/app/models/security.py,sha256=0oYj_cqPcQFsPFDyN4OTsqbXsLlXRcweawjP_iSiRI0,2900
+fractal_server/app/models/v1/__init__.py,sha256=hUI7dEbPaiZGN0IbHW4RSmSicyvtn_xeuevoX7zvUwI,466
 fractal_server/app/models/v1/dataset.py,sha256=99GDgt7njx8yYQApkImqp_7bHA5HH3ElvbR6Oyj9kVI,2017
 fractal_server/app/models/v1/job.py,sha256=QLGXcWdVRHaUHQNDapYYlLpEfw4K7QyD8TmcwhrWw2o,3304
-fractal_server/app/models/v1/project.py,sha256=sDmAFLOBK5o4dLrwsIN681JcT5J1rzoUNTV9QVqwnA8,859
+fractal_server/app/models/v1/project.py,sha256=tf6fniyBH-sb6rBvGiqNl2wgN9ipR4hDEE3OKvxKaoo,804
 fractal_server/app/models/v1/state.py,sha256=ew7xw3iPzBwUnPlzmsOEMiPbPEMsJn_TyZ5cK93jBRQ,1095
 fractal_server/app/models/v1/task.py,sha256=3xZqNeFYUqslh8ddMSXF2nO4nIiOD8T5Ij37wY20kss,2782
 fractal_server/app/models/v1/workflow.py,sha256=dnY5eMaOe3oZv8arn00RNX9qVkBtTLG-vYdWXcQuyo4,3950
@@ -17,20 +17,20 @@ fractal_server/app/models/v2/__init__.py,sha256=uLzdInqATSwi0bS_V4vKB-TqFrOFaXux
 fractal_server/app/models/v2/collection_state.py,sha256=nxb042i8tt8rCpmgbFJoBCYWU-34m0HdUfO9YurTp8k,588
 fractal_server/app/models/v2/dataset.py,sha256=-7sxHEw4IIAvF_uSan7tA3o8hvoakBkQ0SRvqS2iOQU,1455
 fractal_server/app/models/v2/job.py,sha256=ypJmN-qspkKBGhBG7Mt-HypSQqcQ2EmB4Bzzb2-y550,1535
-fractal_server/app/models/v2/project.py,sha256=CqDEKzdVxmFDMee6DnVOyX7WGmdn-dQSLSekzw_OLUc,817
+fractal_server/app/models/v2/project.py,sha256=CRBnZ8QITNp6u1f5bMxvi1_mcvEfXpWyitsWB5f7gn8,759
 fractal_server/app/models/v2/task.py,sha256=9ZPhug3VWyeqgT8wQ9_8ZXQ2crSiiicRipxrxTslOso,3257
 fractal_server/app/models/v2/workflow.py,sha256=YBgFGCziUgU0aJ5EM3Svu9W2c46AewZO9VBlFCHiSps,1069
 fractal_server/app/models/v2/workflowtask.py,sha256=3jEkObsSnlI05Pur_dSsXYdJxRqPL60Z7tK5-EJLOks,1532
 fractal_server/app/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/admin/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/admin/v1.py,sha256=uMupmRkicaoWazX8qSX5fgh00O3MbuSfim8QayP6NkE,13996
-fractal_server/app/routes/admin/v2.py,sha256=T8-bGAL25on-ntZx_Msz9j5jq6NGhkjVl1jp3eRJUbw,9830
+fractal_server/app/routes/admin/v2.py,sha256=e0A6RMWfmTO5dVL95XO-P2EljdEwR00FErxahEPzODQ,13757
 fractal_server/app/routes/api/__init__.py,sha256=EVyZrEq3I_1643QGTPCC5lgCp4xH_auYbrFfogTm4pc,315
 fractal_server/app/routes/api/v1/__init__.py,sha256=Y2HQdG197J0a7DyQEE2jn53IfxD0EHGhzK1I2JZuEck,958
-fractal_server/app/routes/api/v1/_aux_functions.py,sha256=KoSefKiBXximu0df4fJ3l9bKsGaLO8rb3z6xhD8PWj4,11973
+fractal_server/app/routes/api/v1/_aux_functions.py,sha256=lFfGJxbJc-Ryah_pPkiTH2SBncWQ15n0iqVFolzIOCM,11976
 fractal_server/app/routes/api/v1/dataset.py,sha256=HRE-8vPmVkeXf7WFYkI19mDtbY-iJZeJ7PmMiV0LMgY,16923
 fractal_server/app/routes/api/v1/job.py,sha256=NwXyhvvzdPDor0ts8Im__9-I0P1H943s4NXIRgaz7PM,5436
-fractal_server/app/routes/api/v1/project.py,sha256=tb1M2hhAKyHeToV0RwAQQx0ptIDeX6sEjM7dkfjCpXQ,15799
+fractal_server/app/routes/api/v1/project.py,sha256=DKQ6n1CPmHqsKieBaJlKnOhKaHWgQTZIA_asJTT9Uxo,15802
 fractal_server/app/routes/api/v1/task.py,sha256=udbKnenzc-Q10elYCVB9JmOPWATraa9tZi0AaByvWo0,6129
 fractal_server/app/routes/api/v1/task_collection.py,sha256=mFaYyCWtCPRqvs3j6zx_zaiDXn31Uzoa7UHZS-Lu_L0,8882
 fractal_server/app/routes/api/v1/workflow.py,sha256=7r9IoIevg_rvYCrerMOsIsUabSOQatxdPCfLdkP0dRs,10942
@@ -42,8 +42,8 @@ fractal_server/app/routes/api/v2/images.py,sha256=4r_HblPWyuKSZSJZfn8mbDaLv1ncwZ
 fractal_server/app/routes/api/v2/job.py,sha256=BtaxErBDbLwjY2zgGD1I6eRpsffoMonifcS1CMEXmLU,5325
 fractal_server/app/routes/api/v2/project.py,sha256=qyvizYZ4aUFgF3tGdfp4z8AwWgfo19N_KbFEljfUaC8,5594
 fractal_server/app/routes/api/v2/status.py,sha256=osLexiMOSqmYcEV-41tlrwt9ofyFbtRm5HmPS5BU0t4,6394
-fractal_server/app/routes/api/v2/submit.py,sha256=svI1Oa2zIxUEAomzRt7-M66xKC4Pb9NEGcXNrtN6b5g,6940
-fractal_server/app/routes/api/v2/task.py,sha256=gJ0LruSk-Q1iMw8ZOX8C0wrZ4S4DGlQTr_5SdJJud0Q,7130
+fractal_server/app/routes/api/v2/submit.py,sha256=su512HjafuD_lyiLswyxN4T8xwKaMpWOhGsYVPh94sI,7672
+fractal_server/app/routes/api/v2/task.py,sha256=bRTtGgL8BBGbT7csVeRB-a54clgU2xHydi5XpcByDxg,8297
 fractal_server/app/routes/api/v2/task_collection.py,sha256=eN3NkZaZHkrqnLGRKE7Xd5mo0cHc8aK2lojCt26ErOQ,8988
 fractal_server/app/routes/api/v2/task_legacy.py,sha256=P_VJv9v0yzFUBuS-DQHhMVSOe20ecGJJcFBqiiFciOM,1628
 fractal_server/app/routes/api/v2/workflow.py,sha256=2GlcYNjpvCdjwC_Kn7y0UP16B3pOLSNXBvIVsVDtDKM,11863
@@ -63,7 +63,7 @@ fractal_server/app/runner/executors/slurm/_batching.py,sha256=1P6CgrAOCK9u_EvNFT
 fractal_server/app/runner/executors/slurm/_check_jobs_status.py,sha256=8d29a7DQ2xoWxoFQCnFfTpHER-qBX8mEatl4Dw5HU_o,1908
 fractal_server/app/runner/executors/slurm/_executor_wait_thread.py,sha256=J3tjAx33nBgW4eHAXDte7hDs7Oe9FLEZaElEt8inrbg,4421
 fractal_server/app/runner/executors/slurm/_slurm_config.py,sha256=rF37XDImX1QoWx37MC5hSM9AuY_KfHU5gaWwN4vl4Zk,15552
-fractal_server/app/runner/executors/slurm/_subprocess_run_as_user.py,sha256=8CCtxWCuB5UDst3C_WJxBU77xwPrpDyq7iMCZMnodXU,5123
+fractal_server/app/runner/executors/slurm/_subprocess_run_as_user.py,sha256=YwfJzZr_y4FL_hirHJdWK0vWzrldjoZZhXVFlO2AOMU,5131
 fractal_server/app/runner/executors/slurm/executor.py,sha256=267YTDvyeA0yX2n2HffxP8OAu_CQF5uB9K-_AaUG3iU,44655
 fractal_server/app/runner/executors/slurm/remote.py,sha256=wLziIsGdSMiO-jIXM8x77JRK82g_2hx0iBKTiMghuIo,5852
 fractal_server/app/runner/filenames.py,sha256=9lwu3yB4C67yiijYw8XIKaLFn3mJUt6_TCyVFM_aZUQ,206
@@ -80,7 +80,7 @@ fractal_server/app/runner/v1/_slurm/_submit_setup.py,sha256=llTgSOCnCVMvm7Q0SoVp
 fractal_server/app/runner/v1/_slurm/get_slurm_config.py,sha256=6TLWQon8hSicsD7c3yXK4P9xeId0s_H3HOOeMUVGVss,5977
 fractal_server/app/runner/v1/common.py,sha256=_L-vjLnWato80VdlB_BFN4G8P4jSM07u-5cnl1T3S34,3294
 fractal_server/app/runner/v1/handle_failed_job.py,sha256=bHzScC_aIlU3q-bQxGW6rfWV4xbZ2tho_sktjsAs1no,4684
-fractal_server/app/runner/v2/__init__.py,sha256=mnXlC69UBQVpEwEWH3ZbMSsrVLl1yCnROh8_WGnXKUk,12500
+fractal_server/app/runner/v2/__init__.py,sha256=U6FwKhiIF1INKU8LCoGHBCb04S2xOa3rpbltcodWXLw,11952
 fractal_server/app/runner/v2/_local/__init__.py,sha256=Q1s-DwXleUq6w1ZNv6tlh3tZv6cyBqxB_hMvZlqVYaM,5881
 fractal_server/app/runner/v2/_local/_local_config.py,sha256=lR0Js-l63mQUzN9hK0HkfdLsrTf-W6GHvPvbPC64amY,3630
 fractal_server/app/runner/v2/_local/_submit_setup.py,sha256=deagsLSy6A3ZHKaSDcQqrdvbQVM3i4kgyTcbVc0tC5U,1614
@@ -121,14 +121,14 @@ fractal_server/app/schemas/v2/task_collection.py,sha256=sY29NQfJrbjiidmVkVjSIH-2
 fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
 fractal_server/app/schemas/v2/workflowtask.py,sha256=atVuVN4aXsVEOmSd-vyg-8_8OnPmqx-gT75rXcn_AlQ,6552
 fractal_server/app/security/__init__.py,sha256=wxosoHc3mJYPCdPMyWnRD8w_2OgnKYp2aDkdmwrZh5k,11203
-fractal_server/config.py,sha256=lXofyyyMdRQoK39yTBUwVotRT8ptSb5LceHlZrUuK2o,15048
-fractal_server/data_migrations/2_0_3.py,sha256=7EhwLCZTk1yHD_dlU-HIf2uvx6jUIgfDaA5np27QEEM,2918
+fractal_server/config.py,sha256=19CnX1Jyw_zYjEvfXJTaypB7Ape7qfFzKX4B1LZmOe0,15167
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/images/__init__.py,sha256=xO6jTLE4EZKO6cTDdJsBmK9cdeh9hFTaSbSuWgQg7y4,196
 fractal_server/images/models.py,sha256=9ipU5h4N6ogBChoB-2vHoqtL0TXOHCv6kRR-fER3mkM,4167
 fractal_server/images/tools.py,sha256=gxeniYy4Z-cp_ToK2LHPJUTVVUUrdpogYdcBUvBuLiY,2209
-fractal_server/logger.py,sha256=AuCmrwIydaFWpotMTM_tGRNJbExQO5fP8Xolo82Vdbg,4178
-fractal_server/main.py,sha256=u_MngsZWI-1uKrBpNDUYXKyLgaYodyAEw2dKZrIzS_U,3381
+fractal_server/logger/__init__.py,sha256=Q_e03Lj30VWdCqGBJrKw9A2QEeDbCKC_OOkDQVW9Dyw,5132
+fractal_server/logger/gunicorn_logger.py,sha256=vb5s7mruCHPkKWGrTTOPyrB_658Y2Z05ECdHhCCBhp0,644
+fractal_server/main.py,sha256=OostfB8nyFKCySDTnIR64WlHg82eHkoykJgQg6se9xc,3556
 fractal_server/migrations/README,sha256=4rQvyDfqodGhpJw74VYijRmgFP49ji5chyEemWGHsuw,59
 fractal_server/migrations/env.py,sha256=bsl0HGZpjhommztgcs7wQ94sJzI1Orgnij97K8P_uyo,2630
 fractal_server/migrations/script.py.mako,sha256=oMXw9LC3zRbinWWPPDgeZ4z9FJrV2zhRWiYdS5YgNbI,526
@@ -163,8 +163,8 @@ fractal_server/tasks/v2/background_operations.py,sha256=MAMBn6W2bhkdK59kfUGiD7a1
 fractal_server/tasks/v2/get_collection_data.py,sha256=Qhf2T_aaqAfqu9_KpUSlXsS7EJoZQbEPEreHHa2jco8,502
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
-fractal_server-2.0.4.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.0.4.dist-info/METADATA,sha256=4irspCdC-GXbBTPYtUiQ8FIAaFeRfJBlYnuGWYGdKBo,4222
-fractal_server-2.0.4.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.0.4.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.0.4.dist-info/RECORD,,
+fractal_server-2.0.6.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.0.6.dist-info/METADATA,sha256=id7WLlUPHEi6TAgIVSDxZJacFhTvriBOdX86QLLbqPM,4222
+fractal_server-2.0.6.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.0.6.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.0.6.dist-info/RECORD,,

fractal_server/data_migrations/2_0_3.py

@@ -1,79 +0,0 @@
-import logging
-
-from packaging.version import parse
-from sqlalchemy import select
-from sqlalchemy.orm.attributes import flag_modified
-
-import fractal_server
-from fractal_server.app.db import get_sync_db
-from fractal_server.app.models.v1 import ApplyWorkflow
-from fractal_server.app.models.v2 import JobV2
-from fractal_server.app.schemas.v1 import ApplyWorkflowReadV1
-from fractal_server.app.schemas.v2 import JobReadV2
-
-
-def fix_db():
-    logger = logging.getLogger("fix_db")
-    logger.warning("START execution of fix_db function")
-
-    # Check that this module matches with the current version
-    module_version = parse("2.0.3")
-    current_version = parse(fractal_server.__VERSION__)
-    if (
-        current_version.major != module_version.major
-        or current_version.minor != module_version.minor
-        or current_version.micro != module_version.micro
-    ):
-        raise RuntimeError(
-            f"{fractal_server.__VERSION__=} not matching with {__file__=}"
-        )
-
-    with next(get_sync_db()) as db:
-
-        # V1 jobs
-        stm = select(ApplyWorkflow)
-        jobs_v1 = db.execute(stm).scalars().all()
-        for job_v1 in sorted(jobs_v1, key=lambda x: x.id):
-            for KEY in ["history"]:
-                logger.warning(
-                    f"Now removing {KEY} from `input/output_dataset_dump`, "
-                    f"for appplyworkflow.id={job_v1.id}."
-                )
-                if KEY in job_v1.input_dataset_dump.keys():
-                    job_v1.input_dataset_dump.pop(KEY)
-                if KEY in job_v1.output_dataset_dump.keys():
-                    job_v1.output_dataset_dump.pop(KEY)
-            flag_modified(job_v1, "input_dataset_dump")
-            flag_modified(job_v1, "output_dataset_dump")
-            db.add(job_v1)
-            db.commit()
-            db.refresh(job_v1)
-            db.expunge(job_v1)
-            logger.warning(
-                f"Now validating applyworkflow.id={job_v1.id} with "
-                "ApplyWorkflowReadV1."
-            )
-            ApplyWorkflowReadV1(**job_v1.model_dump())
-
-        # V2 jobs
-        stm = select(JobV2)
-        jobs_v2 = db.execute(stm).scalars().all()
-        for job_v2 in sorted(jobs_v2, key=lambda x: x.id):
-            for KEY in ["history", "images"]:
-                logger.warning(
-                    f"Now removing {KEY} from `dataset_dump`, "
-                    f"for jobv2.id={job_v2.id}."
-                )
-                if KEY in job_v2.dataset_dump.keys():
-                    job_v2.dataset_dump.pop(KEY)
-            flag_modified(job_v2, "dataset_dump")
-            db.add(job_v2)
-            db.commit()
-            db.refresh(job_v2)
-            db.expunge(job_v2)
-            logger.warning(
-                f"Now validating jobv2.id={job_v2.id} with JobReadV2."
-            )
-            JobReadV2(**job_v2.model_dump())
-
-    logger.warning("END of execution of fix_db function")