From b53086718c431bed2787e0fe2eb5ead6421fe9e8 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:10:21 +0200
Subject: [PATCH 01/44] Deprecate legacy tasks in V2 workflows - first commit

---
 fractal_server/app/models/v2/workflowtask.py  |   7 +-
 .../app/routes/api/v2/_aux_functions.py       |  51 ++------
 .../app/routes/api/v2/task_legacy.py          |   2 +
 fractal_server/app/routes/api/v2/workflow.py  |  77 ++++--------
 .../app/routes/api/v2/workflowtask.py         |  42 ++-----
 fractal_server/app/runner/v2/__init__.py      |   5 +-
 .../v2/_slurm_common/get_slurm_config.py      |   5 +-
 .../app/runner/v2/handle_failed_job.py        |  11 +-
 fractal_server/app/runner/v2/runner.py        | 112 +++++++-----------
 .../app/runner/v2/runner_functions.py         |  58 ---------
 .../runner/v2/runner_functions_low_level.py   |  28 ++---
 fractal_server/app/runner/v2/v1_compat.py     |  31 -----
 fractal_server/app/schemas/v2/dumps.py        |  25 +---
 fractal_server/app/schemas/v2/workflowtask.py |  33 +-----
 14 files changed, 104 insertions(+), 383 deletions(-)
 delete mode 100644 fractal_server/app/runner/v2/v1_compat.py

diff --git a/fractal_server/app/models/v2/workflowtask.py b/fractal_server/app/models/v2/workflowtask.py
index 75e0f28b2a..ce5abc818a 100644
--- a/fractal_server/app/models/v2/workflowtask.py
+++ b/fractal_server/app/models/v2/workflowtask.py
@@ -8,7 +8,6 @@
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
-from ..v1.task import Task
 from .task import TaskV2
 
 
@@ -37,13 +36,9 @@ class Config:
     )
 
     # Task
-    is_legacy_task: bool
     task_type: str
+    # TODO: Make task_id and task non-Optional, later
     task_id: Optional[int] = Field(foreign_key="taskv2.id")
     task: Optional[TaskV2] = Relationship(
         sa_relationship_kwargs=dict(lazy="selectin")
     )
-    task_legacy_id: Optional[int] = Field(foreign_key="task.id")
-    task_legacy: Optional[Task] = Relationship(
-        sa_relationship_kwargs=dict(lazy="selectin")
-    )
diff --git a/fractal_server/app/routes/api/v2/_aux_functions.py b/fractal_server/app/routes/api/v2/_aux_functions.py
index 944379ffd7..69bedaa55c 100644
--- a/fractal_server/app/routes/api/v2/_aux_functions.py
+++ b/fractal_server/app/routes/api/v2/_aux_functions.py
@@ -13,7 +13,6 @@
 from sqlmodel.sql.expression import SelectOfScalar
 
 from ....db import AsyncSession
-from ....models.v1 import Task
 from ....models.v2 import DatasetV2
 from ....models.v2 import JobV2
 from ....models.v2 import LinkUserProjectV2
@@ -389,7 +388,6 @@ async def _workflow_insert_task(
     *,
     workflow_id: int,
     task_id: int,
-    is_legacy_task: bool = False,
     order: Optional[int] = None,
     meta_parallel: Optional[dict[str, Any]] = None,
     meta_non_parallel: Optional[dict[str, Any]] = None,
@@ -404,7 +402,7 @@ async def _workflow_insert_task(
     Args:
         workflow_id:
         task_id:
-        is_legacy_task:
+
         order:
         meta_parallel:
         meta_non_parallel:
@@ -424,40 +422,13 @@ async def _workflow_insert_task(
     # method
     # NOTE: this logic remains there for V1 tasks only. When we deprecate V1
     # tasks, we can simplify this block
-    if is_legacy_task is True:
-        db_task = await db.get(Task, task_id)
-        if db_task is None:
-            raise ValueError(f"Task {task_id} not found.")
-        task_type = "parallel"
-
-        final_args_parallel = db_task.default_args_from_args_schema.copy()
-        final_args_non_parallel = {}
-        final_meta_parallel = (db_task.meta or {}).copy()
-        final_meta_non_parallel = {}
+    db_task = await db.get(TaskV2, task_id)
+    if db_task is None:
+        raise ValueError(f"TaskV2 {task_id} not found.")
+    task_type = db_task.type
 
-    else:
-        db_task = await db.get(TaskV2, task_id)
-        if db_task is None:
-            raise ValueError(f"TaskV2 {task_id} not found.")
-        task_type = db_task.type
-
-        final_args_non_parallel = {}
-        final_args_parallel = {}
-        final_meta_parallel = (db_task.meta_parallel or {}).copy()
-        final_meta_non_parallel = (db_task.meta_non_parallel or {}).copy()
-
-    # Combine arg_parallel
-    if args_parallel is not None:
-        for k, v in args_parallel.items():
-            final_args_parallel[k] = v
-    if final_args_parallel == {}:
-        final_args_parallel = None
-    # Combine arg_non_parallel
-    if args_non_parallel is not None:
-        for k, v in args_non_parallel.items():
-            final_args_non_parallel[k] = v
-    if final_args_non_parallel == {}:
-        final_args_non_parallel = None
+    final_meta_parallel = (db_task.meta_parallel or {}).copy()
+    final_meta_non_parallel = (db_task.meta_non_parallel or {}).copy()
 
     # Combine meta_parallel (higher priority)
     # and db_task.meta_parallel (lower priority)
@@ -479,11 +450,9 @@ async def _workflow_insert_task(
     # Create DB entry
     wf_task = WorkflowTaskV2(
         task_type=task_type,
-        is_legacy_task=is_legacy_task,
-        task_id=(task_id if not is_legacy_task else None),
-        task_legacy_id=(task_id if is_legacy_task else None),
-        args_non_parallel=final_args_non_parallel,
-        args_parallel=final_args_parallel,
+        task_id=task_id,
+        args_non_parallel=args_non_parallel,
+        args_parallel=args_parallel,
         meta_parallel=final_meta_parallel,
         meta_non_parallel=final_meta_non_parallel,
         **input_filters_kwarg,
diff --git a/fractal_server/app/routes/api/v2/task_legacy.py b/fractal_server/app/routes/api/v2/task_legacy.py
index e518df9aab..939e89e2fd 100644
--- a/fractal_server/app/routes/api/v2/task_legacy.py
+++ b/fractal_server/app/routes/api/v2/task_legacy.py
@@ -16,6 +16,8 @@
 
 logger = set_logger(__name__)
 
+# FIXME 1712: remove this module?
+
 
 @router.get("/", response_model=list[TaskLegacyReadV2])
 async def get_list_task_legacy(
diff --git a/fractal_server/app/routes/api/v2/workflow.py b/fractal_server/app/routes/api/v2/workflow.py
index c9a8603c97..ada8a175b4 100644
--- a/fractal_server/app/routes/api/v2/workflow.py
+++ b/fractal_server/app/routes/api/v2/workflow.py
@@ -11,7 +11,6 @@
 from .....logger import set_logger
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models.v1 import Task as TaskV1
 from ....models.v2 import JobV2
 from ....models.v2 import ProjectV2
 from ....models.v2 import TaskV2
@@ -242,23 +241,13 @@ async def export_worfklow(
     # Emit a warning when exporting a workflow with custom tasks
     logger = set_logger(None)
     for wftask in workflow.task_list:
-        if wftask.is_legacy_task:
-            if wftask.task_legacy.owner is not None:
-                logger.warning(
-                    f"Custom tasks (like the one with "
-                    f"id={wftask.task_legacy_id} and "
-                    f"source='{wftask.task_legacy.source}') are not meant to "
-                    "be portable; re-importing this workflow may not work as "
-                    "expected."
-                )
-        else:
-            if wftask.task.owner is not None:
-                logger.warning(
-                    f"Custom tasks (like the one with id={wftask.task_id} and "
-                    f'source="{wftask.task.source}") are not meant to be '
-                    "portable; re-importing this workflow may not work as "
-                    "expected."
-                )
+        if wftask.task.owner is not None:
+            logger.warning(
+                f"Custom tasks (like the one with id={wftask.task_id} and "
+                f'source="{wftask.task.source}") are not meant to be '
+                "portable; re-importing this workflow may not work as "
+                "expected."
+            )
     reset_logger_handlers(logger)
 
     await db.close()
@@ -296,38 +285,22 @@ async def import_workflow(
 
     # Check that all required tasks are available
     source_to_id = {}
-    source_to_id_legacy = {}
 
     for wf_task in workflow.task_list:
 
-        if wf_task.is_legacy_task is True:
-            source = wf_task.task_legacy.source
-            if source not in source_to_id_legacy.keys():
-                stm = select(TaskV1).where(TaskV1.source == source)
-                tasks_by_source = (await db.execute(stm)).scalars().all()
-                if len(tasks_by_source) != 1:
-                    raise HTTPException(
-                        status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                        detail=(
-                            f"Found {len(tasks_by_source)} tasks legacy "
-                            f"with {source=}."
-                        ),
-                    )
-                source_to_id_legacy[source] = tasks_by_source[0].id
-        else:
-            source = wf_task.task.source
-            if source not in source_to_id.keys():
-                stm = select(TaskV2).where(TaskV2.source == source)
-                tasks_by_source = (await db.execute(stm)).scalars().all()
-                if len(tasks_by_source) != 1:
-                    raise HTTPException(
-                        status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                        detail=(
-                            f"Found {len(tasks_by_source)} tasks "
-                            f"with {source=}."
-                        ),
-                    )
-                source_to_id[source] = tasks_by_source[0].id
+        source = wf_task.task.source
+        if source not in source_to_id.keys():
+            stm = select(TaskV2).where(TaskV2.source == source)
+            tasks_by_source = (await db.execute(stm)).scalars().all()
+            if len(tasks_by_source) != 1:
+                raise HTTPException(
+                    status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                    detail=(
+                        f"Found {len(tasks_by_source)} tasks "
+                        f"with {source=}."
+                    ),
+                )
+            source_to_id[source] = tasks_by_source[0].id
 
     # Create new Workflow (with empty task_list)
     db_workflow = WorkflowV2(
@@ -341,15 +314,11 @@ async def import_workflow(
     # Insert tasks
 
     for wf_task in workflow.task_list:
-        if wf_task.is_legacy_task is True:
-            source = wf_task.task_legacy.source
-            task_id = source_to_id_legacy[source]
-        else:
-            source = wf_task.task.source
-            task_id = source_to_id[source]
+        source = wf_task.task.source
+        task_id = source_to_id[source]
 
         new_wf_task = WorkflowTaskCreateV2(
-            **wf_task.dict(exclude_none=True, exclude={"task", "task_legacy"})
+            **wf_task.dict(exclude_none=True, exclude={"task"})
         )
         # Insert task
         await _workflow_insert_task(
diff --git a/fractal_server/app/routes/api/v2/workflowtask.py b/fractal_server/app/routes/api/v2/workflowtask.py
index 2fd50ad91d..43455c6035 100644
--- a/fractal_server/app/routes/api/v2/workflowtask.py
+++ b/fractal_server/app/routes/api/v2/workflowtask.py
@@ -9,7 +9,6 @@
 
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models.v1 import Task
 from ....models.v2 import TaskV2
 from ....schemas.v2 import WorkflowTaskCreateV2
 from ....schemas.v2 import WorkflowTaskReadV2
@@ -44,27 +43,14 @@ async def create_workflowtask(
         project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
     )
 
-    if new_task.is_legacy_task is True:
-        task = await db.get(Task, task_id)
-        if not task:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND,
-                detail=f"Task {task_id} not found.",
-            )
-        if not task.is_v2_compatible:
-            raise HTTPException(
-                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                detail=f"Task {task_id} is not V2-compatible.",
-            )
-    else:
-        task = await db.get(TaskV2, task_id)
-        if not task:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND,
-                detail=f"TaskV2 {task_id} not found.",
-            )
+    task = await db.get(TaskV2, task_id)
+    if not task:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"TaskV2 {task_id} not found.",
+        )
 
-    if new_task.is_legacy_task is True or task.type == "parallel":
+    if task.type == "parallel":
         if (
             new_task.meta_non_parallel is not None
             or new_task.args_non_parallel is not None
@@ -74,7 +60,7 @@ async def create_workflowtask(
                 detail=(
                     "Cannot set `WorkflowTaskV2.meta_non_parallel` or "
                     "`WorkflowTask.args_non_parallel` if the associated Task "
-                    "is `parallel` (or legacy)."
+                    "is `parallel`."
                 ),
             )
     elif task.type == "non_parallel":
@@ -93,7 +79,6 @@ async def create_workflowtask(
 
     workflow_task = await _workflow_insert_task(
         workflow_id=workflow.id,
-        is_legacy_task=new_task.is_legacy_task,
         task_id=task_id,
         order=new_task.order,
         meta_non_parallel=new_task.meta_non_parallel,
@@ -182,16 +167,7 @@ async def update_workflowtask(
     for key, value in workflow_task_update.dict(exclude_unset=True).items():
         if key == "args_parallel":
             # Get default arguments via a Task property method
-            if db_wf_task.is_legacy_task:
-                default_args = (
-                    db_wf_task.task_legacy.default_args_from_args_schema
-                )
-                actual_args = deepcopy(default_args)
-                if value is not None:
-                    for k, v in value.items():
-                        actual_args[k] = v
-            else:
-                actual_args = deepcopy(value)
+            actual_args = deepcopy(value)
             if not actual_args:
                 actual_args = None
             setattr(db_wf_task, key, actual_args)
diff --git a/fractal_server/app/runner/v2/__init__.py b/fractal_server/app/runner/v2/__init__.py
index eae855a90b..70d7af3aaa 100644
--- a/fractal_server/app/runner/v2/__init__.py
+++ b/fractal_server/app/runner/v2/__init__.py
@@ -212,10 +212,7 @@ async def submit_workflow(
             # Create all tasks subfolders
             for order in range(job.first_task_index, job.last_task_index + 1):
                 this_wftask = workflow.task_list[order]
-                if this_wftask.is_legacy_task:
-                    task_name = this_wftask.task_legacy.name
-                else:
-                    task_name = this_wftask.task.name
+                task_name = this_wftask.task.name
                 subfolder_name = task_subfolder_name(
                     order=order,
                     task_name=task_name,
diff --git a/fractal_server/app/runner/v2/_slurm_common/get_slurm_config.py b/fractal_server/app/runner/v2/_slurm_common/get_slurm_config.py
index 362873cd96..06abb49e16 100644
--- a/fractal_server/app/runner/v2/_slurm_common/get_slurm_config.py
+++ b/fractal_server/app/runner/v2/_slurm_common/get_slurm_config.py
@@ -116,10 +116,7 @@ def get_slurm_config(
         slurm_dict["mem_per_task_MB"] = mem_per_task_MB
 
     # Job name
-    if wftask.is_legacy_task:
-        job_name = wftask.task_legacy.name.replace(" ", "_")
-    else:
-        job_name = wftask.task.name.replace(" ", "_")
+    job_name = wftask.task.name.replace(" ", "_")
     slurm_dict["job_name"] = job_name
 
     # Optional SLURM arguments and extra lines
diff --git a/fractal_server/app/runner/v2/handle_failed_job.py b/fractal_server/app/runner/v2/handle_failed_job.py
index b2deba5aac..0886743de8 100644
--- a/fractal_server/app/runner/v2/handle_failed_job.py
+++ b/fractal_server/app/runner/v2/handle_failed_job.py
@@ -96,15 +96,8 @@ 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", "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()
+        failed_wftask_dump = failed_wftask.model_dump(exclude={"task"})
+        failed_wftask_dump["task"] = failed_wftask.task.model_dump()
         new_history_item = dict(
             workflowtask=failed_wftask_dump,
             status=WorkflowTaskStatusTypeV2.FAILED,
diff --git a/fractal_server/app/runner/v2/runner.py b/fractal_server/app/runner/v2/runner.py
index c6150a71d1..5a87ac8a58 100644
--- a/fractal_server/app/runner/v2/runner.py
+++ b/fractal_server/app/runner/v2/runner.py
@@ -17,7 +17,6 @@
 from ..filenames import HISTORY_FILENAME
 from ..filenames import IMAGES_FILENAME
 from .runner_functions import no_op_submit_setup_call
-from .runner_functions import run_v1_task_parallel
 from .runner_functions import run_v2_task_compound
 from .runner_functions import run_v2_task_non_parallel
 from .runner_functions import run_v2_task_parallel
@@ -53,16 +52,8 @@ def execute_tasks_v2(
 
     for wftask in wf_task_list:
         task = wftask.task
-        task_legacy = wftask.task_legacy
-        if wftask.is_legacy_task:
-            task_name = task_legacy.name
-            logger.debug(
-                f"SUBMIT {wftask.order}-th task "
-                f'(legacy, name="{task_name}")'
-            )
-        else:
-            task_name = task.name
-            logger.debug(f'SUBMIT {wftask.order}-th task (name="{task_name}")')
+        task_name = task.name
+        logger.debug(f'SUBMIT {wftask.order}-th task (name="{task_name}")')
 
         # PRE TASK EXECUTION
 
@@ -78,67 +69,53 @@ def execute_tasks_v2(
             filters=Filters(**pre_filters),
         )
         # Verify that filtered images 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 JobExecutionError(
-                        "Invalid filtered image list\n"
-                        f"Task input types: {task.input_types=}\n"
-                        f'Image zarr_url: {image["zarr_url"]}\n'
-                        f'Image types: {image["types"]}\n'
-                    )
+        for image in filtered_images:
+            if not match_filter(image, Filters(types=task.input_types)):
+                raise JobExecutionError(
+                    "Invalid filtered image list\n"
+                    f"Task input types: {task.input_types=}\n"
+                    f'Image zarr_url: {image["zarr_url"]}\n'
+                    f'Image types: {image["types"]}\n'
+                )
 
         # TASK EXECUTION (V2)
-        if not wftask.is_legacy_task:
-            if task.type == "non_parallel":
-                current_task_output = run_v2_task_non_parallel(
-                    images=filtered_images,
-                    zarr_dir=zarr_dir,
-                    wftask=wftask,
-                    task=task,
-                    workflow_dir_local=workflow_dir_local,
-                    workflow_dir_remote=workflow_dir_remote,
-                    executor=executor,
-                    logger_name=logger_name,
-                    submit_setup_call=submit_setup_call,
-                )
-            elif task.type == "parallel":
-                current_task_output = run_v2_task_parallel(
-                    images=filtered_images,
-                    wftask=wftask,
-                    task=task,
-                    workflow_dir_local=workflow_dir_local,
-                    workflow_dir_remote=workflow_dir_remote,
-                    executor=executor,
-                    logger_name=logger_name,
-                    submit_setup_call=submit_setup_call,
-                )
-            elif task.type == "compound":
-                current_task_output = run_v2_task_compound(
-                    images=filtered_images,
-                    zarr_dir=zarr_dir,
-                    wftask=wftask,
-                    task=task,
-                    workflow_dir_local=workflow_dir_local,
-                    workflow_dir_remote=workflow_dir_remote,
-                    executor=executor,
-                    logger_name=logger_name,
-                    submit_setup_call=submit_setup_call,
-                )
-            else:
-                raise ValueError(f"Unexpected error: Invalid {task.type=}.")
-        # TASK EXECUTION (V1)
-        else:
-            current_task_output = run_v1_task_parallel(
+        if task.type == "non_parallel":
+            current_task_output = run_v2_task_non_parallel(
                 images=filtered_images,
+                zarr_dir=zarr_dir,
                 wftask=wftask,
-                task_legacy=task_legacy,
+                task=task,
+                workflow_dir_local=workflow_dir_local,
+                workflow_dir_remote=workflow_dir_remote,
                 executor=executor,
                 logger_name=logger_name,
+                submit_setup_call=submit_setup_call,
+            )
+        elif task.type == "parallel":
+            current_task_output = run_v2_task_parallel(
+                images=filtered_images,
+                wftask=wftask,
+                task=task,
+                workflow_dir_local=workflow_dir_local,
+                workflow_dir_remote=workflow_dir_remote,
+                executor=executor,
+                logger_name=logger_name,
+                submit_setup_call=submit_setup_call,
+            )
+        elif task.type == "compound":
+            current_task_output = run_v2_task_compound(
+                images=filtered_images,
+                zarr_dir=zarr_dir,
+                wftask=wftask,
+                task=task,
                 workflow_dir_local=workflow_dir_local,
                 workflow_dir_remote=workflow_dir_remote,
+                executor=executor,
+                logger_name=logger_name,
                 submit_setup_call=submit_setup_call,
             )
+        else:
+            raise ValueError(f"Unexpected error: Invalid {task.type=}.")
 
         # POST TASK EXECUTION
 
@@ -191,8 +168,7 @@ def execute_tasks_v2(
                 # Update image attributes/types with task output and manifest
                 updated_attributes.update(image["attributes"])
                 updated_types.update(image["types"])
-                if not wftask.is_legacy_task:
-                    updated_types.update(task.output_types)
+                updated_types.update(task.output_types)
 
                 # Unset attributes with None value
                 updated_attributes = {
@@ -249,8 +225,7 @@ def execute_tasks_v2(
                     if value is not None
                 }
                 updated_types.update(image["types"])
-                if not wftask.is_legacy_task:
-                    updated_types.update(task.output_types)
+                updated_types.update(task.output_types)
                 new_image = dict(
                     zarr_url=image["zarr_url"],
                     origin=image["origin"],
@@ -282,10 +257,7 @@ def execute_tasks_v2(
             )
 
         # Find manifest ouptut types
-        if wftask.is_legacy_task:
-            types_from_manifest = {}
-        else:
-            types_from_manifest = task.output_types
+        types_from_manifest = task.output_types
 
         # Find task-output types
         if current_task_output.filters is not None:
diff --git a/fractal_server/app/runner/v2/runner_functions.py b/fractal_server/app/runner/v2/runner_functions.py
index e7ab2aa819..7d6fce1a4f 100644
--- a/fractal_server/app/runner/v2/runner_functions.py
+++ b/fractal_server/app/runner/v2/runner_functions.py
@@ -16,8 +16,6 @@
 from .runner_functions_low_level import run_single_task
 from .task_interface import InitTaskOutput
 from .task_interface import TaskOutput
-from .v1_compat import convert_v2_args_into_v1
-from fractal_server.app.models.v1 import Task as TaskV1
 from fractal_server.app.models.v2 import TaskV2
 from fractal_server.app.models.v2 import WorkflowTaskV2
 from fractal_server.app.runner.components import _COMPONENT_KEY_
@@ -28,7 +26,6 @@
     "run_v2_task_non_parallel",
     "run_v2_task_parallel",
     "run_v2_task_compound",
-    "run_v1_task_parallel",
 ]
 
 MAX_PARALLELIZATION_LIST_SIZE = 20_000
@@ -317,58 +314,3 @@ def run_v2_task_compound(
 
     merged_output = merge_outputs(outputs)
     return merged_output
-
-
-def run_v1_task_parallel(
-    *,
-    images: list[dict[str, Any]],
-    task_legacy: TaskV1,
-    wftask: WorkflowTaskV2,
-    executor: Executor,
-    workflow_dir_local: Path,
-    workflow_dir_remote: Optional[Path] = None,
-    logger_name: Optional[str] = None,
-    submit_setup_call: Callable = no_op_submit_setup_call,
-) -> TaskOutput:
-
-    _check_parallelization_list_size(images)
-
-    executor_options = _get_executor_options(
-        wftask=wftask,
-        workflow_dir_local=workflow_dir_local,
-        workflow_dir_remote=workflow_dir_remote,
-        submit_setup_call=submit_setup_call,
-        which_type="parallel",
-    )
-
-    list_function_kwargs = []
-    for ind, image in enumerate(images):
-        list_function_kwargs.append(
-            convert_v2_args_into_v1(
-                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)
-
-    results_iterator = executor.map(
-        functools.partial(
-            run_single_task,
-            wftask=wftask,
-            command=task_legacy.command,
-            workflow_dir_local=workflow_dir_local,
-            workflow_dir_remote=workflow_dir_remote,
-            is_task_v1=True,
-        ),
-        list_function_kwargs,
-        **executor_options,
-    )
-    # Explicitly iterate over the whole list, so that all futures are waited
-    list(results_iterator)
-
-    # Ignore any output metadata for V1 tasks, and return an empty object
-    out = TaskOutput()
-    return out
diff --git a/fractal_server/app/runner/v2/runner_functions_low_level.py b/fractal_server/app/runner/v2/runner_functions_low_level.py
index a41afa152b..8ba2d68dc1 100644
--- a/fractal_server/app/runner/v2/runner_functions_low_level.py
+++ b/fractal_server/app/runner/v2/runner_functions_low_level.py
@@ -61,7 +61,6 @@ def run_single_task(
     workflow_dir_local: Path,
     workflow_dir_remote: Optional[Path] = None,
     logger_name: Optional[str] = None,
-    is_task_v1: bool = False,
 ) -> dict[str, Any]:
     """
     Runs within an executor.
@@ -73,10 +72,7 @@ def run_single_task(
     if not workflow_dir_remote:
         workflow_dir_remote = workflow_dir_local
 
-    if is_task_v1:
-        task_name = wftask.task_legacy.name
-    else:
-        task_name = wftask.task.name
+    task_name = wftask.task.name
 
     component = args.pop(_COMPONENT_KEY_, None)
     task_files = get_task_file_paths(
@@ -92,18 +88,11 @@ def run_single_task(
         json.dump(args, f, indent=2)
 
     # Assemble full command
-    if is_task_v1:
-        full_command = (
-            f"{command} "
-            f"--json {task_files.args.as_posix()} "
-            f"--metadata-out {task_files.metadiff.as_posix()}"
-        )
-    else:
-        full_command = (
-            f"{command} "
-            f"--args-json {task_files.args.as_posix()} "
-            f"--out-json {task_files.metadiff.as_posix()}"
-        )
+    full_command = (
+        f"{command} "
+        f"--args-json {task_files.args.as_posix()} "
+        f"--out-json {task_files.metadiff.as_posix()}"
+    )
 
     try:
         _call_command_wrapper(
@@ -113,10 +102,7 @@ def run_single_task(
     except TaskExecutionError as e:
         e.workflow_task_order = wftask.order
         e.workflow_task_id = wftask.id
-        if wftask.is_legacy_task:
-            e.task_name = wftask.task_legacy.name
-        else:
-            e.task_name = wftask.task.name
+        e.task_name = wftask.task.name
         raise e
 
     try:
diff --git a/fractal_server/app/runner/v2/v1_compat.py b/fractal_server/app/runner/v2/v1_compat.py
deleted file mode 100644
index f9accc135b..0000000000
--- a/fractal_server/app/runner/v2/v1_compat.py
+++ /dev/null
@@ -1,31 +0,0 @@
-from copy import deepcopy
-from pathlib import Path
-from typing import 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()
-    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],
-        output_path=input_path,
-        metadata={},
-        component=component,
-    )
-
-    return kwargs_v1
diff --git a/fractal_server/app/schemas/v2/dumps.py b/fractal_server/app/schemas/v2/dumps.py
index 8aa625ed58..1b733b064a 100644
--- a/fractal_server/app/schemas/v2/dumps.py
+++ b/fractal_server/app/schemas/v2/dumps.py
@@ -12,9 +12,7 @@
 
 from pydantic import BaseModel
 from pydantic import Extra
-from pydantic import root_validator
 
-from fractal_server.app.schemas.v1.dumps import TaskDumpV1
 from fractal_server.images import Filters
 
 
@@ -45,29 +43,10 @@ class WorkflowTaskDumpV2(BaseModel):
     workflow_id: int
     order: Optional[int]
 
-    is_legacy_task: bool
-
     input_filters: Filters
 
-    task_id: Optional[int]
-    task: Optional[TaskDumpV2]
-    task_legacy_id: Optional[int]
-    task_legacy: Optional[TaskDumpV1]
-
-    # Validators
-    @root_validator
-    def task_v1_or_v2(cls, values):
-        v1 = values.get("task_legacy_id")
-        v2 = values.get("task_id")
-        if ((v1 is not None) and (v2 is not None)) or (
-            (v1 is None) and (v2 is None)
-        ):
-            message = "both" if (v1 and v2) else "none"
-            raise ValueError(
-                "One and only one must be provided between "
-                f"'task_legacy_id' and 'task_id' (you provided {message})"
-            )
-        return values
+    task_id: int
+    task: TaskDumpV2
 
 
 class WorkflowDumpV2(BaseModel, extra=Extra.forbid):
diff --git a/fractal_server/app/schemas/v2/workflowtask.py b/fractal_server/app/schemas/v2/workflowtask.py
index 9303dca17e..1edd35e2d7 100644
--- a/fractal_server/app/schemas/v2/workflowtask.py
+++ b/fractal_server/app/schemas/v2/workflowtask.py
@@ -5,16 +5,12 @@
 from pydantic import BaseModel
 from pydantic import Extra
 from pydantic import Field
-from pydantic import root_validator
 from pydantic import validator
 
 from .._validators import valdictkeys
 from .._validators import valint
-from ..v1.task import TaskExportV1
-from ..v1.task import TaskImportV1
 from .task import TaskExportV2
 from .task import TaskImportV2
-from .task import TaskLegacyReadV2
 from .task import TaskReadV2
 from fractal_server.images import Filters
 
@@ -49,8 +45,6 @@ class WorkflowTaskCreateV2(BaseModel, extra=Extra.forbid):
     order: Optional[int]
     input_filters: Filters = Field(default_factory=Filters)
 
-    is_legacy_task: bool = False
-
     # Validators
     _meta_non_parallel = validator("meta_non_parallel", allow_reuse=True)(
         valdictkeys("meta_non_parallel")
@@ -88,18 +82,6 @@ def validate_args_parallel(cls, value):
             )
         return value
 
-    @root_validator
-    def validate_legacy_task(cls, values):
-        if values["is_legacy_task"] and (
-            values.get("meta_non_parallel") is not None
-            or values.get("args_non_parallel") is not None
-        ):
-            raise ValueError(
-                "If Task is legacy, 'args_non_parallel' and 'meta_non_parallel"
-                "must be None"
-            )
-        return values
-
 
 class WorkflowTaskReadV2(BaseModel):
 
@@ -115,12 +97,9 @@ class WorkflowTaskReadV2(BaseModel):
 
     input_filters: Filters
 
-    is_legacy_task: bool
     task_type: str
-    task_id: Optional[int]
-    task: Optional[TaskReadV2]
-    task_legacy_id: Optional[int]
-    task_legacy: Optional[TaskLegacyReadV2]
+    task_id: int
+    task: TaskReadV2
 
 
 class WorkflowTaskUpdateV2(BaseModel):
@@ -177,9 +156,7 @@ class WorkflowTaskImportV2(BaseModel):
 
     input_filters: Optional[Filters] = None
 
-    is_legacy_task: bool = False
-    task: Optional[TaskImportV2] = None
-    task_legacy: Optional[TaskImportV1] = None
+    task: TaskImportV2
 
     _meta_non_parallel = validator("meta_non_parallel", allow_reuse=True)(
         valdictkeys("meta_non_parallel")
@@ -203,6 +180,4 @@ class WorkflowTaskExportV2(BaseModel):
     args_parallel: Optional[dict[str, Any]] = None
     input_filters: Filters = Field(default_factory=Filters)
 
-    is_legacy_task: bool = False
-    task: Optional[TaskExportV2]
-    task_legacy: Optional[TaskExportV1]
+    task: TaskExportV2

From 48939271c6178fb218d9bfeccbec9e05dea3c68e Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:12:32 +0200
Subject: [PATCH 02/44] Add db migration script

---
 ...remove_workflowtaskv2_legacy_attributes.py | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 fractal_server/migrations/versions/40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py

diff --git a/fractal_server/migrations/versions/40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py b/fractal_server/migrations/versions/40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py
new file mode 100644
index 0000000000..6f719589ad
--- /dev/null
+++ b/fractal_server/migrations/versions/40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py
@@ -0,0 +1,48 @@
+"""Remove WorkflowTaskV2 legacy attributes
+
+Revision ID: 40b3479ba47f
+Revises: 5bf02391cfef
+Create Date: 2024-09-03 10:11:27.477326
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "40b3479ba47f"
+down_revision = "5bf02391cfef"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_constraint(
+        "fk_workflowtaskv2_task_legacy_id_task",
+        "workflowtaskv2",
+        type_="foreignkey",
+    )
+    op.drop_column("workflowtaskv2", "is_legacy_task")
+    op.drop_column("workflowtaskv2", "task_legacy_id")
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column(
+        "workflowtaskv2",
+        sa.Column("task_legacy_id", sa.INTEGER(), nullable=True),
+    )
+    op.add_column(
+        "workflowtaskv2",
+        sa.Column("is_legacy_task", sa.BOOLEAN(), nullable=False),
+    )
+    op.create_foreign_key(
+        "fk_workflowtaskv2_task_legacy_id_task",
+        "workflowtaskv2",
+        "task",
+        ["task_legacy_id"],
+        ["id"],
+    )
+    # ### end Alembic commands ###

From 643ca87a70ca8a494ccbda91f82932bac245752d Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:13:14 +0200
Subject: [PATCH 03/44] Update `scripts/validate_db_data_with_read_schemas.py`

---
 scripts/validate_db_data_with_read_schemas.py | 21 +++++--------------
 1 file changed, 5 insertions(+), 16 deletions(-)

diff --git a/scripts/validate_db_data_with_read_schemas.py b/scripts/validate_db_data_with_read_schemas.py
index 9d6c613ec6..e0fe4fc8c9 100644
--- a/scripts/validate_db_data_with_read_schemas.py
+++ b/scripts/validate_db_data_with_read_schemas.py
@@ -28,7 +28,6 @@
 from fractal_server.app.schemas.v2 import DatasetReadV2
 from fractal_server.app.schemas.v2 import JobReadV2
 from fractal_server.app.schemas.v2 import ProjectReadV2
-from fractal_server.app.schemas.v2 import TaskLegacyReadV2
 from fractal_server.app.schemas.v2 import TaskReadV2
 from fractal_server.app.schemas.v2 import WorkflowReadV2
 from fractal_server.app.schemas.v2 import WorkflowTaskReadV2
@@ -133,22 +132,12 @@
         # validate task_list
         task_list = []
         for wftask in workflow.task_list:
-            if wftask.is_legacy_task is True:
-                task_list.append(
-                    WorkflowTaskReadV2(
-                        **wftask.model_dump(),
-                        task_legacy=TaskLegacyReadV2(
-                            **wftask.task.model_dump()
-                        ),
-                    )
-                )
-            else:
-                task_list.append(
-                    WorkflowTaskReadV2(
-                        **wftask.model_dump(),
-                        task=TaskReadV2(**wftask.task.model_dump()),
-                    )
+            task_list.append(
+                WorkflowTaskReadV2(
+                    **wftask.model_dump(),
+                    task=TaskReadV2(**wftask.task.model_dump()),
                 )
+            )
 
         WorkflowReadV2(
             **workflow.model_dump(),

From 8e27eef8d5ebc5120e3a1d4bf70bba399d2406bb Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:13:48 +0200
Subject: [PATCH 04/44] Update benchmarks/runner/mocks.py

---
 benchmarks/runner/mocks.py | 44 ++------------------------------------
 1 file changed, 2 insertions(+), 42 deletions(-)

diff --git a/benchmarks/runner/mocks.py b/benchmarks/runner/mocks.py
index c7da9e0eb2..20e16c34a9 100644
--- a/benchmarks/runner/mocks.py
+++ b/benchmarks/runner/mocks.py
@@ -69,59 +69,19 @@ def _set_type(cls, value, values):
                 return "compound"
 
 
-class TaskV1Mock(BaseModel):
-    id: int
-    name: str
-    command: str  # str
-    source: str = Field(unique=True)
-    input_type: str
-    output_type: str
-    meta: Optional[dict[str, Any]] = Field(default_factory=dict)
-
-    @property
-    def parallelization_level(self) -> Optional[str]:
-        try:
-            return self.meta["parallelization_level"]
-        except KeyError:
-            return None
-
-    @property
-    def is_parallel(self) -> bool:
-        return bool(self.parallelization_level)
-
-
 class WorkflowTaskV2Mock(BaseModel):
     args_non_parallel: dict[str, Any] = Field(default_factory=dict)
     args_parallel: dict[str, Any] = Field(default_factory=dict)
     meta_non_parallel: dict[str, Any] = Field(default_factory=dict)
     meta_parallel: dict[str, Any] = Field(default_factory=dict)
-    is_legacy_task: Optional[bool]
     meta_parallel: Optional[dict[str, Any]] = Field()
     meta_non_parallel: Optional[dict[str, Any]] = Field()
-    task: Optional[TaskV2Mock] = None
-    task_legacy: Optional[TaskV1Mock] = None
-    is_legacy_task: bool = False
+    task: TaskV2Mock = None
     input_filters: dict[str, Any] = Field(default_factory=dict)
     order: int
     id: int
     workflow_id: int = 0
-    task_legacy_id: Optional[int]
-    task_id: Optional[int]
-
-    @root_validator(pre=False)
-    def _legacy_or_not(cls, values):
-        is_legacy_task = values["is_legacy_task"]
-        task = values.get("task")
-        task_legacy = values.get("task_legacy")
-        if is_legacy_task:
-            if task_legacy is None or task is not None:
-                raise ValueError(f"Invalid WorkflowTaskV2Mock with {values=}")
-            values["task_legacy_id"] = task_legacy.id
-        else:
-            if task is None or task_legacy is not None:
-                raise ValueError(f"Invalid WorkflowTaskV2Mock with {values=}")
-            values["task_id"] = task.id
-        return values
+    task_id: int
 
     @validator("input_filters", always=True)
     def _default_filters(cls, value):

From 218ff120ce1545e98bb6cf6e5fa7f38eed1022d3 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:17:42 +0200
Subject: [PATCH 05/44] Do not test order of `listdir` output

---
 tests/no_version/test_unit_zip_tools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/no_version/test_unit_zip_tools.py b/tests/no_version/test_unit_zip_tools.py
index f1166e3937..16d7ed2566 100644
--- a/tests/no_version/test_unit_zip_tools.py
+++ b/tests/no_version/test_unit_zip_tools.py
@@ -134,7 +134,7 @@ def test_zip_folder_to_file_and_remove(tmp_path: Path, monkeypatch):
     assert os.listdir(tmp_path) == ["test"]
 
     _zip_folder_to_file_and_remove(test_folder)
-    assert os.listdir(tmp_path) == ["test", "test.zip"]
+    assert set(os.listdir(tmp_path)) == {"test", "test.zip"}
 
     with ZipFile(tmp_path / "test.zip", mode="r") as zipfile:
         assert "file1" in zipfile.namelist()

From 0053a38729f6476b587418f59a2f08e649531eaf Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:24:00 +0200
Subject: [PATCH 06/44] Add FIXMEs

---
 fractal_server/app/models/v2/workflowtask.py                 | 5 ++---
 .../40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py  | 2 ++
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/fractal_server/app/models/v2/workflowtask.py b/fractal_server/app/models/v2/workflowtask.py
index ce5abc818a..8a5e840f30 100644
--- a/fractal_server/app/models/v2/workflowtask.py
+++ b/fractal_server/app/models/v2/workflowtask.py
@@ -37,8 +37,7 @@ class Config:
 
     # Task
     task_type: str
-    # TODO: Make task_id and task non-Optional, later
-    task_id: Optional[int] = Field(foreign_key="taskv2.id")
-    task: Optional[TaskV2] = Relationship(
+    task_id: Optional[int] = Field(foreign_key="taskv2.id")  # FIXME 1712
+    task: Optional[TaskV2] = Relationship(  # FIXME 1712
         sa_relationship_kwargs=dict(lazy="selectin")
     )
diff --git a/fractal_server/migrations/versions/40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py b/fractal_server/migrations/versions/40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py
index 6f719589ad..3d322e6df5 100644
--- a/fractal_server/migrations/versions/40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py
+++ b/fractal_server/migrations/versions/40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py
@@ -18,6 +18,8 @@
 
 def upgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
+
+    # FIXME 1712: adapt to sqlite??
     op.drop_constraint(
         "fk_workflowtaskv2_task_legacy_id_task",
         "workflowtaskv2",

From 9601cfe5d3db3f8e9a84e9246c50aa9f37313ecd Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:26:40 +0200
Subject: [PATCH 07/44] Adapt tests after removing legacy tasks from V2
 workflows

---
 tests/data/example_server_startup/cleanup.sh  |  1 +
 tests/data/import_export/workflow-v2.json     | 12 ----
 tests/fixtures_server_v2.py                   |  1 -
 tests/no_version/test_unit_config.py          |  2 +
 tests/v2/01_schemas/test_unit_schemas_v2.py   | 22 --------
 tests/v2/03_api/test_api_workflow.py          |  2 -
 .../04_runner/test_unit_aux_functions_v2.py   | 55 -------------------
 7 files changed, 3 insertions(+), 92 deletions(-)

diff --git a/tests/data/example_server_startup/cleanup.sh b/tests/data/example_server_startup/cleanup.sh
index 7368e464fe..131f9e9d81 100755
--- a/tests/data/example_server_startup/cleanup.sh
+++ b/tests/data/example_server_startup/cleanup.sh
@@ -4,3 +4,4 @@ rm test.db
 rm -r Tasks
 rm -r Artifacts
 rm logs*
+rm test.db-shm test.db-wal
diff --git a/tests/data/import_export/workflow-v2.json b/tests/data/import_export/workflow-v2.json
index d7a0855f5b..d8ec31b90c 100644
--- a/tests/data/import_export/workflow-v2.json
+++ b/tests/data/import_export/workflow-v2.json
@@ -17,18 +17,6 @@
             "task": {
                 "source": "PKG_SOURCE:dummy2"
             }
-        },
-        {
-            "args_parallel": {
-                "message": "task",
-                "arg": "value"
-            },
-            "meta_parallel": {"key": "value"},
-            "order": 1,
-            "is_legacy_task": true,
-            "task_legacy": {
-                "source": "PKG_SOURCE:dummy1"
-            }
         }
     ]
 }
diff --git a/tests/fixtures_server_v2.py b/tests/fixtures_server_v2.py
index 114d1b8c08..4fba6d62f6 100644
--- a/tests/fixtures_server_v2.py
+++ b/tests/fixtures_server_v2.py
@@ -242,7 +242,6 @@ async def __workflowtask_factory(
         defaults = dict(
             workflow_id=workflow_id,
             task_id=task_id,
-            is_legacy_task=False,
             task_type=task.type,
         )
         args = dict(**defaults)
diff --git a/tests/no_version/test_unit_config.py b/tests/no_version/test_unit_config.py
index 5650159bf4..f0de848655 100644
--- a/tests/no_version/test_unit_config.py
+++ b/tests/no_version/test_unit_config.py
@@ -193,6 +193,8 @@ def test_settings_check(
     settings_dict: dict[str, str], raises: bool, testdata_path: Path
 ):
 
+    debug(settings_dict, raises)
+
     # Workaround to set FRACTAL_SLURM_CONFIG_FILE to a valid path, which
     # requires the value of testdata_path
     if (
diff --git a/tests/v2/01_schemas/test_unit_schemas_v2.py b/tests/v2/01_schemas/test_unit_schemas_v2.py
index 5e773de71c..2d6439da17 100644
--- a/tests/v2/01_schemas/test_unit_schemas_v2.py
+++ b/tests/v2/01_schemas/test_unit_schemas_v2.py
@@ -48,17 +48,6 @@ def test_extra_on_create_models():
         WorkflowTaskCreateV2(foo="bar")
 
 
-def test_validate_legacy_task():
-
-    WorkflowTaskCreateV2(meta_non_parallel={"a": "b"})
-    with pytest.raises(ValidationError):
-        WorkflowTaskCreateV2(is_legacy_task=True, meta_non_parallel={"a": "b"})
-
-    WorkflowTaskCreateV2(args_non_parallel={"a": "b"})
-    with pytest.raises(ValidationError):
-        WorkflowTaskCreateV2(is_legacy_task=True, args_non_parallel={"a": "b"})
-
-
 def test_dictionary_keys_validation():
     args = dict(
         name="name",
@@ -125,23 +114,12 @@ def test_workflow_task_dump():
     WorkflowTaskDumpV2(
         id=1,
         workflow_id=1,
-        is_legacy_task=False,
         input_filters=Filters(),
         task_id=1,
     )
-    with pytest.raises(ValidationError, match="both"):
-        WorkflowTaskDumpV2(
-            id=1,
-            workflow_id=1,
-            is_legacy_task=False,
-            input_filters=Filters(),
-            task_id=1,
-            task_legacy_id=1,
-        )
     with pytest.raises(ValidationError, match="none"):
         WorkflowTaskDumpV2(
             id=1,
             workflow_id=1,
-            is_legacy_task=False,
             input_filters=Filters(),
         )
diff --git a/tests/v2/03_api/test_api_workflow.py b/tests/v2/03_api/test_api_workflow.py
index dd6157040f..b7cd7a8e7f 100644
--- a/tests/v2/03_api/test_api_workflow.py
+++ b/tests/v2/03_api/test_api_workflow.py
@@ -338,8 +338,6 @@ async def test_post_worfkflow_task(
         workflow = await get_workflow(client, project.id, wf_id)
         task_list = workflow["task_list"]
         assert len(task_list) == 4
-        for wftask in task_list:
-            assert wftask["is_legacy_task"] is False
         assert task_list[0]["task"]["name"] == "task0"
         assert task_list[1]["task"]["name"] == "task0b"
         assert task_list[2]["task"]["name"] == "task1"
diff --git a/tests/v2/04_runner/test_unit_aux_functions_v2.py b/tests/v2/04_runner/test_unit_aux_functions_v2.py
index f7fd33de1f..f3407fe560 100644
--- a/tests/v2/04_runner/test_unit_aux_functions_v2.py
+++ b/tests/v2/04_runner/test_unit_aux_functions_v2.py
@@ -1,5 +1,3 @@
-from pathlib import Path
-
 import pytest
 from devtools import debug
 from pydantic import ValidationError
@@ -14,7 +12,6 @@
 )
 from fractal_server.app.runner.v2.task_interface import InitArgsModel
 from fractal_server.app.runner.v2.task_interface import TaskOutput
-from fractal_server.app.runner.v2.v1_compat import convert_v2_args_into_v1
 
 
 def test_deduplicate_list_of_dicts():
@@ -69,58 +66,6 @@ def test_task_output():
         TaskOutput(image_list_removals=["http://url.json"])
 
 
-def test_convert_v2_args_into_v1(tmp_path: Path):
-    kwargs_v2 = dict(
-        zarr_url=(tmp_path / "input_path/plate.zarr/B/03/0").as_posix(),
-        something="else",
-        metadata="this will be overwritten",
-        component="this will be overwritten",
-    )
-
-    # Image
-    kwargs_v1 = convert_v2_args_into_v1(
-        kwargs_v2, parallelization_level="image"
-    )
-    PATH = (tmp_path / "input_path").as_posix()
-    assert kwargs_v1 == {
-        "input_paths": [PATH],
-        "output_path": PATH,
-        "metadata": {},
-        "component": "plate.zarr/B/03/0",
-        "something": "else",
-    }
-
-    # Well
-    kwargs_v1 = convert_v2_args_into_v1(
-        kwargs_v2, parallelization_level="well"
-    )
-    PATH = (tmp_path / "input_path").as_posix()
-    assert kwargs_v1 == {
-        "input_paths": [PATH],
-        "output_path": PATH,
-        "metadata": {},
-        "component": "plate.zarr/B/03",
-        "something": "else",
-    }
-
-    # Plate
-    kwargs_v1 = convert_v2_args_into_v1(
-        kwargs_v2, parallelization_level="plate"
-    )
-    PATH = (tmp_path / "input_path").as_posix()
-    assert kwargs_v1 == {
-        "input_paths": [PATH],
-        "output_path": PATH,
-        "metadata": {},
-        "component": "plate.zarr",
-        "something": "else",
-    }
-
-    # None
-    with pytest.raises(ValueError):
-        convert_v2_args_into_v1(kwargs_v2, parallelization_level=None)
-
-
 def test_cast_and_validate_functions():
 
     _cast_and_validate_TaskOutput(

From f8b7ae4476abe1f15270c1fdec3d7dca4fe0d8a1 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:35:32 +0200
Subject: [PATCH 08/44] Make non-legacy workflowtaskv2 task attributes
 non-optional

---
 fractal_server/app/models/v2/workflowtask.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/fractal_server/app/models/v2/workflowtask.py b/fractal_server/app/models/v2/workflowtask.py
index 8a5e840f30..32f64215a7 100644
--- a/fractal_server/app/models/v2/workflowtask.py
+++ b/fractal_server/app/models/v2/workflowtask.py
@@ -37,7 +37,5 @@ class Config:
 
     # Task
     task_type: str
-    task_id: Optional[int] = Field(foreign_key="taskv2.id")  # FIXME 1712
-    task: Optional[TaskV2] = Relationship(  # FIXME 1712
-        sa_relationship_kwargs=dict(lazy="selectin")
-    )
+    task_id: int = Field(foreign_key="taskv2.id")
+    task: TaskV2 = Relationship(sa_relationship_kwargs=dict(lazy="selectin"))

From 2e0588fe5f7f05e69142df58ecb04b9c59d540de Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:35:42 +0200
Subject: [PATCH 09/44] Update db migration script

---
 ...emove_workflowtaskv2_legacy_attributes.py} | 20 +++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)
 rename fractal_server/migrations/versions/{40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py => a75703146940_remove_workflowtaskv2_legacy_attributes.py} (78%)

diff --git a/fractal_server/migrations/versions/40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py b/fractal_server/migrations/versions/a75703146940_remove_workflowtaskv2_legacy_attributes.py
similarity index 78%
rename from fractal_server/migrations/versions/40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py
rename to fractal_server/migrations/versions/a75703146940_remove_workflowtaskv2_legacy_attributes.py
index 3d322e6df5..34b39b493e 100644
--- a/fractal_server/migrations/versions/40b3479ba47f_remove_workflowtaskv2_legacy_attributes.py
+++ b/fractal_server/migrations/versions/a75703146940_remove_workflowtaskv2_legacy_attributes.py
@@ -1,8 +1,8 @@
 """Remove WorkflowTaskV2 legacy attributes
 
-Revision ID: 40b3479ba47f
+Revision ID: a75703146940
 Revises: 5bf02391cfef
-Create Date: 2024-09-03 10:11:27.477326
+Create Date: 2024-09-03 10:34:51.761372
 
 """
 import sqlalchemy as sa
@@ -10,7 +10,7 @@
 
 
 # revision identifiers, used by Alembic.
-revision = "40b3479ba47f"
+revision = "a75703146940"
 down_revision = "5bf02391cfef"
 branch_labels = None
 depends_on = None
@@ -18,15 +18,16 @@
 
 def upgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
-
-    # FIXME 1712: adapt to sqlite??
+    op.alter_column(
+        "workflowtaskv2", "task_id", existing_type=sa.INTEGER(), nullable=False
+    )
     op.drop_constraint(
         "fk_workflowtaskv2_task_legacy_id_task",
         "workflowtaskv2",
         type_="foreignkey",
     )
-    op.drop_column("workflowtaskv2", "is_legacy_task")
     op.drop_column("workflowtaskv2", "task_legacy_id")
+    op.drop_column("workflowtaskv2", "is_legacy_task")
     # ### end Alembic commands ###
 
 
@@ -34,11 +35,11 @@ def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
     op.add_column(
         "workflowtaskv2",
-        sa.Column("task_legacy_id", sa.INTEGER(), nullable=True),
+        sa.Column("is_legacy_task", sa.BOOLEAN(), nullable=False),
     )
     op.add_column(
         "workflowtaskv2",
-        sa.Column("is_legacy_task", sa.BOOLEAN(), nullable=False),
+        sa.Column("task_legacy_id", sa.INTEGER(), nullable=True),
     )
     op.create_foreign_key(
         "fk_workflowtaskv2_task_legacy_id_task",
@@ -47,4 +48,7 @@ def downgrade() -> None:
         ["task_legacy_id"],
         ["id"],
     )
+    op.alter_column(
+        "workflowtaskv2", "task_id", existing_type=sa.INTEGER(), nullable=True
+    )
     # ### end Alembic commands ###

From b31d9d22fbb8e8eef161cb8b0a48c71f9ee2b45e Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 11:47:53 +0200
Subject: [PATCH 10/44] Remove `Task.is_v2_compatible` and task-legacy
 endpoints

---
 fractal_server/app/models/v1/task.py          |  5 --
 fractal_server/app/routes/admin/v2.py         | 30 ---------
 fractal_server/app/routes/api/v2/__init__.py  |  4 --
 .../app/routes/api/v2/task_legacy.py          | 61 -------------------
 fractal_server/app/schemas/v2/__init__.py     |  1 -
 fractal_server/app/schemas/v2/task.py         |  5 --
 6 files changed, 106 deletions(-)
 delete mode 100644 fractal_server/app/routes/api/v2/task_legacy.py

diff --git a/fractal_server/app/models/v1/task.py b/fractal_server/app/models/v1/task.py
index 0d13b40ddb..21f784c791 100644
--- a/fractal_server/app/models/v1/task.py
+++ b/fractal_server/app/models/v1/task.py
@@ -5,7 +5,6 @@
 
 from pydantic import HttpUrl
 from sqlalchemy import Column
-from sqlalchemy import sql
 from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import SQLModel
@@ -49,10 +48,6 @@ class Task(_TaskBaseV1, SQLModel, table=True):
     docs_info: Optional[str] = None
     docs_link: Optional[HttpUrl] = None
 
-    is_v2_compatible: bool = Field(
-        default=False, sa_column_kwargs={"server_default": sql.false()}
-    )
-
     @property
     def parallelization_level(self) -> Optional[str]:
         try:
diff --git a/fractal_server/app/routes/admin/v2.py b/fractal_server/app/routes/admin/v2.py
index f86ae08244..f1fb6bfce3 100644
--- a/fractal_server/app/routes/admin/v2.py
+++ b/fractal_server/app/routes/admin/v2.py
@@ -25,7 +25,6 @@
 from ...db import AsyncSession
 from ...db import get_async_db
 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
@@ -281,35 +280,6 @@ async def download_job_logs(
     )
 
 
-class TaskCompatibility(BaseModel):
-    is_v2_compatible: bool
-
-
-@router_admin_v2.patch(
-    "/task-v1/{task_id}/",
-    status_code=status.HTTP_200_OK,
-)
-async def flag_task_v1_as_v2_compatible(
-    task_id: int,
-    compatibility: TaskCompatibility,
-    user: User = Depends(current_active_superuser),
-    db: AsyncSession = Depends(get_async_db),
-) -> Response:
-
-    task = await db.get(Task, task_id)
-    if task is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail=f"Task {task_id} not found",
-        )
-
-    task.is_v2_compatible = compatibility.is_v2_compatible
-    await db.commit()
-    await db.close()
-
-    return Response(status_code=status.HTTP_200_OK)
-
-
 class TaskV2Minimal(BaseModel):
 
     id: int
diff --git a/fractal_server/app/routes/api/v2/__init__.py b/fractal_server/app/routes/api/v2/__init__.py
index 9231a17bef..cc4eaa4483 100644
--- a/fractal_server/app/routes/api/v2/__init__.py
+++ b/fractal_server/app/routes/api/v2/__init__.py
@@ -12,7 +12,6 @@
 from .task import router as task_router_v2
 from .task_collection import router as task_collection_router_v2
 from .task_collection_custom import router as task_collection_router_v2_custom
-from .task_legacy import router as task_legacy_router_v2
 from .workflow import router as workflow_router_v2
 from .workflowtask import router as workflowtask_router_v2
 from fractal_server.config import get_settings
@@ -38,9 +37,6 @@
     tags=["V2 Task Collection"],
 )
 router_api_v2.include_router(task_router_v2, prefix="/task", tags=["V2 Task"])
-router_api_v2.include_router(
-    task_legacy_router_v2, prefix="/task-legacy", tags=["V2 Task Legacy"]
-)
 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"])
diff --git a/fractal_server/app/routes/api/v2/task_legacy.py b/fractal_server/app/routes/api/v2/task_legacy.py
deleted file mode 100644
index 939e89e2fd..0000000000
--- a/fractal_server/app/routes/api/v2/task_legacy.py
+++ /dev/null
@@ -1,61 +0,0 @@
-from fastapi import APIRouter
-from fastapi import Depends
-from fastapi import HTTPException
-from fastapi import status
-from sqlmodel import select
-
-from .....logger import set_logger
-from ....db import AsyncSession
-from ....db import get_async_db
-from ....models.v1 import Task as TaskV1
-from ....schemas.v2 import TaskLegacyReadV2
-from ....security import current_active_user
-from ....security import User
-
-router = APIRouter()
-
-logger = set_logger(__name__)
-
-# FIXME 1712: remove this module?
-
-
-@router.get("/", response_model=list[TaskLegacyReadV2])
-async def get_list_task_legacy(
-    args_schema: bool = True,
-    only_v2_compatible: bool = False,
-    user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> list[TaskLegacyReadV2]:
-    """
-    Get list of available legacy tasks
-    """
-    stm = select(TaskV1)
-    if only_v2_compatible:
-        stm = stm.where(TaskV1.is_v2_compatible)
-    res = await db.execute(stm)
-    task_list = res.scalars().all()
-    await db.close()
-    if args_schema is False:
-        for task in task_list:
-            setattr(task, "args_schema", None)
-
-    return task_list
-
-
-@router.get("/{task_id}/", response_model=TaskLegacyReadV2)
-async def get_task_legacy(
-    task_id: int,
-    user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> TaskLegacyReadV2:
-    """
-    Get info on a specific legacy task
-    """
-    task = await db.get(TaskV1, task_id)
-    await db.close()
-    if not task:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail=f"TaskV1[{task_id}] not found",
-        )
-    return task
diff --git a/fractal_server/app/schemas/v2/__init__.py b/fractal_server/app/schemas/v2/__init__.py
index 560e3d7700..1660d48ef7 100644
--- a/fractal_server/app/schemas/v2/__init__.py
+++ b/fractal_server/app/schemas/v2/__init__.py
@@ -20,7 +20,6 @@
 from .task import TaskCreateV2  # noqa F401
 from .task import TaskExportV2  # noqa F401
 from .task import TaskImportV2  # noqa F401
-from .task import TaskLegacyReadV2  # noqa F401
 from .task import TaskReadV2  # noqa F401
 from .task import TaskUpdateV2  # noqa F401
 from .task_collection import CollectionStateReadV2  # noqa F401
diff --git a/fractal_server/app/schemas/v2/task.py b/fractal_server/app/schemas/v2/task.py
index b3b650dd24..55957e5b47 100644
--- a/fractal_server/app/schemas/v2/task.py
+++ b/fractal_server/app/schemas/v2/task.py
@@ -11,7 +11,6 @@
 
 from .._validators import valdictkeys
 from .._validators import valstr
-from ..v1.task import TaskReadV1
 
 
 class TaskCreateV2(BaseModel, extra=Extra.forbid):
@@ -101,10 +100,6 @@ class TaskReadV2(BaseModel):
     output_types: dict[str, bool]
 
 
-class TaskLegacyReadV2(TaskReadV1):
-    is_v2_compatible: bool
-
-
 class TaskUpdateV2(BaseModel):
 
     name: Optional[str]

From 4afa11882672618f38cafaf8b61c98cd815ce383 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 11:48:03 +0200
Subject: [PATCH 11/44] Update tests

---
 tests/v1/02_schemas/test_unit_schemas.py      |   1 -
 tests/v1/03_db/test_unit_db_models.py         |   1 -
 tests/v2/03_api/test_api_admin.py             |  36 -----
 tests/v2/03_api/test_api_task.py              |  76 ----------
 tests/v2/03_api/test_api_workflow.py          | 130 +-----------------
 tests/v2/08_full_workflow/common_functions.py |  30 ++--
 6 files changed, 10 insertions(+), 264 deletions(-)

diff --git a/tests/v1/02_schemas/test_unit_schemas.py b/tests/v1/02_schemas/test_unit_schemas.py
index e7f5b4d6ea..de512089cc 100644
--- a/tests/v1/02_schemas/test_unit_schemas.py
+++ b/tests/v1/02_schemas/test_unit_schemas.py
@@ -507,7 +507,6 @@ def test_workflow_read_non_empty_task_list():
         input_type="input_type",
         output_type="output_type",
         meta=dict(something="else"),
-        is_v2_compatible=False,
     )
     # Create two WorkflowTaskRead
     wft1 = WorkflowTaskReadV1(id=1, task_id=1, workflow_id=1, task=t1)
diff --git a/tests/v1/03_db/test_unit_db_models.py b/tests/v1/03_db/test_unit_db_models.py
index 2f8b063beb..afe0dd16b8 100644
--- a/tests/v1/03_db/test_unit_db_models.py
+++ b/tests/v1/03_db/test_unit_db_models.py
@@ -70,7 +70,6 @@ async def test_tasks(db):
     assert db_task.args_schema_version is None
     assert db_task.docs_info is None
     assert db_task.docs_link is None
-    assert db_task.is_v2_compatible is False
 
     # `Task.source` has unique constraint
     broken_task = Task(**args)  # == task1
diff --git a/tests/v2/03_api/test_api_admin.py b/tests/v2/03_api/test_api_admin.py
index 6a8f7c1969..6361f3ec34 100644
--- a/tests/v2/03_api/test_api_admin.py
+++ b/tests/v2/03_api/test_api_admin.py
@@ -486,42 +486,6 @@ async def test_download_job_logs(
         assert LOG_CONTENT in actual_logs
 
 
-async def test_flag_task_v2_compatible(
-    db,
-    client,
-    MockCurrentUser,
-    task_factory,
-):
-    task = await task_factory()
-    assert task.is_v2_compatible is False
-
-    async with MockCurrentUser(user_kwargs={"is_superuser": True}):
-
-        for _ in range(2):
-            res = await client.patch(
-                f"{PREFIX}/task-v1/{task.id}/",
-                json=dict(is_v2_compatible=True),
-            )
-            assert res.status_code == 200
-            await db.refresh(task)
-            assert task.is_v2_compatible is True
-
-        for _ in range(2):
-            res = await client.patch(
-                f"{PREFIX}/task-v1/{task.id}/",
-                json=dict(is_v2_compatible=False),
-            )
-            assert res.status_code == 200
-            await db.refresh(task)
-            assert task.is_v2_compatible is False
-
-        res = await client.patch(
-            f"{PREFIX}/task-v1/{task.id + 100}/",
-            json=dict(is_v2_compatible=True),
-        )
-        assert res.status_code == 404
-
-
 async def test_task_query(
     db,
     client,
diff --git a/tests/v2/03_api/test_api_task.py b/tests/v2/03_api/test_api_task.py
index 933156cac3..fd3de9228b 100644
--- a/tests/v2/03_api/test_api_task.py
+++ b/tests/v2/03_api/test_api_task.py
@@ -538,79 +538,3 @@ async def test_post_same_source(client, MockCurrentUser):
         # POST v1_c OK
         res = await client.post(V1, json=task_v1_c.dict(exclude_unset=True))
         assert res.status_code == 201
-
-
-async def test_get_legacy_task(
-    task_factory, task_factory_v2, client, MockCurrentUser
-):
-    async with MockCurrentUser():
-
-        # Add 3 task V2
-        await task_factory_v2(source="a")
-        await task_factory_v2(source="b")
-        await task_factory_v2(source="c")
-
-        # Assert
-        res = await client.get("/api/v1/task/")
-        assert len(res.json()) == 0
-        res = await client.get("/api/v2/task/")
-        assert len(res.json()) == 3
-        res = await client.get("/api/v2/task-legacy/")
-        assert len(res.json()) == 0
-        res = await client.get("/api/v2/task-legacy/?only_v2_available=True")
-        assert len(res.json()) == 0
-
-        # Add 2 task V1, not v2-compatibles
-        await task_factory(source="d")
-        await task_factory(source="e")
-        await task_factory(source="f")
-
-        # Assert
-        res = await client.get("/api/v1/task/")
-        assert len(res.json()) == 3
-        for task in res.json():
-            assert "is_v2_compatible" not in task
-
-        res = await client.get("/api/v2/task/")
-        assert len(res.json()) == 3
-
-        res = await client.get("/api/v2/task-legacy/")
-        assert len(res.json()) == 3
-        for task in res.json():
-            assert task["is_v2_compatible"] is False
-
-        res = await client.get("/api/v2/task-legacy/?only_v2_compatible=True")
-        assert len(res.json()) == 0
-
-        # Add 2 task V1 and v2-compatibles
-        await task_factory(source="g", is_v2_compatible=True)
-        await task_factory(
-            source="h", is_v2_compatible=True, args_schema={"args": "schema"}
-        )
-
-        # Assert
-        res = await client.get("/api/v1/task/")
-        assert len(res.json()) == 5
-        for task in res.json():
-            assert "is_v2_compatible" not in task
-
-        res = await client.get("/api/v2/task/")
-        assert len(res.json()) == 3
-
-        res = await client.get("/api/v2/task-legacy/")
-        assert len(res.json()) == 5
-        for task in res.json():
-            assert "is_v2_compatible" in task
-
-        res = await client.get(
-            "/api/v2/task-legacy/?only_v2_compatible=True&args_schema=False"
-        )
-        assert len(res.json()) == 2
-        for task in res.json():
-            assert task["is_v2_compatible"] is True
-            assert task["args_schema"] is None
-            res = await client.get(f"/api/v2/task-legacy/{task['id']}/")
-            assert res.json()["is_v2_compatible"] is True
-
-        res = await client.get("/api/v2/task-legacy/9999999/")
-        assert res.status_code == 404
diff --git a/tests/v2/03_api/test_api_workflow.py b/tests/v2/03_api/test_api_workflow.py
index b7cd7a8e7f..8c4ebe2c24 100644
--- a/tests/v2/03_api/test_api_workflow.py
+++ b/tests/v2/03_api/test_api_workflow.py
@@ -686,80 +686,6 @@ async def test_patch_workflow_task(
             assert "Cannot patch" in res.json()["detail"]
 
 
-async def test_patch_workflow_task_legacy(
-    MockCurrentUser,
-    project_factory_v2,
-    workflow_factory_v2,
-    task_factory,
-    client,
-):
-    """
-    GIVEN a WorkflowTask pointing to a legacy task
-    WHEN the endpoint to PATCH a WorkflowTask is called
-    THEN the WorkflowTask is updated
-
-    In this test, we also include null non-parallel attributes in the PATCH
-    request body. They are not necessary or relevant, but we need to make
-    sure that the endpoint does not fail in this case.
-    """
-    async with MockCurrentUser(user_kwargs=dict(is_verified=True)) as user:
-        # Create task
-        legacy_task = await task_factory(is_v2_compatible=True)
-
-        # Create project and workflow
-        proj = await project_factory_v2(user)
-        wf = await workflow_factory_v2(project_id=proj.id)
-
-        # Add legacy task to workflow
-        res = await client.post(
-            f"{PREFIX}/project/{proj.id}/workflow/{wf.id}/wftask/"
-            f"?task_id={legacy_task.id}",
-            json={"is_legacy_task": True},
-        )
-        assert res.status_code == 201
-        wf_task_id = res.json()["id"]
-
-        res = await client.post(
-            f"{PREFIX}/project/{proj.id}/workflow/{wf.id}/wftask/"
-            "?task_id=123456789",
-            json={"is_legacy_task": True},
-        )
-        assert res.status_code == 404
-
-        workflow = await get_workflow(client, proj.id, wf.id)
-
-        assert workflow["task_list"][0]["args_parallel"] is None
-        assert workflow["task_list"][0]["args_non_parallel"] is None
-        assert workflow["task_list"][0]["meta_non_parallel"] is None
-        assert workflow["task_list"][0]["meta_parallel"] is None
-
-        ARGS = {"c": 333, "d": 444}
-        META = {"executor": "cpu-low"}
-        INPUT_FILTERS = {
-            "attributes": {"a": "b", "c": "d"},
-            "types": {"e": True, "f": False, "g": True},
-        }
-
-        patch_payload = dict(
-            args_non_parallel=None,
-            meta_non_parallel=None,
-            args_parallel=ARGS,
-            meta_parallel=META,
-            input_filters=INPUT_FILTERS,
-        )
-        res = await client.patch(
-            f"{PREFIX}/project/{proj.id}/workflow/{wf.id}/"
-            f"wftask/{wf_task_id}/",
-            json=patch_payload,
-        )
-        debug(res.json())
-        assert res.status_code == 200
-
-        assert res.json()["args_parallel"] == ARGS
-        assert res.json()["meta_parallel"] == META
-        assert res.json()["input_filters"] == INPUT_FILTERS
-
-
 async def test_patch_workflow_task_with_args_schema(
     client, MockCurrentUser, project_factory_v2, task_factory_v2
 ):
@@ -1191,12 +1117,8 @@ async def test_import_export_workflow(
     for wftask in workflow_exported["task_list"]:
         assert "id" not in wftask
         assert "task_id" not in wftask
-        assert "task_legacy_id" not in wftask
         assert "workflow_id" not in wftask
-        if wftask["is_legacy_task"]:
-            assert "id" not in wftask["task_legacy"]
-        else:
-            assert "id" not in wftask["task"]
+        assert "id" not in wftask["task"]
     assert res.status_code == 200
 
     # Check that the exported workflow is an extension of the one in the
@@ -1220,56 +1142,6 @@ async def test_import_export_workflow(
         assert task_old == task_new
 
 
-async def test_task_legacy_is_v2_compatible(
-    MockCurrentUser,
-    client,
-    project_factory_v2,
-    workflow_factory_v2,
-    task_factory,
-    task_factory_v2,
-):
-    # Create tasks
-    task_v1_compatible = await task_factory(
-        id=1, name="task_v1-c", source="source1", is_v2_compatible=True
-    )
-    task_v1_not_compatible = await task_factory(
-        id=2, name="task_v1-good", source="source2", is_v2_compatible=False
-    )
-    task_v2 = await task_factory_v2(id=3, name="task_v2", source="source3")
-    assert task_v1_compatible.is_v2_compatible is True
-    assert task_v1_not_compatible.is_v2_compatible is False
-
-    async with MockCurrentUser() as user:
-
-        project = await project_factory_v2(user)
-        workflow = await workflow_factory_v2(project_id=project.id)
-
-        # Fail adding TaskV1 with is_v2_compatible==False
-        res = await client.post(
-            f"{PREFIX}/project/{project.id}/workflow/{workflow.id}/wftask/"
-            f"?task_id={task_v1_not_compatible.id}",
-            json=dict(is_legacy_task=True),
-        )
-        assert res.status_code == 422
-        assert "compatible" in res.json()["detail"]
-
-        # Succeed adding TaskV1 with is_v2_compatible==True
-        res = await client.post(
-            f"{PREFIX}/project/{project.id}/workflow/{workflow.id}/wftask/"
-            f"?task_id={task_v1_compatible.id}",
-            json=dict(is_legacy_task=True),
-        )
-        assert res.status_code == 201
-
-        # Succeed adding TaskV2
-        res = await client.post(
-            f"{PREFIX}/project/{project.id}/workflow/{workflow.id}/wftask/"
-            f"?task_id={task_v2.id}",
-            json=dict(),
-        )
-        assert res.status_code == 201
-
-
 async def test_export_workflow_log(
     client,
     MockCurrentUser,
diff --git a/tests/v2/08_full_workflow/common_functions.py b/tests/v2/08_full_workflow/common_functions.py
index ead795f835..facba361dc 100644
--- a/tests/v2/08_full_workflow/common_functions.py
+++ b/tests/v2/08_full_workflow/common_functions.py
@@ -395,7 +395,6 @@ async def failing_workflow_UnknownError(
     MockCurrentUser,
     client,
     monkeypatch,
-    legacy,
     project_factory_v2,
     dataset_factory_v2,
     workflow_factory_v2,
@@ -423,18 +422,14 @@ async def failing_workflow_UnknownError(
         workflow_id = workflow.id
 
         # Create task
-        if legacy:
-            task = await task_factory(command="echo", is_v2_compatible=True)
-        else:
-            task = await task_factory_v2(
-                command_non_parallel="echo", type="non_parallel"
-            )
+        task = await task_factory_v2(
+            command_non_parallel="echo", type="non_parallel"
+        )
 
-        payload = dict(is_legacy_task=legacy)
         res = await client.post(
             f"{PREFIX}/project/{project_id}/workflow/{workflow_id}/wftask/"
             f"?task_id={task.id}",
-            json=payload,
+            json={},
         )
         assert res.status_code == 201
         workflow_task_id = res.json()["id"]
@@ -448,18 +443,11 @@ async def failing_workflow_UnknownError(
         def _raise_RuntimeError(*args, **kwargs):
             raise RuntimeError(ERROR_MSG)
 
-        if legacy:
-            monkeypatch.setattr(
-                fractal_server.app.runner.v2.runner,
-                "run_v1_task_parallel",
-                _raise_RuntimeError,
-            )
-        else:
-            monkeypatch.setattr(
-                fractal_server.app.runner.v2.runner,
-                "run_v2_task_non_parallel",
-                _raise_RuntimeError,
-            )
+        monkeypatch.setattr(
+            fractal_server.app.runner.v2.runner,
+            "run_v2_task_non_parallel",
+            _raise_RuntimeError,
+        )
 
         # EXECUTE WORKFLOW
         res = await client.post(

From d9e97b49ae1c8dd0b39bd0340c405213452ff92d Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 12:23:37 +0200
Subject: [PATCH 12/44] Keep removing legacy-task-related tests

---
 tests/data/import_export/workflow-v2.json     |  1 -
 tests/v2/04_runner/fixtures_mocks.py          | 63 --------------
 tests/v2/04_runner/test_fractal_examples.py   | 87 +------------------
 .../test_no_images_parallelization.py         | 11 +--
 tests/v2/04_runner/v2_mock_models.py          | 44 +---------
 ...est_full_workflow_local_experimental_v2.py |  4 -
 .../test_full_workflow_local_v2.py            |  4 -
 .../test_full_workflow_slurm_v2.py            |  4 -
 tests/v2/09_backends/test_slurm_config.py     | 55 +++---------
 9 files changed, 22 insertions(+), 251 deletions(-)

diff --git a/tests/data/import_export/workflow-v2.json b/tests/data/import_export/workflow-v2.json
index d8ec31b90c..f469bcaa5d 100644
--- a/tests/data/import_export/workflow-v2.json
+++ b/tests/data/import_export/workflow-v2.json
@@ -13,7 +13,6 @@
             "meta_parallel": {"key1": "value1"},
             "meta_non_parallel": {"key2": "value2"},
             "order": 0,
-            "is_legacy_task": false,
             "task": {
                 "source": "PKG_SOURCE:dummy2"
             }
diff --git a/tests/v2/04_runner/fixtures_mocks.py b/tests/v2/04_runner/fixtures_mocks.py
index 5544067ff6..3f3075fd1d 100644
--- a/tests/v2/04_runner/fixtures_mocks.py
+++ b/tests/v2/04_runner/fixtures_mocks.py
@@ -1,8 +1,4 @@
-import json
 import logging
-import os
-import sys
-from pathlib import Path
 
 import pytest
 from v2_mock_models import TaskV2Mock
@@ -47,62 +43,3 @@ def fractal_tasks_mock_no_db(
         task.name: TaskV2Mock(id=_id, **task.dict())
         for _id, task in enumerate(fractal_tasks_mock_collection["task_list"])
     }
-
-
-@pytest.fixture
-def fractal_tasks_mock_venv_legacy(testdata_path, tmp_path_factory) -> dict:
-    from v2_mock_models import TaskV1Mock
-
-    basetemp = tmp_path_factory.getbasetemp()
-    venv_name = "venv_fractal_tasks_core_alpha"
-    venv_path = (basetemp / venv_name).as_posix()
-    python_bin = (basetemp / venv_name / "bin/python").as_posix()
-
-    if not os.path.isdir(venv_path):
-        logging.debug(f"venv does not exists ({venv_path=})")
-        # Create venv
-        cmd = f"{sys.executable} -m venv {venv_path}"
-        _run_cmd(cmd=cmd, label="create-venv")
-        # Install fractal-tasks-core-alpha from wheel
-        wheel_file = (
-            testdata_path
-            / "dummy_package_with_args_schemas"
-            / "dist/fractal_tasks_core_alpha-0.0.1a0-py3-none-any.whl"
-        ).as_posix()
-        cmd = f"{python_bin} -m pip install {wheel_file}"
-        _run_cmd(cmd=cmd, label="install-fractal-tasks-core-alpha")
-    else:
-        logging.info("venv already exists")
-
-    # Extract installed-package folder
-    cmd = f"{python_bin} -m pip show fractal_tasks_core_alpha"
-    out = _run_cmd(cmd=cmd, label="extract-pkg-dir")
-    location = next(
-        line for line in out.split("\n") if line.startswith("Location:")
-    )
-    location = location.replace("Location: ", "")
-    src_dir = Path(location) / "fractal_tasks_core_alpha/"
-
-    # Construct TaskV1Mock objects, and store them as a key-value pairs
-    # (indexed by their names)
-    with (src_dir / "__FRACTAL_MANIFEST__.json").open("r") as f:
-        manifest = json.load(f)
-    task_dict = {}
-    for ind, task in enumerate(manifest["task_list"]):
-
-        more_attributes = {}
-        if task["name"] == "dummy parallel":
-            more_attributes["meta"] = {"parallelization_level": "image"}
-
-        task_path = (src_dir / task["executable"]).as_posix()
-        t = TaskV1Mock(
-            id=ind,
-            name=task["name"],
-            source=task["name"].replace(" ", "_"),
-            input_type="Any",
-            output_type="Any",
-            command=f"{python_bin} {task_path}",
-            **more_attributes,
-        )
-        task_dict[t.name] = t
-    return task_dict
diff --git a/tests/v2/04_runner/test_fractal_examples.py b/tests/v2/04_runner/test_fractal_examples.py
index 71abd604c2..7dd3e6e57d 100644
--- a/tests/v2/04_runner/test_fractal_examples.py
+++ b/tests/v2/04_runner/test_fractal_examples.py
@@ -14,7 +14,6 @@
 from fractal_server.app.runner.exceptions import JobExecutionError
 from fractal_server.images import SingleImage
 from fractal_server.images.tools import find_image_by_zarr_url
-from fractal_server.logger import set_logger
 
 
 def execute_tasks_v2(wf_task_list, workflow_dir_local, **kwargs):
@@ -24,14 +23,9 @@ def execute_tasks_v2(wf_task_list, workflow_dir_local, **kwargs):
     )
 
     for wftask in wf_task_list:
-        if wftask.task is not None:
-            subfolder = workflow_dir_local / task_subfolder_name(
-                order=wftask.order, task_name=wftask.task.name
-            )
-        else:
-            subfolder = workflow_dir_local / task_subfolder_name(
-                order=wftask.order, task_name=wftask.task_legacy.name
-            )
+        subfolder = workflow_dir_local / task_subfolder_name(
+            order=wftask.order, task_name=wftask.task.name
+        )
         logging.info(f"Now creating {subfolder.as_posix()}")
         subfolder.mkdir(parents=True)
 
@@ -740,78 +734,3 @@ def test_invalid_filtered_image_list(
             **execute_tasks_v2_args,
         )
     assert "Invalid filtered image list" in str(e.value)
-
-
-def test_legacy_task(
-    tmp_path: Path,
-    executor: Executor,
-    fractal_tasks_mock_no_db,
-    fractal_tasks_mock_venv_legacy,
-    override_settings_factory,
-):
-    """
-    Run a workflow that includes V2 and V1 tasks.
-    """
-
-    # Set up logger
-    override_settings_factory(FRACTAL_LOGGING_LEVEL=logging.INFO)
-    logger_name = "test_legacy_task"
-    log_file_path = (tmp_path / "log").as_posix()
-    set_logger(
-        logger_name=logger_name,
-        log_file_path=log_file_path,
-    )
-
-    execute_tasks_v2_args = dict(
-        executor=executor,
-        workflow_dir_local=tmp_path / "job_dir",
-        workflow_dir_remote=tmp_path / "job_dir",
-        logger_name=logger_name,
-    )
-
-    zarr_dir = (tmp_path / "zarr_dir").as_posix().rstrip("/")
-    dataset_attrs = execute_tasks_v2(
-        wf_task_list=[
-            WorkflowTaskV2Mock(
-                task=fractal_tasks_mock_no_db["create_ome_zarr_compound"],
-                args_non_parallel=dict(image_dir="/tmp/input_images"),
-                id=0,
-                order=0,
-            )
-        ],
-        dataset=DatasetV2Mock(name="dataset", zarr_dir=zarr_dir),
-        **execute_tasks_v2_args,
-    )
-
-    assert _task_names_from_history(dataset_attrs["history"]) == [
-        "create_ome_zarr_compound"
-    ]
-    assert dataset_attrs["filters"]["attributes"] == {}
-    assert dataset_attrs["filters"]["types"] == {}
-    _assert_image_data_exist(dataset_attrs["images"])
-    assert len(dataset_attrs["images"]) == 2
-
-    dataset_attrs = execute_tasks_v2(
-        wf_task_list=[
-            WorkflowTaskV2Mock(
-                task_legacy=fractal_tasks_mock_venv_legacy["dummy parallel"],
-                is_legacy_task=True,
-                id=1,
-                order=1,
-            )
-        ],
-        dataset=DatasetV2Mock(
-            name="dataset", zarr_dir=zarr_dir, **dataset_attrs
-        ),
-        **execute_tasks_v2_args,
-    )
-
-    assert len(dataset_attrs["history"]) == 1
-    assert dataset_attrs["history"][0]["status"] == "done"
-    assert dataset_attrs["history"][0]["workflowtask"]["is_legacy_task"]
-
-    # Check logs
-    with open(log_file_path, "r") as f:
-        lines = f.read()
-    assert 'SUBMIT 1-th task (legacy, name="dummy parallel")' in lines
-    assert 'END    1-th task (name="dummy parallel")' in lines
diff --git a/tests/v2/04_runner/test_no_images_parallelization.py b/tests/v2/04_runner/test_no_images_parallelization.py
index 8d9d3a3866..113894c40e 100644
--- a/tests/v2/04_runner/test_no_images_parallelization.py
+++ b/tests/v2/04_runner/test_no_images_parallelization.py
@@ -15,14 +15,9 @@ def execute_tasks_v2(wf_task_list, workflow_dir_local, **kwargs):
     )
 
     for wftask in wf_task_list:
-        if wftask.task is not None:
-            subfolder = workflow_dir_local / task_subfolder_name(
-                order=wftask.order, task_name=wftask.task.name
-            )
-        else:
-            subfolder = workflow_dir_local / task_subfolder_name(
-                order=wftask.order, task_name=wftask.task_legacy.name
-            )
+        subfolder = workflow_dir_local / task_subfolder_name(
+            order=wftask.order, task_name=wftask.task.name
+        )
         logging.info(f"Now creating {subfolder.as_posix()}")
         subfolder.mkdir(parents=True)
 
diff --git a/tests/v2/04_runner/v2_mock_models.py b/tests/v2/04_runner/v2_mock_models.py
index 21135ab763..9275e40d36 100644
--- a/tests/v2/04_runner/v2_mock_models.py
+++ b/tests/v2/04_runner/v2_mock_models.py
@@ -69,59 +69,19 @@ def _set_type(cls, value, values):
                 return "compound"
 
 
-class TaskV1Mock(BaseModel):
-    id: int
-    name: str
-    command: str  # str
-    source: str = Field(unique=True)
-    input_type: str
-    output_type: str
-    meta: Optional[dict[str, Any]] = Field(default_factory=dict)
-
-    @property
-    def parallelization_level(self) -> Optional[str]:
-        try:
-            return self.meta["parallelization_level"]
-        except KeyError:
-            return None
-
-    @property
-    def is_parallel(self) -> bool:
-        return bool(self.parallelization_level)
-
-
 class WorkflowTaskV2Mock(BaseModel):
     args_non_parallel: dict[str, Any] = Field(default_factory=dict)
     args_parallel: dict[str, Any] = Field(default_factory=dict)
     meta_non_parallel: dict[str, Any] = Field(default_factory=dict)
     meta_parallel: dict[str, Any] = Field(default_factory=dict)
-    is_legacy_task: Optional[bool]
     meta_parallel: Optional[dict[str, Any]] = Field()
     meta_non_parallel: Optional[dict[str, Any]] = Field()
-    task: Optional[TaskV2Mock] = None
-    task_legacy: Optional[TaskV1Mock] = None
-    is_legacy_task: bool = False
+    task: TaskV2Mock
     input_filters: dict[str, Any] = Field(default_factory=dict)
     order: int
     id: int
     workflow_id: int = 0
-    task_legacy_id: Optional[int]
-    task_id: Optional[int]
-
-    @root_validator(pre=False)
-    def _legacy_or_not(cls, values):
-        is_legacy_task = values["is_legacy_task"]
-        task = values.get("task")
-        task_legacy = values.get("task_legacy")
-        if is_legacy_task:
-            if task_legacy is None or task is not None:
-                raise ValueError(f"Invalid WorkflowTaskV2Mock with {values=}")
-            values["task_legacy_id"] = task_legacy.id
-        else:
-            if task is None or task_legacy is not None:
-                raise ValueError(f"Invalid WorkflowTaskV2Mock with {values=}")
-            values["task_id"] = task.id
-        return values
+    task_id: int
 
     @validator("input_filters", always=True)
     def _default_filters(cls, value):
diff --git a/tests/v2/08_full_workflow/test_full_workflow_local_experimental_v2.py b/tests/v2/08_full_workflow/test_full_workflow_local_experimental_v2.py
index 515700ca82..f4ad722352 100644
--- a/tests/v2/08_full_workflow/test_full_workflow_local_experimental_v2.py
+++ b/tests/v2/08_full_workflow/test_full_workflow_local_experimental_v2.py
@@ -1,4 +1,3 @@
-import pytest
 from common_functions import failing_workflow_UnknownError
 from common_functions import full_workflow
 from common_functions import full_workflow_TaskExecutionError
@@ -97,9 +96,7 @@ async def test_non_executable_task_command_local(
     )
 
 
-@pytest.mark.parametrize("legacy", [False, True])
 async def test_failing_workflow_UnknownError_local(
-    legacy: bool,
     client,
     MockCurrentUser,
     tmp777_path,
@@ -124,7 +121,6 @@ async def test_failing_workflow_UnknownError_local(
         MockCurrentUser=MockCurrentUser,
         client=client,
         monkeypatch=monkeypatch,
-        legacy=legacy,
         project_factory_v2=project_factory_v2,
         dataset_factory_v2=dataset_factory_v2,
         workflow_factory_v2=workflow_factory_v2,
diff --git a/tests/v2/08_full_workflow/test_full_workflow_local_v2.py b/tests/v2/08_full_workflow/test_full_workflow_local_v2.py
index 1c2672e430..18d6293989 100644
--- a/tests/v2/08_full_workflow/test_full_workflow_local_v2.py
+++ b/tests/v2/08_full_workflow/test_full_workflow_local_v2.py
@@ -1,4 +1,3 @@
-import pytest
 from common_functions import failing_workflow_UnknownError
 from common_functions import full_workflow
 from common_functions import full_workflow_TaskExecutionError
@@ -97,9 +96,7 @@ async def test_non_executable_task_command_local(
     )
 
 
-@pytest.mark.parametrize("legacy", [False, True])
 async def test_failing_workflow_UnknownError_local(
-    legacy: bool,
     client,
     MockCurrentUser,
     tmp777_path,
@@ -124,7 +121,6 @@ async def test_failing_workflow_UnknownError_local(
         MockCurrentUser=MockCurrentUser,
         client=client,
         monkeypatch=monkeypatch,
-        legacy=legacy,
         project_factory_v2=project_factory_v2,
         dataset_factory_v2=dataset_factory_v2,
         workflow_factory_v2=workflow_factory_v2,
diff --git a/tests/v2/08_full_workflow/test_full_workflow_slurm_v2.py b/tests/v2/08_full_workflow/test_full_workflow_slurm_v2.py
index 45ba68463d..1935e20826 100644
--- a/tests/v2/08_full_workflow/test_full_workflow_slurm_v2.py
+++ b/tests/v2/08_full_workflow/test_full_workflow_slurm_v2.py
@@ -1,7 +1,6 @@
 import shlex
 import subprocess
 
-import pytest
 from common_functions import failing_workflow_UnknownError
 from common_functions import full_workflow
 from common_functions import full_workflow_TaskExecutionError
@@ -254,9 +253,7 @@ async def test_non_executable_task_command_slurm(
     )
 
 
-@pytest.mark.parametrize("legacy", [False, True])
 async def test_failing_workflow_UnknownError_slurm(
-    legacy: bool,
     client,
     MockCurrentUser,
     testdata_path,
@@ -288,7 +285,6 @@ async def test_failing_workflow_UnknownError_slurm(
         user_kwargs={"cache_dir": str(tmp777_path / "user_cache_dir-slurm")},
         client=client,
         monkeypatch=monkeypatch,
-        legacy=legacy,
         project_factory_v2=project_factory_v2,
         dataset_factory_v2=dataset_factory_v2,
         workflow_factory_v2=workflow_factory_v2,
diff --git a/tests/v2/09_backends/test_slurm_config.py b/tests/v2/09_backends/test_slurm_config.py
index bec3d893cf..dbc4754778 100644
--- a/tests/v2/09_backends/test_slurm_config.py
+++ b/tests/v2/09_backends/test_slurm_config.py
@@ -50,56 +50,29 @@ class WorkflowTaskV2Mock(BaseModel, extra=Extra.forbid):
     args_parallel: dict[str, Any] = Field(default_factory=dict)
     meta_non_parallel: dict[str, Any] = Field(default_factory=dict)
     meta_parallel: dict[str, Any] = Field(default_factory=dict)
-    is_legacy_task: Optional[bool]
     meta_parallel: Optional[dict[str, Any]] = Field()
     meta_non_parallel: Optional[dict[str, Any]] = Field()
-    task: Optional[TaskV2Mock] = None
-    task_legacy: Optional[TaskV1Mock] = None
-    is_legacy_task: bool = False
+    task: TaskV2Mock
     input_filters: dict[str, Any] = Field(default_factory=dict)
     order: int = 0
     id: int = 1
     workflow_id: int = 0
-    task_legacy_id: Optional[int]
-    task_id: Optional[int]
-
-    @root_validator(pre=False)
-    def _legacy_or_not(cls, values):
-        is_legacy_task = values["is_legacy_task"]
-        task = values.get("task")
-        task_legacy = values.get("task_legacy")
-        if is_legacy_task:
-            if task_legacy is None or task is not None:
-                raise ValueError(f"Invalid WorkflowTaskV2Mock with {values=}")
-            values["task_legacy_id"] = task_legacy.id
-        else:
-            if task is None or task_legacy is not None:
-                raise ValueError(f"Invalid WorkflowTaskV2Mock with {values=}")
-            values["task_id"] = task.id
-        return values
+    task_id: int
 
     @root_validator(pre=False)
     def merge_meta(cls, values):
-        if values["is_legacy_task"]:
-            task_meta = values["task"].meta
-            if task_meta:
-                values["meta"] = {
-                    **task_meta,
-                    **values["meta"],
-                }
-        else:
-            task_meta_parallel = values["task"].meta_parallel
-            if task_meta_parallel:
-                values["meta_parallel"] = {
-                    **task_meta_parallel,
-                    **values["meta_parallel"],
-                }
-            task_meta_non_parallel = values["task"].meta_non_parallel
-            if task_meta_non_parallel:
-                values["meta_non_parallel"] = {
-                    **task_meta_non_parallel,
-                    **values["meta_non_parallel"],
-                }
+        task_meta_parallel = values["task"].meta_parallel
+        if task_meta_parallel:
+            values["meta_parallel"] = {
+                **task_meta_parallel,
+                **values["meta_parallel"],
+            }
+        task_meta_non_parallel = values["task"].meta_non_parallel
+        if task_meta_non_parallel:
+            values["meta_non_parallel"] = {
+                **task_meta_non_parallel,
+                **values["meta_non_parallel"],
+            }
         return values
 
 

From 9df9c8599dc922c4000ef8135ed0b653da3848fc Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 17:27:18 +0200
Subject: [PATCH 13/44] Add required `task_id` attribute in tests

---
 tests/v2/04_runner/test_dummy_examples.py | 27 +++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/tests/v2/04_runner/test_dummy_examples.py b/tests/v2/04_runner/test_dummy_examples.py
index 7c2122180b..b9f493f283 100644
--- a/tests/v2/04_runner/test_dummy_examples.py
+++ b/tests/v2/04_runner/test_dummy_examples.py
@@ -50,6 +50,9 @@ def test_dummy_insert_single_image(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["dummy_insert_single_image"],
+                task_id=fractal_tasks_mock_no_db[
+                    "dummy_insert_single_image"
+                ].id,
                 id=0,
                 order=0,
             )
@@ -64,6 +67,9 @@ def test_dummy_insert_single_image(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["dummy_insert_single_image"],
+                task_id=fractal_tasks_mock_no_db[
+                    "dummy_insert_single_image"
+                ].id,
                 id=1,
                 order=1,
             )
@@ -80,6 +86,9 @@ def test_dummy_insert_single_image(
             wf_task_list=[
                 WorkflowTaskV2Mock(
                     task=fractal_tasks_mock_no_db["dummy_insert_single_image"],
+                    task_id=fractal_tasks_mock_no_db[
+                        "dummy_insert_single_image"
+                    ].id,
                     args_non_parallel={
                         "full_new_image": dict(
                             zarr_url=IMAGES[0]["zarr_url"], origin="/somewhere"
@@ -116,6 +125,7 @@ def test_dummy_insert_single_image(
             wf_task_list=[
                 WorkflowTaskV2Mock(
                     task=PATCHED_TASK,
+                    task_id=PATCHED_TASK.id,
                     args_non_parallel={"types": {KEY: True}},
                     id=2,
                     order=2,
@@ -140,6 +150,9 @@ def test_dummy_insert_single_image(
             wf_task_list=[
                 WorkflowTaskV2Mock(
                     task=fractal_tasks_mock_no_db["dummy_insert_single_image"],
+                    task_id=fractal_tasks_mock_no_db[
+                        "dummy_insert_single_image"
+                    ].id,
                     args_non_parallel={"fail": True},
                     id=2,
                     order=2,
@@ -158,6 +171,9 @@ def test_dummy_insert_single_image(
             wf_task_list=[
                 WorkflowTaskV2Mock(
                     task=fractal_tasks_mock_no_db["dummy_insert_single_image"],
+                    task_id=fractal_tasks_mock_no_db[
+                        "dummy_insert_single_image"
+                    ].id,
                     args_non_parallel={"fail_2": True},
                     id=3,
                     order=3,
@@ -194,6 +210,7 @@ def test_dummy_remove_images(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["dummy_remove_images"],
+                task_id=fractal_tasks_mock_no_db["dummy_remove_images"].id,
                 id=0,
                 order=0,
             )
@@ -213,6 +230,7 @@ def test_dummy_remove_images(
             wf_task_list=[
                 WorkflowTaskV2Mock(
                     task=fractal_tasks_mock_no_db["dummy_remove_images"],
+                    task_id=fractal_tasks_mock_no_db["dummy_remove_images"].id,
                     id=1,
                     order=1,
                     args_non_parallel=dict(
@@ -257,6 +275,7 @@ def test_dummy_unset_attribute(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["dummy_unset_attribute"],
+                task_id=fractal_tasks_mock_no_db["dummy_unset_attribute"].id,
                 args_non_parallel=dict(attribute="key2"),
                 id=0,
                 order=0,
@@ -273,6 +292,7 @@ def test_dummy_unset_attribute(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["dummy_unset_attribute"],
+                task_id=fractal_tasks_mock_no_db["dummy_unset_attribute"].id,
                 args_non_parallel=dict(attribute="missing-attribute"),
                 id=1,
                 order=1,
@@ -304,6 +324,9 @@ def test_dummy_insert_single_image_none_attribute(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["dummy_insert_single_image"],
+                task_id=fractal_tasks_mock_no_db[
+                    "dummy_insert_single_image"
+                ].id,
                 args_non_parallel=dict(attributes={"attribute-name": None}),
                 id=0,
                 order=0,
@@ -334,6 +357,9 @@ def test_dummy_insert_single_image_normalization(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["dummy_insert_single_image"],
+                task_id=fractal_tasks_mock_no_db[
+                    "dummy_insert_single_image"
+                ].id,
                 id=0,
                 order=0,
                 args_non_parallel={"trailing_slash": True},
@@ -372,6 +398,7 @@ def test_default_inclusion_of_images(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["generic_task_parallel"],
+                task_id=fractal_tasks_mock_no_db["generic_task_parallel"].id,
                 id=0,
                 order=0,
             )

From a4eebf100bf88b30a127bffed1889d2aef6aeb11 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 17:30:40 +0200
Subject: [PATCH 14/44] Update test_unit_schemas_v2.py

---
 tests/v2/01_schemas/test_unit_schemas_v2.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/tests/v2/01_schemas/test_unit_schemas_v2.py b/tests/v2/01_schemas/test_unit_schemas_v2.py
index 2d6439da17..d80f1eee8f 100644
--- a/tests/v2/01_schemas/test_unit_schemas_v2.py
+++ b/tests/v2/01_schemas/test_unit_schemas_v2.py
@@ -6,6 +6,7 @@
 from fractal_server.app.schemas.v2 import ProjectCreateV2
 from fractal_server.app.schemas.v2 import TaskCollectPipV2
 from fractal_server.app.schemas.v2 import TaskCreateV2
+from fractal_server.app.schemas.v2 import TaskDumpV2
 from fractal_server.app.schemas.v2 import TaskUpdateV2
 from fractal_server.app.schemas.v2 import WorkflowCreateV2
 from fractal_server.app.schemas.v2 import WorkflowTaskCreateV2
@@ -116,10 +117,12 @@ def test_workflow_task_dump():
         workflow_id=1,
         input_filters=Filters(),
         task_id=1,
-    )
-    with pytest.raises(ValidationError, match="none"):
-        WorkflowTaskDumpV2(
+        task=TaskDumpV2(
             id=1,
-            workflow_id=1,
-            input_filters=Filters(),
-        )
+            name="name",
+            type="type",
+            source="source",
+            input_types={},
+            output_types={},
+        ),
+    )

From 216949d8a34b809348979463040e4ab12efb97e0 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 3 Sep 2024 17:39:19 +0200
Subject: [PATCH 15/44] Fix some more WorkflowTaskV2Mock required attributes in
 tests

---
 tests/v2/04_runner/test_fractal_examples.py   | 49 +++++++++++++++++++
 .../test_no_images_parallelization.py         |  2 +
 tests/v2/09_backends/test_slurm_config.py     | 13 +++--
 3 files changed, 61 insertions(+), 3 deletions(-)

diff --git a/tests/v2/04_runner/test_fractal_examples.py b/tests/v2/04_runner/test_fractal_examples.py
index 7dd3e6e57d..ac90971130 100644
--- a/tests/v2/04_runner/test_fractal_examples.py
+++ b/tests/v2/04_runner/test_fractal_examples.py
@@ -79,6 +79,9 @@ def test_fractal_demos_01(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["create_ome_zarr_compound"],
+                task_id=fractal_tasks_mock_no_db[
+                    "create_ome_zarr_compound"
+                ].id,
                 args_non_parallel=dict(image_dir="/tmp/input_images"),
                 args_parallel={},
                 id=0,
@@ -101,6 +104,7 @@ def test_fractal_demos_01(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["illumination_correction"],
+                task_id=fractal_tasks_mock_no_db["illumination_correction"].id,
                 args_parallel=dict(overwrite_input=True),
                 id=1,
                 order=1,
@@ -146,6 +150,7 @@ def test_fractal_demos_01(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["MIP_compound"],
+                task_id=fractal_tasks_mock_no_db["MIP_compound"].id,
                 args_non_parallel=dict(suffix="mip"),
                 args_parallel={},
                 id=2,
@@ -190,6 +195,7 @@ def test_fractal_demos_01(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["cellpose_segmentation"],
+                task_id=fractal_tasks_mock_no_db["cellpose_segmentation"].id,
                 args_parallel={},
                 id=3,
                 order=3,
@@ -228,6 +234,9 @@ def test_fractal_demos_01_no_overwrite(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["create_ome_zarr_compound"],
+                task_id=fractal_tasks_mock_no_db[
+                    "create_ome_zarr_compound"
+                ].id,
                 args_non_parallel=dict(image_dir="/tmp/input_images"),
                 id=0,
                 order=0,
@@ -247,6 +256,7 @@ def test_fractal_demos_01_no_overwrite(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["illumination_correction"],
+                task_id=fractal_tasks_mock_no_db["illumination_correction"].id,
                 args_parallel=dict(overwrite_input=False),
                 id=1,
                 order=1,
@@ -323,6 +333,7 @@ def test_fractal_demos_01_no_overwrite(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["MIP_compound"],
+                task_id=fractal_tasks_mock_no_db["MIP_compound"].id,
                 args_non_parallel=dict(suffix="mip"),
                 id=2,
                 order=2,
@@ -388,6 +399,7 @@ def test_fractal_demos_01_no_overwrite(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["cellpose_segmentation"],
+                task_id=fractal_tasks_mock_no_db["cellpose_segmentation"].id,
                 id=3,
                 order=3,
             )
@@ -422,6 +434,9 @@ def test_registration_no_overwrite(
                 task=fractal_tasks_mock_no_db[
                     "create_ome_zarr_multiplex_compound"
                 ],
+                task_id=fractal_tasks_mock_no_db[
+                    "create_ome_zarr_multiplex_compound"
+                ].id,
                 args_non_parallel=dict(image_dir="/tmp/input_images"),
                 id=0,
                 order=0,
@@ -438,6 +453,9 @@ def test_registration_no_overwrite(
                 task=fractal_tasks_mock_no_db[
                     "calculate_registration_compound"
                 ],
+                task_id=fractal_tasks_mock_no_db[
+                    "calculate_registration_compound"
+                ].id,
                 args_non_parallel={"ref_acquisition": 0},
                 id=1,
                 order=1,
@@ -463,6 +481,9 @@ def test_registration_no_overwrite(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["find_registration_consensus"],
+                task_id=fractal_tasks_mock_no_db[
+                    "find_registration_consensus"
+                ].id,
                 id=2,
                 order=2,
             )
@@ -485,6 +506,9 @@ def test_registration_no_overwrite(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["apply_registration_to_image"],
+                task_id=fractal_tasks_mock_no_db[
+                    "apply_registration_to_image"
+                ].id,
                 args_parallel={"overwrite_input": False},
                 id=3,
                 order=3,
@@ -520,6 +544,9 @@ def test_registration_overwrite(
                 task=fractal_tasks_mock_no_db[
                     "create_ome_zarr_multiplex_compound"
                 ],
+                task_id=fractal_tasks_mock_no_db[
+                    "create_ome_zarr_multiplex_compound"
+                ].id,
                 args_non_parallel=dict(image_dir="/tmp/input_images"),
                 id=0,
                 order=0,
@@ -536,6 +563,9 @@ def test_registration_overwrite(
                 task=fractal_tasks_mock_no_db[
                     "calculate_registration_compound"
                 ],
+                task_id=fractal_tasks_mock_no_db[
+                    "calculate_registration_compound"
+                ].id,
                 args_non_parallel={"ref_acquisition": 0},
                 order=1,
                 id=1,
@@ -561,6 +591,9 @@ def test_registration_overwrite(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["find_registration_consensus"],
+                task_id=fractal_tasks_mock_no_db[
+                    "find_registration_consensus"
+                ].id,
                 id=2,
                 order=2,
             )
@@ -583,6 +616,9 @@ def test_registration_overwrite(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["apply_registration_to_image"],
+                task_id=fractal_tasks_mock_no_db[
+                    "apply_registration_to_image"
+                ].id,
                 args_parallel={"overwrite_input": True},
                 id=3,
                 order=3,
@@ -615,6 +651,9 @@ def test_channel_parallelization_with_overwrite(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["create_ome_zarr_compound"],
+                task_id=fractal_tasks_mock_no_db[
+                    "create_ome_zarr_compound"
+                ].id,
                 args_non_parallel=dict(image_dir="/tmp/input_images"),
                 id=0,
                 order=0,
@@ -631,6 +670,9 @@ def test_channel_parallelization_with_overwrite(
                 task=fractal_tasks_mock_no_db[
                     "illumination_correction_compound"
                 ],
+                task_id=fractal_tasks_mock_no_db[
+                    "illumination_correction_compound"
+                ].id,
                 args_non_parallel=dict(overwrite_input=True),
                 args_parallel=dict(another_argument="something"),
                 id=1,
@@ -662,6 +704,9 @@ def test_channel_parallelization_no_overwrite(
         wf_task_list=[
             WorkflowTaskV2Mock(
                 task=fractal_tasks_mock_no_db["create_ome_zarr_compound"],
+                task_id=fractal_tasks_mock_no_db[
+                    "create_ome_zarr_compound"
+                ].id,
                 args_non_parallel=dict(image_dir="/tmp/input_images"),
                 id=0,
                 order=0,
@@ -678,6 +723,9 @@ def test_channel_parallelization_no_overwrite(
                 task=fractal_tasks_mock_no_db[
                     "illumination_correction_compound"
                 ],
+                task_id=fractal_tasks_mock_no_db[
+                    "illumination_correction_compound"
+                ].id,
                 args_non_parallel=dict(overwrite_input=False),
                 args_parallel=dict(another_argument="something"),
                 id=1,
@@ -724,6 +772,7 @@ def test_invalid_filtered_image_list(
                         type="non_parallel",
                         input_types=dict(invalid=True),
                     ),
+                    task_id=0,
                     id=0,
                     order=0,
                 )
diff --git a/tests/v2/04_runner/test_no_images_parallelization.py b/tests/v2/04_runner/test_no_images_parallelization.py
index 113894c40e..b744176cc6 100644
--- a/tests/v2/04_runner/test_no_images_parallelization.py
+++ b/tests/v2/04_runner/test_no_images_parallelization.py
@@ -52,6 +52,7 @@ def test_parallelize_on_no_images(tmp_path: Path, executor: Executor):
                     id=0,
                     source="source",
                 ),
+                task_id=0,
                 id=0,
                 order=0,
             )
@@ -86,6 +87,7 @@ def test_parallelize_on_no_images_compound(tmp_path: Path, executor: Executor):
                     id=0,
                     source="source",
                 ),
+                task_id=0,
                 id=0,
                 order=0,
             )
diff --git a/tests/v2/09_backends/test_slurm_config.py b/tests/v2/09_backends/test_slurm_config.py
index dbc4754778..601977c032 100644
--- a/tests/v2/09_backends/test_slurm_config.py
+++ b/tests/v2/09_backends/test_slurm_config.py
@@ -153,6 +153,7 @@ def test_get_slurm_config(tmp_path: Path):
     )
     mywftask = WorkflowTaskV2Mock(
         task=mytask,
+        task_id=mytask.id,
         args_non_parallel=dict(message="test"),
         meta_non_parallel=meta_non_parallel,
     )
@@ -214,6 +215,7 @@ def test_get_slurm_config_fail(tmp_path):
     get_slurm_config(
         wftask=WorkflowTaskV2Mock(
             task=TaskV2Mock(),
+            task_id=TaskV2Mock().id,
             meta_non_parallel={},
         ),
         config_path=config_path_valid,
@@ -231,6 +233,7 @@ def test_get_slurm_config_fail(tmp_path):
         get_slurm_config(
             wftask=WorkflowTaskV2Mock(
                 task=TaskV2Mock(),
+                task_id=TaskV2Mock().id,
                 meta_non_parallel={},
             ),
             config_path=config_path_invalid,
@@ -294,6 +297,7 @@ def test_get_slurm_config_wftask_meta_none(tmp_path):
     )
     mywftask = WorkflowTaskV2Mock(
         task=TaskV2Mock(meta_non_parallel=None),
+        task_id=TaskV2Mock(meta_non_parallel=None).id,
         args_non_parallel=dict(message="test"),
         meta_non_parallel=meta_non_parallel,
     )
@@ -335,7 +339,7 @@ def test_slurm_submit_setup(
     )
 
     # No account in `wftask.meta` --> OK
-    wftask = WorkflowTaskV2Mock(task=TaskV2Mock())
+    wftask = WorkflowTaskV2Mock(task=TaskV2Mock(), task_id=TaskV2Mock().id)
     slurm_config = _slurm_submit_setup(
         wftask=wftask,
         workflow_dir_local=tmp_path,
@@ -349,6 +353,7 @@ def test_slurm_submit_setup(
     wftask = WorkflowTaskV2Mock(
         meta_non_parallel=dict(key="value", account="MyFakeAccount"),
         task=TaskV2Mock(),
+        task_id=TaskV2Mock().id,
     )
     with pytest.raises(SlurmConfigError) as e:
         _slurm_submit_setup(
@@ -398,7 +403,7 @@ def test_get_slurm_config_gpu_options(tmp_path: Path):
         json.dump(slurm_config_dict, f)
 
     # In absence of `needs_gpu`, parameters in `gpu_slurm_config` are not used
-    mywftask = WorkflowTaskV2Mock(task=TaskV2Mock())
+    mywftask = WorkflowTaskV2Mock(task=TaskV2Mock(), task_id=TaskV2Mock().id)
     slurm_config = get_slurm_config(
         wftask=mywftask,
         config_path=config_path,
@@ -410,7 +415,9 @@ def test_get_slurm_config_gpu_options(tmp_path: Path):
 
     # When `needs_gpu` is set, parameters in `gpu_slurm_config` are used
     mywftask = WorkflowTaskV2Mock(
-        meta_non_parallel=dict(needs_gpu=True), task=TaskV2Mock()
+        meta_non_parallel=dict(needs_gpu=True),
+        task=TaskV2Mock(),
+        task_id=TaskV2Mock().id,
     )
     slurm_config = get_slurm_config(
         wftask=mywftask,

From 650df6a37fdcc10e697de59eac789f0db6c133d7 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 4 Sep 2024 08:44:46 +0200
Subject: [PATCH 16/44] Merge two migration scripts

---
 ...42_remove_link_between_v1_and_v2_tasks_.py} | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)
 rename fractal_server/migrations/versions/{a75703146940_remove_workflowtaskv2_legacy_attributes.py => 9e081c49e542_remove_link_between_v1_and_v2_tasks_.py} (76%)

diff --git a/fractal_server/migrations/versions/a75703146940_remove_workflowtaskv2_legacy_attributes.py b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
similarity index 76%
rename from fractal_server/migrations/versions/a75703146940_remove_workflowtaskv2_legacy_attributes.py
rename to fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
index 34b39b493e..b33aa4e24f 100644
--- a/fractal_server/migrations/versions/a75703146940_remove_workflowtaskv2_legacy_attributes.py
+++ b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
@@ -1,8 +1,8 @@
-"""Remove WorkflowTaskV2 legacy attributes
+"""Remove link between v1 and v2 tasks/workflowtasks tables
 
-Revision ID: a75703146940
+Revision ID: 9e081c49e542
 Revises: 5bf02391cfef
-Create Date: 2024-09-03 10:34:51.761372
+Create Date: 2024-09-04 08:44:12.471028
 
 """
 import sqlalchemy as sa
@@ -10,7 +10,7 @@
 
 
 # revision identifiers, used by Alembic.
-revision = "a75703146940"
+revision = "9e081c49e542"
 down_revision = "5bf02391cfef"
 branch_labels = None
 depends_on = None
@@ -18,6 +18,7 @@
 
 def upgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("task", "is_v2_compatible")
     op.alter_column(
         "workflowtaskv2", "task_id", existing_type=sa.INTEGER(), nullable=False
     )
@@ -51,4 +52,13 @@ def downgrade() -> None:
     op.alter_column(
         "workflowtaskv2", "task_id", existing_type=sa.INTEGER(), nullable=True
     )
+    op.add_column(
+        "task",
+        sa.Column(
+            "is_v2_compatible",
+            sa.BOOLEAN(),
+            server_default=sa.text("(false)"),
+            nullable=False,
+        ),
+    )
     # ### end Alembic commands ###

From a9644d5e76982a3abdf56767c9a66a4b8db3c01d Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 4 Sep 2024 09:20:47 +0200
Subject: [PATCH 17/44] Make migration script work for sqlite (ref #1722)

---
 ...42_remove_link_between_v1_and_v2_tasks_.py | 43 ++++++++++++++-----
 1 file changed, 32 insertions(+), 11 deletions(-)

diff --git a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
index b33aa4e24f..0e24d3253a 100644
--- a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
@@ -17,20 +17,41 @@
 
 
 def upgrade() -> None:
+
+    # We modified the auto generated commands because sqlite does not support
+    # "alter table". They would have worked fine with postgresql.
+
     # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_column("task", "is_v2_compatible")
-    op.alter_column(
-        "workflowtaskv2", "task_id", existing_type=sa.INTEGER(), nullable=False
-    )
-    op.drop_constraint(
-        "fk_workflowtaskv2_task_legacy_id_task",
-        "workflowtaskv2",
-        type_="foreignkey",
-    )
-    op.drop_column("workflowtaskv2", "task_legacy_id")
-    op.drop_column("workflowtaskv2", "is_legacy_task")
+    # op.drop_column("task", "is_v2_compatible")
+    # op.alter_column(
+    #     "workflowtaskv2",
+    #     "task_id",
+    #     existing_type=sa.INTEGER(),
+    #     nullable=False,
+    # )
+    # op.drop_constraint(
+    #     "fk_workflowtaskv2_task_legacy_id_task",
+    #     "workflowtaskv2",
+    #     type_="foreignkey",
+    # )
+    # op.drop_column("workflowtaskv2", "task_legacy_id")
+    # op.drop_column("workflowtaskv2", "is_legacy_task")
     # ### end Alembic commands ###
 
+    with op.batch_alter_table("task", schema=None) as batch_op:
+        batch_op.drop_column("is_v2_compatible")
+
+    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "task_id", existing_type=sa.INTEGER(), nullable=False
+        )
+        batch_op.drop_column("task_legacy_id")
+        batch_op.drop_column("is_legacy_task")
+
+        batch_op.drop_constraint(
+            "fk_workflowtaskv2_task_legacy_id_task",
+        )
+
 
 def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###

From 5efb6077f7be3b9fed0e1cb67de5a7287a8063de Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 4 Sep 2024 09:23:24 +0200
Subject: [PATCH 18/44] Change sqlite-motivated order of migration script
 statements

---
 .../9e081c49e542_remove_link_between_v1_and_v2_tasks_.py     | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
index 0e24d3253a..ddd580f7af 100644
--- a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
@@ -45,12 +45,11 @@ def upgrade() -> None:
         batch_op.alter_column(
             "task_id", existing_type=sa.INTEGER(), nullable=False
         )
-        batch_op.drop_column("task_legacy_id")
-        batch_op.drop_column("is_legacy_task")
-
         batch_op.drop_constraint(
             "fk_workflowtaskv2_task_legacy_id_task",
         )
+        batch_op.drop_column("task_legacy_id")
+        batch_op.drop_column("is_legacy_task")
 
 
 def downgrade() -> None:

From c8b38d82f5ead54b1c9d95a305709eaf4430296e Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 4 Sep 2024 09:27:00 +0200
Subject: [PATCH 19/44] Do not explicitly drop foreign-key constraint, since we
 are already dropping column

---
 .../9e081c49e542_remove_link_between_v1_and_v2_tasks_.py       | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
index ddd580f7af..7c2eeccfb4 100644
--- a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
@@ -45,9 +45,6 @@ def upgrade() -> None:
         batch_op.alter_column(
             "task_id", existing_type=sa.INTEGER(), nullable=False
         )
-        batch_op.drop_constraint(
-            "fk_workflowtaskv2_task_legacy_id_task",
-        )
         batch_op.drop_column("task_legacy_id")
         batch_op.drop_column("is_legacy_task")
 

From da6443cd97fdd19ad0eef22596f2945f95a2e7ab Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 4 Sep 2024 09:30:34 +0200
Subject: [PATCH 20/44] Change sqlite-motivated order of migration script
 statements

---
 .../9e081c49e542_remove_link_between_v1_and_v2_tasks_.py     | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
index 7c2eeccfb4..d581cc4259 100644
--- a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
@@ -41,6 +41,11 @@ def upgrade() -> None:
     with op.batch_alter_table("task", schema=None) as batch_op:
         batch_op.drop_column("is_v2_compatible")
 
+    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+        batch_op.drop_constraint(
+            "fk_workflowtaskv2_task_legacy_id_task",
+        )
+
     with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
         batch_op.alter_column(
             "task_id", existing_type=sa.INTEGER(), nullable=False

From 1edff7b5473ec4d89c43f4b43bdba4e7e7c3d596 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 4 Sep 2024 09:36:35 +0200
Subject: [PATCH 21/44] Add info about current sqlite version to warning
 message

---
 fractal_server/app/db/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/fractal_server/app/db/__init__.py b/fractal_server/app/db/__init__.py
index e501c12af8..b0e9137b39 100644
--- a/fractal_server/app/db/__init__.py
+++ b/fractal_server/app/db/__init__.py
@@ -2,6 +2,7 @@
 `db` module, loosely adapted from
 https://testdriven.io/blog/fastapi-sqlmodel/#async-sqlmodel
 """
+import sqlite3
 from typing import AsyncGenerator
 from typing import Generator
 
@@ -21,7 +22,9 @@
 logger = set_logger(__name__)
 
 SQLITE_WARNING_MESSAGE = (
-    "SQLite is supported (for version >=3.37) but discouraged in production. "
+    "SQLite is supported (supported version >=3.37, "
+    f"current {sqlite3.sqlite_version=}) "
+    "but discouraged in production. "
     "Given its partial support for ForeignKey constraints, "
     "database consistency cannot be guaranteed."
 )

From 905cb950ad6c3fa283ec6a256fe9732137e6ad59 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 10:14:43 +0200
Subject: [PATCH 22/44] add _type to migration

---
 .../9e081c49e542_remove_link_between_v1_and_v2_tasks_.py       | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
index d581cc4259..39f043aea8 100644
--- a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
@@ -8,7 +8,6 @@
 import sqlalchemy as sa
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "9e081c49e542"
 down_revision = "5bf02391cfef"
@@ -43,7 +42,7 @@ def upgrade() -> None:
 
     with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
         batch_op.drop_constraint(
-            "fk_workflowtaskv2_task_legacy_id_task",
+            "fk_workflowtaskv2_task_legacy_id_task", type_="foreignkey"
         )
 
     with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:

From def9f1ca5fd5a8520a51387ee35d8bfb88d2060e Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 11:27:23 +0200
Subject: [PATCH 23/44] avoit drop_constraint in sqlite

---
 ...2_remove_link_between_v1_and_v2_tasks_.py} | 44 ++++++-------------
 1 file changed, 13 insertions(+), 31 deletions(-)
 rename fractal_server/migrations/versions/{9e081c49e542_remove_link_between_v1_and_v2_tasks_.py => 820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py} (60%)

diff --git a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py
similarity index 60%
rename from fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
rename to fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py
index 39f043aea8..39c3b9f494 100644
--- a/fractal_server/migrations/versions/9e081c49e542_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py
@@ -1,56 +1,38 @@
 """Remove link between v1 and v2 tasks/workflowtasks tables
 
-Revision ID: 9e081c49e542
+Revision ID: 820d66a50cc2
 Revises: 5bf02391cfef
-Create Date: 2024-09-04 08:44:12.471028
+Create Date: 2024-09-09 11:21:59.311683
 
 """
 import sqlalchemy as sa
 from alembic import op
+from sqlalchemy.dialects import sqlite
+
 
 # revision identifiers, used by Alembic.
-revision = "9e081c49e542"
+revision = "820d66a50cc2"
 down_revision = "5bf02391cfef"
 branch_labels = None
 depends_on = None
 
 
 def upgrade() -> None:
-
-    # We modified the auto generated commands because sqlite does not support
-    # "alter table". They would have worked fine with postgresql.
-
     # ### commands auto generated by Alembic - please adjust! ###
-    # op.drop_column("task", "is_v2_compatible")
-    # op.alter_column(
-    #     "workflowtaskv2",
-    #     "task_id",
-    #     existing_type=sa.INTEGER(),
-    #     nullable=False,
-    # )
-    # op.drop_constraint(
-    #     "fk_workflowtaskv2_task_legacy_id_task",
-    #     "workflowtaskv2",
-    #     type_="foreignkey",
-    # )
-    # op.drop_column("workflowtaskv2", "task_legacy_id")
-    # op.drop_column("workflowtaskv2", "is_legacy_task")
-    # ### end Alembic commands ###
-
-    with op.batch_alter_table("task", schema=None) as batch_op:
-        batch_op.drop_column("is_v2_compatible")
-
-    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
-        batch_op.drop_constraint(
-            "fk_workflowtaskv2_task_legacy_id_task", type_="foreignkey"
-        )
-
+    op.drop_column("task", "is_v2_compatible")
     with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
         batch_op.alter_column(
             "task_id", existing_type=sa.INTEGER(), nullable=False
         )
         batch_op.drop_column("task_legacy_id")
         batch_op.drop_column("is_legacy_task")
+    if not isinstance(op.get_bind().dialect, sqlite.dialect):
+        op.drop_constraint(
+            "fk_workflowtaskv2_task_legacy_id_task",
+            "workflowtaskv2",
+            type_="foreignkey",
+        )
+    # ### end Alembic commands ###
 
 
 def downgrade() -> None:

From 02c13a8f2dfe2c6a366c3f5d73d495c06a2a3072 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 11:29:55 +0200
Subject: [PATCH 24/44] move check up

---
 ...d66a50cc2_remove_link_between_v1_and_v2_tasks_.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py
index 39c3b9f494..da1a4cc467 100644
--- a/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py
@@ -21,17 +21,17 @@ def upgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
     op.drop_column("task", "is_v2_compatible")
     with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+        if not isinstance(op.get_bind().dialect, sqlite.dialect):
+            batch_op.drop_constraint(
+                "fk_workflowtaskv2_task_legacy_id_task",
+                "workflowtaskv2",
+                type_="foreignkey",
+            )
         batch_op.alter_column(
             "task_id", existing_type=sa.INTEGER(), nullable=False
         )
         batch_op.drop_column("task_legacy_id")
         batch_op.drop_column("is_legacy_task")
-    if not isinstance(op.get_bind().dialect, sqlite.dialect):
-        op.drop_constraint(
-            "fk_workflowtaskv2_task_legacy_id_task",
-            "workflowtaskv2",
-            type_="foreignkey",
-        )
     # ### end Alembic commands ###
 
 

From 5f9848cf223eda0d1933e0295667086e297f6b91 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 11:37:47 +0200
Subject: [PATCH 25/44] move check up again

---
 ...d66a50cc2_remove_link_between_v1_and_v2_tasks_.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py
index da1a4cc467..75f999064a 100644
--- a/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py
@@ -20,13 +20,13 @@
 def upgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
     op.drop_column("task", "is_v2_compatible")
+    if not isinstance(op.get_bind().dialect, sqlite.dialect):
+        op.drop_constraint(
+            "fk_workflowtaskv2_task_legacy_id_task",
+            "workflowtaskv2",
+            type_="foreignkey",
+        )
     with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
-        if not isinstance(op.get_bind().dialect, sqlite.dialect):
-            batch_op.drop_constraint(
-                "fk_workflowtaskv2_task_legacy_id_task",
-                "workflowtaskv2",
-                type_="foreignkey",
-            )
         batch_op.alter_column(
             "task_id", existing_type=sa.INTEGER(), nullable=False
         )

From 1cbe911e5f5d642c08aa8e4a7b09fa96e0685d36 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 14:20:31 +0200
Subject: [PATCH 26/44] render_as_batch=True

---
 fractal_server/migrations/env.py              |  2 +
 ...c2_remove_link_between_v1_and_v2_tasks_.py | 67 -------------------
 2 files changed, 2 insertions(+), 67 deletions(-)
 delete mode 100644 fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py

diff --git a/fractal_server/migrations/env.py b/fractal_server/migrations/env.py
index 390d177bb9..825d3198c0 100644
--- a/fractal_server/migrations/env.py
+++ b/fractal_server/migrations/env.py
@@ -58,6 +58,7 @@ def run_migrations_offline() -> None:
         target_metadata=target_metadata,
         literal_binds=True,
         dialect_opts={"paramstyle": "named"},
+        render_as_batch=True,
     )
 
     with context.begin_transaction():
@@ -68,6 +69,7 @@ def do_run_migrations(connection: Connection) -> None:
     context.configure(
         connection=connection,
         target_metadata=target_metadata,
+        render_as_batch=True,
     )
 
     with context.begin_transaction():
diff --git a/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py
deleted file mode 100644
index 75f999064a..0000000000
--- a/fractal_server/migrations/versions/820d66a50cc2_remove_link_between_v1_and_v2_tasks_.py
+++ /dev/null
@@ -1,67 +0,0 @@
-"""Remove link between v1 and v2 tasks/workflowtasks tables
-
-Revision ID: 820d66a50cc2
-Revises: 5bf02391cfef
-Create Date: 2024-09-09 11:21:59.311683
-
-"""
-import sqlalchemy as sa
-from alembic import op
-from sqlalchemy.dialects import sqlite
-
-
-# revision identifiers, used by Alembic.
-revision = "820d66a50cc2"
-down_revision = "5bf02391cfef"
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_column("task", "is_v2_compatible")
-    if not isinstance(op.get_bind().dialect, sqlite.dialect):
-        op.drop_constraint(
-            "fk_workflowtaskv2_task_legacy_id_task",
-            "workflowtaskv2",
-            type_="foreignkey",
-        )
-    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
-        batch_op.alter_column(
-            "task_id", existing_type=sa.INTEGER(), nullable=False
-        )
-        batch_op.drop_column("task_legacy_id")
-        batch_op.drop_column("is_legacy_task")
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.add_column(
-        "workflowtaskv2",
-        sa.Column("is_legacy_task", sa.BOOLEAN(), nullable=False),
-    )
-    op.add_column(
-        "workflowtaskv2",
-        sa.Column("task_legacy_id", sa.INTEGER(), nullable=True),
-    )
-    op.create_foreign_key(
-        "fk_workflowtaskv2_task_legacy_id_task",
-        "workflowtaskv2",
-        "task",
-        ["task_legacy_id"],
-        ["id"],
-    )
-    op.alter_column(
-        "workflowtaskv2", "task_id", existing_type=sa.INTEGER(), nullable=True
-    )
-    op.add_column(
-        "task",
-        sa.Column(
-            "is_v2_compatible",
-            sa.BOOLEAN(),
-            server_default=sa.text("(false)"),
-            nullable=False,
-        ),
-    )
-    # ### end Alembic commands ###

From 7a79d8951e7a49824f484634da7fdde9db8f778a Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 14:23:46 +0200
Subject: [PATCH 27/44] autogenerated review

---
 ...42_remove_link_between_v1_and_v2_tasks_.py | 53 +++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 fractal_server/migrations/versions/d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py

diff --git a/fractal_server/migrations/versions/d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py
new file mode 100644
index 0000000000..e96fa6b7c6
--- /dev/null
+++ b/fractal_server/migrations/versions/d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py
@@ -0,0 +1,53 @@
+"""Remove link between v1 and v2 tasks/workflowtasks tables
+
+Revision ID: d9a140db5d42
+Revises: 5bf02391cfef
+Create Date: 2024-09-09 14:15:34.415926
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "d9a140db5d42"
+down_revision = "5bf02391cfef"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "task_id", existing_type=sa.INTEGER(), nullable=False
+        )
+        batch_op.drop_constraint(
+            "fk_workflowtaskv2_task_legacy_id_task", type_="foreignkey"
+        )
+        batch_op.drop_column("is_legacy_task")
+        batch_op.drop_column("task_legacy_id")
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column("task_legacy_id", sa.INTEGER(), nullable=True)
+        )
+        batch_op.add_column(
+            sa.Column("is_legacy_task", sa.BOOLEAN(), nullable=False)
+        )
+        batch_op.create_foreign_key(
+            "fk_workflowtaskv2_task_legacy_id_task",
+            "task",
+            ["task_legacy_id"],
+            ["id"],
+        )
+        batch_op.alter_column(
+            "task_id", existing_type=sa.INTEGER(), nullable=True
+        )
+
+    # ### end Alembic commands ###

From 7b834d6bcf09ef6af03239e607f31167c981b5cd Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 14:32:39 +0200
Subject: [PATCH 28/44] if branch in migration

---
 ...140db5d42_remove_link_between_v1_and_v2_tasks_.py | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/fractal_server/migrations/versions/d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py
index e96fa6b7c6..a3160d4866 100644
--- a/fractal_server/migrations/versions/d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py
@@ -7,7 +7,7 @@
 """
 import sqlalchemy as sa
 from alembic import op
-
+from sqlalchemy.dialects import sqlite
 
 # revision identifiers, used by Alembic.
 revision = "d9a140db5d42"
@@ -17,19 +17,17 @@
 
 
 def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
     with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
         batch_op.alter_column(
             "task_id", existing_type=sa.INTEGER(), nullable=False
         )
-        batch_op.drop_constraint(
-            "fk_workflowtaskv2_task_legacy_id_task", type_="foreignkey"
-        )
+        if not isinstance(op.get_bind().dialect, sqlite.dialect):
+            batch_op.drop_constraint(
+                "fk_workflowtaskv2_task_legacy_id_task", type_="foreignkey"
+            )
         batch_op.drop_column("is_legacy_task")
         batch_op.drop_column("task_legacy_id")
 
-    # ### end Alembic commands ###
-
 
 def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###

From 883ddeeed220fe9560d70dd4743386f9a0561882 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 15:49:49 +0200
Subject: [PATCH 29/44] NAMING_CONVENTION in separate file

---
 fractal_server/migrations/env.py                  |  9 ++-------
 fractal_server/migrations/naming_convention.py    |  7 +++++++
 ...fcd85_remove_link_between_v1_and_v2_tasks_.py} | 15 ++++++++-------
 3 files changed, 17 insertions(+), 14 deletions(-)
 create mode 100644 fractal_server/migrations/naming_convention.py
 rename fractal_server/migrations/versions/{d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py => 501961cfcd85_remove_link_between_v1_and_v2_tasks_.py} (77%)

diff --git a/fractal_server/migrations/env.py b/fractal_server/migrations/env.py
index 825d3198c0..ac909554bb 100644
--- a/fractal_server/migrations/env.py
+++ b/fractal_server/migrations/env.py
@@ -7,6 +7,7 @@
 
 from fractal_server.app import models  # noqa
 from fractal_server.config import get_settings
+from fractal_server.migrations.naming_convention import NAMING_CONVENTION
 from fractal_server.syringe import Inject
 
 # this is the Alembic Config object, which provides
@@ -25,13 +26,7 @@
 # from myapp import mymodel
 # target_metadata = mymodel.Base.metadata
 target_metadata = SQLModel.metadata
-target_metadata.naming_convention = {
-    "ix": "ix_%(column_0_label)s",
-    "uq": "uq_%(table_name)s_%(column_0_name)s",
-    "ck": "ck_%(table_name)s_`%(constraint_name)s`",
-    "fk": "fk_%(table_name)s_%(column_0_name)s_%(referred_table_name)s",
-    "pk": "pk_%(table_name)s",
-}
+target_metadata.naming_convention = NAMING_CONVENTION
 
 # other values from the config, defined by the needs of env.py,
 # can be acquired:
diff --git a/fractal_server/migrations/naming_convention.py b/fractal_server/migrations/naming_convention.py
new file mode 100644
index 0000000000..9787bfc2e6
--- /dev/null
+++ b/fractal_server/migrations/naming_convention.py
@@ -0,0 +1,7 @@
+NAMING_CONVENTION = {
+    "ix": "ix_%(column_0_label)s",
+    "uq": "uq_%(table_name)s_%(column_0_name)s",
+    "ck": "ck_%(table_name)s_`%(constraint_name)s`",
+    "fk": "fk_%(table_name)s_%(column_0_name)s_%(referred_table_name)s",
+    "pk": "pk_%(table_name)s",
+}
diff --git a/fractal_server/migrations/versions/d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
similarity index 77%
rename from fractal_server/migrations/versions/d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py
rename to fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
index a3160d4866..625e24f64b 100644
--- a/fractal_server/migrations/versions/d9a140db5d42_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
@@ -7,7 +7,8 @@
 """
 import sqlalchemy as sa
 from alembic import op
-from sqlalchemy.dialects import sqlite
+
+from fractal_server.migrations.naming_convention import NAMING_CONVENTION
 
 # revision identifiers, used by Alembic.
 revision = "d9a140db5d42"
@@ -17,16 +18,16 @@
 
 
 def upgrade() -> None:
-    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+    with op.batch_alter_table(
+        "workflowtaskv2", schema=None, naming_convention=NAMING_CONVENTION
+    ) as batch_op:
         batch_op.alter_column(
             "task_id", existing_type=sa.INTEGER(), nullable=False
         )
-        if not isinstance(op.get_bind().dialect, sqlite.dialect):
-            batch_op.drop_constraint(
-                "fk_workflowtaskv2_task_legacy_id_task", type_="foreignkey"
-            )
+        batch_op.drop_constraint(
+            "fk_workflowtaskv2_task_legacy_id_task", type_="foreignkey"
+        )
         batch_op.drop_column("is_legacy_task")
-        batch_op.drop_column("task_legacy_id")
 
 
 def downgrade() -> None:

From 978429b38ff8092a55e47d0d47bf6a366d902189 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 16:07:02 +0200
Subject: [PATCH 30/44] add one missing piece to migration

---
 ...961cfcd85_remove_link_between_v1_and_v2_tasks_.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
index 625e24f64b..aafc2ec740 100644
--- a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
@@ -29,9 +29,21 @@ def upgrade() -> None:
         )
         batch_op.drop_column("is_legacy_task")
 
+    with op.batch_alter_table("task", schema=None) as batch_op:
+        batch_op.drop_column("is_v2_compatible")
+
 
 def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("task", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "is_v2_compatible",
+                sa.BOOLEAN(),
+                server_default=sa.text("(false)"),
+                nullable=False,
+            )
+        )
     with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
         batch_op.add_column(
             sa.Column("task_legacy_id", sa.INTEGER(), nullable=True)

From 2f1616943015557f3141c2b1f05c90613f393495 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 16:23:57 +0200
Subject: [PATCH 31/44] remove index

---
 .../501961cfcd85_remove_link_between_v1_and_v2_tasks_.py      | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
index aafc2ec740..93909a185a 100644
--- a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
@@ -18,6 +18,7 @@
 
 
 def upgrade() -> None:
+
     with op.batch_alter_table(
         "workflowtaskv2", schema=None, naming_convention=NAMING_CONVENTION
     ) as batch_op:
@@ -27,6 +28,9 @@ def upgrade() -> None:
         batch_op.drop_constraint(
             "fk_workflowtaskv2_task_legacy_id_task", type_="foreignkey"
         )
+        batch_op.drop_index("idx_workflowtaskv2_task_legacy_id")
+
+        batch_op.drop_column("task_legacy_id")
         batch_op.drop_column("is_legacy_task")
 
     with op.batch_alter_table("task", schema=None) as batch_op:

From de47a461fee2b4e494646430fda70fa587be1720 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 16:26:52 +0200
Subject: [PATCH 32/44] if branch

---
 .../501961cfcd85_remove_link_between_v1_and_v2_tasks_.py       | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
index 93909a185a..8f2ac64c36 100644
--- a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
@@ -28,7 +28,8 @@ def upgrade() -> None:
         batch_op.drop_constraint(
             "fk_workflowtaskv2_task_legacy_id_task", type_="foreignkey"
         )
-        batch_op.drop_index("idx_workflowtaskv2_task_legacy_id")
+        if op.get_bind().dialect.name == "sqlite":
+            batch_op.drop_index("idx_workflowtaskv2_task_legacy_id")
 
         batch_op.drop_column("task_legacy_id")
         batch_op.drop_column("is_legacy_task")

From 146e31c2f8d8cd55aa2984dd5ca1a4cd5b5f540c Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Mon, 9 Sep 2024 16:43:28 +0200
Subject: [PATCH 33/44] check for index

---
 ...61cfcd85_remove_link_between_v1_and_v2_tasks_.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
index 8f2ac64c36..2e530223b8 100644
--- a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
@@ -28,7 +28,18 @@ def upgrade() -> None:
         batch_op.drop_constraint(
             "fk_workflowtaskv2_task_legacy_id_task", type_="foreignkey"
         )
-        if op.get_bind().dialect.name == "sqlite":
+
+        if (
+            op.get_bind().dialect.name == "sqlite"
+            and op.get_bind()
+            .execute(
+                sa.text(
+                    "SELECT name FROM sqlite_master WHERE type='index' "
+                    "AND name='idx_workflowtaskv2_task_legacy_id'"
+                )
+            )
+            .fetchone()
+        ):
             batch_op.drop_index("idx_workflowtaskv2_task_legacy_id")
 
         batch_op.drop_column("task_legacy_id")

From 8330543e93aaef17852905e332ebafe42769a19c Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Tue, 10 Sep 2024 09:28:39 +0200
Subject: [PATCH 34/44] fix revision order

---
 .../501961cfcd85_remove_link_between_v1_and_v2_tasks_.py        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
index 2e530223b8..8e93884e6c 100644
--- a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
@@ -12,7 +12,7 @@
 
 # revision identifiers, used by Alembic.
 revision = "d9a140db5d42"
-down_revision = "5bf02391cfef"
+down_revision = "091b01f51f88"
 branch_labels = None
 depends_on = None
 

From a3f069080699ff8161ac70e5e8298a199359d310 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Tue, 10 Sep 2024 09:57:04 +0200
Subject: [PATCH 35/44] Literal for WorkflowTaskV2.task_type

---
 fractal_server/app/models/v2/workflowtask.py | 2 +-
 fractal_server/app/runner/v2/runner.py       | 4 +---
 tests/v2/03_api/test_unit_aux_functions.py   | 5 +++++
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/fractal_server/app/models/v2/workflowtask.py b/fractal_server/app/models/v2/workflowtask.py
index 32f64215a7..22caee0285 100644
--- a/fractal_server/app/models/v2/workflowtask.py
+++ b/fractal_server/app/models/v2/workflowtask.py
@@ -36,6 +36,6 @@ class Config:
     )
 
     # Task
-    task_type: str
+    task_type: Literal["parallel", "non_parallel", "compound"]
     task_id: int = Field(foreign_key="taskv2.id")
     task: TaskV2 = Relationship(sa_relationship_kwargs=dict(lazy="selectin"))
diff --git a/fractal_server/app/runner/v2/runner.py b/fractal_server/app/runner/v2/runner.py
index 5a87ac8a58..966e69f8ac 100644
--- a/fractal_server/app/runner/v2/runner.py
+++ b/fractal_server/app/runner/v2/runner.py
@@ -102,7 +102,7 @@ def execute_tasks_v2(
                 logger_name=logger_name,
                 submit_setup_call=submit_setup_call,
             )
-        elif task.type == "compound":
+        else:  # task.type == "compound"
             current_task_output = run_v2_task_compound(
                 images=filtered_images,
                 zarr_dir=zarr_dir,
@@ -114,8 +114,6 @@ def execute_tasks_v2(
                 logger_name=logger_name,
                 submit_setup_call=submit_setup_call,
             )
-        else:
-            raise ValueError(f"Unexpected error: Invalid {task.type=}.")
 
         # POST TASK EXECUTION
 
diff --git a/tests/v2/03_api/test_unit_aux_functions.py b/tests/v2/03_api/test_unit_aux_functions.py
index fd6d4feb6d..1250eb0d4e 100644
--- a/tests/v2/03_api/test_unit_aux_functions.py
+++ b/tests/v2/03_api/test_unit_aux_functions.py
@@ -270,6 +270,11 @@ async def test_get_job_check_owner(
 
         workflow = await workflow_factory_v2(project_id=project.id)
         t = await task_factory_v2()
+
+        with pytest.raises(ValueError):
+            await _workflow_insert_task(
+                workflow_id=workflow.id, task_id=9999, db=db
+            )
         await _workflow_insert_task(
             workflow_id=workflow.id, task_id=t.id, db=db
         )

From e23335503f006e787437ce0389ceac4752cc227e Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Tue, 10 Sep 2024 09:59:33 +0200
Subject: [PATCH 36/44] rollback Literal

---
 fractal_server/app/models/v2/workflowtask.py | 2 +-
 fractal_server/app/runner/v2/runner.py       | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/fractal_server/app/models/v2/workflowtask.py b/fractal_server/app/models/v2/workflowtask.py
index 22caee0285..32f64215a7 100644
--- a/fractal_server/app/models/v2/workflowtask.py
+++ b/fractal_server/app/models/v2/workflowtask.py
@@ -36,6 +36,6 @@ class Config:
     )
 
     # Task
-    task_type: Literal["parallel", "non_parallel", "compound"]
+    task_type: str
     task_id: int = Field(foreign_key="taskv2.id")
     task: TaskV2 = Relationship(sa_relationship_kwargs=dict(lazy="selectin"))
diff --git a/fractal_server/app/runner/v2/runner.py b/fractal_server/app/runner/v2/runner.py
index 966e69f8ac..5a87ac8a58 100644
--- a/fractal_server/app/runner/v2/runner.py
+++ b/fractal_server/app/runner/v2/runner.py
@@ -102,7 +102,7 @@ def execute_tasks_v2(
                 logger_name=logger_name,
                 submit_setup_call=submit_setup_call,
             )
-        else:  # task.type == "compound"
+        elif task.type == "compound":
             current_task_output = run_v2_task_compound(
                 images=filtered_images,
                 zarr_dir=zarr_dir,
@@ -114,6 +114,8 @@ def execute_tasks_v2(
                 logger_name=logger_name,
                 submit_setup_call=submit_setup_call,
             )
+        else:
+            raise ValueError(f"Unexpected error: Invalid {task.type=}.")
 
         # POST TASK EXECUTION
 

From 80022a63d3765efc4cd195ff99d253612e1b1ddb Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 10 Sep 2024 10:50:48 +0200
Subject: [PATCH 37/44] Update logs

---
 fractal_server/__main__.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/fractal_server/__main__.py b/fractal_server/__main__.py
index 0b7473656c..210273a8f6 100644
--- a/fractal_server/__main__.py
+++ b/fractal_server/__main__.py
@@ -86,11 +86,11 @@ def set_db():
     alembic_args = ["-c", alembic_ini.as_posix(), "upgrade", "head"]
     print(f"START: Run alembic.config, with argv={alembic_args}")
     alembic.config.main(argv=alembic_args)
-    print("END: alembic.config")
+    print("END: alembic.config\n")
     # Insert default group
     print("START: Default group creation")
     _create_first_group()
-    print("END: Default group creation")
+    print("END: Default group creation\n")
     # NOTE: It will be fixed with #1739
     settings = Inject(get_settings)
     print("START: First user creation")
@@ -103,7 +103,7 @@ def set_db():
             is_verified=True,
         )
     )
-    print("END: First user creation")
+    print("END: First user creation\n")
 
 
 def update_db_data():

From e68049557eb769e0aa7a3c66574407bf597ded4d Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 10 Sep 2024 10:51:05 +0200
Subject: [PATCH 38/44] Update migration name

---
 .../091b01f51f88_add_usergroup_and_linkusergroup_table.py       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_table.py b/fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_table.py
index 45d4565fdb..e45bfcc434 100644
--- a/fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_table.py
+++ b/fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_table.py
@@ -1,4 +1,4 @@
-"""“Add_usergroup_and_linkusergroup_table”
+"""Add_usergroup_and_linkusergroup_table
 
 Revision ID: 091b01f51f88
 Revises: 5bf02391cfef

From 82f395a5ba8c8fbf7ce70429ca911ac1fa0c09ee Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 10 Sep 2024 10:51:46 +0200
Subject: [PATCH 39/44] Update `remove_link_between_v1_and_v2_tasks` migration
 script for sqlite

---
 ...85_remove_link_between_v1_and_v2_tasks_.py | 52 ++++++++++++-------
 1 file changed, 34 insertions(+), 18 deletions(-)

diff --git a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
index 8e93884e6c..fceeedbd55 100644
--- a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
@@ -18,35 +18,51 @@
 
 
 def upgrade() -> None:
+    with op.batch_alter_table("task") as batch_op:
+        batch_op.drop_column("is_v2_compatible")
 
-    with op.batch_alter_table(
-        "workflowtaskv2", schema=None, naming_convention=NAMING_CONVENTION
-    ) as batch_op:
+    with op.batch_alter_table("workflowtaskv2") as batch_op:
         batch_op.alter_column(
             "task_id", existing_type=sa.INTEGER(), nullable=False
         )
+
+    # NOTE: in sqlite, this `drop_constraint` only works if
+    # `batch_alter_table` has a `naming_convention` set. Ref
+    # https://alembic.sqlalchemy.org/en/latest/batch.html#dropping-unnamed-or-named-foreign-key-constraints
+    with op.batch_alter_table(
+        "workflowtaskv2", naming_convention=NAMING_CONVENTION
+    ) as batch_op:
         batch_op.drop_constraint(
             "fk_workflowtaskv2_task_legacy_id_task", type_="foreignkey"
         )
 
-        if (
-            op.get_bind().dialect.name == "sqlite"
-            and op.get_bind()
-            .execute(
-                sa.text(
-                    "SELECT name FROM sqlite_master WHERE type='index' "
-                    "AND name='idx_workflowtaskv2_task_legacy_id'"
-                )
+    # NOTE: in sqlite, the `drop_index` command fails if the existing table
+    # has zero rows, while it succeeds if there are already some rows
+    if op.get_bind().dialect.name == "sqlite":
+        import sqlite3
+        import logging
+
+        logger = logging.getLogger("alembic.runtime.migration")
+        logger.warning(
+            f"Using sqlite, with {sqlite3.version=} and "
+            f"{sqlite3.sqlite_version=}"
+        )
+        logger.warning("Now drop index 'idx_workflowtaskv2_task_legacy_id'")
+        try:
+            with op.batch_alter_table("workflowtaskv2") as batch_op:
+                batch_op.drop_index("idx_workflowtaskv2_task_legacy_id")
+        except sa.exc.OperationalError:
+            logger.warning(
+                "Could not drop index; "
+                "this is expected, when the database is empty."
             )
-            .fetchone()
-        ):
-            batch_op.drop_index("idx_workflowtaskv2_task_legacy_id")
+            logger.warning("Continue.")
 
-        batch_op.drop_column("task_legacy_id")
+    with op.batch_alter_table(
+        "workflowtaskv2", schema=None, naming_convention=NAMING_CONVENTION
+    ) as batch_op:
         batch_op.drop_column("is_legacy_task")
-
-    with op.batch_alter_table("task", schema=None) as batch_op:
-        batch_op.drop_column("is_v2_compatible")
+        batch_op.drop_column("task_legacy_id")
 
 
 def downgrade() -> None:

From 00950261ec018063fba5cb49be6781aa2323ba99 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Tue, 10 Sep 2024 10:57:18 +0200
Subject: [PATCH 40/44] Re-order migration statements

---
 .../501961cfcd85_remove_link_between_v1_and_v2_tasks_.py     | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
index fceeedbd55..41db4dffe7 100644
--- a/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
+++ b/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py
@@ -18,8 +18,6 @@
 
 
 def upgrade() -> None:
-    with op.batch_alter_table("task") as batch_op:
-        batch_op.drop_column("is_v2_compatible")
 
     with op.batch_alter_table("workflowtaskv2") as batch_op:
         batch_op.alter_column(
@@ -64,6 +62,9 @@ def upgrade() -> None:
         batch_op.drop_column("is_legacy_task")
         batch_op.drop_column("task_legacy_id")
 
+    with op.batch_alter_table("task") as batch_op:
+        batch_op.drop_column("is_v2_compatible")
+
 
 def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###

From 9a9d2b6fdaa1ed1df34bf4c29f457e20cf2cbe53 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 11 Sep 2024 09:12:51 +0200
Subject: [PATCH 41/44] Clean up old explanation comment

---
 fractal_server/app/routes/api/v2/_aux_functions.py | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/fractal_server/app/routes/api/v2/_aux_functions.py b/fractal_server/app/routes/api/v2/_aux_functions.py
index 5bd6f1046c..c3280162bf 100644
--- a/fractal_server/app/routes/api/v2/_aux_functions.py
+++ b/fractal_server/app/routes/api/v2/_aux_functions.py
@@ -418,25 +418,21 @@ async def _workflow_insert_task(
     if order is None:
         order = len(db_workflow.task_list)
 
-    # Get task from db, and extract default arguments via a Task property
-    # method
-    # NOTE: this logic remains there for V1 tasks only. When we deprecate V1
-    # tasks, we can simplify this block
+    # Get task from db
     db_task = await db.get(TaskV2, task_id)
     if db_task is None:
         raise ValueError(f"TaskV2 {task_id} not found.")
     task_type = db_task.type
 
-    final_meta_parallel = (db_task.meta_parallel or {}).copy()
-    final_meta_non_parallel = (db_task.meta_non_parallel or {}).copy()
-
     # Combine meta_parallel (higher priority)
     # and db_task.meta_parallel (lower priority)
+    final_meta_parallel = (db_task.meta_parallel or {}).copy()
     final_meta_parallel.update(meta_parallel or {})
     if final_meta_parallel == {}:
         final_meta_parallel = None
     # Combine meta_non_parallel (higher priority)
     # and db_task.meta_non_parallel (lower priority)
+    final_meta_non_parallel = (db_task.meta_non_parallel or {}).copy()
     final_meta_non_parallel.update(meta_non_parallel or {})
     if final_meta_non_parallel == {}:
         final_meta_non_parallel = None

From e28d9ef919427e726676e5d015fb5404bf908f10 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 11 Sep 2024 09:44:32 +0200
Subject: [PATCH 42/44] Update CHANGELOG [skip ci]

---
 CHANGELOG.md | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a44ffebdef..ec0a149b52 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,7 +1,28 @@
 **Note**: Numbers like (\#1234) point to closed Pull Requests on the fractal-server repository.
 
+# 2.5.0 (unreleased)
+
+This release removes support for including V1 tasks in V2 workflows. This comes
+with changes to the database (data and metadata), to the API, and to the V2
+runner.
+
+* Runner:
+    * Deprecate running v1 tasks within v2 workflows (\#1721).
+* Database:
+    * Remove `Task.is_v2_compatible` column (\#1721).
+    * For table `WorkflowTaskV2`, drop `is_legacy_task` and `task_legacy_id` columns, remove `task_legacy` ORM attribute, make `task_id` required, make `task` required (\#1721).
+* API:
+    * Drop v1-v2-task-compatibility admin endpoint (\#1721).
+    * Drop `/task-legacy/` endpoint (\#1721).
+    * Remove legacy task code branches from `WorkflowTaskV2` CRUD endpoints (\#1721).
+
 # 2.4.0
 
+This release introduces support for user groups, but without linking it to any
+access-control rules (which will be introduced later).
+
+> NOTE: This release requires running the `fractalctl update-db-data` script.
+
 * App:
     * Move creation of first user from application startup into `fractalctl set-db` command (\#1738, \#1748).
     * Add creation of default user group into `fractalctl set-db` command (\#1738).

From d973896ab5dd28031a25a204af82b77fd626f91e Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Fri, 13 Sep 2024 13:28:15 +0200
Subject: [PATCH 43/44] Update CHANGELOG.md [skip ci]

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a2b2f26bf2..d5be8b2dae 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
 **Note**: Numbers like (\#1234) point to closed Pull Requests on the fractal-server repository.
 
-# 2.5.0 (unreleased)
+# 2.5.0
 
 This release removes support for including V1 tasks in V2 workflows. This comes
 with changes to the database (data and metadata), to the API, and to the V2

From e49247d64d106ba031ba13c59268eef5fa5d1716 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Fri, 13 Sep 2024 13:28:46 +0200
Subject: [PATCH 44/44] Update __main__.py

---
 fractal_server/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fractal_server/__main__.py b/fractal_server/__main__.py
index 1dba1c2293..b239a0e60e 100644
--- a/fractal_server/__main__.py
+++ b/fractal_server/__main__.py
@@ -86,7 +86,7 @@ def set_db():
     alembic_args = ["-c", alembic_ini.as_posix(), "upgrade", "head"]
     print(f"START: Run alembic.config, with argv={alembic_args}")
     alembic.config.main(argv=alembic_args)
-    print("END: alembic.config\n")
+    print("END: alembic.config")
     # Insert default group
     print()
     _create_first_group()