fractal-server 2.14.3__py3-none-any.whl → 2.14.4__py3-none-any.whl

fractal_server/types/__init__.py

@@ -0,0 +1,87 @@
+from typing import Annotated
+from typing import Any
+from typing import Optional
+from typing import Union
+
+from pydantic import AfterValidator
+from pydantic.types import NonNegativeInt
+from pydantic.types import StringConstraints
+
+from ..urls import normalize_url
+from .validators import val_absolute_path
+from .validators import val_http_url
+from .validators import val_unique_list
+from .validators import valdict_keys
+from .validators import validate_attribute_filters
+from .validators import validate_wft_args
+
+NonEmptyStr = Annotated[
+    str,
+    StringConstraints(min_length=1, strip_whitespace=True),
+]
+
+AbsolutePathStr = Annotated[
+    NonEmptyStr,
+    AfterValidator(val_absolute_path),
+]
+HttpUrlStr = Annotated[
+    NonEmptyStr,
+    AfterValidator(val_http_url),
+]
+ZarrUrlStr = Annotated[
+    NonEmptyStr,
+    AfterValidator(normalize_url),
+]
+ZarrDirStr = Annotated[
+    NonEmptyStr,
+    AfterValidator(normalize_url),
+]
+
+DictStrAny = Annotated[
+    dict[str, Any],
+    AfterValidator(valdict_keys),
+]
+DictStrStr = Annotated[
+    dict[str, NonEmptyStr],
+    AfterValidator(valdict_keys),
+]
+
+ListUniqueNonEmptyString = Annotated[
+    list[NonEmptyStr],
+    AfterValidator(val_unique_list),
+]
+ListUniqueNonNegativeInt = Annotated[
+    list[NonNegativeInt],
+    AfterValidator(val_unique_list),
+]
+ListUniqueAbsolutePathStr = Annotated[
+    list[AbsolutePathStr],
+    AfterValidator(val_unique_list),
+]
+
+WorkflowTaskArgument = Annotated[
+    DictStrAny,
+    AfterValidator(validate_wft_args),
+]
+
+ImageAttributeValue = Union[int, float, str, bool]
+ImageAttributes = Annotated[
+    dict[str, ImageAttributeValue],
+    AfterValidator(valdict_keys),
+]
+ImageAttributesWithNone = Annotated[
+    dict[str, Optional[ImageAttributeValue]],
+    AfterValidator(valdict_keys),
+]
+AttributeFilters = Annotated[
+    dict[str, list[ImageAttributeValue]],
+    AfterValidator(validate_attribute_filters),
+]
+TypeFilters = Annotated[
+    dict[str, bool],
+    AfterValidator(valdict_keys),
+]
+ImageTypes = Annotated[
+    dict[str, bool],
+    AfterValidator(valdict_keys),
+]

fractal_server/types/validators/__init__.py

@@ -0,0 +1,6 @@
+from ._common_validators import val_absolute_path  # noqa F401
+from ._common_validators import val_http_url  # noqa F401
+from ._common_validators import val_unique_list  # noqa F401
+from ._common_validators import valdict_keys  # noqa F401
+from ._filter_validators import validate_attribute_filters  # noqa F401
+from ._workflow_task_arguments_validators import validate_wft_args  # noqa F401

fractal_server/types/validators/_common_validators.py

@@ -0,0 +1,42 @@
+import os
+from typing import Any
+
+from pydantic import HttpUrl
+
+
+def valdict_keys(d: dict[str, Any]) -> dict[str, Any]:
+    """
+    Strip every key of the dictionary, and fail if there are identical keys
+    """
+    old_keys = list(d.keys())
+    new_keys = [key.strip() for key in old_keys]
+    if any(k == "" for k in new_keys):
+        raise ValueError(f"Empty string in {new_keys}.")
+    if len(new_keys) != len(set(new_keys)):
+        raise ValueError(
+            f"Dictionary contains multiple identical keys: '{d}'."
+        )
+    for old_key, new_key in zip(old_keys, new_keys):
+        if new_key != old_key:
+            d[new_key] = d.pop(old_key)
+    return d
+
+
+def val_absolute_path(path: str) -> str:
+    """
+    Check that a string attribute is an absolute path
+    """
+    if not os.path.isabs(path):
+        raise ValueError(f"String must be an absolute path (given '{path}').")
+    return path
+
+
+def val_unique_list(must_be_unique: list) -> list:
+    if len(set(must_be_unique)) != len(must_be_unique):
+        raise ValueError("List has repetitions")
+    return must_be_unique
+
+
+def val_http_url(value: str) -> str:
+    HttpUrl(value)
+    return value

fractal_server/types/validators/_filter_validators.py

@@ -0,0 +1,24 @@
+from typing import Any
+from typing import Union
+
+from ._common_validators import valdict_keys
+
+
+def validate_attribute_filters(
+    attribute_filters: dict[str, list[Union[int, float, str, bool]]]
+) -> dict[str, list[Any]]:
+    attribute_filters = valdict_keys(attribute_filters)
+    for key, values in attribute_filters.items():
+        if values == []:
+            raise ValueError(
+                f"attribute_filters[{key}] cannot be an empty list."
+            )
+        else:
+            # values is a non-empty list, and its items must homogeneous
+            _type = type(values[0])
+            if not all(type(value) is _type for value in values):
+                raise ValueError(
+                    f"attribute_filters[{key}] has values with "
+                    f"non-homogeneous types: {values}."
+                )
+    return attribute_filters

fractal_server/types/validators/_workflow_task_arguments_validators.py

@@ -0,0 +1,10 @@
+def validate_wft_args(value: dict) -> dict:
+    RESERVED_ARGUMENTS = {"zarr_dir", "zarr_url", "zarr_urls", "init_args"}
+    args_keys = set(value.keys())
+    intersect_keys = RESERVED_ARGUMENTS.intersection(args_keys)
+    if intersect_keys:
+        raise ValueError(
+            "`args` contains the following forbidden keys: "
+            f"{intersect_keys}"
+        )
+    return value

{fractal_server-2.14.3.dist-info → fractal_server-2.14.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.14.3
+Version: 2.14.4
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin

{fractal_server-2.14.3.dist-info → fractal_server-2.14.4.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=20SgG8fPO0eewuM_dSHcBRp5Xaupoj5yomTxw0STcSI,23
+fractal_server/__init__.py,sha256=1GpRTVyXaEa3G3t4ruCfoTeyVcAd3cK5jro1DmuxzU0,23
 fractal_server/__main__.py,sha256=rkM8xjY1KeS3l63irB8yCrlVobR-73uDapC4wvrIlxI,6957
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -13,7 +13,7 @@ fractal_server/app/models/v2/__init__.py,sha256=vjHwek7-IXmaZZL9VF0nD30YL9ca4wNc
 fractal_server/app/models/v2/accounting.py,sha256=f2ALxfKKBNxFLJTtC2-YqRepVK253x68y7zkD2V_Nls,1115
 fractal_server/app/models/v2/dataset.py,sha256=Xa3YLmqvSChBJoqlSsjmt-5x0zC-6rSx2eafFnMukfo,1240
 fractal_server/app/models/v2/history.py,sha256=6yuYhsXgahHxv5FmDdv__aFndT228_rBFjTtkS-3Ohg,2082
-fractal_server/app/models/v2/job.py,sha256=JWrEjX_E4iRFr5MbmtV_aY28J-5D469awLr0rfa5Kig,2052
+fractal_server/app/models/v2/job.py,sha256=8BYqjeKUrAUVnt3RYHAqNdtl2GO-qGCRX4jWunLjsnU,2036
 fractal_server/app/models/v2/project.py,sha256=rAHoh5KfYwIaW7rTX0_O0jvWmxEvfo1BafvmcXuSSRk,786
 fractal_server/app/models/v2/task.py,sha256=8KEROaadgccXRZIP7EriBp2j1FgzYkgiirOi5_fG79M,1494
 fractal_server/app/models/v2/task_group.py,sha256=yIzKAyJIFYYhG_K3AO-WGWYftygrk5D8H_WvAB7QnQk,3541
@@ -37,9 +37,9 @@ fractal_server/app/routes/api/v2/_aux_functions_task_lifecycle.py,sha256=qdXCb6I
 fractal_server/app/routes/api/v2/_aux_functions_tasks.py,sha256=uhNSs-jcS7ndIUFKiOC1yrDiViw3uvKEXi9UL04BMks,11642
 fractal_server/app/routes/api/v2/dataset.py,sha256=h5AhE0sdhQ20ZlIbEJsFnHIOUW0S1VHFpoflpBkVScs,8936
 fractal_server/app/routes/api/v2/history.py,sha256=pDztvwQFOh3JChtSk9GIG3H17yg4G5pk1mq14qXF4Ck,17793
-fractal_server/app/routes/api/v2/images.py,sha256=BGpO94gVd8BTpCN6Mun2RXmjrPmfkIp73m8RN7uiGW4,8361
+fractal_server/app/routes/api/v2/images.py,sha256=Ly5Q4yzzm3w-roJi_ZBdzvcP_XUC7pwLPHMv8RnhI6Q,7743
 fractal_server/app/routes/api/v2/job.py,sha256=MU1sHIKk_89WrD0TD44d4ufzqnywot7On_W71KjyUbQ,6500
-fractal_server/app/routes/api/v2/pre_submission_checks.py,sha256=WyJAco9-96c15ImjgvsNfhd2169gG29CXkwtCTVLs38,4816
+fractal_server/app/routes/api/v2/pre_submission_checks.py,sha256=8pG8DbO5Ipk85VaNN9sfVTwXHGAWwk65OrsyRN4iWSo,4800
 fractal_server/app/routes/api/v2/project.py,sha256=uAZgATiHcOvbnRX-vv1D3HoaEUvLUd7vzVmGcqOP8ZY,4602
 fractal_server/app/routes/api/v2/status_legacy.py,sha256=0QlbBErOT2Idf-LT0EvOiPtTjrm6WmIY0k69NOgjmWk,6355
 fractal_server/app/routes/api/v2/submit.py,sha256=hCwwC6bXP7EyhgGyVLv1ClybRH1YytDVoPunOzpsf0s,8822
@@ -67,7 +67,6 @@ fractal_server/app/routes/aux/validate_user_settings.py,sha256=FLVi__8YFcm_6c_K5
 fractal_server/app/routes/pagination.py,sha256=L8F5JqekF39qz-LpeScdlhb57MQnSRXjK4ZEtsZqYLk,1210
 fractal_server/app/runner/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/components.py,sha256=-Ii5l8d_V6f5DFOd-Zsr8VYmOsyqw0Hox9fEFQiuqxY,66
-fractal_server/app/runner/compress_folder.py,sha256=3X8eyC5sdTJqOgWiMKCu-1wI658gVMXRuHKBcqHpFWo,3811
 fractal_server/app/runner/exceptions.py,sha256=JC5ufHyeA1hYD_rkZUscI30DD8D903ncag7Z3AArmUY,4215
 fractal_server/app/runner/executors/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/base_runner.py,sha256=4xxMpYycIeAOz5niaJj2xtVW_Cq-shCxP1qk4g-KwOM,5137
@@ -84,59 +83,57 @@ fractal_server/app/runner/executors/slurm_common/remote.py,sha256=Z7cnAlhYi9Orge
 fractal_server/app/runner/executors/slurm_common/slurm_job_task_models.py,sha256=RoxHLKOn0_wGjnY0Sv0a9nDSiqxYZHKRoMkT3p9_G1E,3607
 fractal_server/app/runner/executors/slurm_common/utils_executors.py,sha256=naPyJI0I3lD-sYHbSXbMFGUBK4h_SggA5V91Z1Ch1Xg,1416
 fractal_server/app/runner/executors/slurm_ssh/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/app/runner/executors/slurm_ssh/runner.py,sha256=yKK_cjskHDiasn_QQ-k14GhplP3tNaK7Kp4yiVn44Y0,9437
+fractal_server/app/runner/executors/slurm_ssh/run_subprocess.py,sha256=vlkJ0S37wYOmLG6gKC5-x8mBivYcgK7HTVvaroBnqLk,1030
+fractal_server/app/runner/executors/slurm_ssh/runner.py,sha256=IJ6fHidj8Yv0H59NzOgd3ZIgYuCiOmlkB1_Rt8Jt-Qo,7901
+fractal_server/app/runner/executors/slurm_ssh/tar_commands.py,sha256=g173siyv7qtjov5i-CjTVRT8d19ibK8re3RVWbsdHYA,1845
 fractal_server/app/runner/executors/slurm_sudo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm_sudo/_subprocess_run_as_user.py,sha256=BlOz4NElv3v7rUYefyeki33uaJxcSDk6rPuVZx9ocdw,2776
 fractal_server/app/runner/executors/slurm_sudo/runner.py,sha256=zT-DH61oPEq4dvo08EMnXv3QMYpwAZ3teY7R3MJ5G_8,6291
-fractal_server/app/runner/extract_archive.py,sha256=8h6ZX7Gy0Vqv5KmrEGbWGPuA0MvW207cQZ-8CPYjwXc,2800
 fractal_server/app/runner/filenames.py,sha256=lPnxKHtdRizr6FqG3zOdjDPyWA7GoaJGTtiuJV0gA8E,70
-fractal_server/app/runner/run_subprocess.py,sha256=c3JbYXq3hX2aaflQU19qJ5Xs6J6oXGNvnTEoAfv2bxc,959
 fractal_server/app/runner/set_start_and_last_task_index.py,sha256=-q4zVybAj8ek2XlbENKlfOAJ39hT_zoJoZkqzDqiAMY,1254
 fractal_server/app/runner/shutdown.py,sha256=9pfSKHDNdIcm0eY-opgRTi7y0HmvfPmYiu9JR6Idark,2082
 fractal_server/app/runner/task_files.py,sha256=27xFuPzSJc1Pw912CfSMPOhOIpvNwpkyLCnycqdo9lw,4365
 fractal_server/app/runner/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/app/runner/v2/_local.py,sha256=Ggdxx_XOlMya3bgXn_vGd2WMNVmLQaO3w9ZPaxYlRQk,3088
-fractal_server/app/runner/v2/_slurm_ssh.py,sha256=CEaJLajwdDjdpxY1_7aTLb9wqgzeOuxLlSewScMEx_Y,3322
-fractal_server/app/runner/v2/_slurm_sudo.py,sha256=TVihkQKMX6YWEWxXJjQo0WEQOjVy7FVVLmbM3MCulR0,3037
+fractal_server/app/runner/v2/_local.py,sha256=fJfSpY72BJeO_hGISIK1jE5q7lx3z3fv9_hlhNcJHLM,3072
+fractal_server/app/runner/v2/_slurm_ssh.py,sha256=zQYvuTF_pNuBm9t73CSnhxvh1z_fgp2EkXJWclHiI5I,3306
+fractal_server/app/runner/v2/_slurm_sudo.py,sha256=KmRBGFw9NDNMuMLp4H72iSj4NA3hm9f6OHJHkrMQmHM,3021
 fractal_server/app/runner/v2/db_tools.py,sha256=du5dKhMMFMErQXbGIgu9JvO_vtMensodyPsyDeqz1yQ,3324
 fractal_server/app/runner/v2/deduplicate_list.py,sha256=IVTE4abBU1bUprFTkxrTfYKnvkNTanWQ-KWh_etiT08,645
 fractal_server/app/runner/v2/merge_outputs.py,sha256=D1L4Taieq9i71SPQyNc1kMokgHh-sV_MqF3bv7QMDBc,907
-fractal_server/app/runner/v2/runner.py,sha256=tYG-LB9Dm9_Lz3uYgAhcIeeFLy5I6xMqCdVuUKNXyII,17717
+fractal_server/app/runner/v2/runner.py,sha256=2NQhcaGDw6XJ6Mnmiubru0yq2PpgF6fWFIE5hOVnOY0,17701
 fractal_server/app/runner/v2/runner_functions.py,sha256=AzsE7VF6NMz_5qc0htQkfow5_2rr-wkx50vFJTndj8I,19250
 fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=_h_OOffq3d7V0uHa8Uvs0mj31y1GSZBUXjDDF3WjVjY,3620
 fractal_server/app/runner/v2/submit_workflow.py,sha256=QywUGIoHAHnrWgfnyX8W9kVqKY-RvVyNLpzrbsXZOZ4,13075
-fractal_server/app/runner/v2/task_interface.py,sha256=IXdQTI8rXFgXv1Ez0js4CjKFf3QwO2GCHRTuwiFtiTQ,2891
+fractal_server/app/runner/v2/task_interface.py,sha256=vVNSLiUTnImo82dp910KqP4gYLX3aoiLSJsfvdzGems,2561
 fractal_server/app/runner/versions.py,sha256=dSaPRWqmFPHjg20kTCHmi_dmGNcCETflDtDLronNanU,852
 fractal_server/app/schemas/__init__.py,sha256=stURAU_t3AOBaH0HSUbV-GKhlPKngnnIMoqWc3orFyI,135
-fractal_server/app/schemas/_filter_validators.py,sha256=Gkf2USrkuxZx1TWeeMRmhgfmG60AAIDQfbaWslLsvJQ,1572
-fractal_server/app/schemas/_validators.py,sha256=ZzTlTTzRATzf9Snx4Xp67aDmG77GaM2ewssFtlxQaaY,2680
-fractal_server/app/schemas/user.py,sha256=oCftAKeHdFFowpLyh1G-RiylR8cIO7fTn0PkT5xjs0E,2494
-fractal_server/app/schemas/user_group.py,sha256=Uao1igRYflBu7Dg6Zs0kaFU3zBFJzIwDLrkFfaJk6z8,2176
-fractal_server/app/schemas/user_settings.py,sha256=z7hx54yTrWfjo98oX_1lkeRh1UGrC1dSRH6yIOpnCsY,2772
+fractal_server/app/schemas/user.py,sha256=0e4fWin0EdStjlbUnNWl7GsvnVfKMJPmVPCt-Mm_9tg,1945
+fractal_server/app/schemas/user_group.py,sha256=ejk5qHLbmmDotXT6_--kkoDHVm-T5nS9GDtivJ4LjZU,1456
+fractal_server/app/schemas/user_settings.py,sha256=KgfFdYI36_4OPeBrqxj5l-J5xYuRj7QORPtviLqHSM4,1948
 fractal_server/app/schemas/v2/__init__.py,sha256=wXS4ZEzobWx5dh-XLjMZWpd-JMwWFPODUeUVoMQGRv4,3099
 fractal_server/app/schemas/v2/accounting.py,sha256=Wylt7uWTiDIFlHJOh4XEtYitk2FjFlmnodDrJDxcr0E,397
-fractal_server/app/schemas/v2/dataset.py,sha256=xNWdOW8hhL5Wx-iwyUPrZfWcC8fFuGDgdOHvZLbGVME,2782
+fractal_server/app/schemas/v2/dataset.py,sha256=WSG9QQtcoC6ueDHxXH4mIJhFhlePpAo4N3sWJbluthY,1762
 fractal_server/app/schemas/v2/dumps.py,sha256=uc9itXekO5IFfR6UucpQ5BX9NZZ8erE4hRR6S6aXlOc,2284
 fractal_server/app/schemas/v2/history.py,sha256=Y3rc96DOPGQGZWJtBYVHiBjMQEhFtMq4WGkV4vs1oDE,1675
-fractal_server/app/schemas/v2/job.py,sha256=OXPB4oPiMVWYgZu0lGzM_LGACvhWBavsW7c3MmivdDM,4556
-fractal_server/app/schemas/v2/manifest.py,sha256=8mmB0QwxEgAeGgwKD_fT-o-wFy7lb6HxNXbp17IJqNY,7281
-fractal_server/app/schemas/v2/project.py,sha256=ulgCmUnX0w-0jrSjVYIT7sxeK95CSNGh2msXydhsgYI,885
+fractal_server/app/schemas/v2/job.py,sha256=Km7Im3i5OxI8NfBkIxAZFot_4LEBZNfL40Y-sFm5c0k,3363
+fractal_server/app/schemas/v2/manifest.py,sha256=wYYNLkcyc93AtcxTg4PhjlKRIKRwGGrTWrCwM8D2Uqw,6880
+fractal_server/app/schemas/v2/project.py,sha256=l96-3bCfB3knhITaLj1WSyBgbzP_k8CdtvgX_5jO_fU,657
 fractal_server/app/schemas/v2/status_legacy.py,sha256=vc6C3Xri8222bb9OmsghMz05CNuEalO-t2s_nKo341s,954
-fractal_server/app/schemas/v2/task.py,sha256=8vc8c3ZL6dJo9kyCrfKozgO_pF37BBLvD5XYIXynlEc,6551
-fractal_server/app/schemas/v2/task_collection.py,sha256=dLu4sy-su5k5vDJqCZdJMW8mLT5TX2SV60l_RAvKhwY,5930
-fractal_server/app/schemas/v2/task_group.py,sha256=A3SFHNHLKPJyrnDz-wbnQvycetafKltp6UsH1u-euwA,3850
-fractal_server/app/schemas/v2/workflow.py,sha256=ZpM43zTMyLRnEUtkbr_J5DYP00NwjItaC8gweB7GGAA,2172
-fractal_server/app/schemas/v2/workflowtask.py,sha256=rVbmNihDAJL_Sckbt1hBK2JEcb-8Xpxn3McvaomZLmQ,7429
+fractal_server/app/schemas/v2/task.py,sha256=5soZ3vp82f4myXi2Jj8Ob7iuGV0zaHbDXoKcARKsf4Y,4336
+fractal_server/app/schemas/v2/task_collection.py,sha256=N1G5C8qNd93D5XVtK8gwDzrwdgpePlCIGl8Y7rOBBKk,4196
+fractal_server/app/schemas/v2/task_group.py,sha256=FdIB9RSdoMIrfPkiCM60QpUdUjoVCLESeAxxAL-QAIs,3260
+fractal_server/app/schemas/v2/workflow.py,sha256=sJWwjmlNN2gRvO8gA0w7wKd_MCucBgEA5iXtu0vPycQ,1806
+fractal_server/app/schemas/v2/workflowtask.py,sha256=Q_2wM89QLMX19uthrnOigh-bxLYV5mdP-mUZPTgVJpM,3784
 fractal_server/app/security/__init__.py,sha256=e2cveg5hQpieGD3bSPd5GTOMthvJ-HXH3buSb9WVfEU,14096
 fractal_server/app/security/signup_email.py,sha256=Xd6QYxcdmg0PHpDwmUE8XQmPcOj3Xjy5oROcIMhmltM,1472
 fractal_server/app/user_settings.py,sha256=OP1yiYKtPadxwM51_Q0hdPk3z90TCN4z1BLpQsXyWiU,1316
-fractal_server/config.py,sha256=A3j1bxa2inTNqIp5Ry0sY6DS72k7X_AKA3OUaDwoYbA,28439
+fractal_server/config.py,sha256=McwfsTwRUzQOfN97ZjTLOHVyUvJKBqKY8xc9vK_eACA,26437
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/data_migrations/tools.py,sha256=LeMeASwYGtEqd-3wOLle6WARdTGAimoyMmRbbJl-hAM,572
 fractal_server/gunicorn_fractal.py,sha256=u6U01TLGlXgq1v8QmEpLih3QnsInZD7CqphgJ_GrGzc,1230
 fractal_server/images/__init__.py,sha256=-_wjoKtSX02P1KjDxDP_EXKvmbONTRmbf7iGVTsyBpM,154
-fractal_server/images/models.py,sha256=jdGKMPi8WlO9Kvns4grIOU5LjujnvwIGjMFMC0wNy08,3501
-fractal_server/images/tools.py,sha256=-zFDzRv6cbbRo21OrD0eZY5qWcoMX8dxgEnfyI3tOcg,4140
+fractal_server/images/models.py,sha256=AOIwwhleUtpuP6f_CNlOJEP517Grra9oWRqcBRk75xM,1280
+fractal_server/images/tools.py,sha256=oapI8j9DmMdIxVsDQQMpo_HXCTVElsn8TvmVBP5iX5s,4120
 fractal_server/logger.py,sha256=2QxBu5mB6xN3qWqj60nuxdrxcbxwzlx0xL47jKHB5PU,5385
 fractal_server/main.py,sha256=FD9KzTTsXTQnTW0z3Hu7y0Nj_oAkBeZEInKDXFd4hjE,4561
 fractal_server/migrations/env.py,sha256=nfyBpMIOT3kny6t-b-tUjyRjZ4k906bb1_wCQ7me1BI,1353
@@ -179,7 +176,7 @@ fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.p
 fractal_server/migrations/versions/fbce16ff4e47_new_history_items.py,sha256=TDWCaIoM0Q4SpRWmR9zr_rdp3lJXhCfBPTMhtrP5xYE,3950
 fractal_server/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/ssh/__init__.py,sha256=sVUmzxf7_DuXG1xoLQ1_00fo5NPhi2LJipSmU5EAkPs,124
-fractal_server/ssh/_fabric.py,sha256=jF7Nny0r3_PL1WjM1Zlw1I73Uqerx-mTaDWQlOaOpa0,23324
+fractal_server/ssh/_fabric.py,sha256=wLjOh2kBnaBjpmGB6lbrPdcWq9D5BzbaS2vKYwOfxEo,23498
 fractal_server/string_tools.py,sha256=niViRrrZAOo0y6pEFI9L_eUYS1PoOiQZUBtngiLc2_k,1877
 fractal_server/syringe.py,sha256=3qSMW3YaMKKnLdgnooAINOPxnCOxP7y2jeAQYB21Gdo,2786
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
@@ -206,11 +203,16 @@ fractal_server/tasks/v2/utils_database.py,sha256=yi7793Uue32O59OBVUgomO42oUrVKdS
 fractal_server/tasks/v2/utils_package_names.py,sha256=RDg__xrvQs4ieeVzmVdMcEh95vGQYrv9Hfal-5EDBM8,2393
 fractal_server/tasks/v2/utils_python_interpreter.py,sha256=5_wrlrTqXyo1YuLZvAW9hrSoh5MyLOzdPVUlUwM7uDQ,955
 fractal_server/tasks/v2/utils_templates.py,sha256=Kc_nSzdlV6KIsO0CQSPs1w70zLyENPqJeTQEFiz4bOg,3124
+fractal_server/types/__init__.py,sha256=BK12yh5d-8pecRWQOdey7l9QqXTCD21Eff62ypRoTjw,2057
+fractal_server/types/validators/__init__.py,sha256=5uj6KJ9MelFZgyoq3MzXLhgWCl0yiriS7XKmb0gathg,392
+fractal_server/types/validators/_common_validators.py,sha256=MpxyaP2kwgbyCTOaVRjYnJ74Lfi0f2X0q3rjX9w3vTk,1170
+fractal_server/types/validators/_filter_validators.py,sha256=El8NuMqEy7CPYpWcN-n40DmMOA8cZtpFkUYL0uSjO5w,859
+fractal_server/types/validators/_workflow_task_arguments_validators.py,sha256=HL7NgV8d56XbcD6gG5PVFUPMHjDm5Q-d7cXhVLdFAGU,387
 fractal_server/urls.py,sha256=QjIKAC1a46bCdiPMu3AlpgFbcv6a4l3ABcd5xz190Og,471
 fractal_server/utils.py,sha256=PMwrxWFxRTQRl1b9h-NRIbFGPKqpH_hXnkAT3NfZdpY,3571
 fractal_server/zip_tools.py,sha256=GjDgo_sf6V_DDg6wWeBlZu5zypIxycn_l257p_YVKGc,4876
-fractal_server-2.14.3.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.14.3.dist-info/METADATA,sha256=jWGz8N3CZga8UzjSeagUSYuLxxqDbZSBnkZnd15zrTo,4560
-fractal_server-2.14.3.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
-fractal_server-2.14.3.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.14.3.dist-info/RECORD,,
+fractal_server-2.14.4.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.14.4.dist-info/METADATA,sha256=eKfSXb3fH8Ac8Y_quuf64HUx8osvyiiK_CXVtjBoqPw,4560
+fractal_server-2.14.4.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
+fractal_server-2.14.4.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.14.4.dist-info/RECORD,,

fractal_server/app/runner/compress_folder.py

@@ -1,125 +0,0 @@
-"""
-Wrap `tar` compression command.
-
-This module is used both locally (in the environment where `fractal-server`
-is running) and remotely (as a standalon Python module, executed over SSH).
-
-This is a twin-module of `extract_archive.py`.
-
-The reason for using the `tar` command via `subprocess` rather than Python
-built-in `tarfile` library has to do with performance issues we observed
-when handling files which were just created within a SLURM job, and in the
-context of a CephFS filesystem.
-"""
-import sys
-import time
-from pathlib import Path
-
-from fractal_server.app.runner.run_subprocess import run_subprocess
-from fractal_server.logger import set_logger
-
-
-def compress_folder(
-    subfolder_path: Path,
-    filelist_path: str | None,
-    default_logging_level: int | None = None,
-) -> str:
-    """
-    Compress e.g. `/path/archive` into `/path/archive.tar.gz`
-
-    Note that `/path/archive.tar.gz` may already exist. In this case, it will
-    be overwritten.
-
-    Args:
-        subfolder_path: Absolute path to the folder to compress.
-        remote_to_local: If `True`, exclude some files from the tar.gz archive.
-        default_logging_level:
-
-    Returns:
-        Absolute path to the tar.gz archive.
-    """
-
-    # Assign an almost-unique label to the logger name, to simplify grepping
-    # logs when several `compress_folder` functions are run concurrently
-    label = round(time.time(), 2)
-    logger_name = f"compress_folder_{label}"
-    logger = set_logger(
-        logger_name,
-        default_logging_level=default_logging_level,
-    )
-    logger.debug("START")
-    t_start = time.perf_counter()
-
-    subfolder_name = subfolder_path.name
-    tarfile_path = (
-        subfolder_path.parent / f"{subfolder_name}.tar.gz"
-    ).as_posix()
-
-    logger.debug(f"{subfolder_path=}")
-    logger.debug(f"{tarfile_path=}")
-
-    if filelist_path is None:
-        cmd_tar = (
-            f"tar -c -z -f {tarfile_path} "
-            f"--directory={subfolder_path.as_posix()} "
-            "."
-        )
-    else:
-        cmd_tar = (
-            f"tar -c -z -f {tarfile_path} "
-            f"--directory={subfolder_path.as_posix()} "
-            f"--files-from={filelist_path} --ignore-failed-read"
-        )
-    logger.debug(f"{cmd_tar=}")
-
-    try:
-        run_subprocess(cmd=cmd_tar, logger_name=logger_name)
-        elapsed = time.perf_counter() - t_start
-        logger.debug(f"END {elapsed=} s ({tarfile_path})")
-        return tarfile_path
-    except Exception as e:
-        logger.debug(f"ERROR: {str(e)}")
-        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)}."
-            )
-
-        sys.exit(1)
-
-
-def main(
-    sys_argv: list[str],
-    default_logging_level: int | None = None,
-):
-
-    help_msg = (
-        "Expected use:\n"
-        "python -m fractal_server.app.runner.compress_folder "
-        "path/to/folder [--filelist /path/to/filelist]\n"
-    )
-    num_args = len(sys_argv[1:])
-    if num_args == 0:
-        sys.exit(f"Invalid argument.\n{help_msg}\nProvided: {sys_argv[1:]=}")
-    elif num_args == 1:
-        compress_folder(
-            subfolder_path=Path(sys_argv[1]),
-            filelist_path=None,
-            default_logging_level=default_logging_level,
-        )
-    elif num_args == 3 and sys_argv[2] == "--filelist":
-        compress_folder(
-            subfolder_path=Path(sys_argv[1]),
-            filelist_path=sys_argv[3],
-            default_logging_level=default_logging_level,
-        )
-    else:
-        sys.exit(f"Invalid argument.\n{help_msg}\nProvided: {sys_argv[1:]=}")
-
-
-if __name__ == "__main__":
-    import logging
-
-    main(sys.argv, default_logging_level=logging.DEBUG)

fractal_server/app/runner/extract_archive.py

@@ -1,99 +0,0 @@
-"""
-Wrap `tar` extraction command.
-
-This module is used both locally (in the environment where `fractal-server`
-is running) and remotely (as a standalon Python module, executed over SSH).
-
-This is a twin-module of `compress_folder.py`.
-
-The reason for using the `tar` command via `subprocess` rather than Python
-built-in `tarfile` library has to do with performance issues we observed
-when handling files which were just created within a SLURM job, and in the
-context of a CephFS filesystem.
-"""
-import sys
-from pathlib import Path
-
-from .run_subprocess import run_subprocess
-from fractal_server.logger import set_logger
-
-
-def _remove_suffix(*, string: str, suffix: str) -> str:
-    if string.endswith(suffix):
-        return string[: -len(suffix)]
-    else:
-        raise ValueError(f"Cannot remove {suffix=} from {string=}.")
-
-
-def extract_archive(
-    archive_path: Path,
-    default_logging_level: int | None = None,
-):
-    """
-    Extract e.g. `/path/archive.tar.gz` archive into `/path/archive` folder
-
-    Note that `/path/archive` may already exist. In this case, files with
-    the same name are overwritten and new files are added.
-
-    Arguments:
-        archive_path: Absolute path to the archive file.
-        default_logging_level
-    """
-
-    logger_name = "extract_archive"
-    logger = set_logger(
-        logger_name,
-        default_logging_level=default_logging_level,
-    )
-
-    logger.debug("START")
-    logger.debug(f"{archive_path.as_posix()=}")
-
-    # Check archive_path is valid
-    if not archive_path.exists():
-        sys.exit(f"Missing file {archive_path.as_posix()}.")
-
-    # Prepare subfolder path
-    parent_dir = archive_path.parent
-    subfolder_name = _remove_suffix(string=archive_path.name, suffix=".tar.gz")
-    subfolder_path = parent_dir / subfolder_name
-    logger.debug(f"{subfolder_path.as_posix()=}")
-
-    # Create subfolder
-    subfolder_path.mkdir(exist_ok=True)
-
-    # Run tar command
-    cmd_tar = (
-        f"tar -xzvf {archive_path} --directory={subfolder_path.as_posix()}"
-    )
-    logger.debug(f"{cmd_tar=}")
-    run_subprocess(cmd=cmd_tar, logger_name=logger_name)
-
-    logger.debug("END")
-
-
-def main(
-    sys_argv: list[str],
-    default_logging_level: int | None = None,
-):
-    help_msg = (
-        "Expected use:\n"
-        "python -m fractal_server.app.runner.extract_archive "
-        "path/to/archive.tar.gz"
-    )
-
-    if len(sys_argv[1:]) != 1 or not sys_argv[1].endswith(".tar.gz"):
-        sys.exit(f"Invalid argument.\n{help_msg}\nProvided: {sys_argv[1:]=}")
-    else:
-        tarfile_path = Path(sys_argv[1])
-        extract_archive(
-            tarfile_path,
-            default_logging_level=default_logging_level,
-        )
-
-
-if __name__ == "__main__":
-
-    import logging
-
-    main(sys.argv, default_logging_level=logging.DEBUG)

fractal_server/app/schemas/_filter_validators.py

@@ -1,46 +0,0 @@
-from typing import Optional
-
-from ._validators import valdict_keys
-from fractal_server.images.models import AttributeFiltersType
-
-
-def validate_type_filters(
-    cls, type_filters: Optional[dict[str, bool]]
-) -> dict[str, bool]:
-    if type_filters is None:
-        raise ValueError("'type_filters' cannot be 'None'.")
-
-    type_filters = valdict_keys("type_filters")(cls, type_filters)
-    return type_filters
-
-
-def validate_attribute_filters(
-    cls,
-    attribute_filters: Optional[AttributeFiltersType],
-) -> AttributeFiltersType:
-    if attribute_filters is None:
-        raise ValueError("'attribute_filters' cannot be 'None'.")
-
-    attribute_filters = valdict_keys("attribute_filters")(
-        cls, attribute_filters
-    )
-    for key, values in attribute_filters.items():
-        if values == []:
-            raise ValueError(
-                f"attribute_filters[{key}] cannot be an empty list."
-            )
-        else:
-            # values is a non-empty list, and its items must all be of the
-            # same scalar non-None type
-            _type = type(values[0])
-            if not all(type(value) is _type for value in values):
-                raise ValueError(
-                    f"attribute_filters[{key}] has values with "
-                    f"non-homogeneous types: {values}."
-                )
-            if _type not in (int, float, str, bool):
-                raise ValueError(
-                    f"attribute_filters[{key}] has values with "
-                    f"invalid types: {values}."
-                )
-    return attribute_filters