fractal-server 1.4.9__py3-none-any.whl → 2.0.0a0__py3-none-any.whl

fractal_server/app/schemas/v2/workflow.py

@@ -0,0 +1,78 @@
+from datetime import datetime
+from typing import Optional
+
+from pydantic import BaseModel
+from pydantic import validator
+
+from .._validators import valstr
+from .._validators import valutc
+from ..v1.project import ProjectReadV1
+from .workflowtask import WorkflowTaskExportV2
+from .workflowtask import WorkflowTaskImportV2
+from .workflowtask import WorkflowTaskReadV2
+
+
+class WorkflowCreateV2(BaseModel):
+
+    name: str
+
+    # Validators
+    _name = validator("name", allow_reuse=True)(valstr("name"))
+
+
+class WorkflowReadV2(BaseModel):
+
+    id: int
+    name: str
+    project_id: int
+    task_list: list[WorkflowTaskReadV2]
+    project: ProjectReadV1
+    timestamp_created: datetime
+
+    _timestamp_created = validator("timestamp_created", allow_reuse=True)(
+        valutc("timestamp_created")
+    )
+
+
+class WorkflowUpdateV2(BaseModel):
+
+    name: Optional[str]
+    reordered_workflowtask_ids: Optional[list[int]]
+
+    # Validators
+    _name = validator("name", allow_reuse=True)(valstr("name"))
+
+    @validator("reordered_workflowtask_ids")
+    def check_positive_and_unique(cls, value):
+        if any(i < 0 for i in value):
+            raise ValueError("Negative `id` in `reordered_workflowtask_ids`")
+        if len(value) != len(set(value)):
+            raise ValueError("`reordered_workflowtask_ids` has repetitions")
+        return value
+
+
+class WorkflowImportV2(BaseModel):
+    """
+    Class for `Workflow` import.
+
+    Attributes:
+        task_list:
+    """
+
+    name: str
+    task_list: list[WorkflowTaskImportV2]
+
+    # Validators
+    _name = validator("name", allow_reuse=True)(valstr("name"))
+
+
+class WorkflowExportV2(BaseModel):
+    """
+    Class for `Workflow` export.
+
+    Attributes:
+        task_list:
+    """
+
+    name: str
+    task_list: list[WorkflowTaskExportV2]

fractal_server/app/schemas/v2/workflowtask.py

@@ -0,0 +1,118 @@
+from enum import Enum
+from typing import Any
+from typing import Optional
+
+from pydantic import BaseModel
+from pydantic import Field
+from pydantic import validator
+
+from .._validators import valint
+from ..v1.task import TaskExportV1
+from ..v1.task import TaskImportV1
+from ..v1.task import TaskReadV1
+from .task import TaskExportV2
+from .task import TaskImportV2
+from .task import TaskReadV2
+from fractal_server.images import Filters
+
+
+class WorkflowTaskStatusTypeV2(str, Enum):
+    """
+    Define the available values for the status of a `WorkflowTask`.
+
+    This model is used within the `Dataset.history` attribute, which is
+    constructed in the runner and then used in the API (e.g. in the
+    `api/v2/project/{project_id}/dataset/{dataset_id}/status` endpoint).
+
+    Attributes:
+        SUBMITTED: The `WorkflowTask` is part of a running job.
+        DONE: The most-recent execution of this `WorkflowTask` was successful.
+        FAILED: The most-recent execution of this `WorkflowTask` failed.
+    """
+
+    SUBMITTED = "submitted"
+    DONE = "done"
+    FAILED = "failed"
+
+
+class WorkflowTaskCreateV2(BaseModel):
+
+    meta_parallel: Optional[dict[str, Any]]
+    meta_non_parallel: Optional[dict[str, Any]]
+    args_non_parallel: Optional[dict[str, Any]]
+    args_parallel: Optional[dict[str, Any]]
+    order: Optional[int]
+    input_filters: Filters = Field(default_factory=Filters)
+
+    is_legacy_task: bool = False
+
+    # Validators
+
+    _order = validator("order", allow_reuse=True)(valint("order", min_val=0))
+    # FIXME validate: if `is_legacy_task`, `args_non_parallel` must be None
+
+
+class WorkflowTaskReadV2(BaseModel):
+
+    id: int
+
+    workflow_id: int
+    order: Optional[int]
+    meta_parallel: Optional[dict[str, Any]]
+    meta_non_parallel: Optional[dict[str, Any]]
+
+    args_non_parallel: Optional[dict[str, Any]]
+    args_parallel: Optional[dict[str, Any]]
+
+    input_filters: Filters
+
+    is_legacy_task: bool
+    task_type: str
+    task_id: Optional[int]
+    task: Optional[TaskReadV2]
+    task_legacy_id: Optional[int]
+    task_legacy: Optional[TaskReadV1]
+
+
+class WorkflowTaskUpdateV2(BaseModel):
+
+    meta_parallel: Optional[dict[str, Any]]
+    meta_non_parallel: Optional[dict[str, Any]]
+    args_non_parallel: Optional[dict[str, Any]]
+    args_parallel: Optional[dict[str, Any]]
+    input_filters: Optional[Filters]
+
+    # Validators
+
+    @validator("meta_parallel", "meta_non_parallel")
+    def check_no_parallelisation_level(cls, m):
+        if "parallelization_level" in m:
+            raise ValueError(
+                "Overriding task parallelization level currently not allowed"
+            )
+        return m
+
+
+class WorkflowTaskImportV2(BaseModel):
+
+    meta_parallel: Optional[dict[str, Any]] = None
+    meta_non_parallel: Optional[dict[str, Any]] = None
+    args: Optional[dict[str, Any]] = None  # FIXME
+
+    input_filters: Optional[Filters] = None
+
+    is_legacy_task: bool = False
+    task: Optional[TaskImportV2] = None
+    task_legacy: Optional[TaskImportV1] = None
+
+
+class WorkflowTaskExportV2(BaseModel):
+
+    meta_parallel: Optional[dict[str, Any]] = None
+    meta_non_parallel: Optional[dict[str, Any]] = None
+    args: Optional[dict[str, Any]] = None  # FIXME
+    input_filters: Filters = Field(default_factory=Filters)
+
+    is_legacy_task: bool = False
+    task: Optional[TaskExportV2]
+    task_legacy: Optional[TaskExportV1]

fractal_server/config.py

@@ -390,12 +390,11 @@ class Settings(BaseSettings):
 
         info = f"FRACTAL_RUNNER_BACKEND={self.FRACTAL_RUNNER_BACKEND}"
         if self.FRACTAL_RUNNER_BACKEND == "slurm":
-            try:
-                import cfut  # noqa: F401
-            except ModuleNotFoundError:
-                raise FractalConfigurationError(
-                    f"{info} but `clusterfutures` is not available"
-                )
+
+            from fractal_server.app.runner.executors.slurm._slurm_config import (  # noqa: E501
+                load_slurm_config_file,
+            )
+
             if not self.FRACTAL_SLURM_CONFIG_FILE:
                 raise FractalConfigurationError(
                     f"Must set FRACTAL_SLURM_CONFIG_FILE when {info}"
@@ -407,10 +406,6 @@ class Settings(BaseSettings):
                         f"{self.FRACTAL_SLURM_CONFIG_FILE} not found."
                     )
 
-                from fractal_server.app.runner._slurm._slurm_config import (
-                    load_slurm_config_file,
-                )
-
                 load_slurm_config_file(self.FRACTAL_SLURM_CONFIG_FILE)
                 if not shutil.which("sbatch"):
                     raise FractalConfigurationError(

fractal_server/images/__init__.py

@@ -0,0 +1,50 @@
+from typing import Any
+from typing import Optional
+from typing import Union
+
+from pydantic import BaseModel
+from pydantic import Field
+from pydantic import validator
+
+
+class SingleImage(BaseModel):
+
+    path: str
+    origin: Optional[str] = None
+
+    attributes: dict[str, Any] = Field(default_factory=dict)
+    types: dict[str, bool] = Field(default_factory=dict)
+
+    @validator("attributes")
+    def validate_attributes(
+        cls, v: dict[str, Any]
+    ) -> dict[str, Union[int, float, str, bool]]:
+        for key, value in v.items():
+            if not isinstance(value, (int, float, str, bool)):
+                raise ValueError(
+                    f"SingleImage.attributes[{key}] must be a scalar "
+                    f"(int, float, str or bool). Given {value} ({type(value)})"
+                )
+        return v
+
+
+class Filters(BaseModel):
+    attributes: dict[str, Any] = Field(default_factory=dict)
+    types: dict[str, bool] = Field(default_factory=dict)
+
+    class Config:
+        extra = "forbid"
+
+    # Validators
+    @validator("attributes")
+    def validate_attributes(
+        cls, v: dict[str, Any]
+    ) -> dict[str, Union[int, float, str, bool, None]]:
+        for key, value in v.items():
+            if not isinstance(value, (int, float, str, bool, type(None))):
+                raise ValueError(
+                    f"Filters.attributes[{key}] must be a scalar "
+                    "(int, float, str, bool, or None). "
+                    f"Given {value} ({type(value)})"
+                )
+        return v

fractal_server/images/tools.py

@@ -0,0 +1,86 @@
+from copy import copy
+from typing import Any
+from typing import Optional
+from typing import Union
+
+from fractal_server.images import Filters
+from fractal_server.images import SingleImage
+
+
+def find_image_by_path(
+    *,
+    images: list[dict[str, Any]],
+    path: str,
+) -> Optional[dict[str, Union[int, dict[str, Any]]]]:
+    """
+    Return a copy of the image with a given path and its positional index.
+
+    Args:
+        images: List of images.
+        path: Path that the returned image must have.
+
+    Returns:
+        The first image from `images` which has path equal to `path`.
+    """
+    image_paths = [img["path"] for img in images]
+    try:
+        ind = image_paths.index(path)
+    except ValueError:
+        return None
+    return dict(image=copy(images[ind]), index=ind)
+
+
+def match_filter(image: dict[str, Any], filters: Filters):
+    for key, value in filters.types.items():
+        if image["types"].get(key, False) != value:
+            return False
+    for key, value in filters.attributes.items():
+        if value is None:
+            continue
+        if image["attributes"].get(key) != value:
+            return False
+    return True
+
+
+def _filter_image_list(
+    images: list[dict[str, Any]],
+    filters: Filters,
+) -> list[dict[str, Any]]:
+
+    # When no filter is provided, return all images
+    if filters.attributes == {} and filters.types == {}:
+        return images
+
+    filtered_images = []
+    for this_image in images:
+        if match_filter(this_image, filters=filters):
+            filtered_images.append(copy(this_image))
+    return filtered_images
+
+
+def match_filter_SingleImage(image: SingleImage, filters: Filters):
+    for key, value in filters.types.items():
+        if image.types.get(key, False) != value:
+            return False
+    for key, value in filters.attributes.items():
+        if value is None:
+            continue
+        if image.attributes.get(key) != value:
+            return False
+    return True
+
+
+def _filter_image_list_SingleImage(
+    images: list[SingleImage],
+    filters: Filters,
+) -> list[SingleImage]:
+
+    # When no filter is provided, return all images
+    if filters.attributes == {} and filters.types == {}:
+        return images
+
+    filtered_images = []
+    for this_image in images:
+        if match_filter_SingleImage(this_image, filters=filters):
+            filtered_images.append(copy(this_image))
+    return filtered_images

fractal_server/main.py

@@ -32,13 +32,21 @@ def collect_routers(app: FastAPI) -> None:
     """
     from .app.routes.api import router_api
     from .app.routes.api.v1 import router_api_v1
-    from .app.routes.admin import router_admin
+    from .app.routes.api.v2 import router_api_v2
+    from .app.routes.admin.v1 import router_admin_v1
+    from .app.routes.admin.v2 import router_admin_v2
     from .app.routes.auth import router_auth
 
     app.include_router(router_api, prefix="/api")
     app.include_router(router_api_v1, prefix="/api/v1")
-    app.include_router(router_admin, prefix="/admin", tags=["Admin area"])
-    app.include_router(router_auth, prefix="/auth", tags=["auth"])
+    app.include_router(router_api_v2, prefix="/api/v2")
+    app.include_router(
+        router_admin_v1, prefix="/admin/v1", tags=["V1 Admin area"]
+    )
+    app.include_router(
+        router_admin_v2, prefix="/admin/v2", tags=["V2 Admin area"]
+    )
+    app.include_router(router_auth, prefix="/auth", tags=["Authentication"])
 
 
 def check_settings() -> None:

fractal_server/migrations/versions/4b35c5cefbe3_tmp_is_v2_compatible.py

@@ -0,0 +1,39 @@
+"""TMP - is_v2_compatible
+
+Revision ID: 4b35c5cefbe3
+Revises: 876f28db9d4e
+Create Date: 2024-03-28 15:26:33.436724
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "4b35c5cefbe3"
+down_revision = "876f28db9d4e"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("task", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "is_v2_compatible",
+                sa.Boolean(),
+                server_default=sa.text("false"),
+                nullable=False,
+            )
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("task", schema=None) as batch_op:
+        batch_op.drop_column("is_v2_compatible")
+
+    # ### end Alembic commands ###

fractal_server/migrations/versions/56af171b0159_v2.py

@@ -0,0 +1,217 @@
+"""v2
+
+Revision ID: 56af171b0159
+Revises: 9fd26a2b0de4
+Create Date: 2024-03-22 11:09:02.458011
+
+"""
+import sqlalchemy as sa
+import sqlmodel
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "56af171b0159"
+down_revision = "9fd26a2b0de4"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "projectv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
+        sa.Column("read_only", sa.Boolean(), nullable=False),
+        sa.Column(
+            "timestamp_created", sa.DateTime(timezone=True), nullable=False
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_table(
+        "taskv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
+        sa.Column(
+            "command_non_parallel",
+            sqlmodel.sql.sqltypes.AutoString(),
+            nullable=True,
+        ),
+        sa.Column(
+            "command_parallel",
+            sqlmodel.sql.sqltypes.AutoString(),
+            nullable=True,
+        ),
+        sa.Column(
+            "source", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column("meta", sa.JSON(), nullable=True),
+        sa.Column("owner", sqlmodel.sql.sqltypes.AutoString(), nullable=True),
+        sa.Column(
+            "version", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column("args_schema", sa.JSON(), nullable=True),
+        sa.Column(
+            "args_schema_version",
+            sqlmodel.sql.sqltypes.AutoString(),
+            nullable=True,
+        ),
+        sa.Column(
+            "docs_info", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column(
+            "docs_link", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column("input_types", sa.JSON(), nullable=True),
+        sa.Column("output_types", sa.JSON(), nullable=True),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("source"),
+    )
+    op.create_table(
+        "datasetv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
+        sa.Column("project_id", sa.Integer(), nullable=False),
+        sa.Column("history", sa.JSON(), server_default="[]", nullable=False),
+        sa.Column("read_only", sa.Boolean(), nullable=False),
+        sa.Column(
+            "timestamp_created", sa.DateTime(timezone=True), nullable=False
+        ),
+        sa.Column(
+            "zarr_dir", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column("images", sa.JSON(), server_default="[]", nullable=False),
+        sa.Column(
+            "filters",
+            sa.JSON(),
+            server_default='{"attributes": {}, "types": {}}',
+            nullable=False,
+        ),
+        sa.ForeignKeyConstraint(
+            ["project_id"],
+            ["projectv2.id"],
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_table(
+        "linkuserprojectv2",
+        sa.Column("project_id", sa.Integer(), nullable=False),
+        sa.Column("user_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["project_id"],
+            ["projectv2.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["user_id"],
+            ["user_oauth.id"],
+        ),
+        sa.PrimaryKeyConstraint("project_id", "user_id"),
+    )
+    op.create_table(
+        "workflowv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
+        sa.Column("project_id", sa.Integer(), nullable=False),
+        sa.Column(
+            "timestamp_created", sa.DateTime(timezone=True), nullable=False
+        ),
+        sa.ForeignKeyConstraint(
+            ["project_id"],
+            ["projectv2.id"],
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_table(
+        "jobv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("project_id", sa.Integer(), nullable=True),
+        sa.Column("workflow_id", sa.Integer(), nullable=True),
+        sa.Column("dataset_id", sa.Integer(), nullable=True),
+        sa.Column(
+            "user_email", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column(
+            "slurm_account", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column("dataset_dump", sa.JSON(), nullable=False),
+        sa.Column("workflow_dump", sa.JSON(), nullable=False),
+        sa.Column("project_dump", sa.JSON(), nullable=False),
+        sa.Column(
+            "worker_init", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column(
+            "working_dir", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column(
+            "working_dir_user",
+            sqlmodel.sql.sqltypes.AutoString(),
+            nullable=True,
+        ),
+        sa.Column("first_task_index", sa.Integer(), nullable=False),
+        sa.Column("last_task_index", sa.Integer(), nullable=False),
+        sa.Column(
+            "start_timestamp", sa.DateTime(timezone=True), nullable=False
+        ),
+        sa.Column("end_timestamp", sa.DateTime(timezone=True), nullable=True),
+        sa.Column(
+            "status", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column("log", sqlmodel.sql.sqltypes.AutoString(), nullable=True),
+        sa.ForeignKeyConstraint(
+            ["dataset_id"],
+            ["datasetv2.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["project_id"],
+            ["projectv2.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["workflow_id"],
+            ["workflowv2.id"],
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_table(
+        "workflowtaskv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("workflow_id", sa.Integer(), nullable=False),
+        sa.Column("order", sa.Integer(), nullable=True),
+        sa.Column("meta", sa.JSON(), nullable=True),
+        sa.Column("args", sa.JSON(), nullable=True),
+        sa.Column(
+            "input_filters",
+            sa.JSON(),
+            server_default='{"attributes": {}, "types": {}}',
+            nullable=False,
+        ),
+        sa.Column("is_legacy_task", sa.Boolean(), nullable=False),
+        sa.Column("task_id", sa.Integer(), nullable=True),
+        sa.Column("task_legacy_id", sa.Integer(), nullable=True),
+        sa.ForeignKeyConstraint(
+            ["task_id"],
+            ["taskv2.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["task_legacy_id"],
+            ["task.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["workflow_id"],
+            ["workflowv2.id"],
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table("workflowtaskv2")
+    op.drop_table("jobv2")
+    op.drop_table("workflowv2")
+    op.drop_table("linkuserprojectv2")
+    op.drop_table("datasetv2")
+    op.drop_table("taskv2")
+    op.drop_table("projectv2")
+    # ### end Alembic commands ###