fractal-server 2.17.1a0__py3-none-any.whl → 2.17.2__py3-none-any.whl

fractal_server/types/__init__.py

@@ -6,7 +6,8 @@ from pydantic import AfterValidator
 from pydantic.types import NonNegativeInt
 from pydantic.types import StringConstraints
 
-from ..urls import normalize_url
+from fractal_server.urls import normalize_url
+
 from .validators import val_absolute_path
 from .validators import val_http_url
 from .validators import val_unique_list
@@ -18,69 +19,143 @@ NonEmptyStr = Annotated[
     str,
     StringConstraints(min_length=1, strip_whitespace=True),
 ]
+"""
+A non-empty string, with no leading/trailing whitespaces.
+"""
+
 
 AbsolutePathStr = Annotated[
     NonEmptyStr,
     AfterValidator(val_absolute_path),
 ]
+"""
+String representing an absolute path.
+"""
+
+
 HttpUrlStr = Annotated[
     NonEmptyStr,
     AfterValidator(val_http_url),
 ]
+"""
+String representing an URL.
+"""
+
+
 ZarrUrlStr = Annotated[
     NonEmptyStr,
     AfterValidator(normalize_url),
 ]
+"""
+String representing a zarr URL/path.
+"""
+
+
 ZarrDirStr = Annotated[
     NonEmptyStr,
     AfterValidator(normalize_url),
 ]
+"""
+String representing a `zarr_dir` path.
+"""
 
 DictStrAny = Annotated[
     dict[str, Any],
     AfterValidator(valdict_keys),
 ]
+"""
+Dictionary where keys are strings with no leading/trailing whitespaces.
+"""
+
+
 DictStrStr = Annotated[
     dict[str, NonEmptyStr],
     AfterValidator(valdict_keys),
 ]
+"""
+Dictionary where keys are strings with no leading/trailing whitespaces and
+values are non-empty strings.
+"""
 
 ListUniqueNonEmptyString = Annotated[
     list[NonEmptyStr],
     AfterValidator(val_unique_list),
 ]
+"""
+List of unique non-empty-string items.
+"""
+
+
 ListUniqueNonNegativeInt = Annotated[
     list[NonNegativeInt],
     AfterValidator(val_unique_list),
 ]
+"""
+List of unique non-negative-integer items.
+"""
+
+
 ListUniqueAbsolutePathStr = Annotated[
     list[AbsolutePathStr],
     AfterValidator(val_unique_list),
 ]
+"""
+List of unique absolute-path-string items.
+"""
 
 WorkflowTaskArgument = Annotated[
     DictStrAny,
     AfterValidator(validate_wft_args),
 ]
+"""
+Dictionary with no keys from a given forbid-list.
+"""
 
 ImageAttributeValue = Union[int, float, str, bool]
+"""
+Possible values for image attributes.
+"""
+
 ImageAttributes = Annotated[
     dict[str, ImageAttributeValue],
     AfterValidator(valdict_keys),
 ]
+"""
+Image-attributes dictionary.
+"""
+
+
 ImageAttributesWithNone = Annotated[
     dict[str, ImageAttributeValue | None],
     AfterValidator(valdict_keys),
 ]
+"""
+Image-attributes dictionary, including `None` attributes.
+"""
+
+
 AttributeFilters = Annotated[
     dict[str, list[ImageAttributeValue]],
     AfterValidator(validate_attribute_filters),
 ]
+"""
+Image-attributes filters.
+"""
+
+
 TypeFilters = Annotated[
     dict[str, bool],
     AfterValidator(valdict_keys),
 ]
+"""
+Image-type filters.
+"""
+
+
 ImageTypes = Annotated[
     dict[str, bool],
     AfterValidator(valdict_keys),
 ]
+"""
+Image types.
+"""

fractal_server/types/validators/_common_validators.py

@@ -13,9 +13,7 @@ def valdict_keys(d: dict[str, Any]) -> dict[str, Any]:
     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}'."
-        )
+        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)

fractal_server/types/validators/_workflow_task_arguments_validators.py

@@ -4,7 +4,6 @@ def validate_wft_args(value: dict) -> dict:
     intersect_keys = RESERVED_ARGUMENTS.intersection(args_keys)
     if intersect_keys:
         raise ValueError(
-            "`args` contains the following forbidden keys: "
-            f"{intersect_keys}"
+            f"`args` contains the following forbidden keys: {intersect_keys}"
         )
     return value

fractal_server/utils.py

@@ -13,6 +13,7 @@
 This module provides general purpose utilities that are not specific to any
 subsystem.
 """
+
 import shlex
 import subprocess  # nosec
 from datetime import datetime

fractal_server/zip_tools.py

@@ -1,5 +1,6 @@
 import os
 import shutil
+import subprocess  # nosec
 from collections.abc import Iterator
 from io import BytesIO
 from pathlib import Path
@@ -144,3 +145,36 @@ def _zip_folder_to_file_and_remove(folder: str) -> None:
         logger.info(f"Removing folder '{folder}'.")
         shutil.rmtree(folder)
         logger.info("Folder removed.")
+
+
+def _read_single_file_from_zip(*, file_path: str, archive_path: str) -> str:
+    """
+    Reads and returns the contents of a single file from a ZIP archive using
+    `unzip -p`.
+
+    Args:
+        file_path:
+            relative to the archive
+        archive_path:
+
+    Returns:
+        The file content
+
+    Raises:
+        FileNotFoundError:
+            if the file is not inside the archive
+    """
+    result = subprocess.run(  # nosec
+        ["unzip", "-p", archive_path, file_path],
+        capture_output=True,
+        encoding="utf-8",
+        check=False,
+    )
+
+    if result.returncode != 0:
+        # The caller function should handle this error
+        raise FileNotFoundError(
+            f"File '{file_path}' not found inside archive '{archive_path}'."
+        )
+
+    return result.stdout

{fractal_server-2.17.1a0.dist-info → fractal_server-2.17.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.17.1a0
+Version: 2.17.2
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE

fractal_server-2.17.2.dist-info/RECORD

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fractal_server/app/models/user_settings.py

@@ -1,37 +0,0 @@
-from sqlalchemy import Column
-from sqlalchemy.dialects.postgresql import JSONB
-from sqlmodel import Field
-from sqlmodel import SQLModel
-
-
-# TODO-2.17.1: Drop `UserSettings`
-class UserSettings(SQLModel, table=True):
-    """
-    Comprehensive list of user settings.
-
-    Attributes:
-        id: ID of database object
-        slurm_accounts:
-            List of SLURM accounts, to be used upon Fractal job submission.
-        ssh_host: SSH-reachable host where a SLURM client is available.
-        ssh_username: User on `ssh_host`.
-        ssh_private_key_path: Path of private SSH key for `ssh_username`.
-        slurm_user: Local user, to be impersonated via `sudo -u`
-        project_dir: Folder where `slurm_user` can write.
-    """
-
-    __tablename__ = "user_settings"
-
-    id: int | None = Field(default=None, primary_key=True)
-    slurm_accounts: list[str] = Field(
-        sa_column=Column(JSONB, server_default="[]", nullable=False)
-    )
-    ssh_host: str | None = None
-    ssh_username: str | None = None
-    ssh_private_key_path: str | None = None
-
-    slurm_user: str | None = None
-    project_dir: str | None = None
-
-    ssh_tasks_dir: str | None = None
-    ssh_jobs_dir: str | None = None

fractal_server/app/routes/admin/v2/project.py

@@ -1,41 +0,0 @@
-from fastapi import APIRouter
-from fastapi import Depends
-from sqlmodel import select
-
-from fractal_server.app.db import AsyncSession
-from fractal_server.app.db import get_async_db
-from fractal_server.app.models import UserOAuth
-from fractal_server.app.models.v2 import ProjectV2
-from fractal_server.app.routes.auth import current_superuser_act
-from fractal_server.app.schemas.v2 import ProjectReadV2
-
-router = APIRouter()
-
-
-@router.get("/", response_model=list[ProjectReadV2])
-async def view_project(
-    id: int | None = None,
-    user_id: int | None = None,
-    user: UserOAuth = Depends(current_superuser_act),
-    db: AsyncSession = Depends(get_async_db),
-) -> list[ProjectReadV2]:
-    """
-    Query `ProjectV2` table.
-
-    Args:
-        id: If not `None`, select a given `project.id`.
-        user_id: If not `None`, select a given `project.user_id`.
-    """
-
-    stm = select(ProjectV2)
-
-    if id is not None:
-        stm = stm.where(ProjectV2.id == id)
-    if user_id is not None:
-        stm = stm.where(ProjectV2.user_list.any(UserOAuth.id == user_id))
-
-    res = await db.execute(stm)
-    project_list = res.scalars().all()
-    await db.close()
-
-    return project_list