fractal-server 2.14.0a3__py3-none-any.whl → 2.14.0a4__py3-none-any.whl

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Files changed (47) hide show
  1. fractal_server/__init__.py +1 -1
  2. fractal_server/__main__.py +3 -1
  3. fractal_server/app/history/__init__.py +4 -4
  4. fractal_server/app/history/image_updates.py +124 -143
  5. fractal_server/app/history/status_enum.py +2 -2
  6. fractal_server/app/models/v2/__init__.py +6 -4
  7. fractal_server/app/models/v2/history.py +44 -20
  8. fractal_server/app/routes/api/__init__.py +1 -1
  9. fractal_server/app/routes/api/v2/__init__.py +4 -0
  10. fractal_server/app/routes/api/v2/_aux_functions_history.py +49 -0
  11. fractal_server/app/routes/api/v2/dataset.py +0 -12
  12. fractal_server/app/routes/api/v2/history.py +301 -186
  13. fractal_server/app/routes/api/v2/project.py +0 -25
  14. fractal_server/app/routes/api/v2/status_legacy.py +168 -0
  15. fractal_server/app/routes/api/v2/workflow.py +2 -17
  16. fractal_server/app/routes/api/v2/workflowtask.py +41 -71
  17. fractal_server/app/routes/auth/oauth.py +5 -3
  18. fractal_server/app/runner/executors/local/runner.py +10 -55
  19. fractal_server/app/runner/executors/slurm_sudo/runner.py +171 -108
  20. fractal_server/app/runner/v2/__init__.py +0 -20
  21. fractal_server/app/runner/v2/runner.py +45 -58
  22. fractal_server/app/runner/v2/runner_functions.py +164 -22
  23. fractal_server/app/schemas/_validators.py +13 -24
  24. fractal_server/app/schemas/user.py +10 -7
  25. fractal_server/app/schemas/user_settings.py +9 -21
  26. fractal_server/app/schemas/v2/dataset.py +8 -6
  27. fractal_server/app/schemas/v2/job.py +9 -5
  28. fractal_server/app/schemas/v2/manifest.py +2 -6
  29. fractal_server/app/schemas/v2/project.py +9 -7
  30. fractal_server/app/schemas/v2/task.py +41 -77
  31. fractal_server/app/schemas/v2/task_collection.py +14 -32
  32. fractal_server/app/schemas/v2/task_group.py +10 -9
  33. fractal_server/app/schemas/v2/workflow.py +10 -11
  34. fractal_server/app/security/signup_email.py +2 -2
  35. fractal_server/config.py +31 -32
  36. fractal_server/migrations/versions/fbce16ff4e47_new_history_items.py +120 -0
  37. fractal_server/tasks/v2/templates/2_pip_install.sh +1 -1
  38. fractal_server/tasks/v2/utils_templates.py +6 -0
  39. {fractal_server-2.14.0a3.dist-info → fractal_server-2.14.0a4.dist-info}/METADATA +1 -1
  40. {fractal_server-2.14.0a3.dist-info → fractal_server-2.14.0a4.dist-info}/RECORD +43 -44
  41. fractal_server/app/runner/executors/slurm_sudo/_executor_wait_thread.py +0 -130
  42. fractal_server/app/schemas/v2/history.py +0 -23
  43. fractal_server/migrations/versions/87cd72a537a2_add_historyitem_table.py +0 -68
  44. fractal_server/migrations/versions/954ddc64425a_image_status.py +0 -63
  45. {fractal_server-2.14.0a3.dist-info → fractal_server-2.14.0a4.dist-info}/LICENSE +0 -0
  46. {fractal_server-2.14.0a3.dist-info → fractal_server-2.14.0a4.dist-info}/WHEEL +0 -0
  47. {fractal_server-2.14.0a3.dist-info → fractal_server-2.14.0a4.dist-info}/entry_points.txt +0 -0
fractal_server/app/schemas/v2/history.py DELETED
@@ -1,23 +0,0 @@
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- from datetime import datetime
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- from typing import Any
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-
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- from pydantic import BaseModel
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- from pydantic import field_serializer
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- from pydantic.types import AwareDatetime
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-
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-
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- class HistoryItemV2Read(BaseModel):
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- id: int
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- dataset_id: int
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- workflowtask_id: int
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- timestamp_started: AwareDatetime
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- parameters_hash: str
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- num_available_images: int
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- num_current_images: int
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- images: dict[str, str]
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- workflowtask_dump: dict[str, Any]
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- task_group_dump: dict[str, Any]
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-
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- @field_serializer("timestamp_started")
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- def serialize_datetime(v: datetime) -> str:
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- return v.isoformat()
fractal_server/migrations/versions/87cd72a537a2_add_historyitem_table.py DELETED
@@ -1,68 +0,0 @@
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- """Add HistoryItem table
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-
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- Revision ID: 87cd72a537a2
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- Revises: af1ef1c83c9b
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- Create Date: 2025-02-18 10:48:16.401995
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-
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- """
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- import sqlalchemy as sa
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- import sqlmodel
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- from alembic import op
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- from sqlalchemy.dialects import postgresql
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-
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- # revision identifiers, used by Alembic.
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- revision = "87cd72a537a2"
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- down_revision = "af1ef1c83c9b"
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- branch_labels = None
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- depends_on = None
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-
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-
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- def upgrade() -> None:
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- # ### commands auto generated by Alembic - please adjust! ###
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- op.create_table(
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- "historyitemv2",
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- sa.Column("id", sa.Integer(), nullable=False),
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- sa.Column("dataset_id", sa.Integer(), nullable=False),
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- sa.Column("workflowtask_id", sa.Integer(), nullable=True),
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- sa.Column(
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- "timestamp_started", sa.DateTime(timezone=True), nullable=False
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- ),
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- sa.Column(
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- "workflowtask_dump",
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- postgresql.JSONB(astext_type=sa.Text()),
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- nullable=False,
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- ),
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- sa.Column(
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- "task_group_dump",
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- postgresql.JSONB(astext_type=sa.Text()),
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- nullable=False,
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- ),
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- sa.Column(
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- "parameters_hash",
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- sqlmodel.sql.sqltypes.AutoString(),
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- nullable=False,
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- ),
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- sa.Column("num_available_images", sa.Integer(), nullable=False),
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- sa.Column("num_current_images", sa.Integer(), nullable=False),
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- sa.Column(
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- "images", postgresql.JSONB(astext_type=sa.Text()), nullable=False
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- ),
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- sa.ForeignKeyConstraint(
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- ["dataset_id"],
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- ["datasetv2.id"],
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- name=op.f("fk_historyitemv2_dataset_id_datasetv2"),
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- ),
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- sa.ForeignKeyConstraint(
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- ["workflowtask_id"],
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- ["workflowtaskv2.id"],
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- name=op.f("fk_historyitemv2_workflowtask_id_workflowtaskv2"),
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- ),
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- sa.PrimaryKeyConstraint("id", name=op.f("pk_historyitemv2")),
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- )
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- # ### end Alembic commands ###
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-
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-
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- def downgrade() -> None:
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- # ### commands auto generated by Alembic - please adjust! ###
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- op.drop_table("historyitemv2")
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- # ### end Alembic commands ###
fractal_server/migrations/versions/954ddc64425a_image_status.py DELETED
@@ -1,63 +0,0 @@
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- """image status
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-
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- Revision ID: 954ddc64425a
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- Revises: 87cd72a537a2
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- Create Date: 2025-02-28 16:37:38.765883
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-
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- """
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- import sqlalchemy as sa
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- import sqlmodel
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- from alembic import op
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-
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-
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- # revision identifiers, used by Alembic.
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- revision = "954ddc64425a"
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- down_revision = "87cd72a537a2"
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- branch_labels = None
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- depends_on = None
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-
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-
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- def upgrade() -> None:
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- # ### commands auto generated by Alembic - please adjust! ###
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- op.create_table(
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- "imagestatus",
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- sa.Column(
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- "zarr_url", sqlmodel.sql.sqltypes.AutoString(), nullable=False
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- ),
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- sa.Column("workflowtask_id", sa.Integer(), nullable=False),
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- sa.Column("dataset_id", sa.Integer(), nullable=False),
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- sa.Column(
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- "parameters_hash",
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- sqlmodel.sql.sqltypes.AutoString(),
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- nullable=False,
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- ),
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- sa.Column(
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- "status", sqlmodel.sql.sqltypes.AutoString(), nullable=False
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- ),
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- sa.Column(
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- "logfile", sqlmodel.sql.sqltypes.AutoString(), nullable=True
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- ),
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- sa.ForeignKeyConstraint(
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- ["dataset_id"],
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- ["datasetv2.id"],
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- name=op.f("fk_imagestatus_dataset_id_datasetv2"),
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- ),
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- sa.ForeignKeyConstraint(
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- ["workflowtask_id"],
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- ["workflowtaskv2.id"],
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- name=op.f("fk_imagestatus_workflowtask_id_workflowtaskv2"),
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- ),
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- sa.PrimaryKeyConstraint(
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- "zarr_url",
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- "workflowtask_id",
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- "dataset_id",
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- name=op.f("pk_imagestatus"),
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- ),
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- )
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- # ### end Alembic commands ###
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-
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-
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- def downgrade() -> None:
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- # ### commands auto generated by Alembic - please adjust! ###
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- op.drop_table("imagestatus")
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- # ### end Alembic commands ###