fractal-server 2.0.0a8__py3-none-any.whl → 2.0.0a10__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.0.0a8"
+__VERSION__ = "2.0.0a10"

fractal_server/app/models/v2/workflow.py

@@ -33,11 +33,3 @@ class WorkflowV2(SQLModel, table=True):
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),
     )
-
-    @property
-    def input_types(self):
-        return self.task_list[0].task.input_types
-
-    @property
-    def output_types(self):
-        return self.task_list[-1].task.output_types

fractal_server/app/models/v2/workflowtask.py

@@ -51,14 +51,13 @@ class WorkflowTaskV2(SQLModel, table=True):
 
     @validator("args_non_parallel")
     def validate_args_non_parallel(cls, value):
-        """
-        FIXME V2 this requires an update
-        """
         if value is None:
             return
         forbidden_args_keys = {
-            "metadata",
-            "component",
+            "zarr_dir",
+            "zarr_url",
+            "zarr_urls",
+            "init_args",
         }
         args_keys = set(value.keys())
         intersect_keys = forbidden_args_keys.intersection(args_keys)
@@ -71,14 +70,13 @@ class WorkflowTaskV2(SQLModel, table=True):
 
     @validator("args_parallel")
     def validate_args_parallel(cls, value):
-        """
-        FIXME V2 this requires an update
-        """
         if value is None:
             return
         forbidden_args_keys = {
-            "metadata",
-            "component",
+            "zarr_dir",
+            "zarr_url",
+            "zarr_urls",
+            "init_args",
         }
         args_keys = set(value.keys())
         intersect_keys = forbidden_args_keys.intersection(args_keys)

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

@@ -7,6 +7,7 @@ from .dataset import router as dataset_router_v2
 from .images import router as images_routes_v2
 from .job import router as job_router_v2
 from .project import router as project_router_v2
+from .status import router as status_router_v2
 from .submit import router as submit_job_router_v2
 from .task import router as task_router_v2
 from .task_collection import router as task_collection_router_v2
@@ -30,3 +31,4 @@ router_api_v2.include_router(
 )
 router_api_v2.include_router(workflow_router_v2, tags=["V2 Workflow"])
 router_api_v2.include_router(workflowtask_router_v2, tags=["V2 WorkflowTask"])
+router_api_v2.include_router(status_router_v2, tags=["V2 Status"])

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

@@ -1,5 +1,3 @@
-import json
-from pathlib import Path
 from typing import Optional
 
 from fastapi import APIRouter
@@ -17,15 +15,13 @@ from ....models.v2 import ProjectV2
 from ....schemas.v2 import DatasetCreateV2
 from ....schemas.v2 import DatasetReadV2
 from ....schemas.v2 import DatasetUpdateV2
-from ....schemas.v2.dataset import DatasetStatusReadV2
-from ....schemas.v2.dataset import WorkflowTaskStatusTypeV2
+from ....schemas.v2.dataset import DatasetExportV2
+from ....schemas.v2.dataset import DatasetImportV2
 from ....security import current_active_user
 from ....security import User
 from ._aux_functions import _get_dataset_check_owner
 from ._aux_functions import _get_project_check_owner
 from ._aux_functions import _get_submitted_jobs_statement
-from ._aux_functions import _get_workflow_check_owner
-from fractal_server.app.runner.filenames import HISTORY_FILENAME
 
 router = APIRouter()
 
@@ -227,91 +223,61 @@ async def get_user_datasets(
 
 
 @router.get(
-    "/project/{project_id}/dataset/{dataset_id}/status/",
-    response_model=DatasetStatusReadV2,
+    "/project/{project_id}/dataset/{dataset_id}/export/",
+    response_model=DatasetExportV2,
 )
-async def get_workflowtask_status(
+async def export_dataset(
     project_id: int,
     dataset_id: int,
     user: User = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[DatasetStatusReadV2]:
+) -> Optional[DatasetExportV2]:
     """
-    Extract the status of all `WorkflowTask`s that ran on a given `DatasetV2`.
+    Export an existing dataset
     """
-    # Get the dataset DB entry
-    output = await _get_dataset_check_owner(
+    dict_dataset_project = await _get_dataset_check_owner(
         project_id=project_id,
         dataset_id=dataset_id,
         user_id=user.id,
         db=db,
     )
-    dataset = output["dataset"]
+    await db.close()
 
-    # Check whether there exists a job such that
-    # 1. `job.dataset_id == dataset_id`, and
-    # 2. `job.status` is submitted
-    # If one such job exists, it will be used later. If there are multiple
-    # jobs, raise an error.
-    stm = _get_submitted_jobs_statement().where(JobV2.dataset_id == dataset_id)
-    res = await db.execute(stm)
-    running_jobs = res.scalars().all()
-    if len(running_jobs) == 0:
-        running_job = None
-    elif len(running_jobs) == 1:
-        running_job = running_jobs[0]
-    else:
-        string_ids = str([job.id for job in running_jobs])[1:-1]
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                f"Cannot get WorkflowTaskV2 statuses as DatasetV2 {dataset.id}"
-                f" is linked to multiple active jobs: {string_ids}."
-            ),
-        )
+    dataset = dict_dataset_project["dataset"]
 
-    # Initialize empty dictionary for WorkflowTaskV2 status
-    workflow_tasks_status_dict: dict = {}
-
-    # Lowest priority: read status from DB, which corresponds to jobs that are
-    # not running
-    history = dataset.history
-    for history_item in history:
-        wftask_id = history_item["workflowtask"]["id"]
-        wftask_status = history_item["status"]
-        workflow_tasks_status_dict[wftask_id] = wftask_status
-
-    # If a job is running, then gather more up-to-date information
-    if running_job is not None:
-        # Get the workflow DB entry
-        running_workflow = await _get_workflow_check_owner(
-            project_id=project_id,
-            workflow_id=running_job.workflow_id,
-            user_id=user.id,
-            db=db,
-        )
-        # Mid priority: Set all WorkflowTask's that are part of the running job
-        # as "submitted"
-        start = running_job.first_task_index
-        end = running_job.last_task_index + 1
-        for wftask in running_workflow.task_list[start:end]:
-            workflow_tasks_status_dict[
-                wftask.id
-            ] = WorkflowTaskStatusTypeV2.SUBMITTED
-
-        # Highest priority: Read status updates coming from the running-job
-        # temporary file. Note: this file only contains information on
-        # # WorkflowTask's that ran through successfully.
-        tmp_file = Path(running_job.working_dir) / HISTORY_FILENAME
-        try:
-            with tmp_file.open("r") as f:
-                history = json.load(f)
-        except FileNotFoundError:
-            history = []
-        for history_item in history:
-            wftask_id = history_item["workflowtask"]["id"]
-            wftask_status = history_item["status"]
-            workflow_tasks_status_dict[wftask_id] = wftask_status
-
-    response_body = DatasetStatusReadV2(status=workflow_tasks_status_dict)
-    return response_body
+    return dataset
+
+
+@router.post(
+    "/project/{project_id}/dataset/import/",
+    response_model=DatasetReadV2,
+    status_code=status.HTTP_201_CREATED,
+)
+async def import_dataset(
+    project_id: int,
+    dataset: DatasetImportV2,
+    user: User = Depends(current_active_user),
+    db: AsyncSession = Depends(get_async_db),
+) -> Optional[DatasetReadV2]:
+    """
+    Import an existing dataset into a project
+    """
+
+    # Preliminary checks
+    await _get_project_check_owner(
+        project_id=project_id,
+        user_id=user.id,
+        db=db,
+    )
+
+    # Create new Dataset
+    db_dataset = DatasetV2(
+        project_id=project_id,
+        **dataset.dict(exclude_none=True),
+    )
+    db.add(db_dataset)
+    await db.commit()
+    await db.refresh(db_dataset)
+    await db.close()
+
+    return db_dataset

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

@@ -66,6 +66,14 @@ async def post_new_image(
                 f"{dataset.zarr_dir}."
             ),
         )
+    elif new_image.zarr_url == dataset.zarr_dir:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                "`SingleImage.zarr_url` cannot be equal to `Dataset.zarr_dir`:"
+                f" {dataset.zarr_dir}"
+            ),
+        )
 
     if new_image.zarr_url in dataset.image_zarr_urls:
         raise HTTPException(

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

@@ -0,0 +1,150 @@
+import json
+from pathlib import Path
+from typing import Optional
+
+from fastapi import APIRouter
+from fastapi import Depends
+from fastapi import HTTPException
+from fastapi import status
+
+from ....db import AsyncSession
+from ....db import get_async_db
+from ....models.v2 import JobV2
+from ....schemas.v2.dataset import WorkflowTaskStatusTypeV2
+from ....schemas.v2.status import StatusReadV2
+from ....security import current_active_user
+from ....security import User
+from ._aux_functions import _get_dataset_check_owner
+from ._aux_functions import _get_submitted_jobs_statement
+from ._aux_functions import _get_workflow_check_owner
+from fractal_server.app.runner.filenames import HISTORY_FILENAME
+
+router = APIRouter()
+
+
+@router.get(
+    "/project/{project_id}/status/",
+    response_model=StatusReadV2,
+)
+async def get_workflowtask_status(
+    project_id: int,
+    dataset_id: int,
+    workflow_id: int,
+    user: User = Depends(current_active_user),
+    db: AsyncSession = Depends(get_async_db),
+) -> Optional[StatusReadV2]:
+    """
+    Extract the status of all `WorkflowTaskV2` of a given `WorkflowV2` that ran
+    on a given `DatasetV2`.
+
+    *NOTE*: the current endpoint is not guaranteed to provide consistent
+    results if the workflow task list is modified in a non-trivial way
+    (that is, by adding intermediate tasks, removing tasks, or changing their
+    order). See fractal-server GitHub issues: 793, 1083.
+    """
+    # Get the dataset DB entry
+    output = await _get_dataset_check_owner(
+        project_id=project_id,
+        dataset_id=dataset_id,
+        user_id=user.id,
+        db=db,
+    )
+    dataset = output["dataset"]
+
+    # Get the workflow DB entry
+    workflow = await _get_workflow_check_owner(
+        project_id=project_id,
+        workflow_id=workflow_id,
+        user_id=user.id,
+        db=db,
+    )
+
+    # Check whether there exists a submitted job associated to this
+    # workflow/dataset pair. If it does exist, it will be used later.
+    # If there are multiple jobs, raise an error.
+    stm = _get_submitted_jobs_statement()
+    stm = stm.where(JobV2.dataset_id == dataset_id)
+    stm = stm.where(JobV2.workflow_id == workflow_id)
+    res = await db.execute(stm)
+    running_jobs = res.scalars().all()
+    if len(running_jobs) == 0:
+        running_job = None
+    elif len(running_jobs) == 1:
+        running_job = running_jobs[0]
+    else:
+        string_ids = str([job.id for job in running_jobs])[1:-1]
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                f"Cannot get WorkflowTaskV2 statuses as DatasetV2 {dataset.id}"
+                f" is linked to multiple active jobs: {string_ids}."
+            ),
+        )
+
+    # Initialize empty dictionary for WorkflowTaskV2 status
+    workflow_tasks_status_dict: dict = {}
+
+    # Lowest priority: read status from DB, which corresponds to jobs that are
+    # not running
+    history = dataset.history
+    for history_item in history:
+        wftask_id = history_item["workflowtask"]["id"]
+        wftask_status = history_item["status"]
+        workflow_tasks_status_dict[wftask_id] = wftask_status
+
+    if running_job is None:
+        # If no job is running, the chronological-last history item is also the
+        # positional-last workflow task to be included in the response.
+        if len(dataset.history) > 0:
+            last_valid_wftask_id = dataset.history[-1]["workflowtask"]["id"]
+        else:
+            last_valid_wftask_id = None
+    else:
+        # If a job is running, then gather more up-to-date information
+
+        # Mid priority: Set all WorkflowTask's that are part of the running job
+        # as "submitted"
+        start = running_job.first_task_index
+        end = running_job.last_task_index + 1
+        for wftask in workflow.task_list[start:end]:
+            workflow_tasks_status_dict[
+                wftask.id
+            ] = WorkflowTaskStatusTypeV2.SUBMITTED
+
+        # The last workflow task that is included in the submitted job is also
+        # the positional-last workflow task to be included in the response.
+        last_valid_wftask_id = workflow.task_list[end - 1]
+
+        # Highest priority: Read status updates coming from the running-job
+        # temporary file. Note: this file only contains information on
+        # WorkflowTask's that ran through successfully.
+        tmp_file = Path(running_job.working_dir) / HISTORY_FILENAME
+        try:
+            with tmp_file.open("r") as f:
+                history = json.load(f)
+        except FileNotFoundError:
+            history = []
+        for history_item in history:
+            wftask_id = history_item["workflowtask"]["id"]
+            wftask_status = history_item["status"]
+            workflow_tasks_status_dict[wftask_id] = wftask_status
+
+    # Based on previously-gathered information, clean up the response body
+    clean_workflow_tasks_status_dict = {}
+    for wf_task in workflow.task_list:
+        wf_task_status = workflow_tasks_status_dict.get(wf_task.id)
+        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
+        if wf_task_status == WorkflowTaskStatusTypeV2.FAILED:
+            # Starting from the beginning of `workflow.task_list`, stop the
+            # first time that you hit a failed job
+            break
+        if wf_task.id == last_valid_wftask_id:
+            # Starting from the beginning of `workflow.task_list`, stop the
+            # first time that you hit `last_valid_wftask_id``
+            break
+
+    response_body = StatusReadV2(status=clean_workflow_tasks_status_dict)
+    return response_body

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

@@ -200,9 +200,15 @@ async def update_workflowtask(
             setattr(db_wf_task, key, actual_args)
         elif key == "args_non_parallel":
             # Get default arguments via a Task property method
-            default_args = deepcopy(
-                db_wf_task.task.default_args_non_parallel_from_args_schema
-            )
+            if db_wf_task.is_legacy_task:
+                # This is only needed so that we don't have to modify the rest
+                # of this block, but legacy task cannot take any non-parallel
+                # args (see checks above).
+                default_args = {}
+            else:
+                default_args = deepcopy(
+                    db_wf_task.task.default_args_non_parallel_from_args_schema
+                )
             # Override default_args with args value items
             actual_args = default_args.copy()
             if value is not None:

fractal_server/app/runner/v2/_slurm/get_slurm_config.py

@@ -125,7 +125,10 @@ def get_slurm_config(
         slurm_dict["mem_per_task_MB"] = mem_per_task_MB
 
     # Job name
-    job_name = wftask.task.name.replace(" ", "_")
+    if wftask.is_legacy_task:
+        job_name = wftask.task_legacy.name.replace(" ", "_")
+    else:
+        job_name = wftask.task.name.replace(" ", "_")
     slurm_dict["job_name"] = job_name
 
     # Optional SLURM arguments and extra lines

fractal_server/app/runner/v2/handle_failed_job.py

@@ -96,8 +96,15 @@ def assemble_history_failed_job(
 
     # Part 3/B: Append failed task to history
     if failed_wftask is not None:
-        failed_wftask_dump = failed_wftask.model_dump(exclude={"task"})
-        failed_wftask_dump["task"] = failed_wftask.task.model_dump()
+        failed_wftask_dump = failed_wftask.model_dump(
+            exclude={"task", "task_legacy"}
+        )
+        if failed_wftask.is_legacy_task:
+            failed_wftask_dump[
+                "task_legacy"
+            ] = failed_wftask.task_legacy.model_dump()
+        else:
+            failed_wftask_dump["task"] = failed_wftask.task.model_dump()
         new_history_item = dict(
             workflowtask=failed_wftask_dump,
             status=WorkflowTaskStatusTypeV2.FAILED,

fractal_server/app/runner/v2/runner.py

@@ -1,4 +1,5 @@
 import json
+import logging
 from concurrent.futures import ThreadPoolExecutor
 from copy import copy
 from copy import deepcopy
@@ -37,6 +38,8 @@ def execute_tasks_v2(
     submit_setup_call: Callable = no_op_submit_setup_call,
 ) -> DatasetV2:
 
+    logger = logging.getLogger(logger_name)
+
     if not workflow_dir.exists():  # FIXME: this should have already happened
         workflow_dir.mkdir()
 
@@ -48,6 +51,9 @@ def execute_tasks_v2(
 
     for wftask in wf_task_list:
         task = wftask.task
+        task_legacy = wftask.task_legacy
+        task_name = task_legacy.name if wftask.is_legacy_task else task.name
+        logger.debug(f'SUBMIT {wftask.order}-th task (name="{task_name}")')
 
         # PRE TASK EXECUTION
 
@@ -63,12 +69,13 @@ def execute_tasks_v2(
             filters=Filters(**pre_filters),
         )
         # Verify that filtered images comply with task input_types
-        for image in filtered_images:
-            if not match_filter(image, Filters(types=task.input_types)):
-                raise ValueError(
-                    f"Filtered images include {image}, which does "
-                    f"not comply with {task.input_types=}."
-                )
+        if not wftask.is_legacy_task:
+            for image in filtered_images:
+                if not match_filter(image, Filters(types=task.input_types)):
+                    raise ValueError(
+                        f"Filtered images include {image}, which does "
+                        f"not comply with {task.input_types=}."
+                    )
 
         # TASK EXECUTION (V2)
         if not wftask.is_legacy_task:
@@ -77,7 +84,7 @@ def execute_tasks_v2(
                     images=filtered_images,
                     zarr_dir=zarr_dir,
                     wftask=wftask,
-                    task=wftask.task,
+                    task=task,
                     workflow_dir=workflow_dir,
                     workflow_dir_user=workflow_dir_user,
                     executor=executor,
@@ -88,7 +95,7 @@ def execute_tasks_v2(
                 current_task_output = run_v2_task_parallel(
                     images=filtered_images,
                     wftask=wftask,
-                    task=wftask.task,
+                    task=task,
                     workflow_dir=workflow_dir,
                     workflow_dir_user=workflow_dir_user,
                     executor=executor,
@@ -100,7 +107,7 @@ def execute_tasks_v2(
                     images=filtered_images,
                     zarr_dir=zarr_dir,
                     wftask=wftask,
-                    task=wftask.task,
+                    task=task,
                     workflow_dir=workflow_dir,
                     workflow_dir_user=workflow_dir_user,
                     executor=executor,
@@ -114,9 +121,11 @@ def execute_tasks_v2(
             current_task_output = run_v1_task_parallel(
                 images=filtered_images,
                 wftask=wftask,
-                task_legacy=wftask.task_legacy,
+                task_legacy=task_legacy,
                 executor=executor,
                 logger_name=logger_name,
+                workflow_dir=workflow_dir,
+                workflow_dir_user=workflow_dir_user,
                 submit_setup_call=submit_setup_call,
             )
 
@@ -155,7 +164,8 @@ def execute_tasks_v2(
                 # Update image attributes/types with task output and manifest
                 updated_attributes.update(image["attributes"])
                 updated_types.update(image["types"])
-                updated_types.update(task.output_types)
+                if not wftask.is_legacy_task:
+                    updated_types.update(task.output_types)
 
                 # Unset attributes with None value
                 updated_attributes = {
@@ -182,6 +192,11 @@ def execute_tasks_v2(
                         f"{zarr_dir} is not a parent directory of "
                         f"{image['zarr_url']}"
                     )
+                # Check that image['zarr_url'] is not equal to zarr_dir
+                if image["zarr_url"] == zarr_dir:
+                    raise ValueError(
+                        "image['zarr_url'] cannot be equal to zarr_dir"
+                    )
                 # Propagate attributes and types from `origin` (if any)
                 updated_attributes = {}
                 updated_types = {}
@@ -202,7 +217,8 @@ def execute_tasks_v2(
                     if value is not None
                 }
                 updated_types.update(image["types"])
-                updated_types.update(task.output_types)
+                if not wftask.is_legacy_task:
+                    updated_types.update(task.output_types)
                 new_image = dict(
                     zarr_url=image["zarr_url"],
                     origin=image["origin"],
@@ -277,6 +293,8 @@ def execute_tasks_v2(
         with open(workflow_dir / IMAGES_FILENAME, "w") as f:
             json.dump(tmp_images, f, indent=2)
 
+        logger.debug(f'END    {wftask.order}-th task (name="{task_name}")')
+
     # NOTE: tmp_history only contains the newly-added history items (to be
     # appended to the original history), while tmp_filters and tmp_images
     # represent the new attributes (to replace the original ones)

fractal_server/app/runner/v2/runner_functions.py

@@ -146,6 +146,9 @@ def run_v2_task_parallel(
     submit_setup_call: Callable = no_op_submit_setup_call,
 ) -> TaskOutput:
 
+    if len(images) == 0:
+        return TaskOutput()
+
     _check_parallelization_list_size(images)
 
     executor_options = _get_executor_options(
@@ -249,6 +252,9 @@ def run_v2_task_compound(
     # 3/B: parallel part of a compound task
     _check_parallelization_list_size(parallelization_list)
 
+    if len(parallelization_list) == 0:
+        return TaskOutput()
+
     list_function_kwargs = []
     for ind, parallelization_item in enumerate(parallelization_list):
         list_function_kwargs.append(
@@ -313,10 +319,11 @@ def run_v1_task_parallel(
     for ind, image in enumerate(images):
         list_function_kwargs.append(
             convert_v2_args_into_v1(
-                dict(
+                kwargs_v2=dict(
                     zarr_url=image["zarr_url"],
                     **(wftask.args_parallel or {}),
-                )
+                ),
+                parallelization_level=task_legacy.parallelization_level,
             ),
         )
         list_function_kwargs[-1][_COMPONENT_KEY_] = _index_to_component(ind)

fractal_server/app/runner/v2/runner_functions_low_level.py

@@ -116,7 +116,10 @@ def run_single_task(
     except TaskExecutionError as e:
         e.workflow_task_order = wftask.order
         e.workflow_task_id = wftask.id
-        e.task_name = wftask.task.name
+        if wftask.is_legacy_task:
+            e.task_name = wftask.task_legacy.name
+        else:
+            e.task_name = wftask.task.name
         raise e
 
     try:

fractal_server/app/runner/v2/v1_compat.py

@@ -3,13 +3,23 @@ from pathlib import Path
 from typing import Any
 
 
-def convert_v2_args_into_v1(kwargs_v2: dict[str, Any]) -> dict[str, Any]:
-
+def convert_v2_args_into_v1(
+    kwargs_v2: dict[str, Any],
+    parallelization_level: str = "image",
+) -> dict[str, Any]:
     kwargs_v1 = deepcopy(kwargs_v2)
 
     zarr_url = kwargs_v1.pop("zarr_url")
     input_path = Path(zarr_url).parents[3].as_posix()
-    component = zarr_url.replace(input_path, "").lstrip("/")
+    image_component = zarr_url.replace(input_path, "").lstrip("/")
+    if parallelization_level == "image":
+        component = image_component
+    elif parallelization_level == "well":
+        component = str(Path(image_component).parent)
+    elif parallelization_level == "plate":
+        component = str(Path(image_component).parents[2])
+    else:
+        raise ValueError(f"Invalid {parallelization_level=}.")
 
     kwargs_v1.update(
         input_paths=[input_path],

fractal_server/app/schemas/v2/dataset.py

@@ -12,6 +12,7 @@ from .dumps import WorkflowTaskDumpV2
 from .project import ProjectReadV2
 from .workflowtask import WorkflowTaskStatusTypeV2
 from fractal_server.images import Filters
+from fractal_server.images import SingleImage
 from fractal_server.urls import normalize_url
 
 
@@ -25,20 +26,6 @@ class _DatasetHistoryItemV2(BaseModel):
     parallelization: Optional[dict]
 
 
-class DatasetStatusReadV2(BaseModel):
-    """
-    Response type for the
-    `/project/{project_id}/dataset/{dataset_id}/status/` endpoint
-    """
-
-    status: Optional[
-        dict[
-            str,
-            WorkflowTaskStatusTypeV2,
-        ]
-    ] = None
-
-
 # CRUD
 
 
@@ -95,3 +82,40 @@ class DatasetUpdateV2(BaseModel):
         return v
 
     _name = validator("name", allow_reuse=True)(valstr("name"))
+
+
+class DatasetImportV2(BaseModel):
+    """
+    Class for `Dataset` import.
+
+    Attributes:
+        name:
+        zarr_dir:
+        images:
+        filters:
+    """
+
+    class Config:
+        extra = "forbid"
+
+    name: str
+    zarr_dir: str
+    images: list[SingleImage] = Field(default_factory=[])
+    filters: Filters = Field(default_factory=Filters)
+
+
+class DatasetExportV2(BaseModel):
+    """
+    Class for `Dataset` export.
+
+    Attributes:
+        name:
+        zarr_dir:
+        images:
+        filters:
+    """
+
+    name: str
+    zarr_dir: str
+    images: list[SingleImage]
+    filters: Filters

fractal_server/app/schemas/v2/dumps.py

@@ -45,6 +45,8 @@ class WorkflowTaskDumpV2(BaseModel):
     workflow_id: int
     order: Optional[int]
 
+    is_legacy_task: bool
+
     input_filters: Filters
 
     task_id: Optional[int]

fractal_server/app/schemas/v2/status.py

@@ -0,0 +1,16 @@
+from pydantic import BaseModel
+from pydantic import Field
+
+from .workflowtask import WorkflowTaskStatusTypeV2
+
+
+class StatusReadV2(BaseModel):
+    """
+    Response type for the
+    `/project/{project_id}/status/` endpoint
+    """
+
+    status: dict[
+        str,
+        WorkflowTaskStatusTypeV2,
+    ] = Field(default_factory=dict)

{fractal_server-2.0.0a8.dist-info → fractal_server-2.0.0a10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.0.0a8
+Version: 2.0.0a10
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -23,7 +23,7 @@ Requires-Dist: cloudpickle (>=3.0.0,<3.1.0)
 Requires-Dist: clusterfutures (>=0.5,<0.6)
 Requires-Dist: fastapi (>=0.110.0,<0.111.0)
 Requires-Dist: fastapi-users[oauth] (>=12.1.0,<13.0.0)
-Requires-Dist: gunicorn (>=21.2.0,<22.0.0) ; extra == "gunicorn"
+Requires-Dist: gunicorn (>=21.2,<23.0) ; extra == "gunicorn"
 Requires-Dist: packaging (>=23.2,<24.0)
 Requires-Dist: psycopg2 (>=2.9.5,<3.0.0) ; extra == "postgres"
 Requires-Dist: pydantic (>=1.10.8,<2)

{fractal_server-2.0.0a8.dist-info → fractal_server-2.0.0a10.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=K1rg40LWC0HcWGPng5LXrwtqh2Z-3XITlzdSqTIPpeQ,24
+fractal_server/__init__.py,sha256=Ndyws1HQt0rbkLhMYPxRDuKeooalmEoA6oesT2NmbbU,25
 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
@@ -18,8 +18,8 @@ fractal_server/app/models/v2/dataset.py,sha256=-7sxHEw4IIAvF_uSan7tA3o8hvoakBkQ0
 fractal_server/app/models/v2/job.py,sha256=PCJf0_NYIc5boXL6e6P72BvYJGydCZOGKnW2DT4Sw9g,1535
 fractal_server/app/models/v2/project.py,sha256=CqDEKzdVxmFDMee6DnVOyX7WGmdn-dQSLSekzw_OLUc,817
 fractal_server/app/models/v2/task.py,sha256=9ZPhug3VWyeqgT8wQ9_8ZXQ2crSiiicRipxrxTslOso,3257
-fractal_server/app/models/v2/workflow.py,sha256=4pSTeZC78OQbgHHC5S0ge6pK1AP6ak7Qew_0ZNM9xuw,1256
-fractal_server/app/models/v2/workflowtask.py,sha256=f2a85MSAyBAdC7oG6SR8mViMNqlomQWaIB08n3ZhT-0,2727
+fractal_server/app/models/v2/workflow.py,sha256=YBgFGCziUgU0aJ5EM3Svu9W2c46AewZO9VBlFCHiSps,1069
+fractal_server/app/models/v2/workflowtask.py,sha256=kEm2k1LI0KK9vlTH7DL1NddaEUpIvMkFi42vahwDpd8,2695
 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=uY6H1znlAlrM9e1MG2EThTqwciCl87Twew34JM5W6IU,13981
@@ -34,18 +34,19 @@ fractal_server/app/routes/api/v1/task.py,sha256=4zUXMtq5M95XjaZs1t9oibYHiDIwxpM-
 fractal_server/app/routes/api/v1/task_collection.py,sha256=_cY3pPRGchdWPuJ1XudMZMVJ0IC0_XVH0XwLTiAbRGg,8873
 fractal_server/app/routes/api/v1/workflow.py,sha256=ZObifWTPi100oRQ1wEER8Sgsr3Neo8QVdCCFQnWMNZ0,10930
 fractal_server/app/routes/api/v1/workflowtask.py,sha256=ox-DIIqYV4K35hCu86eGa2SHnR5IQml-I00UHEwnmHQ,5579
-fractal_server/app/routes/api/v2/__init__.py,sha256=x56HcY1uBNCgq4BRVj-0j6bAj6OsTN97RNDqY8NefJ8,1373
+fractal_server/app/routes/api/v2/__init__.py,sha256=UNgODxoEXfQpQDjvsnMvHaUWbZOrcHhEXNisLcU-0tE,1487
 fractal_server/app/routes/api/v2/_aux_functions.py,sha256=TCHf3aM-KQxaNJen10CGX1Da5IIra00xRF39FUTU698,14301
-fractal_server/app/routes/api/v2/dataset.py,sha256=BmNKrhHUVoy0EuEYZpdocR_aG7U2tNuOpoAVimaGIBY,10008
-fractal_server/app/routes/api/v2/images.py,sha256=LX9-EYOGN4NHSARNXYGgSK4_vvAVFwzTiwVM5KuVukA,7589
+fractal_server/app/routes/api/v2/dataset.py,sha256=0JGRnK1DRQKgVA3FDhK8VdoRglLYFxgkMQOaoWI-tiQ,7853
+fractal_server/app/routes/api/v2/images.py,sha256=4r_HblPWyuKSZSJZfn8mbDaLv1ncwZU0gWdKneZcNG4,7894
 fractal_server/app/routes/api/v2/job.py,sha256=9mXaKCX_N3FXM0GIxdE49nWl_hJZ8CBLBIaMMhaCKOM,5334
 fractal_server/app/routes/api/v2/project.py,sha256=i9a19HAqE36N92G60ZYgObIP9nv-hR7Jt5nd9Dkhz1g,6024
+fractal_server/app/routes/api/v2/status.py,sha256=3bqQejJ3TnIMan5wK6jr9sv4ypsQr9WWU8xqlvTgDCE,5739
 fractal_server/app/routes/api/v2/submit.py,sha256=iszII5CvWDEjGPTphBgH9FVS1pNb5m11Xc8xozGgjgI,6901
 fractal_server/app/routes/api/v2/task.py,sha256=gJ0LruSk-Q1iMw8ZOX8C0wrZ4S4DGlQTr_5SdJJud0Q,7130
 fractal_server/app/routes/api/v2/task_collection.py,sha256=iw74UF8qdQa9pJf0DvSjihng6ri2k2HtW2UhMS_a8Zc,8904
 fractal_server/app/routes/api/v2/task_legacy.py,sha256=P_VJv9v0yzFUBuS-DQHhMVSOe20ecGJJcFBqiiFciOM,1628
 fractal_server/app/routes/api/v2/workflow.py,sha256=sw-1phO_rrmDAcWX9Zqb9M8SfrWF78-02AuLB1-D1PU,11845
-fractal_server/app/routes/api/v2/workflowtask.py,sha256=L4hYpb-ihKNfPxM5AnZqPhCdiojI9Eq5TR0wf-0vP_s,8414
+fractal_server/app/routes/api/v2/workflowtask.py,sha256=I1nrIV5J_DW1IeBq0q9VmUeBDo7P6x7qYO_Ocls2Pno,8720
 fractal_server/app/routes/auth.py,sha256=Xv80iqdyfY3lyicYs2Y8B6zEDEnyUu_H6_6psYtv3R4,4885
 fractal_server/app/routes/aux/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/aux/_job.py,sha256=5gKgvArAruSkMQuPN34Vvzi89WJbwWPsx0oDAa_iXu4,1248
@@ -85,15 +86,15 @@ fractal_server/app/runner/v2/_local/_submit_setup.py,sha256=deagsLSy6A3ZHKaSDcQq
 fractal_server/app/runner/v2/_local/executor.py,sha256=QrJlD77G6q4WohoJQO7XXbvi2RlCUsNvMnPDEZIoAqA,3620
 fractal_server/app/runner/v2/_slurm/__init__.py,sha256=srxn5-KdQxqD8cWJmOJlSoctbXYlyCMM249xWGY9bhI,4409
 fractal_server/app/runner/v2/_slurm/_submit_setup.py,sha256=tsZHQdVy3VxENMdsBzHltrVWzugBppq0cFrHtaVzoUA,2793
-fractal_server/app/runner/v2/_slurm/get_slurm_config.py,sha256=sqP-hs58TPt849rx10VRFKWX_DgLDPQcKZJcE0zKBXs,6621
+fractal_server/app/runner/v2/_slurm/get_slurm_config.py,sha256=I_lOS75iGYyJ74-gNwwcPadvZ9vI9HYe04WMln5GJ5Q,6726
 fractal_server/app/runner/v2/deduplicate_list.py,sha256=-imwO7OB7ATADEnqVbTElUwoY0YIJCTf_SbWJNN9OZg,639
-fractal_server/app/runner/v2/handle_failed_job.py,sha256=fipRJT5Y8UY0US4bXUX-4ORTAQ1AetZcCAOVCjDO3_c,5202
+fractal_server/app/runner/v2/handle_failed_job.py,sha256=M1r3dnrbUMo_AI2qjaVuGhieMAyLh5gcvB10YOBpjvI,5415
 fractal_server/app/runner/v2/merge_outputs.py,sha256=IHuHqbKmk97K35BFvTrKVBs60z3e_--OzXTnsvmA02c,1281
-fractal_server/app/runner/v2/runner.py,sha256=rBRehRDduGU0TUOkgQN6WbIGhDWZ6GOat4bv7IVB8cA,11784
-fractal_server/app/runner/v2/runner_functions.py,sha256=LfO1-FJF70_Qh78NQTCHJWyzyr011wvvtnzB6nTj5ZM,10087
-fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=Pp3hsj1i1t4ExDMcUBkQ27yEi7kjlvymY6q6eDiC8DM,3845
+fractal_server/app/runner/v2/runner.py,sha256=K6bmWbQRSZwbO6ZI2Bp7wNxYdkHcXxhWwBObMxJ0iSU,12599
+fractal_server/app/runner/v2/runner_functions.py,sha256=qVGG9KlH8ObX4Y0kr0q6qE8OpWFwf4RnOHhgPRRdj5M,10293
+fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=djNKD1y_EE0Q9Jkzh1QdKpjM66JVsLQgX2_zJT0xQlA,3947
 fractal_server/app/runner/v2/task_interface.py,sha256=TZLVJs6CNFo2lFhr-lsDxe585cEhRv48eA490LS9aqc,1746
-fractal_server/app/runner/v2/v1_compat.py,sha256=6UijuRYbB2ry2mM073u1fW4CSTeelB11lmoj_TOGtm4,511
+fractal_server/app/runner/v2/v1_compat.py,sha256=t0ficzAHUFaaeI56nqTb4YEKxfARF7L9Y6ijtJCwjP8,912
 fractal_server/app/schemas/__init__.py,sha256=VL55f3CTFngXHYkOsFaLBEEkEEewEWI5ODlcGTI7cqA,157
 fractal_server/app/schemas/_validators.py,sha256=1dTOYr1IZykrxuQSV2-zuEMZbKe_nGwrfS7iUrsh-sE,3461
 fractal_server/app/schemas/state.py,sha256=t4XM04aqxeluh8MfvD7LfEc-8-dOmUVluZHhLsfxxkc,692
@@ -108,11 +109,12 @@ fractal_server/app/schemas/v1/task.py,sha256=7BxOZ_qoRQ8n3YbQpDvB7VMcxB5fSYQmR5R
 fractal_server/app/schemas/v1/task_collection.py,sha256=uvq9bcMaGD_qHsh7YtcpoSAkVAbw12eY4DocIO3MKOg,3057
 fractal_server/app/schemas/v1/workflow.py,sha256=tuOs5E5Q_ozA8if7YPZ07cQjzqB_QMkBS4u92qo4Ro0,4618
 fractal_server/app/schemas/v2/__init__.py,sha256=zlCYrplCWwnCL9-BYsExRMfVzhBy21IMBfdHPMgJZYk,1752
-fractal_server/app/schemas/v2/dataset.py,sha256=V04_2bXgD12L53aW4_Ls8rnGLLgCaiVAFoAedx5of8Q,2086
-fractal_server/app/schemas/v2/dumps.py,sha256=Xen0OPf1Ax9i_7ItrAPvCk1OCNcUsnhlLRiyny89aLM,1997
+fractal_server/app/schemas/v2/dataset.py,sha256=MGv0bdzEIQFNy8ARqiDn_neC1mJJTMXFzbb9M5l4xxg,2474
+fractal_server/app/schemas/v2/dumps.py,sha256=IpIT_2KxJd7qTgW2NllDknGeP7vBAJDfyz1I5p3TytU,2023
 fractal_server/app/schemas/v2/job.py,sha256=zfF9K3v4jWUJ7M482ta2CkqUJ4tVT4XfVt60p9IRhP0,3250
 fractal_server/app/schemas/v2/manifest.py,sha256=N37IWohcfO3_y2l8rVM0h_1nZq7m4Izxk9iL1vtwBJw,6243
 fractal_server/app/schemas/v2/project.py,sha256=u7S4B-bote1oGjzAGiZ-DuQIyeRAGqJsI71Tc1EtYE0,736
+fractal_server/app/schemas/v2/status.py,sha256=SQaUpQkjFq5c5k5J4rOjNhuQaDOEg8lksPhkKmPU5VU,332
 fractal_server/app/schemas/v2/task.py,sha256=7IfxiZkaVqlARy7WYE_H8m7j_IEcuQaZORUrs6b5YuY,4672
 fractal_server/app/schemas/v2/task_collection.py,sha256=sY29NQfJrbjiidmVkVjSIH-20wIsmh7G1QOdr05KoDQ,3171
 fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
@@ -159,8 +161,8 @@ fractal_server/tasks/v2/background_operations.py,sha256=zr6j3uoWmCeW2EA9auxWNZ0s
 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-2.0.0a8.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.0.0a8.dist-info/METADATA,sha256=sKsPtIdIowQ-avbzi1OajV7Qet2IIuHXM9duIYpxpyA,4204
-fractal_server-2.0.0a8.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-fractal_server-2.0.0a8.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.0.0a8.dist-info/RECORD,,
+fractal_server-2.0.0a10.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.0.0a10.dist-info/METADATA,sha256=rZurMguM3pZbihOJYXyhi3zM3aRVhRrzDc_kuoTh910,4201
+fractal_server-2.0.0a10.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+fractal_server-2.0.0a10.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.0.0a10.dist-info/RECORD,,