fractal-server 2.14.0a9__py3-none-any.whl → 2.14.0a11__py3-none-any.whl

fractal_server/app/schemas/v2/dumps.py

@@ -15,7 +15,6 @@ from pydantic import Field
 
 from .task import TaskTypeType
 from .task_group import TaskGroupV2OriginEnum
-from fractal_server.images.models import AttributeFiltersType
 
 
 class ProjectDumpV2(BaseModel):
@@ -65,15 +64,17 @@ class WorkflowDumpV2(BaseModel):
 
 
 class DatasetDumpV2(BaseModel):
-    model_config = ConfigDict(extra="forbid")
+    """
+    We do not include 'model_config = ConfigDict(extra="forbid")' because
+    legacy data may include 'type_filters' or 'attribute_filters' and we
+    want to avoid response-validation errors.
+    """
+
     id: int
     name: str
     project_id: int
     timestamp_created: str
-
     zarr_dir: str
-    type_filters: dict[str, bool]
-    attribute_filters: AttributeFiltersType
 
 
 class TaskGroupDumpV2(BaseModel):

fractal_server/app/schemas/v2/job.py

@@ -13,6 +13,7 @@ from pydantic.types import AwareDatetime
 from pydantic.types import StrictStr
 
 from .._filter_validators import validate_attribute_filters
+from .._filter_validators import validate_type_filters
 from .._validators import cant_set_none
 from .._validators import NonEmptyString
 from .._validators import root_validate_dict_keys
@@ -44,7 +45,6 @@ class JobStatusTypeV2(str, Enum):
 
 
 class JobCreateV2(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     first_task_index: Optional[int] = None
@@ -53,6 +53,7 @@ class JobCreateV2(BaseModel):
     worker_init: Optional[NonEmptyString] = None
 
     attribute_filters: AttributeFiltersType = Field(default_factory=dict)
+    type_filters: dict[str, bool] = Field(default_factory=dict)
 
     # Validators
 
@@ -67,6 +68,9 @@ class JobCreateV2(BaseModel):
     _attribute_filters = field_validator("attribute_filters")(
         classmethod(validate_attribute_filters)
     )
+    _type_filters = field_validator("type_filters")(
+        classmethod(validate_type_filters)
+    )
 
     @field_validator("first_task_index")
     @classmethod
@@ -104,7 +108,6 @@ class JobCreateV2(BaseModel):
 
 
 class JobReadV2(BaseModel):
-
     id: int
     project_id: Optional[int] = None
     project_dump: ProjectDumpV2
@@ -124,6 +127,7 @@ class JobReadV2(BaseModel):
     last_task_index: Optional[int] = None
     worker_init: Optional[str] = None
     attribute_filters: AttributeFiltersType
+    type_filters: dict[str, bool]
 
     @field_serializer("start_timestamp")
     def serialize_datetime_start(v: datetime) -> str:
@@ -138,7 +142,6 @@ class JobReadV2(BaseModel):
 
 
 class JobUpdateV2(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     status: JobStatusTypeV2

fractal_server/migrations/versions/47351f8c7ebc_drop_dataset_filters.py

@@ -0,0 +1,50 @@
+"""Drop dataset filters
+
+Revision ID: 47351f8c7ebc
+Revises: fbce16ff4e47
+Create Date: 2025-03-26 11:10:17.869028
+
+"""
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = "47351f8c7ebc"
+down_revision = "fbce16ff4e47"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("datasetv2", schema=None) as batch_op:
+        batch_op.drop_column("type_filters")
+        batch_op.drop_column("attribute_filters")
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("datasetv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "attribute_filters",
+                postgresql.JSON(astext_type=sa.Text()),
+                server_default=sa.text("'{}'::json"),
+                autoincrement=False,
+                nullable=False,
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "type_filters",
+                postgresql.JSON(astext_type=sa.Text()),
+                server_default=sa.text("'{}'::json"),
+                autoincrement=False,
+                nullable=False,
+            )
+        )
+
+    # ### end Alembic commands ###

fractal_server/migrations/versions/e81103413827_add_job_type_filters.py

@@ -0,0 +1,36 @@
+"""Add job.type_filters
+
+Revision ID: e81103413827
+Revises: 47351f8c7ebc
+Create Date: 2025-03-26 11:10:41.748248
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "e81103413827"
+down_revision = "47351f8c7ebc"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("jobv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "type_filters", sa.JSON(), server_default="{}", nullable=False
+            )
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("jobv2", schema=None) as batch_op:
+        batch_op.drop_column("type_filters")
+
+    # ### end Alembic commands ###

{fractal_server-2.14.0a9.dist-info → fractal_server-2.14.0a11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.14.0a9
+Version: 2.14.0a11
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin

{fractal_server-2.14.0a9.dist-info → fractal_server-2.14.0a11.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=E9dF_7reewiCJauBwZifrX9piwxy4gBB_Eqz9YpzK1M,25
+fractal_server/__init__.py,sha256=GtuXF0xAIDTX9AXSJY7o0G6jQtfGliAzZf-nkCVjhSg,26
 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
@@ -11,9 +11,9 @@ fractal_server/app/models/security.py,sha256=mMb_HiwWY74QZrs9xuyno0CVSmk4GYQWk5F
 fractal_server/app/models/user_settings.py,sha256=Y-ZV-uZAFLZqXxy8c5_Qeh_F7zQuZDWOgLpU6Zs6iqU,1316
 fractal_server/app/models/v2/__init__.py,sha256=vjHwek7-IXmaZZL9VF0nD30YL9ca4wNc8P4RXJK_kDc,832
 fractal_server/app/models/v2/accounting.py,sha256=f2ALxfKKBNxFLJTtC2-YqRepVK253x68y7zkD2V_Nls,1115
-fractal_server/app/models/v2/dataset.py,sha256=O5_6YfNeX6JM7PUcEZhbeV4JCvuAhFCQbOOuefpVnqc,1544
+fractal_server/app/models/v2/dataset.py,sha256=ld8MruHCThSXVW2IYv7VqEljBsiWoctpaqkAOLlLSaU,1220
 fractal_server/app/models/v2/history.py,sha256=C0pqn_S5yqc8PjayoyRNcsk5Mt_SxvHitdQznuxJvGM,2044
-fractal_server/app/models/v2/job.py,sha256=L0P1mrztMqqb-6qdPEbuHXhCsf2mxVUct_ehcXrREGg,1844
+fractal_server/app/models/v2/job.py,sha256=6DMc0wehg0blhteHcEOUCSrCpNsUwqbWGb3gu_64ACo,1961
 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=f-JiqAQAmXP2LOVKQM7Yq3qcEjI1KA-HFYsyLpBASGs,3499
@@ -30,24 +30,25 @@ fractal_server/app/routes/admin/v2/task.py,sha256=QOwgyDU9m7T_wLMwkdgfFaoMjNxcDg
 fractal_server/app/routes/admin/v2/task_group.py,sha256=XTjdqgABXZcx9EenaoqSmHh12BXSentUus3SV0oxBMs,7929
 fractal_server/app/routes/admin/v2/task_group_lifecycle.py,sha256=0e0ZJ_k75TVHaT2o8Xk33DPDSgh-eBhZf-y4y7t-Adg,9429
 fractal_server/app/routes/api/__init__.py,sha256=B8l6PSAhR10iZqHEiyTat-_0tkeKdrCigIE6DJGP5b8,638
-fractal_server/app/routes/api/v2/__init__.py,sha256=Q65mxJOfuexzj53m6IB5fNl9PDec-Asu97W0bBxrRMM,2324
+fractal_server/app/routes/api/v2/__init__.py,sha256=9o9zxTU2IJrC_JQ8GUMft3niiBZ39YLvODUeraiRRdQ,2465
 fractal_server/app/routes/api/v2/_aux_functions.py,sha256=eE-TdEMI_UX3LBDUGwjG5NyUcihDVaHYlG15NlTJ9DI,12872
 fractal_server/app/routes/api/v2/_aux_functions_history.py,sha256=nWO4jBoL3MWuMMwS-6TwxlTHzgRr8Xed30RSeetLvP8,4199
 fractal_server/app/routes/api/v2/_aux_functions_task_lifecycle.py,sha256=qdXCb6IP8-qPEAxGZKljtjIqNzIAyRaAsQSRi5VqFHM,6773
 fractal_server/app/routes/api/v2/_aux_functions_tasks.py,sha256=uhNSs-jcS7ndIUFKiOC1yrDiViw3uvKEXi9UL04BMks,11642
 fractal_server/app/routes/api/v2/dataset.py,sha256=osoWJIA5SZH4aAr-0TG6Uc3877wzsgCLB_Oek59hRjk,9230
-fractal_server/app/routes/api/v2/history.py,sha256=9oux9P_BloLLFs0t-bSiKfjaWEH1Al0kzQSr4wFUxac,13042
-fractal_server/app/routes/api/v2/images.py,sha256=wUhYomNLGtJTtu_pD2oQorcH2LISxo64Wxo6ogc4IXc,8185
+fractal_server/app/routes/api/v2/history.py,sha256=DvIor59lWTgQ76EUJD-jPItIPKKHBvwFoZ7QPb93hc0,13285
+fractal_server/app/routes/api/v2/images.py,sha256=R0ccsHMeMyvZ3Sh23zGXyfqniMFOTVmwNWMzaQxc6t8,8239
 fractal_server/app/routes/api/v2/job.py,sha256=MU1sHIKk_89WrD0TD44d4ufzqnywot7On_W71KjyUbQ,6500
 fractal_server/app/routes/api/v2/project.py,sha256=hMvL9QLPUcAAiPGy6ta2LBLTVRozJsfvBPl5D06_MHg,6666
 fractal_server/app/routes/api/v2/status_legacy.py,sha256=Q5ZWQNfeZKL8Xgtou2Xr80iaF1uO-r4oSKgq5H42V_8,6349
-fractal_server/app/routes/api/v2/submit.py,sha256=K4OjcSg476JXIeeMUaYdTDk8Qpj5IO5UULvfErI7Y5Y,8624
+fractal_server/app/routes/api/v2/submit.py,sha256=hCwwC6bXP7EyhgGyVLv1ClybRH1YytDVoPunOzpsf0s,8822
 fractal_server/app/routes/api/v2/task.py,sha256=O7pquZhXIS4lRs5XqHvstiwe8BiCuS-B3ZKJI1g6EJU,6985
 fractal_server/app/routes/api/v2/task_collection.py,sha256=IDNF6sjDuU37HIQ0TuQA-TZIuf7nfHAQXUUNmkrlhLM,12706
 fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=cctW61-C2QYF2KXluS15lLhZJS_kt30Ca6UGLFO32z0,6207
 fractal_server/app/routes/api/v2/task_group.py,sha256=j3zDvVZizB7NWEgVgZU42JCXETkaVkk2ImJPr0jS7BQ,8164
 fractal_server/app/routes/api/v2/task_group_lifecycle.py,sha256=3o9bCC8ubMwffQPPaxQZy-CjH9IB2RkIReIecI6L2_w,9300
-fractal_server/app/routes/api/v2/workflow.py,sha256=2ZqpKTbr4hUuoXDm7WEIX7j_BLVC78ssnHKOqa4tiEg,10459
+fractal_server/app/routes/api/v2/verify_image_types.py,sha256=IOB96X3_FYBd9L_QiyVSEoV13ZP7YGS4WlBIDA1Op4I,1979
+fractal_server/app/routes/api/v2/workflow.py,sha256=dVXVuEajW8acmaFyr_yWYhG_qnbqkm1UqjDoGWf4bZ0,10568
 fractal_server/app/routes/api/v2/workflow_import.py,sha256=INmnhlMEBJp-vHPR0f940DANPmIidts3OfcooeM_aNA,11205
 fractal_server/app/routes/api/v2/workflowtask.py,sha256=7_syX2EO7ibF6Xkm7HBPhsUYq6aYnKNeC5iSaafQhG4,11342
 fractal_server/app/routes/auth/__init__.py,sha256=fao6CS0WiAjHDTvBzgBVV_bSXFpEAeDBF6Z6q7rRkPc,1658
@@ -65,48 +66,49 @@ fractal_server/app/routes/aux/_runner.py,sha256=spNudutueHTBJPhm55RlOuYzb31Dhyhe
 fractal_server/app/routes/aux/validate_user_settings.py,sha256=FLVi__8YFcm_6c_K5uMQo7raWWXQLBcZtx8yaPO4jaE,2301
 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=ZF8ct_Ky5k8IAcrmpYOZ-bc6OBgdELEighYVqFDEbZg,119
+fractal_server/app/runner/components.py,sha256=-Ii5l8d_V6f5DFOd-Zsr8VYmOsyqw0Hox9fEFQiuqxY,66
 fractal_server/app/runner/compress_folder.py,sha256=HSc1tv7x2DBjBoXwugZlC79rm9GNBIWtQKK9yWn5ZBI,3991
-fractal_server/app/runner/exceptions.py,sha256=_qZ_t8O4umAdJ1ikockiF5rDJuxnEskrGrLjZcnQl7A,4159
+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=v-uUHEvJgRnipTEvU9AmIMkYbkkazqkjm4iAF1GXHEM,4562
+fractal_server/app/runner/executors/base_runner.py,sha256=WhS7MLOkSHy8vjrGZGRHkounziJoYsqUlPkAdUQIs44,4511
 fractal_server/app/runner/executors/local/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/app/runner/executors/local/_local_config.py,sha256=8dyg2Gh8L2FlG_jJRYLMkcMgVHGEY2w7DME9aaKXFFo,3688
-fractal_server/app/runner/executors/local/_submit_setup.py,sha256=pDc9Q6axXL8_5JAV0byXzGOLOB0bZF88_L9LZykOgwM,1220
-fractal_server/app/runner/executors/local/runner.py,sha256=LNql8q6M-Cn_hEV4IMkNP57XFPQJ6eaVd0YIDKJLk60,5621
+fractal_server/app/runner/executors/local/get_local_config.py,sha256=wbrIYuGOvABOStrE7jNrC4ULPhtBQ5Q7Y3aKm_icomg,3508
+fractal_server/app/runner/executors/local/runner.py,sha256=KHmG6tw1TCb1HLtUhUC4FYcK_OdJk-SDdXtLkX_G4-4,7939
 fractal_server/app/runner/executors/slurm_common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm_common/_batching.py,sha256=ZY020JZlDS5mfpgpWTChQkyHU7iLE5kx2HVd57_C6XA,8850
+fractal_server/app/runner/executors/slurm_common/_check_jobs_status.py,sha256=bzpqx8mxT-2xRIGQK6YLMIvMN-SM6OeYWUs97W0iRno,2103
 fractal_server/app/runner/executors/slurm_common/_job_states.py,sha256=nuV-Zba38kDrRESOVB3gaGbrSPZc4q7YGichQaeqTW0,238
 fractal_server/app/runner/executors/slurm_common/_slurm_config.py,sha256=fZaFUUXqDH0p3DndCFUpFqTqyD2tMVCuSYgYLAycpVw,15897
-fractal_server/app/runner/executors/slurm_common/_submit_setup.py,sha256=crbfAAvXbxe_9PaokXkkVdPV65lSCFbInZ0RlT6uyHI,2746
 fractal_server/app/runner/executors/slurm_common/get_slurm_config.py,sha256=-fAX1DZMB5RZnyYanIJD72mWOJAPkh21jd4loDXKJw4,5994
 fractal_server/app/runner/executors/slurm_common/remote.py,sha256=iXLu4d-bWzn7qmDaOjKFkcuaSHLjPESAMSLcg6c99fc,5852
 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/_check_job_status_ssh.py,sha256=81e4kYpnNlONUw0a3o0o5kTu35Dshelc61y6Gf63m2M,1899
 fractal_server/app/runner/executors/slurm_ssh/_executor_wait_thread.py,sha256=lnW8dNNPqqbpQvojVBQaNJm4wN3Qkw02RWBZ1w68Hyw,3755
 fractal_server/app/runner/executors/slurm_ssh/_slurm_job.py,sha256=IL1C52dezEiincVX2yKryNiPHi4YOMURNLdQO_QPdGw,4406
-fractal_server/app/runner/executors/slurm_ssh/executor.py,sha256=VXMDaQRijYaeKyxly4RkBkRg2inLBZ75rfuODg0Mgr8,53602
+fractal_server/app/runner/executors/slurm_ssh/executor.py,sha256=StEX6vN9jY79nTxqRDb5OEhkTVd3jYhT4X0_luZSqd4,53678
+fractal_server/app/runner/executors/slurm_ssh/runner.py,sha256=LON7H3RGPYwqmDj0gEcPg7CtBGQzClU8o0fubsXk-Rw,24482
 fractal_server/app/runner/executors/slurm_sudo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/app/runner/executors/slurm_sudo/_check_jobs_status.py,sha256=eZd9lxbObsqc1M3B96IGMJ-1oC0jo8lBOX4Nto97VvE,2036
 fractal_server/app/runner/executors/slurm_sudo/_subprocess_run_as_user.py,sha256=O1bNg1DiSDJmQE0RmOk2Ii47DagiXp5ryd0R6KxO2OM,3177
-fractal_server/app/runner/executors/slurm_sudo/runner.py,sha256=niDcezFNQ7awfv_7nqABmVhG3oLIf8Z7BwlLxM-chZo,21833
+fractal_server/app/runner/executors/slurm_sudo/runner.py,sha256=hjHn09Gvw1xZ-mmSRRaye-0-JInA-YhM45ohCZ_8WYY,27911
 fractal_server/app/runner/extract_archive.py,sha256=tLpjDrX47OjTNhhoWvm6iNukg8KoieWyTb7ZfvE9eWU,2483
 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=5enzBqiQct1AUGwrGX-rxFCxnhW3SPYIUylMYwyVfrE,2482
-fractal_server/app/runner/v2/__init__.py,sha256=ro5C4ro7gXuV-H7p8SrV90vBsS52IfukWn-b2FxJ9F4,13293
-fractal_server/app/runner/v2/_db_tools.py,sha256=_8Mt4WbItew8EEtRwHdZidfIm4MvfM49FsMPf2JYol4,1361
-fractal_server/app/runner/v2/_local.py,sha256=Zas2RS_f9mfdkXszBpzISHylLX1bX8pFuoLA1fHLFqQ,2945
-fractal_server/app/runner/v2/_slurm_ssh.py,sha256=5w_lwQzySx-R3kVg2Bf-21n5JpWjJAgMtYP2BROvWJo,3227
-fractal_server/app/runner/v2/_slurm_sudo.py,sha256=CzWUeC6at_Sj-wU1myjA68ZRKMiLZYBTLv9I9odUxBU,2914
+fractal_server/app/runner/task_files.py,sha256=pGqaFsSXg-3kywf_FGqgjx_8pPLwIn0MpjQ3009fkus,2741
+fractal_server/app/runner/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fractal_server/app/runner/v2/_local.py,sha256=DK8yagbvd6HHjcDVhUzTy0f7MURlTkQha-NM6OZKgJc,3044
+fractal_server/app/runner/v2/_slurm_ssh.py,sha256=RhfV1quXGGU4bYioRF7UKAdrzOI_stgsFdXdcTegrv0,3310
+fractal_server/app/runner/v2/_slurm_sudo.py,sha256=vjvOA-6_0vSKp704wM1O0ubEDpKZZ0vJG5ZfUi9-wSA,2997
+fractal_server/app/runner/v2/db_tools.py,sha256=yPF2KgkrEdvAc380YL-wux68O0Ej9cY-usTSd-m_evE,2400
 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=hsXBFQmoo8fqZC13DxlEwLLSVwsr7AvgTrTfiQXcXyk,15570
-fractal_server/app/runner/v2/runner_functions.py,sha256=9i7fHMr3BFrgguptJ-Pz3Gu68Okp5e3JvIIEqhdrG3Q,22120
-fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=dvvRK7od8iQ8vdPf80uGUxs3i5i0buGjCodBxSjZ7PQ,3671
-fractal_server/app/runner/v2/task_interface.py,sha256=e1GGQSYd0MyBj1EZvEVzqv-HpVE4YffXOq82WLrCaOc,1866
+fractal_server/app/runner/v2/runner.py,sha256=tCBGtUjExhlAplFLw3AlxEr7NZmpAj9QIwSh2xstIO8,15153
+fractal_server/app/runner/v2/runner_functions.py,sha256=xnc1rpuECwUEDuD4oLF7PpyenHUe3kTVD41xjZa2r_0,16490
+fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=9t1CHN3EyfsGRWfG257YPY5WjQ6zuztsw_KZrpEAFPo,3703
+fractal_server/app/runner/v2/submit_workflow.py,sha256=PTLXNT_ZoEd9GTZ5C4Ai0imOFJOfY4E9Yg1rB-gsl7I,13340
+fractal_server/app/runner/v2/task_interface.py,sha256=IXdQTI8rXFgXv1Ez0js4CjKFf3QwO2GCHRTuwiFtiTQ,2891
 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
@@ -116,10 +118,10 @@ fractal_server/app/schemas/user_group.py,sha256=Uao1igRYflBu7Dg6Zs0kaFU3zBFJzIwD
 fractal_server/app/schemas/user_settings.py,sha256=z7hx54yTrWfjo98oX_1lkeRh1UGrC1dSRH6yIOpnCsY,2772
 fractal_server/app/schemas/v2/__init__.py,sha256=Q1Sozuh6escPbU3SIsmiJbQMFl9kfIcfK-3Ctb-1wXQ,2988
 fractal_server/app/schemas/v2/accounting.py,sha256=Wylt7uWTiDIFlHJOh4XEtYitk2FjFlmnodDrJDxcr0E,397
-fractal_server/app/schemas/v2/dataset.py,sha256=9yc-tte70yPPk4CSfy2imykYVbCW8-23K499pi9z2e0,5206
-fractal_server/app/schemas/v2/dumps.py,sha256=AhCSo4jaGyCdcNkmRvtIZ_QnIl4elu-KUAFlmP5I2rg,2261
+fractal_server/app/schemas/v2/dataset.py,sha256=xNWdOW8hhL5Wx-iwyUPrZfWcC8fFuGDgdOHvZLbGVME,2782
+fractal_server/app/schemas/v2/dumps.py,sha256=uc9itXekO5IFfR6UucpQ5BX9NZZ8erE4hRR6S6aXlOc,2284
 fractal_server/app/schemas/v2/history.py,sha256=aCzr68OdNtHzNHrW43F5uxSCCcT6dMaq-_Dq9GpuJ6k,1100
-fractal_server/app/schemas/v2/job.py,sha256=KhxQOfncpE_SAu7Wed8CXS2G6onh0v875GkotBvKBTY,4304
+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/status_legacy.py,sha256=vc6C3Xri8222bb9OmsghMz05CNuEalO-t2s_nKo341s,954
@@ -147,6 +149,7 @@ fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_
 fractal_server/migrations/versions/19eca0dd47a9_user_settings_project_dir.py,sha256=Q1Gj1cJ0UrdLBJ5AXfFK9QpxTtmcv-4Z3NEGDnxOme4,961
 fractal_server/migrations/versions/1eac13a26c83_drop_v1_tables.py,sha256=ok8dl4IkI-dfsyE_NZ8IndjQrnQ_g6CDZo4PwozpIwE,1605
 fractal_server/migrations/versions/316140ff7ee1_remove_usersettings_cache_dir.py,sha256=lANgTox0rz459_yo1Rw7fGCT1qw5sUCUXTLUMc_Bzf8,911
+fractal_server/migrations/versions/47351f8c7ebc_drop_dataset_filters.py,sha256=vePkVm1iUHiPNKLQ3KR7BBLdHruqBdl87j_tUCbMbEA,1414
 fractal_server/migrations/versions/4c308bcaea2b_add_task_args_schema_and_task_args_.py,sha256=-wHe-fOffmYeAm0JXVl_lxZ7hhDkaEVqxgxpHkb_uL8,954
 fractal_server/migrations/versions/4cedeb448a53_workflowtask_foreign_keys_not_nullables.py,sha256=Mob8McGYAcmgvrseyyYOa54E6Gsgr-4SiGdC-r9O4_A,1157
 fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py,sha256=5ROUgcoZOdjf8kMt6cxuvPhzHmV6xaCxvZEbhUEyZM4,3271
@@ -170,6 +173,7 @@ fractal_server/migrations/versions/d4fe3708d309_make_applyworkflow_workflow_dump
 fractal_server/migrations/versions/da2cb2ac4255_user_group_viewer_paths.py,sha256=yGWSA2HIHUybcVy66xBITk08opV2DFYSCIIrulaUZhI,901
 fractal_server/migrations/versions/db09233ad13a_split_filters_and_keep_old_columns.py,sha256=NumyjvciIjgShLZcmpDvh3ggJxnc-W1kc7vofrpcNOs,2906
 fractal_server/migrations/versions/e75cac726012_make_applyworkflow_start_timestamp_not_.py,sha256=lOggSvzGWqQvnxxFuSM6W50Ui49R918A-uBuiZJ0pNM,963
+fractal_server/migrations/versions/e81103413827_add_job_type_filters.py,sha256=t4ImlKNHx5JMgBL2sTpLWunv1gwY8OCFOKd3G338mdE,890
 fractal_server/migrations/versions/efa89c30e0a4_add_project_timestamp_created.py,sha256=jilQW3QIqYQ4Q6hCnUiG7UtNMpA41ujqrB3tPFiPM1Q,1221
 fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.py,sha256=9BwqUS9Gf7UW_KjrzHbtViC880qhD452KAytkHWWZyk,746
 fractal_server/migrations/versions/fbce16ff4e47_new_history_items.py,sha256=TDWCaIoM0Q4SpRWmR9zr_rdp3lJXhCfBPTMhtrP5xYE,3950
@@ -205,8 +209,8 @@ fractal_server/tasks/v2/utils_templates.py,sha256=Kc_nSzdlV6KIsO0CQSPs1w70zLyENP
 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-2.14.0a9.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.14.0a9.dist-info/METADATA,sha256=ZeOIxRJewSWlF3Y1yfC767EtZrhOzPGW97Hjpo_0ewI,4562
-fractal_server-2.14.0a9.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
-fractal_server-2.14.0a9.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.14.0a9.dist-info/RECORD,,
+fractal_server-2.14.0a11.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.14.0a11.dist-info/METADATA,sha256=_yK06nJ_yK0gkC42b3nVAtSD0_TQTlD7VJwUl9rlzf0,4563
+fractal_server-2.14.0a11.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
+fractal_server-2.14.0a11.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.14.0a11.dist-info/RECORD,,

fractal_server/app/runner/executors/local/_submit_setup.py

@@ -1,46 +0,0 @@
-from pathlib import Path
-from typing import Any
-from typing import Literal
-
-from ...task_files import TaskFiles
-from ._local_config import get_local_backend_config
-from fractal_server.app.models.v2 import WorkflowTaskV2
-
-
-def _local_submit_setup(
-    *,
-    wftask: WorkflowTaskV2,
-    root_dir_local: Path,
-    root_dir_remote: Path,
-    which_type: Literal["non_parallel", "parallel"],
-) -> dict[str, Any]:
-    """
-    Collect WorkflowTask-specific configuration parameters from different
-    sources, and inject them for execution.
-
-    FIXME
-
-    Arguments:
-        wftask: WorkflowTask for which the configuration is to be assembled
-        root_dir_local:
-        root_dir_rempote: Not used in this function.
-        which_type: Whether it is a parallel or non-parallel task.
-    """
-
-    local_backend_config = get_local_backend_config(
-        wftask=wftask,
-        which_type=which_type,
-    )
-
-    # Get TaskFiles object
-    task_files = TaskFiles(
-        root_dir_local=root_dir_local,
-        root_dir_remote=root_dir_local,
-        task_order=wftask.order,
-        task_name=wftask.task.name,
-    )
-
-    return dict(
-        local_backend_config=local_backend_config,
-        task_files=task_files,
-    )

fractal_server/app/runner/executors/slurm_common/_submit_setup.py

@@ -1,84 +0,0 @@
-# Copyright 2022 (C) Friedrich Miescher Institute for Biomedical Research and
-# University of Zurich
-#
-# Original authors:
-# Jacopo Nespolo <jacopo.nespolo@exact-lab.it>
-# Tommaso Comparin <tommaso.comparin@exact-lab.it>
-#
-# This file is part of Fractal and was originally developed by eXact lab S.r.l.
-# <exact-lab.it> under contract with Liberali Lab from the Friedrich Miescher
-# Institute for Biomedical Research and Pelkmans Lab from the University of
-# Zurich.
-"""
-Submodule to define _slurm_submit_setup, which is also the reference
-implementation of `submit_setup_call`.
-"""
-from pathlib import Path
-from typing import Any
-from typing import Literal
-
-from ...task_files import TaskFiles
-from fractal_server.app.models.v2 import WorkflowTaskV2
-from fractal_server.app.runner.executors.slurm_common.get_slurm_config import (
-    get_slurm_config,
-)
-
-
-def _slurm_submit_setup(
-    *,
-    wftask: WorkflowTaskV2,
-    root_dir_local: Path,
-    root_dir_remote: Path,
-    which_type: Literal["non_parallel", "parallel"],
-) -> dict[str, Any]:
-    """
-    Collect WorkflowTask-specific configuration parameters from different
-    sources, and inject them for execution.
-
-    FIXME
-
-    Here goes all the logic for reading attributes from the appropriate sources
-    and transforming them into an appropriate `SlurmConfig` object (encoding
-    SLURM configuration) and `TaskFiles` object (with details e.g. about file
-    paths or filename prefixes).
-
-    For now, this is the reference implementation for the argument
-    `submit_setup_call` of
-    [fractal_server.app.runner.v2.runner][].
-
-    Arguments:
-        wftask:
-            WorkflowTask for which the configuration is to be assembled
-        workflow_dir_local:
-            Server-owned directory to store all task-execution-related relevant
-            files (inputs, outputs, errors, and all meta files related to the
-            job execution). Note: users cannot write directly to this folder.
-        workflow_dir_remote:
-            User-side directory with the same scope as `workflow_dir_local`,
-            and where a user can write.
-
-    Returns:
-        submit_setup_dict:
-            A dictionary that will be passed on to
-            `FractalSlurmExecutor.submit` and `FractalSlurmExecutor.map`, so
-            as to set extra options.
-    """
-
-    # Get SlurmConfig object
-    slurm_config = get_slurm_config(
-        wftask=wftask,
-        which_type=which_type,
-    )
-
-    # Get TaskFiles object
-    task_files = TaskFiles(
-        root_dir_local=root_dir_local,
-        root_dir_remote=root_dir_remote,
-        task_order=wftask.order,
-        task_name=wftask.task.name,
-    )
-
-    return dict(
-        slurm_config=slurm_config,
-        task_files=task_files,
-    )

fractal_server/app/runner/v2/_db_tools.py

@@ -1,48 +0,0 @@
-from typing import Any
-
-from sqlalchemy.dialects.postgresql import insert as pg_insert
-from sqlalchemy.orm import Session
-
-from fractal_server.app.models.v2 import HistoryImageCache
-
-
-def bulk_upsert_image_cache_fast(
-    *,
-    list_upsert_objects: list[dict[str, Any]],
-    db: Session,
-) -> None:
-    """
-    Insert or update many objects into `HistoryImageCache` and commit
-
-    This function is an optimized version of
-
-    ```python
-    for obj in list_upsert_objects:
-        db.merge(**obj)
-    db.commit()
-    ```
-
-    See docs at
-    https://docs.sqlalchemy.org/en/20/dialects/postgresql.html#insert-on-conflict-upsert
-
-    FIXME: we tried to replace `index_elements` with
-    `constraint="pk_historyimagecache"`, but it did not work as expected.
-
-    Arguments:
-        list_upsert_objects:
-            List of dictionaries for objects to be upsert-ed.
-        db: A sync database session
-    """
-    if len(list_upsert_objects) == 0:
-        return None
-    stmt = pg_insert(HistoryImageCache).values(list_upsert_objects)
-    stmt = stmt.on_conflict_do_update(
-        index_elements=[
-            HistoryImageCache.zarr_url,
-            HistoryImageCache.dataset_id,
-            HistoryImageCache.workflowtask_id,
-        ],
-        set_=dict(latest_history_unit_id=stmt.excluded.latest_history_unit_id),
-    )
-    db.execute(stmt)
-    db.commit()