fractal-server 2.17.1a1__py3-none-any.whl → 2.17.2__py3-none-any.whl

fractal_server/tasks/v2/ssh/reactivate_pixi.py

@@ -2,12 +2,6 @@ import time
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
-from ..utils_background import fail_and_cleanup
-from ..utils_background import get_activity_and_task_group
-from ..utils_pixi import SOURCE_DIR_NAME
-from ._pixi_slurm_ssh import run_script_on_remote_slurm
-from ._utils import check_ssh_or_fail_and_cleanup
-from ._utils import edit_pyproject_toml_in_place_ssh
 from fractal_server.app.db import get_sync_db
 from fractal_server.app.models import Profile
 from fractal_server.app.models import Resource
@@ -21,10 +15,17 @@ from fractal_server.tasks.utils import get_log_path
 from fractal_server.tasks.v2.ssh._utils import _customize_and_run_template
 from fractal_server.tasks.v2.ssh._utils import _customize_and_send_template
 from fractal_server.tasks.v2.utils_background import add_commit_refresh
+from fractal_server.tasks.v2.utils_background import fail_and_cleanup
+from fractal_server.tasks.v2.utils_background import get_activity_and_task_group
 from fractal_server.tasks.v2.utils_background import get_current_log
+from fractal_server.tasks.v2.utils_pixi import SOURCE_DIR_NAME
 from fractal_server.tasks.v2.utils_templates import SCRIPTS_SUBFOLDER
 from fractal_server.utils import get_timestamp
 
+from ._pixi_slurm_ssh import run_script_on_remote_slurm
+from ._utils import check_ssh_or_fail_and_cleanup
+from ._utils import edit_pyproject_toml_in_place_ssh
+
 
 def reactivate_ssh_pixi(
     *,
@@ -233,9 +234,7 @@ def reactivate_ssh_pixi(
                             remote_script3_path,
                             f"chmod -R 755 {source_dir}",
                         ],
-                        slurm_config=resource.tasks_pixi_config[
-                            "SLURM_CONFIG"
-                        ],
+                        slurm_config=resource.tasks_pixi_config["SLURM_CONFIG"],
                         fractal_ssh=fractal_ssh,
                         logger_name=LOGGER_NAME,
                         prefix=common_args["prefix"],

fractal_server/tasks/v2/templates/1_create_venv.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 set -e
 
 write_log(){

fractal_server/tasks/v2/templates/2_pip_install.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 set -e
 
 write_log(){

fractal_server/tasks/v2/templates/3_pip_freeze.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 set -e
 
 # Variables to be filled within fractal-server

fractal_server/tasks/v2/templates/4_pip_show.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 set -e
 
 write_log(){

fractal_server/tasks/v2/templates/5_get_venv_size_and_file_number.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 set -e
 
 # Variables to be filled within fractal-server
@@ -7,4 +9,4 @@ PACKAGE_ENV_DIR=__PACKAGE_ENV_DIR__
 ENV_DISK_USAGE=$(du -sk "${PACKAGE_ENV_DIR}" | cut -f1)
 ENV_FILE_NUMBER=$(find "${PACKAGE_ENV_DIR}" -type f | wc -l)
 
-echo $ENV_DISK_USAGE $ENV_FILE_NUMBER
+echo "$ENV_DISK_USAGE" "$ENV_FILE_NUMBER"

fractal_server/tasks/v2/templates/6_pip_install_from_freeze.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 set -e
 
 write_log(){

fractal_server/tasks/v2/templates/pixi_1_extract.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 set -e
 
 write_log(){

fractal_server/tasks/v2/templates/pixi_2_install.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 set -e
 
 write_log(){

fractal_server/tasks/v2/templates/pixi_3_post_install.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 set -e
 
 write_log(){

fractal_server/tasks/v2/utils_background.py

@@ -112,9 +112,9 @@ def prepare_tasks_metadata(
         if package_version is not None:
             task_attributes["version"] = package_version
         if package_manifest.has_args_schemas:
-            task_attributes[
-                "args_schema_version"
-            ] = package_manifest.args_schema_version
+            task_attributes["args_schema_version"] = (
+                package_manifest.args_schema_version
+            )
         # Set command attributes
         if _task.executable_non_parallel is not None:
             non_parallel_path = package_root / _task.executable_non_parallel

fractal_server/tasks/v2/utils_package_names.py

@@ -62,8 +62,7 @@ def compare_package_names(
         return
 
     logger.warning(
-        f"Package name mismatch: "
-        f"{pkg_name_task_group=}, {pkg_name_pip_show=}."
+        f"Package name mismatch: {pkg_name_task_group=}, {pkg_name_pip_show=}."
     )
     normalized_pkg_name_pip = normalize_package_name(pkg_name_pip_show)
     normalized_pkg_name_taskgroup = normalize_package_name(pkg_name_task_group)

fractal_server/tasks/v2/utils_pixi.py

@@ -95,9 +95,7 @@ def simplify_pyproject_toml(
             if key == pixi_environment
         }
         if pixi_data["environments"] == {}:
-            raise ValueError(
-                f"No '{pixi_environment}' pixi environment found."
-            )
+            raise ValueError(f"No '{pixi_environment}' pixi environment found.")
     except KeyError:
         logger.info("KeyError for workspace/platforms - skip.")
 

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-2.17.1a1.dist-info → fractal_server-2.17.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.17.1a1
+Version: 2.17.2
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE