fractal-server 2.16.5__py3-none-any.whl → 2.17.0a0__py3-none-any.whl

fractal_server/tasks/v2/ssh/deactivate.py

@@ -10,6 +10,8 @@ from ._utils import _copy_wheel_file_ssh
 from ._utils import _customize_and_run_template
 from ._utils import check_ssh_or_fail_and_cleanup
 from fractal_server.app.db import get_sync_db
+from fractal_server.app.models import Profile
+from fractal_server.app.models import Resource
 from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
 from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.app.schemas.v2.task_group import TaskGroupActivityStatusV2
@@ -28,8 +30,8 @@ def deactivate_ssh(
     *,
     task_group_activity_id: int,
     task_group_id: int,
-    ssh_config: SSHConfig,
-    tasks_base_dir: str,
+    resource: Resource,
+    profile: Profile,
 ) -> None:
     """
     Deactivate a task group venv.
@@ -37,13 +39,10 @@ def deactivate_ssh(
     This function is run as a background task, therefore exceptions must be
     handled.
 
-    Arguments:
+    Args:
         task_group_id:
         task_group_activity_id:
         ssh_config:
-        tasks_base_dir:
-            Only used as a `safe_root` in `remove_dir`, and typically set to
-            `user_settings.ssh_tasks_dir`.
     """
 
     LOGGER_NAME = f"{__name__}.ID{task_group_activity_id}"
@@ -66,7 +65,11 @@ def deactivate_ssh(
                 return
 
             with SingleUseFractalSSH(
-                ssh_config=ssh_config,
+                ssh_config=SSHConfig(
+                    user=profile.username,
+                    host=resource.host,
+                    key_path=profile.ssh_key_path,
+                ),
                 logger_name=LOGGER_NAME,
             ) as fractal_ssh:
                 try:
@@ -110,6 +113,7 @@ def deactivate_ssh(
                         replacements = get_collection_replacements(
                             task_group=task_group,
                             python_bin="/not/applicable",
+                            resource=resource,
                         )
 
                         # Define script_dir_remote and create it if missing
@@ -255,7 +259,7 @@ def deactivate_ssh(
                     logger.info(f"Now removing {task_group.venv_path}.")
                     fractal_ssh.remove_folder(
                         folder=task_group.venv_path,
-                        safe_root=tasks_base_dir,
+                        safe_root=profile.tasks_remote_dir,
                     )
                     logger.info(f"All good, {task_group.venv_path} removed.")
                     activity.status = TaskGroupActivityStatusV2.OK

fractal_server/tasks/v2/ssh/deactivate_pixi.py

@@ -7,6 +7,8 @@ from ..utils_background import get_activity_and_task_group
 from ..utils_pixi import SOURCE_DIR_NAME
 from ._utils import check_ssh_or_fail_and_cleanup
 from fractal_server.app.db import get_sync_db
+from fractal_server.app.models import Profile
+from fractal_server.app.models import Resource
 from fractal_server.app.schemas.v2.task_group import TaskGroupActivityStatusV2
 from fractal_server.logger import reset_logger_handlers
 from fractal_server.logger import set_logger
@@ -21,8 +23,8 @@ def deactivate_ssh_pixi(
     *,
     task_group_activity_id: int,
     task_group_id: int,
-    ssh_config: SSHConfig,
-    tasks_base_dir: str,
+    resource: Resource,
+    profile: Profile,
 ) -> None:
     """
     Deactivate a pixi task group venv.
@@ -30,13 +32,11 @@ def deactivate_ssh_pixi(
     This function is run as a background task, therefore exceptions must be
     handled.
 
-    Arguments:
-        task_group_id:
+    Args:
         task_group_activity_id:
-        ssh_config:
-        tasks_base_dir:
-            Only used as a `safe_root` in `remove_dir`, and typically set to
-            `user_settings.ssh_tasks_dir`.
+        task_group_id:
+        resource:
+        profile:
     """
 
     LOGGER_NAME = f"{__name__}.ID{task_group_activity_id}"
@@ -59,7 +59,11 @@ def deactivate_ssh_pixi(
                 return
 
             with SingleUseFractalSSH(
-                ssh_config=ssh_config,
+                ssh_config=SSHConfig(
+                    host=resource.host,
+                    user=profile.username,
+                    key_path=profile.ssh_key_path,
+                ),
                 logger_name=LOGGER_NAME,
             ) as fractal_ssh:
                 try:
@@ -101,7 +105,7 @@ def deactivate_ssh_pixi(
                     logger.info(f"Now removing {source_dir}.")
                     fractal_ssh.remove_folder(
                         folder=source_dir,
-                        safe_root=tasks_base_dir,
+                        safe_root=profile.tasks_remote_dir,
                     )
                     logger.info(f"All good, {source_dir} removed.")
                     activity.status = TaskGroupActivityStatusV2.OK

fractal_server/tasks/v2/ssh/delete.py

@@ -6,6 +6,8 @@ from ..utils_background import fail_and_cleanup
 from ..utils_background import get_activity_and_task_group
 from ._utils import check_ssh_or_fail_and_cleanup
 from fractal_server.app.db import get_sync_db
+from fractal_server.app.models import Profile
+from fractal_server.app.models import Resource
 from fractal_server.app.schemas.v2 import TaskGroupActivityStatusV2
 from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.logger import reset_logger_handlers
@@ -21,8 +23,8 @@ def delete_ssh(
     *,
     task_group_activity_id: int,
     task_group_id: int,
-    ssh_config: SSHConfig,
-    tasks_base_dir: str,
+    resource: Resource,
+    profile: Profile,
 ) -> None:
     """
     Delete a task group.
@@ -30,13 +32,10 @@ def delete_ssh(
     This function is run as a background task, therefore exceptions must be
     handled.
 
-    Arguments:
+    Args:
         task_group_id:
         task_group_activity_id:
         ssh_config:
-        tasks_base_dir:
-            Only used as a `safe_root` in `remove_dir`, and typically set to
-            `user_settings.ssh_tasks_dir`.
     """
 
     LOGGER_NAME = f"{__name__}.ID{task_group_activity_id}"
@@ -59,7 +58,11 @@ def delete_ssh(
                 return
 
             with SingleUseFractalSSH(
-                ssh_config=ssh_config,
+                ssh_config=SSHConfig(
+                    host=resource.host,
+                    user=profile.username,
+                    key_path=profile.ssh_key_path,
+                ),
                 logger_name=LOGGER_NAME,
             ) as fractal_ssh:
                 try:
@@ -86,11 +89,11 @@ def delete_ssh(
                     if task_group.origin != TaskGroupV2OriginEnum.OTHER:
                         logger.debug(
                             f"Removing remote {task_group.path=} "
-                            f"(with {tasks_base_dir=})."
+                            f"(with {profile.tasks_remote_dir=})."
                         )
                         fractal_ssh.remove_folder(
                             folder=task_group.path,
-                            safe_root=tasks_base_dir,
+                            safe_root=profile.tasks_remote_dir,
                         )
                         logger.debug(f"Remote {task_group.path=} removed.")
 

fractal_server/tasks/v2/ssh/reactivate.py

@@ -9,6 +9,8 @@ from ..utils_templates import get_collection_replacements
 from ._utils import _customize_and_run_template
 from ._utils import check_ssh_or_fail_and_cleanup
 from fractal_server.app.db import get_sync_db
+from fractal_server.app.models import Profile
+from fractal_server.app.models import Resource
 from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
 from fractal_server.app.schemas.v2.task_group import TaskGroupActivityStatusV2
 from fractal_server.logger import reset_logger_handlers
@@ -18,7 +20,7 @@ from fractal_server.ssh._fabric import SSHConfig
 from fractal_server.tasks.utils import get_log_path
 from fractal_server.tasks.v2.utils_background import get_current_log
 from fractal_server.tasks.v2.utils_python_interpreter import (
-    get_python_interpreter_v2,
+    get_python_interpreter,
 )
 from fractal_server.tasks.v2.utils_templates import SCRIPTS_SUBFOLDER
 from fractal_server.utils import get_timestamp
@@ -28,8 +30,8 @@ def reactivate_ssh(
     *,
     task_group_activity_id: int,
     task_group_id: int,
-    ssh_config: SSHConfig,
-    tasks_base_dir: str,
+    resource: Resource,
+    profile: Profile,
 ) -> None:
     """
     Reactivate a task group venv.
@@ -37,13 +39,10 @@ def reactivate_ssh(
     This function is run as a background task, therefore exceptions must be
     handled.
 
-    Arguments:
+    Args:
         task_group_id:
         task_group_activity_id:
         ssh_config:
-        tasks_base_dir:
-            Only used as a `safe_root` in `remove_dir`, and typically set to
-            `user_settings.ssh_tasks_dir`.
     """
 
     LOGGER_NAME = f"{__name__}.ID{task_group_activity_id}"
@@ -67,7 +66,11 @@ def reactivate_ssh(
                 return
 
             with SingleUseFractalSSH(
-                ssh_config=ssh_config,
+                ssh_config=SSHConfig(
+                    host=resource.host,
+                    user=profile.username,
+                    key_path=profile.ssh_key_path,
+                ),
                 logger_name=LOGGER_NAME,
             ) as fractal_ssh:
                 try:
@@ -102,11 +105,14 @@ def reactivate_ssh(
                     activity = add_commit_refresh(obj=activity, db=db)
 
                     # Prepare replacements for templates
+                    python_bin = get_python_interpreter(
+                        python_version=task_group.python_version,
+                        resource=resource,
+                    )
                     replacements = get_collection_replacements(
                         task_group=task_group,
-                        python_bin=get_python_interpreter_v2(
-                            python_version=task_group.python_version
-                        ),
+                        python_bin=python_bin,
+                        resource=resource,
                     )
 
                     # Prepare replacements for templates
@@ -181,7 +187,7 @@ def reactivate_ssh(
                         )
                         fractal_ssh.remove_folder(
                             folder=task_group.venv_path,
-                            safe_root=tasks_base_dir,
+                            safe_root=profile.tasks_remote_dir,
                         )
                         logger.info(f"Deleted folder {task_group.venv_path}")
                     except Exception as rm_e:

fractal_server/tasks/v2/ssh/reactivate_pixi.py

@@ -9,14 +9,14 @@ 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
 from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
 from fractal_server.app.schemas.v2 import TaskGroupActivityStatusV2
-from fractal_server.config import get_settings
 from fractal_server.logger import reset_logger_handlers
 from fractal_server.logger import set_logger
 from fractal_server.ssh._fabric import SingleUseFractalSSH
 from fractal_server.ssh._fabric import SSHConfig
-from fractal_server.syringe import Inject
 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
@@ -30,8 +30,8 @@ def reactivate_ssh_pixi(
     *,
     task_group_activity_id: int,
     task_group_id: int,
-    ssh_config: SSHConfig,
-    tasks_base_dir: str,
+    resource: Resource,
+    profile: Profile,
 ) -> None:
     """
     Reactivate a task group venv.
@@ -39,13 +39,11 @@ def reactivate_ssh_pixi(
     This function is run as a background task, therefore exceptions must be
     handled.
 
-    Arguments:
+    Args:
         task_group_id:
         task_group_activity_id:
-        ssh_config:
-        tasks_base_dir:
-            Only used as a `safe_root` in `remove_dir`, and typically set to
-            `user_settings.ssh_tasks_dir`.
+        resource:
+        profile:
     """
 
     LOGGER_NAME = f"{__name__}.ID{task_group_activity_id}"
@@ -69,7 +67,11 @@ def reactivate_ssh_pixi(
                 return
 
             with SingleUseFractalSSH(
-                ssh_config=ssh_config,
+                ssh_config=SSHConfig(
+                    host=resource.host,
+                    user=profile.username,
+                    key_path=profile.ssh_key_path,
+                ),
                 logger_name=LOGGER_NAME,
             ) as fractal_ssh:
                 try:
@@ -103,11 +105,12 @@ def reactivate_ssh_pixi(
                         )
                         return
 
-                    settings = Inject(get_settings)
                     replacements = {
                         (
                             "__PIXI_HOME__",
-                            settings.pixi.versions[task_group.pixi_version],
+                            resource.tasks_pixi_config["versions"][
+                                task_group.pixi_version
+                            ],
                         ),
                         ("__PACKAGE_DIR__", task_group.path),
                         ("__TAR_GZ_PATH__", task_group.archive_path),
@@ -119,15 +122,27 @@ def reactivate_ssh_pixi(
                         ("__FROZEN_OPTION__", "--frozen"),
                         (
                             "__TOKIO_WORKER_THREADS__",
-                            str(settings.pixi.TOKIO_WORKER_THREADS),
+                            str(
+                                resource.tasks_pixi_config[
+                                    "TOKIO_WORKER_THREADS"
+                                ]
+                            ),
                         ),
                         (
                             "__PIXI_CONCURRENT_SOLVES__",
-                            str(settings.pixi.PIXI_CONCURRENT_SOLVES),
+                            str(
+                                resource.tasks_pixi_config[
+                                    "PIXI_CONCURRENT_SOLVES"
+                                ]
+                            ),
                         ),
                         (
                             "__PIXI_CONCURRENT_DOWNLOADS__",
-                            str(settings.pixi.PIXI_CONCURRENT_DOWNLOADS),
+                            str(
+                                resource.tasks_pixi_config[
+                                    "PIXI_CONCURRENT_DOWNLOADS"
+                                ]
+                            ),
                         ),
                     }
 
@@ -172,6 +187,7 @@ def reactivate_ssh_pixi(
                     edit_pyproject_toml_in_place_ssh(
                         fractal_ssh=fractal_ssh,
                         pyproject_toml_path=pyproject_toml_path,
+                        resource=resource,
                     )
                     # Write pixi.lock into `source_dir`
                     pixi_lock_local = Path(tmpdir, "pixi.lock").as_posix()
@@ -217,13 +233,16 @@ def reactivate_ssh_pixi(
                             remote_script3_path,
                             f"chmod -R 755 {source_dir}",
                         ],
-                        slurm_config=settings.pixi.SLURM_CONFIG,
+                        slurm_config=resource.tasks_pixi_config[
+                            "SLURM_CONFIG"
+                        ],
                         fractal_ssh=fractal_ssh,
                         logger_name=LOGGER_NAME,
                         prefix=common_args["prefix"],
                         db=db,
                         activity=activity,
                         log_file_path=log_file_path,
+                        poll_interval=resource.jobs_poll_interval,
                     )
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
@@ -244,7 +263,7 @@ def reactivate_ssh_pixi(
                         logger.info(f"Now delete folder {source_dir}")
                         fractal_ssh.remove_folder(
                             folder=source_dir,
-                            safe_root=tasks_base_dir,
+                            safe_root=profile.tasks_remote_dir,
                         )
                         logger.info(f"Deleted folder {source_dir}")
                     except Exception as rm_e:

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

@@ -17,21 +17,19 @@ VENVPYTHON=${PACKAGE_ENV_DIR}/bin/python
 write_log "Python interpreter: $VENVPYTHON"
 echo
 
-# FIXME: only run pip-show once!
-
 # Extract information about paths
 # WARNING: this block will fail for paths which include whitespace characters
 write_log "START pip show"
-$VENVPYTHON -m pip show ${PACKAGE_NAME}
+PIP_SHOW_OUTPUT=$($VENVPYTHON -m pip show ${PACKAGE_NAME})
 write_log "END   pip show"
 echo
-PACKAGE_NAME=$($VENVPYTHON -m pip show "$PACKAGE_NAME" | grep "Name:" | cut -d ":" -f 2 | tr -d "[:space:]")
+PACKAGE_NAME=$(echo "$PIP_SHOW_OUTPUT" | grep "Name:" | cut -d ":" -f 2 | tr -d "[:space:]")
 write_log "Package name: $PACKAGE_NAME"
 echo
-PACKAGE_VERSION=$($VENVPYTHON -m pip show "$PACKAGE_NAME" | grep "Version:" | cut -d ":" -f 2 | tr -d "[:space:]")
+PACKAGE_VERSION=$(echo "$PIP_SHOW_OUTPUT" | grep "Version:" | cut -d ":" -f 2 | tr -d "[:space:]")
 write_log "Package version: $PACKAGE_VERSION"
 echo
-PACKAGE_PARENT_FOLDER=$($VENVPYTHON -m pip show "$PACKAGE_NAME" | grep "Location:" | cut -d ":" -f 2 | tr -d "[:space:]")
+PACKAGE_PARENT_FOLDER=$(echo "$PIP_SHOW_OUTPUT" | grep "Location:" | cut -d ":" -f 2 | tr -d "[:space:]")
 write_log "Package parent folder: $PACKAGE_PARENT_FOLDER"
 echo
 MANIFEST_RELATIVE_PATH=$($VENVPYTHON -m pip show "$PACKAGE_NAME" --files | grep "__FRACTAL_MANIFEST__.json" | tr -d "[:space:]")

fractal_server/tasks/v2/utils_database.py

@@ -15,7 +15,7 @@ def create_db_tasks_and_update_task_group_sync(
     """
     Create a `TaskGroupV2` with N `TaskV2`s, and insert them into the database.
 
-    Arguments:
+    Args:
         task_group_id: ID of an existing `TaskGroupV2` object.
         task_list: List of `TaskCreateV2` objects to be inserted into the db.
         db: Synchronous database session
@@ -42,7 +42,7 @@ async def create_db_tasks_and_update_task_group_async(
     """
     Create a `TaskGroupV2` with N `TaskV2`s, and insert them into the database.
 
-    Arguments:
+    Args:
         task_group_id: ID of an existing `TaskGroupV2` object.
         task_list: List of `TaskCreateV2` objects to be inserted into the db.
         db: Synchronous database session

fractal_server/tasks/v2/utils_python_interpreter.py

@@ -1,11 +1,9 @@
-from typing import Literal
+from fractal_server.app.models import Resource
 
-from fractal_server.config import get_settings
-from fractal_server.syringe import Inject
 
-
-def get_python_interpreter_v2(
-    python_version: Literal["3.9", "3.10", "3.11", "3.12"],
+def get_python_interpreter(
+    python_version: str,
+    resource: Resource,
 ) -> str:
     """
     Return the path to the Python interpreter
@@ -21,13 +19,7 @@ def get_python_interpreter_v2(
         interpreter: string representing the python executable or its path
     """
 
-    if python_version not in ["3.9", "3.10", "3.11", "3.12", "3.13"]:
-        raise ValueError(f"Invalid {python_version=}.")
-
-    settings = Inject(get_settings)
-    version_underscore = python_version.replace(".", "_")
-    key = f"FRACTAL_TASKS_PYTHON_{version_underscore}"
-    value = getattr(settings, key)
-    if value is None:
-        raise ValueError(f"Requested {python_version=}, but {key}={value}.")
-    return value
+    python_path = resource.tasks_python_config["versions"].get(python_version)
+    if python_path is None:
+        raise ValueError(f"Requested {python_version=} is not available.")
+    return python_path

fractal_server/tasks/v2/utils_templates.py

@@ -1,9 +1,8 @@
 from pathlib import Path
 
+from fractal_server.app.models import Resource
 from fractal_server.app.models.v2 import TaskGroupV2
-from fractal_server.config import get_settings
 from fractal_server.logger import set_logger
-from fractal_server.syringe import Inject
 
 TEMPLATES_DIR = Path(__file__).parent / "templates"
 
@@ -12,7 +11,7 @@ SCRIPTS_SUBFOLDER = "scripts"
 logger = set_logger(__name__)
 
 
-def _check_pixi_frozen_option(replacements: list[tuple[str, str]]):
+def _check_pixi_frozen_option(replacements: set[tuple[str, str]]):
     try:
         replacement = next(
             rep for rep in replacements if rep[0] == "__FROZEN_OPTION__"
@@ -28,7 +27,7 @@ def customize_template(
     template_name: str,
     replacements: set[tuple[str, str]],
     script_path: str,
-) -> str:
+) -> None:
     """
     Customize a bash-script template and write it to disk.
 
@@ -84,16 +83,14 @@ def parse_script_pip_show_stdout(stdout: str) -> dict[str, str]:
 
 
 def get_collection_replacements(
-    *, task_group: TaskGroupV2, python_bin: str
-) -> dict[str, str]:
-    settings = Inject(get_settings)
-
+    *, task_group: TaskGroupV2, python_bin: str, resource: Resource
+) -> list[tuple[str, str]]:
     replacements = [
         ("__PACKAGE_NAME__", task_group.pkg_name),
         ("__PACKAGE_ENV_DIR__", task_group.venv_path),
         ("__PYTHON__", python_bin),
         ("__INSTALL_STRING__", task_group.pip_install_string),
-        ("__FRACTAL_PIP_CACHE_DIR_ARG__", settings.PIP_CACHE_DIR_ARG),
+        ("__FRACTAL_PIP_CACHE_DIR_ARG__", resource.pip_cache_dir_arg),
         (
             "__PINNED_PACKAGE_LIST_PRE__",
             task_group.pinned_package_versions_pre_string,
@@ -104,6 +101,6 @@ def get_collection_replacements(
         ),
     ]
     logger.info(
-        f"Cache-dir argument for `pip install`: {settings.PIP_CACHE_DIR_ARG}"
+        f"Cache-dir argument for `pip install`: {resource.pip_cache_dir_arg}"
     )
     return replacements

fractal_server/utils.py

@@ -41,7 +41,7 @@ def execute_command_sync(
     If the command returns a return code different from zero, a `RuntimeError`
     is raised.
 
-    Arguments:
+    Args:
         command: Command to be executed.
         logger_name: Name of the logger.
         allow_char: Argument propagated to `validate_cmd`.

{fractal_server-2.16.5.dist-info → fractal_server-2.17.0a0.dist-info}/METADATA

@@ -1,12 +1,12 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.16.5
+Version: 2.17.0a0
 Summary: Backend component of the Fractal analytics platform
-License: BSD-3-Clause
+License-Expression: BSD-3-Clause
+License-File: LICENSE
 Author: Tommaso Comparin
 Author-email: tommaso.comparin@exact-lab.it
 Requires-Python: >=3.11,<3.14
-Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -19,7 +19,7 @@ Requires-Dist: fastapi-users[oauth] (>=14,<15)
 Requires-Dist: gunicorn (>=23.0,<24.0)
 Requires-Dist: packaging (>=25.0.0,<26.0.0)
 Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0)
-Requires-Dist: pydantic (>=2.11.0,<2.12.0)
+Requires-Dist: pydantic (>=2.12.0,<2.13.0)
 Requires-Dist: pydantic-settings (==2.11.0)
 Requires-Dist: python-dotenv (>=1.1.0,<1.2.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)