fractal-server 2.11.1__py3-none-any.whl → 2.12.0__py3-none-any.whl

fractal_server/app/schemas/v1/project.py

@@ -1,66 +0,0 @@
-from datetime import datetime
-from typing import Optional
-
-from pydantic import BaseModel
-from pydantic import validator
-
-from .._validators import valstr
-
-
-__all__ = (
-    "ProjectCreateV1",
-    "ProjectReadV1",
-    "ProjectUpdateV1",
-)
-
-
-class _ProjectBaseV1(BaseModel):
-    """
-    Base class for `Project`.
-
-    Attributes:
-        name:
-        read_only:
-    """
-
-    name: str
-    read_only: bool = False
-
-
-class ProjectCreateV1(_ProjectBaseV1):
-    """
-    Class for `Project` creation.
-    """
-
-    # Validators
-    _name = validator("name", allow_reuse=True)(valstr("name"))
-
-
-class ProjectReadV1(_ProjectBaseV1):
-    """
-    Class for `Project` read from database.
-
-    Attributes:
-        id:
-        name:
-        read_only:
-    """
-
-    id: int
-    timestamp_created: datetime
-
-
-class ProjectUpdateV1(_ProjectBaseV1):
-    """
-    Class for `Project` update.
-
-    Attributes:
-        name:
-        read_only:
-    """
-
-    name: Optional[str]
-    read_only: Optional[bool]
-
-    # Validators
-    _name = validator("name", allow_reuse=True)(valstr("name"))

fractal_server/app/schemas/v1/state.py

@@ -1,18 +0,0 @@
-from datetime import datetime
-from typing import Any
-from typing import Optional
-
-from pydantic import BaseModel
-
-
-class StateRead(BaseModel):
-    """
-    Class for `State` read from database.
-
-    Attributes:
-        id:
-    """
-
-    id: Optional[int]
-    data: dict[str, Any]
-    timestamp: datetime

fractal_server/app/schemas/v1/task.py

@@ -1,167 +0,0 @@
-from typing import Any
-from typing import Optional
-
-from pydantic import BaseModel
-from pydantic import Field
-from pydantic import HttpUrl
-from pydantic import validator
-
-from .._validators import valstr
-
-__all__ = (
-    "TaskCreateV1",
-    "TaskUpdateV1",
-    "TaskReadV1",
-    "TaskImportV1",
-    "TaskExportV1",
-)
-
-
-class _TaskBaseV1(BaseModel):
-    """
-
-    Base class for `Task`.
-
-    Attributes:
-        source:
-            This is the information is used to match tasks across fractal
-            installations when a workflow is imported.
-    """
-
-    source: str
-    _source = validator("source", allow_reuse=True)(valstr("source"))
-
-
-class TaskUpdateV1(_TaskBaseV1):
-    """
-    Class for `Task` update.
-
-    Attributes:
-        name:
-        input_type:
-        output_type:
-        command:
-        source:
-        meta:
-        version:
-        args_schema:
-        args_schema_version:
-        docs_info:
-        docs_link:
-    """
-
-    name: Optional[str]
-    input_type: Optional[str]
-    output_type: Optional[str]
-    command: Optional[str]
-    source: Optional[str]
-    meta: Optional[dict[str, Any]]
-    version: Optional[str]
-    args_schema: Optional[dict[str, Any]]
-    args_schema_version: Optional[str]
-    docs_info: Optional[str]
-    docs_link: Optional[HttpUrl]
-
-    # Validators
-    _name = validator("name", allow_reuse=True)(valstr("name"))
-    _input_type = validator("input_type", allow_reuse=True)(
-        valstr("input_type")
-    )
-    _output_type = validator("output_type", allow_reuse=True)(
-        valstr("output_type")
-    )
-    _command = validator("command", allow_reuse=True)(valstr("command"))
-    _version = validator("version", allow_reuse=True)(
-        valstr("version", accept_none=True)
-    )
-
-
-class TaskImportV1(_TaskBaseV1):
-    """
-    Class for `Task` import.
-    """
-
-    pass
-
-
-class TaskExportV1(_TaskBaseV1):
-    """
-    Class for `Task` export.
-    """
-
-    pass
-
-
-class TaskReadV1(_TaskBaseV1):
-    """
-    Class for `Task` read from database.
-
-    Attributes:
-        id:
-        name:
-        command:
-        input_type:
-        output_type:
-        meta:
-        version:
-        args_schema:
-        args_schema_version:
-        docs_info:
-        docs_link:
-    """
-
-    id: int
-    name: str
-    command: str
-    input_type: str
-    output_type: str
-    meta: Optional[dict[str, Any]] = Field(default={})
-    owner: Optional[str]
-    version: Optional[str]
-    args_schema: Optional[dict[str, Any]]
-    args_schema_version: Optional[str]
-    docs_info: Optional[str]
-    docs_link: Optional[HttpUrl]
-
-
-class TaskCreateV1(_TaskBaseV1):
-    """
-    Class for `Task` creation.
-
-    Attributes:
-        name:
-        command:
-        input_type:
-        output_type:
-        meta:
-        version:
-        args_schema:
-        args_schema_version:
-        docs_info:
-        docs_link:
-    """
-
-    name: str
-    command: str
-    input_type: str
-    output_type: str
-    meta: Optional[dict[str, Any]] = Field(default={})
-    version: Optional[str]
-    args_schema: Optional[dict[str, Any]]
-    args_schema_version: Optional[str]
-    docs_info: Optional[str]
-    docs_link: Optional[HttpUrl]
-
-    # Validators
-    _name = validator("name", allow_reuse=True)(valstr("name"))
-    _input_type = validator("input_type", allow_reuse=True)(
-        valstr("input_type")
-    )
-    _output_type = validator("output_type", allow_reuse=True)(
-        valstr("output_type")
-    )
-    _command = validator("command", allow_reuse=True)(valstr("command"))
-    _version = validator("version", allow_reuse=True)(valstr("version"))
-    _args_schema_version = validator("args_schema_version", allow_reuse=True)(
-        valstr("args_schema_version")
-    )

fractal_server/app/schemas/v1/task_collection.py

@@ -1,110 +0,0 @@
-from pathlib import Path
-from typing import Literal
-from typing import Optional
-
-from pydantic import BaseModel
-from pydantic import Field
-from pydantic import validator
-
-from .._validators import valstr
-from .task import TaskReadV1
-
-__all__ = (
-    "TaskCollectPipV1",
-    "TaskCollectStatusV1",
-)
-
-
-class TaskCollectPipV1(BaseModel):
-    """
-    TaskCollectPip class
-
-    This class only encodes the attributes required to trigger a
-    task-collection operation. Other attributes (that are assigned *during*
-    task collection) are defined as part of fractal-server.
-
-    Two cases are supported:
-
-        1. `package` is the path of a local wheel file;
-        2. `package` is the name of a package that can be installed via `pip`.
-
-
-    Attributes:
-        package:
-            The name of a `pip`-installable package, or the path to a local
-            wheel file.
-        package_version: Version of the package
-        package_extras: Package extras to include in the `pip install` command
-        python_version: Python version to install and run the package tasks
-        pinned_package_versions:
-            dictionary 'package':'version' used to pin versions for specific
-            packages.
-
-    """
-
-    package: str
-    package_version: Optional[str] = None
-    package_extras: Optional[str] = None
-    python_version: Optional[str] = None
-    pinned_package_versions: Optional[dict[str, str]] = None
-
-    _package_extras = validator("package_extras", allow_reuse=True)(
-        valstr("package_extras")
-    )
-    _python_version = validator("python_version", allow_reuse=True)(
-        valstr("python_version")
-    )
-
-    @validator("package")
-    def package_validator(cls, value):
-        if "/" in value:
-            if not value.endswith(".whl"):
-                raise ValueError(
-                    "Local-package path must be a wheel file "
-                    f"(given {value})."
-                )
-            if not Path(value).is_absolute():
-                raise ValueError(
-                    f"Local-package path must be absolute: (given {value})."
-                )
-        return value
-
-    @validator("package_version")
-    def package_version_validator(cls, v, values):
-
-        valstr("package_version")(v)
-
-        if values["package"].endswith(".whl"):
-            raise ValueError(
-                "Cannot provide version when package is a Wheel file."
-            )
-        return v
-
-
-class TaskCollectStatusV1(BaseModel):
-    """
-    TaskCollectStatus class
-
-    Attributes:
-        status:
-        package:
-        venv_path:
-        task_list:
-        log:
-        info:
-    """
-
-    status: Literal["pending", "installing", "collecting", "fail", "OK"]
-    package: str
-    venv_path: Path
-    task_list: Optional[list[TaskReadV1]] = Field(default=[])
-    log: Optional[str]
-    info: Optional[str]
-
-    def sanitised_dict(self):
-        """
-        Return `self.dict()` after casting `self.venv_path` to a string
-        """
-        d = self.dict()
-        d["venv_path"] = str(self.venv_path)
-        return d

fractal_server/app/schemas/v1/workflow.py

@@ -1,212 +0,0 @@
-from datetime import datetime
-from enum import Enum
-from typing import Any
-from typing import Optional
-
-from pydantic import BaseModel
-from pydantic import validator
-
-from .._validators import valint
-from .._validators import valstr
-from .project import ProjectReadV1
-from .task import TaskExportV1
-from .task import TaskImportV1
-from .task import TaskReadV1
-
-__all__ = (
-    "WorkflowCreateV1",
-    "WorkflowReadV1",
-    "WorkflowUpdateV1",
-    "WorkflowImportV1",
-    "WorkflowExportV1",
-    "WorkflowTaskCreateV1",
-    "WorkflowTaskImportV1",
-    "WorkflowTaskExportV1",
-    "WorkflowTaskReadV1",
-    "WorkflowTaskUpdateV1",
-    "WorkflowTaskStatusTypeV1",
-)
-
-
-class _WorkflowTaskBaseV1(BaseModel):
-    """
-    Base class for `WorkflowTask`.
-    """
-
-    meta: Optional[dict[str, Any]] = None
-    args: Optional[dict[str, Any]] = None
-
-
-class WorkflowTaskCreateV1(_WorkflowTaskBaseV1):
-    """
-    Class for `WorkflowTask` creation.
-
-    Attributes:
-        order:
-    """
-
-    order: Optional[int]
-    # Validators
-    _order = validator("order", allow_reuse=True)(valint("order", min_val=0))
-
-
-class WorkflowTaskReadV1(_WorkflowTaskBaseV1):
-    """
-    Class for `WorkflowTask` read from database.
-
-    Attributes:
-        id:
-        order:
-        workflow_id:
-        task_id:
-        task:
-    """
-
-    id: int
-    order: Optional[int]
-    workflow_id: int
-    task_id: int
-    task: TaskReadV1
-
-
-class WorkflowTaskImportV1(_WorkflowTaskBaseV1):
-    """
-    Class for `WorkflowTask` import.
-
-    Attributes:
-        task:
-    """
-
-    task: TaskImportV1
-
-
-class WorkflowTaskExportV1(_WorkflowTaskBaseV1):
-    """
-    Class for `WorkflowTask` export.
-
-    Attributes:
-        task:
-    """
-
-    task: TaskExportV1
-
-
-class WorkflowTaskUpdateV1(_WorkflowTaskBaseV1):
-    """
-    Class for `WorkflowTask` update.
-    """
-
-    # Validators
-    @validator("meta")
-    def check_no_parallelisation_level(cls, m):
-        if "parallelization_level" in m:
-            raise ValueError(
-                "Overriding task parallelization level currently not allowed"
-            )
-        return m
-
-
-class _WorkflowBaseV1(BaseModel):
-    """
-    Base class for `Workflow`.
-
-    Attributes:
-        name: Workflow name.
-    """
-
-    name: str
-
-
-class WorkflowReadV1(_WorkflowBaseV1):
-    """
-    Task for `Workflow` read from database.
-
-    Attributes:
-        id:
-        project_id:
-        task_list:
-        project:
-    """
-
-    id: int
-    project_id: int
-    task_list: list[WorkflowTaskReadV1]
-    project: ProjectReadV1
-    timestamp_created: datetime
-
-
-class WorkflowCreateV1(_WorkflowBaseV1):
-    """
-    Task for `Workflow` creation.
-    """
-
-    # Validators
-    _name = validator("name", allow_reuse=True)(valstr("name"))
-
-
-class WorkflowUpdateV1(_WorkflowBaseV1):
-    """
-    Task for `Workflow` update.
-
-    Attributes:
-        name:
-        reordered_workflowtask_ids:
-    """
-
-    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 WorkflowImportV1(_WorkflowBaseV1):
-    """
-    Class for `Workflow` import.
-
-    Attributes:
-        task_list:
-    """
-
-    task_list: list[WorkflowTaskImportV1]
-
-    # Validators
-    _name = validator("name", allow_reuse=True)(valstr("name"))
-
-
-class WorkflowExportV1(_WorkflowBaseV1):
-    """
-    Class for `Workflow` export.
-
-    Attributes:
-        task_list:
-    """
-
-    task_list: list[WorkflowTaskExportV1]
-
-
-class WorkflowTaskStatusTypeV1(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/v1/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"

fractal_server/tasks/v1/_TaskCollectPip.py

@@ -1,103 +0,0 @@
-from pathlib import Path
-from typing import Optional
-
-from pydantic import root_validator
-
-from fractal_server.app.schemas.v1 import ManifestV1
-from fractal_server.app.schemas.v1 import TaskCollectPipV1
-
-
-class _TaskCollectPip(TaskCollectPipV1):
-    """
-    Internal TaskCollectPip schema
-
-    Differences with its parent class (`TaskCollectPip`):
-
-        1. We check if the package corresponds to a path in the filesystem, and
-           whether it exists (via new validator `check_local_package`, new
-           method `is_local_package` and new attribute `package_path`).
-        2. We include an additional `package_manifest` attribute.
-        3. We expose an additional attribute `package_name`, which is filled
-           during task collection.
-    """
-
-    package_name: Optional[str] = None
-    package_path: Optional[Path] = None
-    package_manifest: Optional[ManifestV1] = None
-
-    @property
-    def is_local_package(self) -> bool:
-        return bool(self.package_path)
-
-    @root_validator(pre=True)
-    def check_local_package(cls, values):
-        """
-        Checks if package corresponds to an existing path on the filesystem
-
-        In this case, the user is providing directly a package file, rather
-        than a remote one from PyPI. We set the `package_path` attribute and
-        get the actual package name and version from the package file name.
-        """
-        if "/" in values["package"]:
-            package_path = Path(values["package"])
-            if not package_path.is_absolute():
-                raise ValueError("Package path must be absolute")
-            if package_path.exists():
-                values["package_path"] = package_path
-                (
-                    values["package"],
-                    values["version"],
-                    *_,
-                ) = package_path.name.split("-")
-            else:
-                raise ValueError(f"Package {package_path} does not exist.")
-        return values
-
-    @property
-    def package_source(self) -> str:
-        """
-        NOTE: As of PR #1188 in `fractal-server`, the attribute
-        `self.package_name` is normalized; this means e.g. that `_` is
-        replaced by `-`. To guarantee backwards compatibility with
-        `Task.source` attributes created before this change, we still replace
-        `-` with `_` upon generation of the `source` attribute, in this
-        method.
-        """
-        if not self.package_name or not self.package_version:
-            raise ValueError(
-                "Cannot construct `package_source` property with "
-                f"{self.package_name=} and {self.package_version=}."
-            )
-        if self.is_local_package:
-            collection_type = "pip_local"
-        else:
-            collection_type = "pip_remote"
-
-        package_extras = self.package_extras or ""
-        if self.python_version:
-            python_version = f"py{self.python_version}"
-        else:
-            python_version = ""
-
-        source = ":".join(
-            (
-                collection_type,
-                self.package_name.replace("-", "_"),  # see method docstring
-                self.package_version,
-                package_extras,
-                python_version,
-            )
-        )
-        return source
-
-    def check(self):
-        """
-        Verify that the package has all attributes that are needed to continue
-        with task collection
-        """
-        if not self.package_name:
-            raise ValueError("`package_name` attribute is not set")
-        if not self.package_version:
-            raise ValueError("`package_version` attribute is not set")
-        if not self.package_manifest:
-            raise ValueError("`package_manifest` attribute is not set")