fractal-server 2.14.1__tar.gz → 2.14.3a0__tar.gz

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.14.1
+Version: 2.14.3a0
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin

fractal_server-2.14.3a0/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.14.3a0"

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/app/routes/admin/v2/job.py

@@ -154,7 +154,7 @@ async def update_job(
     if job_update.status != JobStatusTypeV2.FAILED:
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=f"Cannot set job status to {job_update.status}",
+            detail=f"Cannot set job status to {job_update.status.value}",
         )
 
     setattr(job, "status", job_update.status)

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/app/routes/api/v2/pre_submission_checks.py

@@ -98,11 +98,19 @@ async def check_workflowtask(
     )
 
     if db_workflow_task.order == 0:
+        # Skip check for first task in the workflow
         return JSONResponse(status_code=200, content=[])
 
     previous_wft = db_workflow.task_list[db_workflow_task.order - 1]
 
     if previous_wft.task.output_types != {}:
+        # Skip check if previous task has non-trivial `output_types`
+        return JSONResponse(status_code=200, content=[])
+    elif previous_wft.task.type in [
+        "converter_compound",
+        "converter_non_parallel",
+    ]:
+        # Skip check if previous task is converter
         return JSONResponse(status_code=200, content=[])
 
     res = await _get_dataset_check_owner(

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/app/routes/api/v2/status_legacy.py

@@ -118,8 +118,8 @@ async def get_workflowtask_status(
             )
         except ValueError:
             logger.warning(
-                f"Job {running_job.id} is submitted but its task list does "
-                f"not contain a {WorkflowTaskStatusTypeV2.SUBMITTED} task."
+                f"Job {running_job.id} is submitted but its task list does not"
+                f" contain a {WorkflowTaskStatusTypeV2.SUBMITTED.value} task."
             )
             first_submitted_index = 0
 

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/app/routes/api/v2/task_collection_custom.py

@@ -1,3 +1,4 @@
+import os
 import shlex
 import subprocess  # nosec
 from pathlib import Path
@@ -65,25 +66,36 @@ async def collect_task_custom(
                 detail="Cannot infer 'package_root' with 'slurm_ssh' backend.",
             )
     else:
-        if not Path(task_collect.python_interpreter).is_file():
+        if not os.access(
+            task_collect.python_interpreter, os.X_OK
+        ) or not os.access(task_collect.python_interpreter, os.R_OK):
             raise HTTPException(
                 status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
                 detail=(
                     f"{task_collect.python_interpreter=} "
-                    "doesn't exist or is not a file."
+                    "is not accessible to the Fractal user "
+                    "or it is not executable."
                 ),
             )
-        if (
-            task_collect.package_root is not None
-            and not Path(task_collect.package_root).is_dir()
-        ):
+        if not Path(task_collect.python_interpreter).is_file():
             raise HTTPException(
                 status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                detail=(
-                    f"{task_collect.package_root=} "
-                    "doesn't exist or is not a directory."
-                ),
+                detail=f"{task_collect.python_interpreter=} is not a file.",
             )
+        if task_collect.package_root is not None:
+            if not os.access(task_collect.package_root, os.R_OK):
+                raise HTTPException(
+                    status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                    detail=(
+                        f"{task_collect.package_root=} "
+                        "is not accessible to the Fractal user."
+                    ),
+                )
+            if not Path(task_collect.package_root).is_dir():
+                raise HTTPException(
+                    status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                    detail=f"{task_collect.package_root=} is not a directory.",
+                )
 
     if task_collect.package_root is None:
 

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/app/runner/compress_folder.py

@@ -20,20 +20,9 @@ from fractal_server.logger import get_logger
 from fractal_server.logger import set_logger
 
 
-def _copy_subfolder(src: Path, dest: Path, logger_name: str):
-    t_start = time.perf_counter()
-    cmd_cp = f"cp -r {src.as_posix()} {dest.as_posix()}"
-    logger = get_logger(logger_name=logger_name)
-    logger.debug(f"{cmd_cp=}")
-    res = run_subprocess(cmd=cmd_cp, logger_name=logger_name)
-    elapsed = time.perf_counter() - t_start
-    logger.debug(f"[_copy_subfolder] END {elapsed=} s ({dest.as_posix()})")
-    return res
-
-
 def _create_tar_archive(
     tarfile_path: str,
-    subfolder_path_tmp_copy: Path,
+    subfolder_path: Path,
     logger_name: str,
     filelist_path: str | None,
 ):
@@ -44,39 +33,26 @@ def _create_tar_archive(
     if filelist_path is None:
         cmd_tar = (
             f"tar -c -z -f {tarfile_path} "
-            f"--directory={subfolder_path_tmp_copy.as_posix()} "
+            f"--directory={subfolder_path.as_posix()} "
             "."
         )
     else:
         cmd_tar = (
             f"tar -c -z -f {tarfile_path} "
-            f"--directory={subfolder_path_tmp_copy.as_posix()} "
+            f"--directory={subfolder_path.as_posix()} "
             f"--files-from={filelist_path} --ignore-failed-read"
         )
 
     logger.debug(f"cmd tar:\n{cmd_tar}")
 
-    run_subprocess(cmd=cmd_tar, logger_name=logger_name, allow_char="*")
+    run_subprocess(
+        cmd=cmd_tar,
+        logger_name=logger_name,
+    )
     elapsed = time.perf_counter() - t_start
     logger.debug(f"[_create_tar_archive] END {elapsed=} s ({tarfile_path})")
 
 
-def _remove_temp_subfolder(subfolder_path_tmp_copy: Path, logger_name: str):
-    logger = get_logger(logger_name)
-    t_start = time.perf_counter()
-    try:
-        cmd_rm = f"rm -rf {subfolder_path_tmp_copy}"
-        logger.debug(f"cmd rm:\n{cmd_rm}")
-        run_subprocess(cmd=cmd_rm, logger_name=logger_name, allow_char="*")
-    except Exception as e:
-        logger.debug(f"ERROR during {cmd_rm}: {e}")
-    elapsed = time.perf_counter() - t_start
-    logger.debug(
-        f"[_remove_temp_subfolder] END {elapsed=} s "
-        f"({subfolder_path_tmp_copy=})"
-    )
-
-
 def compress_folder(
     subfolder_path: Path,
     filelist_path: str | None,
@@ -110,18 +86,11 @@ def compress_folder(
     tarfile_path = (parent_dir / f"{subfolder_name}.tar.gz").as_posix()
     logger.debug(f"{tarfile_path=}")
 
-    subfolder_path_tmp_copy = (
-        subfolder_path.parent / f"{subfolder_path.name}_copy"
-    )
     try:
-        _copy_subfolder(
-            subfolder_path,
-            subfolder_path_tmp_copy,
-            logger_name=logger_name,
-        )
+
         _create_tar_archive(
             tarfile_path,
-            subfolder_path_tmp_copy,
+            subfolder_path,
             logger_name=logger_name,
             filelist_path=filelist_path,
         )
@@ -129,12 +98,15 @@ def compress_folder(
 
     except Exception as e:
         logger.debug(f"ERROR: {e}")
-        sys.exit(1)
+        cmd_rm = f"rm {tarfile_path}"
+        try:
+            run_subprocess(cmd=cmd_rm, logger_name=logger_name)
+        except Exception as e_rm:
+            logger.error(
+                f"Running {cmd_rm=} failed, original error: {str(e_rm)}."
+            )
 
-    finally:
-        _remove_temp_subfolder(
-            subfolder_path_tmp_copy, logger_name=logger_name
-        )
+        sys.exit(1)
 
 
 def main(

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/app/runner/executors/slurm_common/remote.py

@@ -18,7 +18,6 @@ import logging
 import os
 import sys
 from typing import Literal
-from typing import Optional
 from typing import Union
 
 import cloudpickle
@@ -91,7 +90,6 @@ def worker(
     *,
     in_fname: str,
     out_fname: str,
-    extra_import_paths: Optional[str] = None,
 ) -> None:
     """
     Execute a job, possibly on a remote node.
@@ -99,7 +97,6 @@ def worker(
     Arguments:
         in_fname: Absolute path to the input pickle file (must be readable).
         out_fname: Absolute path of the output pickle file (must be writeable).
-        extra_import_paths: Additional import paths
     """
 
     # Create output folder, if missing
@@ -108,10 +105,6 @@ def worker(
         logging.debug(f"_slurm.remote.worker: create {out_dir=}")
         os.mkdir(out_dir)
 
-    if extra_import_paths:
-        _extra_import_paths = extra_import_paths.split(":")
-        sys.path[:0] = _extra_import_paths
-
     # Execute the job and capture exceptions
     try:
         with open(in_fname, "rb") as f:
@@ -167,18 +160,11 @@ if __name__ == "__main__":
         help="Path of output pickle file",
         required=True,
     )
-    parser.add_argument(
-        "--extra-import-paths",
-        type=str,
-        help="Extra import paths",
-        required=False,
-    )
     parsed_args = parser.parse_args()
     logging.debug(f"{parsed_args=}")
 
     kwargs = dict(
-        in_fname=parsed_args.input_file, out_fname=parsed_args.output_file
+        in_fname=parsed_args.input_file,
+        out_fname=parsed_args.output_file,
     )
-    if parsed_args.extra_import_paths:
-        kwargs["extra_import_paths"] = parsed_args.extra_import_paths
     worker(**kwargs)

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/app/runner/v2/runner.py

@@ -9,6 +9,7 @@ from typing import Optional
 
 from sqlalchemy.orm.attributes import flag_modified
 from sqlmodel import delete
+from sqlmodel import update
 
 from ....images import SingleImage
 from ....images.tools import filter_image_list
@@ -25,6 +26,7 @@ from fractal_server.app.models.v2 import AccountingRecord
 from fractal_server.app.models.v2 import DatasetV2
 from fractal_server.app.models.v2 import HistoryImageCache
 from fractal_server.app.models.v2 import HistoryRun
+from fractal_server.app.models.v2 import HistoryUnit
 from fractal_server.app.models.v2 import TaskGroupV2
 from fractal_server.app.models.v2 import WorkflowTaskV2
 from fractal_server.app.runner.executors.base_runner import BaseRunner
@@ -219,139 +221,160 @@ def execute_tasks_v2(
             num_tasks = 0
 
         # POST TASK EXECUTION
-
-        non_failed_task_outputs = [
-            value.task_output
-            for value in outcomes_dict.values()
-            if value.task_output is not None
-        ]
-        if len(non_failed_task_outputs) > 0:
-            current_task_output = merge_outputs(non_failed_task_outputs)
-            # If `current_task_output` includes no images (to be created or
-            # removed), then flag all the input images as modified.
-            # See fractal-server issues #1374 and #2409.
-            if (
-                current_task_output.image_list_updates == []
-                and current_task_output.image_list_removals == []
-            ):
-                current_task_output = TaskOutput(
-                    image_list_updates=[
-                        dict(zarr_url=img["zarr_url"])
-                        for img in filtered_images
-                    ],
-                )
-        else:
-            current_task_output = TaskOutput()
-
-        # Update image list
-        num_new_images = 0
-        current_task_output.check_zarr_urls_are_unique()
-        # NOTE: In principle we could make the task-output processing more
-        # granular, and also associate output-processing failures to history
-        # status.
-        for image_obj in current_task_output.image_list_updates:
-            image = image_obj.model_dump()
-            if image["zarr_url"] in [img["zarr_url"] for img in tmp_images]:
-                img_search = find_image_by_zarr_url(
-                    images=tmp_images,
-                    zarr_url=image["zarr_url"],
-                )
-                if img_search is None:
-                    raise ValueError(
-                        "Unexpected error: "
-                        f"Image with zarr_url {image['zarr_url']} not found, "
-                        "while updating image list."
-                    )
-                existing_image_index = img_search["index"]
-
+        try:
+            non_failed_task_outputs = [
+                value.task_output
+                for value in outcomes_dict.values()
+                if value.task_output is not None
+            ]
+            if len(non_failed_task_outputs) > 0:
+                current_task_output = merge_outputs(non_failed_task_outputs)
+                # If `current_task_output` includes no images (to be created or
+                # removed), then flag all the input images as modified.
+                # See fractal-server issues #1374 and #2409.
                 if (
-                    image["origin"] is None
-                    or image["origin"] == image["zarr_url"]
+                    current_task_output.image_list_updates == []
+                    and current_task_output.image_list_removals == []
                 ):
-                    # CASE 1: Edit existing image
-                    existing_image = img_search["image"]
-                    new_attributes = copy(existing_image["attributes"])
-                    new_types = copy(existing_image["types"])
-                    new_image = dict(
+                    current_task_output = TaskOutput(
+                        image_list_updates=[
+                            dict(zarr_url=img["zarr_url"])
+                            for img in filtered_images
+                        ],
+                    )
+            else:
+                current_task_output = TaskOutput()
+
+            # Update image list
+            num_new_images = 0
+            current_task_output.check_zarr_urls_are_unique()
+            # NOTE: In principle we could make the task-output processing more
+            # granular, and also associate output-processing failures to
+            # history status.
+            for image_obj in current_task_output.image_list_updates:
+                image = image_obj.model_dump()
+                if image["zarr_url"] in [
+                    img["zarr_url"] for img in tmp_images
+                ]:
+                    img_search = find_image_by_zarr_url(
+                        images=tmp_images,
                         zarr_url=image["zarr_url"],
                     )
-                    if "origin" in existing_image.keys():
-                        new_image["origin"] = existing_image["origin"]
+                    if img_search is None:
+                        raise ValueError(
+                            "Unexpected error: "
+                            f"Image with zarr_url {image['zarr_url']} not "
+                            "found, while updating image list."
+                        )
+                    existing_image_index = img_search["index"]
+
+                    if (
+                        image["origin"] is None
+                        or image["origin"] == image["zarr_url"]
+                    ):
+                        # CASE 1: Edit existing image
+                        existing_image = img_search["image"]
+                        new_attributes = copy(existing_image["attributes"])
+                        new_types = copy(existing_image["types"])
+                        new_image = dict(
+                            zarr_url=image["zarr_url"],
+                        )
+                        if "origin" in existing_image.keys():
+                            new_image["origin"] = existing_image["origin"]
+                    else:
+                        # CASE 2: Re-create existing image based on `origin`
+                        # Propagate attributes and types from `origin` (if any)
+                        (
+                            new_attributes,
+                            new_types,
+                        ) = get_origin_attribute_and_types(
+                            origin_url=image["origin"],
+                            images=tmp_images,
+                        )
+                        new_image = dict(
+                            zarr_url=image["zarr_url"],
+                            origin=image["origin"],
+                        )
+                    # Update attributes
+                    new_attributes.update(image["attributes"])
+                    new_attributes = drop_none_attributes(new_attributes)
+                    new_image["attributes"] = new_attributes
+                    # Update types
+                    new_types.update(image["types"])
+                    new_types.update(task.output_types)
+                    new_image["types"] = new_types
+                    # Validate new image
+                    SingleImage(**new_image)
+                    # Update image in the dataset image list
+                    tmp_images[existing_image_index] = new_image
+
                 else:
-                    # CASE 2: Re-create existing image based on `origin`
+                    # CASE 3: Add new image
+                    # Check that image['zarr_url'] is a subfolder of zarr_dir
+                    if (
+                        not image["zarr_url"].startswith(zarr_dir)
+                        or image["zarr_url"] == zarr_dir
+                    ):
+                        raise JobExecutionError(
+                            "Cannot create image if zarr_url is not a "
+                            "subfolder of zarr_dir.\n"
+                            f"zarr_dir: {zarr_dir}\n"
+                            f"zarr_url: {image['zarr_url']}"
+                        )
+
                     # Propagate attributes and types from `origin` (if any)
                     new_attributes, new_types = get_origin_attribute_and_types(
                         origin_url=image["origin"],
                         images=tmp_images,
                     )
+                    # Prepare new image
+                    new_attributes.update(image["attributes"])
+                    new_attributes = drop_none_attributes(new_attributes)
+                    new_types.update(image["types"])
+                    new_types.update(task.output_types)
                     new_image = dict(
                         zarr_url=image["zarr_url"],
                         origin=image["origin"],
+                        attributes=new_attributes,
+                        types=new_types,
                     )
-                # Update attributes
-                new_attributes.update(image["attributes"])
-                new_attributes = drop_none_attributes(new_attributes)
-                new_image["attributes"] = new_attributes
-                # Update types
-                new_types.update(image["types"])
-                new_types.update(task.output_types)
-                new_image["types"] = new_types
-                # Validate new image
-                SingleImage(**new_image)
-                # Update image in the dataset image list
-                tmp_images[existing_image_index] = new_image
+                    # Validate new image
+                    SingleImage(**new_image)
+                    # Add image into the dataset image list
+                    tmp_images.append(new_image)
+                    num_new_images += 1
 
-            else:
-                # CASE 3: Add new image
-                # Check that image['zarr_url'] is a subfolder of zarr_dir
-                if (
-                    not image["zarr_url"].startswith(zarr_dir)
-                    or image["zarr_url"] == zarr_dir
-                ):
+            # Remove images from tmp_images
+            for img_zarr_url in current_task_output.image_list_removals:
+                img_search = find_image_by_zarr_url(
+                    images=tmp_images, zarr_url=img_zarr_url
+                )
+                if img_search is None:
                     raise JobExecutionError(
-                        "Cannot create image if zarr_url is not a subfolder "
-                        "of zarr_dir.\n"
-                        f"zarr_dir: {zarr_dir}\n"
-                        f"zarr_url: {image['zarr_url']}"
+                        "Cannot remove missing image "
+                        f"(zarr_url={img_zarr_url})."
                     )
+                else:
+                    tmp_images.pop(img_search["index"])
 
-                # Propagate attributes and types from `origin` (if any)
-                new_attributes, new_types = get_origin_attribute_and_types(
-                    origin_url=image["origin"],
-                    images=tmp_images,
-                )
-                # Prepare new image
-                new_attributes.update(image["attributes"])
-                new_attributes = drop_none_attributes(new_attributes)
-                new_types.update(image["types"])
-                new_types.update(task.output_types)
-                new_image = dict(
-                    zarr_url=image["zarr_url"],
-                    origin=image["origin"],
-                    attributes=new_attributes,
-                    types=new_types,
-                )
-                # Validate new image
-                SingleImage(**new_image)
-                # Add image into the dataset image list
-                tmp_images.append(new_image)
-                num_new_images += 1
-
-        # Remove images from tmp_images
-        for img_zarr_url in current_task_output.image_list_removals:
-            img_search = find_image_by_zarr_url(
-                images=tmp_images, zarr_url=img_zarr_url
+            # Update type_filters based on task-manifest output_types
+            type_filters_from_task_manifest = task.output_types
+            current_dataset_type_filters.update(
+                type_filters_from_task_manifest
             )
-            if img_search is None:
-                raise JobExecutionError(
-                    f"Cannot remove missing image (zarr_url={img_zarr_url})."
+        except Exception as e:
+            logger.error(
+                "Unexpected error in post-task-execution block. "
+                f"Original error: {str(e)}"
+            )
+            with next(get_sync_db()) as db:
+                db.execute(
+                    update(HistoryUnit)
+                    .where(HistoryUnit.history_run_id == history_run_id)
+                    .values(status=HistoryUnitStatus.FAILED)
                 )
-            else:
-                tmp_images.pop(img_search["index"])
-
-        # Update type_filters based on task-manifest output_types
-        type_filters_from_task_manifest = task.output_types
-        current_dataset_type_filters.update(type_filters_from_task_manifest)
+                db.commit()
+            raise e
 
         with next(get_sync_db()) as db:
             # Write current dataset images into the database.

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/tasks/v2/local/collect.py

@@ -132,7 +132,7 @@ def collect_local(
                     ).as_posix(),
                     prefix=(
                         f"{int(time.time())}_"
-                        f"{TaskGroupActivityActionV2.COLLECT}_"
+                        f"{TaskGroupActivityActionV2.COLLECT.value}_"
                     ),
                     logger_name=LOGGER_NAME,
                 )

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/tasks/v2/local/deactivate.py

@@ -107,7 +107,7 @@ def deactivate_local(
                         ).as_posix(),
                         prefix=(
                             f"{int(time.time())}_"
-                            f"{TaskGroupActivityActionV2.DEACTIVATE}_"
+                            f"{TaskGroupActivityActionV2.DEACTIVATE.value}_"
                         ),
                         logger_name=LOGGER_NAME,
                     )

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/tasks/v2/local/reactivate.py

@@ -107,7 +107,7 @@ def reactivate_local(
                     ).as_posix(),
                     prefix=(
                         f"{int(time.time())}_"
-                        f"{TaskGroupActivityActionV2.REACTIVATE}_"
+                        f"{TaskGroupActivityActionV2.REACTIVATE.value}_"
                     ),
                     logger_name=LOGGER_NAME,
                 )

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/tasks/v2/ssh/collect.py

@@ -166,7 +166,7 @@ def collect_ssh(
                     script_dir_remote=script_dir_remote,
                     prefix=(
                         f"{int(time.time())}_"
-                        f"{TaskGroupActivityActionV2.COLLECT}"
+                        f"{TaskGroupActivityActionV2.COLLECT.value}"
                     ),
                     fractal_ssh=fractal_ssh,
                     logger_name=LOGGER_NAME,

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/tasks/v2/ssh/deactivate.py

@@ -136,7 +136,7 @@ def deactivate_ssh(
                         script_dir_remote=script_dir_remote,
                         prefix=(
                             f"{int(time.time())}_"
-                            f"{TaskGroupActivityActionV2.DEACTIVATE}"
+                            f"{TaskGroupActivityActionV2.DEACTIVATE.value}"
                         ),
                         fractal_ssh=fractal_ssh,
                         logger_name=LOGGER_NAME,

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/fractal_server/tasks/v2/ssh/reactivate.py

@@ -144,7 +144,7 @@ def reactivate_ssh(
                     script_dir_remote=script_dir_remote,
                     prefix=(
                         f"{int(time.time())}_"
-                        f"{TaskGroupActivityActionV2.REACTIVATE}"
+                        f"{TaskGroupActivityActionV2.REACTIVATE.value}"
                     ),
                     fractal_ssh=fractal_ssh,
                     logger_name=LOGGER_NAME,

{fractal_server-2.14.1 → fractal_server-2.14.3a0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.14.1"
+version = "2.14.3a0"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -95,7 +95,7 @@ filterwarnings = [
 markers = ["container", "ssh"]
 
 [tool.bumpver]
-current_version = "2.14.1"
+current_version = "2.14.3a0"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.14.1/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.14.1"