fractal-server 2.9.1__tar.gz → 2.9.2__tar.gz

{fractal_server-2.9.1 → fractal_server-2.9.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.9.1
+Version: 2.9.2
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

fractal_server-2.9.2/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.9.2"

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/models/security.py

@@ -76,7 +76,6 @@ class UserOAuth(SQLModel, table=True):
         is_verified:
         slurm_user:
         slurm_accounts:
-        cache_dir:
         username:
         oauth_accounts:
     """

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/models/user_settings.py

@@ -20,7 +20,7 @@ class UserSettings(SQLModel, table=True):
         ssh_tasks_dir: Task-venvs base folder on `ssh_host`.
         ssh_jobs_dir: Jobs base folder on `ssh_host`.
         slurm_user: Local user, to be impersonated via `sudo -u`
-        cache_dir: Folder where `slurm_user` can write.
+        project_dir: Folder where `slurm_user` can write.
     """
 
     __tablename__ = "user_settings"
@@ -35,5 +35,4 @@ class UserSettings(SQLModel, table=True):
     ssh_tasks_dir: Optional[str] = None
     ssh_jobs_dir: Optional[str] = None
     slurm_user: Optional[str] = None
-    cache_dir: Optional[str] = None
     project_dir: Optional[str] = None

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/routes/api/v1/project.py

@@ -448,6 +448,12 @@ async def apply_workflow(
     await db.commit()
     await db.refresh(job)
 
+    cache_dir = (
+        f"{user_settings.project_dir}/.fractal_cache"
+        if user_settings.project_dir is not None
+        else None
+    )
+
     background_tasks.add_task(
         submit_workflow,
         workflow_id=workflow.id,
@@ -456,7 +462,7 @@ async def apply_workflow(
         job_id=job.id,
         worker_init=apply_workflow.worker_init,
         slurm_user=user_settings.slurm_user,
-        user_cache_dir=user_settings.cache_dir,
+        user_cache_dir=cache_dir,
     )
     request.app.state.jobsV1.append(job.id)
     logger.info(

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/routes/api/v2/_aux_functions_task_lifecycle.py

@@ -182,8 +182,8 @@ async def check_no_submitted_job(
     Find submitted jobs which include tasks from a given task group.
 
     Arguments:
-        task_id_list: List of TaskV2 IDs
-        db: Database session
+        task_group_id: ID of the `TaskGroupV2` object.
+        db: Asynchronous database session.
     """
     stm = (
         select(func.count(JobV2.id))

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/routes/api/v2/submit.py

@@ -186,18 +186,22 @@ async def apply_workflow(
         f"_{timestamp_string}"
     )
 
+    cache_dir = (
+        Path(user_settings.project_dir) / ".fractal_cache"
+        if user_settings.project_dir is not None
+        else None
+    )
+
     # Define user-side job directory
     if FRACTAL_RUNNER_BACKEND == "local":
         WORKFLOW_DIR_REMOTE = WORKFLOW_DIR_LOCAL
     elif FRACTAL_RUNNER_BACKEND == "local_experimental":
         WORKFLOW_DIR_REMOTE = WORKFLOW_DIR_LOCAL
     elif FRACTAL_RUNNER_BACKEND == "slurm":
-        WORKFLOW_DIR_REMOTE = (
-            Path(user_settings.cache_dir) / f"{WORKFLOW_DIR_LOCAL.name}"
-        )
+        WORKFLOW_DIR_REMOTE = cache_dir / WORKFLOW_DIR_LOCAL.name
     elif FRACTAL_RUNNER_BACKEND == "slurm_ssh":
         WORKFLOW_DIR_REMOTE = (
-            Path(user_settings.ssh_jobs_dir) / f"{WORKFLOW_DIR_LOCAL.name}"
+            Path(user_settings.ssh_jobs_dir) / WORKFLOW_DIR_LOCAL.name
         )
 
     # Update job folders in the db
@@ -229,7 +233,7 @@ async def apply_workflow(
         user_settings=user_settings,
         worker_init=job.worker_init,
         slurm_user=user_settings.slurm_user,
-        user_cache_dir=user_settings.cache_dir,
+        user_cache_dir=cache_dir.as_posix() if cache_dir else None,
         fractal_ssh=fractal_ssh,
     )
     request.app.state.jobsV2.append(job.id)

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/routes/api/v2/workflow_import.py

@@ -68,11 +68,8 @@ async def _get_task_by_source(
     Find task with a given source.
 
     Args:
-        task_import: Info on task to be imported.
-        user_id: ID of current user.
-        default_group_id: ID of default user group.
-        task_group_list: Current list of valid task groups.
-        db: Asynchronous db session
+        source: `source` of the task to be imported.
+        task_groups_list: Current list of valid task groups.
 
     Return:
         `id` of the matching task, or `None`.
@@ -172,10 +169,10 @@ async def _get_task_by_taskimport(
 
     Args:
         task_import: Info on task to be imported.
+        task_groups_list: Current list of valid task groups.
         user_id: ID of current user.
         default_group_id: ID of default user group.
-        task_group_list: Current list of valid task groups.
-        db: Asynchronous db session
+        db: Asynchronous database session.
 
     Return:
         `id` of the matching task, or `None`.

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/runner/executors/slurm/_slurm_config.py

@@ -327,7 +327,7 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
         script.
 
         Arguments:
-            user_cache_dir:
+            remote_export_dir:
                 Base directory for exports defined in
                 `self.user_local_exports`.
         """
@@ -378,7 +378,7 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
         if self.user_local_exports:
             if remote_export_dir is None:
                 raise ValueError(
-                    f"user_cache_dir=None but {self.user_local_exports=}"
+                    f"remote_export_dir=None but {self.user_local_exports=}"
                 )
             for key, value in self.user_local_exports.items():
                 tmp_value = str(Path(remote_export_dir) / value)

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/runner/executors/slurm/ssh/executor.py

@@ -917,7 +917,7 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         thread via `fut.set_exception(...)`.
 
         Arguments:
-            jobid: ID of the SLURM job
+            job_ids: IDs of the SLURM jobs to handle.
         """
         # Handle all uncaught exceptions in this broad try/except block
         try:
@@ -1109,8 +1109,9 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         Fetch a remote folder via tar+sftp+tar
 
         Arguments:
-            job:
-                `SlurmJob` object (needed for its prefixes-related attributes).
+            jobs:
+                List of `SlurmJob` object (needed for their prefix-related
+                attributes).
         """
 
         # Check that the subfolder is unique

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/runner/v1/_common.py

@@ -524,8 +524,7 @@ def execute_tasks(
 
     **Note:** At the end of each task, write current metadata to
     `workflow_dir_local / METADATA_FILENAME`, so that they can be read as part
-    of the [`get_job`
-    endpoint](../../api/v1/job/#fractal_server.app.routes.api.v1.job.get_job).
+    of the `get_job` endpoint.
 
     Arguments:
         executor:

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/runner/v2/_local/__init__.py

@@ -44,10 +44,6 @@ def _process_workflow(
     Internal processing routine
 
     Schedules the workflow using a `FractalThreadPoolExecutor`.
-
-    Cf.
-    [process_workflow][fractal_server.app.runner.v2._local.process_workflow]
-    for the call signature.
     """
 
     with FractalThreadPoolExecutor() as executor:

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/runner/v2/_slurm_ssh/__init__.py

@@ -55,9 +55,6 @@ def _process_workflow(
     workflow working dir and user to impersonate. It then schedules the
     workflow tasks and returns the new dataset attributes
 
-    Cf.
-    [process_workflow][fractal_server.app.runner.v2._local.process_workflow]
-
     Returns:
         new_dataset_attributes:
     """
@@ -115,9 +112,6 @@ async def process_workflow(
 ) -> dict:
     """
     Process workflow (SLURM backend public interface)
-
-    Cf.
-    [process_workflow][fractal_server.app.runner.v2._local.process_workflow]
     """
 
     # Set values of first_task_index and last_task_index

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/runner/v2/_slurm_sudo/__init__.py

@@ -51,9 +51,6 @@ def _process_workflow(
     workflow working dir and user to impersonate. It then schedules the
     workflow tasks and returns the new dataset attributes
 
-    Cf.
-    [process_workflow][fractal_server.app.runner.v2._local.process_workflow]
-
     Returns:
         new_dataset_attributes:
     """
@@ -106,10 +103,7 @@ async def process_workflow(
     worker_init: Optional[str] = None,
 ) -> dict:
     """
-    Process workflow (SLURM backend public interface)
-
-    Cf.
-    [process_workflow][fractal_server.app.runner.v2._local.process_workflow]
+    Process workflow (SLURM backend public interface).
     """
 
     # Set values of first_task_index and last_task_index

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/schemas/user_settings.py

@@ -31,14 +31,12 @@ class UserSettingsRead(BaseModel):
     ssh_jobs_dir: Optional[str] = None
     slurm_user: Optional[str] = None
     slurm_accounts: list[str]
-    cache_dir: Optional[str] = None
     project_dir: Optional[str] = None
 
 
 class UserSettingsReadStrict(BaseModel):
     slurm_user: Optional[str] = None
     slurm_accounts: list[str]
-    cache_dir: Optional[str] = None
     ssh_username: Optional[str] = None
     project_dir: Optional[str] = None
 
@@ -55,7 +53,6 @@ class UserSettingsUpdate(BaseModel, extra=Extra.forbid):
     ssh_jobs_dir: Optional[str] = None
     slurm_user: Optional[str] = None
     slurm_accounts: Optional[list[StrictStr]] = None
-    cache_dir: Optional[str] = None
     project_dir: Optional[str] = None
 
     _ssh_host = validator("ssh_host", allow_reuse=True)(
@@ -87,13 +84,6 @@ class UserSettingsUpdate(BaseModel, extra=Extra.forbid):
             value[i] = valstr(f"slurm_accounts[{i}]")(item)
         return val_unique_list("slurm_accounts")(value)
 
-    @validator("cache_dir")
-    def cache_dir_validator(cls, value):
-        if value is None:
-            return None
-        validate_cmd(value)
-        return val_absolute_path("cache_dir")(value)
-
     @validator("project_dir")
     def project_dir_validator(cls, value):
         if value is None:
@@ -104,15 +94,7 @@ class UserSettingsUpdate(BaseModel, extra=Extra.forbid):
 
 class UserSettingsUpdateStrict(BaseModel, extra=Extra.forbid):
     slurm_accounts: Optional[list[StrictStr]] = None
-    cache_dir: Optional[str] = None
 
     _slurm_accounts = validator("slurm_accounts", allow_reuse=True)(
         val_unique_list("slurm_accounts")
     )
-
-    @validator("cache_dir")
-    def cache_dir_validator(cls, value):
-        if value is None:
-            return value
-        validate_cmd(value)
-        return val_absolute_path("cache_dir")(value)

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/app/user_settings.py

@@ -32,11 +32,11 @@ class SlurmSudoUserSettings(BaseModel):
 
     Attributes:
         slurm_user: User to be impersonated via `sudo -u`.
-        cache_dir: Folder where `slurm_user` can write.
+        project_dir: Folder where `slurm_user` can write.
         slurm_accounts:
             List of SLURM accounts, to be used upon Fractal job submission.
     """
 
     slurm_user: str
-    cache_dir: str
+    project_dir: str
     slurm_accounts: list[str]

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/config.py

@@ -302,8 +302,7 @@ class Settings(BaseSettings):
     """
     Logging-level threshold for logging
 
-    Only logs of with this level (or higher) will appear in the console logs;
-    see details [here](../internals/logs/).
+    Only logs of with this level (or higher) will appear in the console logs.
     """
 
     FRACTAL_LOCAL_CONFIG_FILE: Optional[Path]

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/logger.py

@@ -66,10 +66,8 @@ def set_logger(
 
     * The attribute `Logger.propagate` set to `False`;
     * One and only one `logging.StreamHandler` handler, with severity level set
-    to
-    [`FRACTAL_LOGGING_LEVEL`](../../../../configuration/#fractal_server.config.Settings.FRACTAL_LOGGING_LEVEL)
-    and formatter set as in the `logger.LOG_FORMAT` variable from the current
-    module;
+    to `FRACTAL_LOGGING_LEVEL` and formatter set as in the `logger.LOG_FORMAT`
+    variable from the current module;
     * One or many `logging.FileHandler` handlers, including one pointint to
     `log_file_path` (if set); all these handlers have severity level set to
     `logging.DEBUG`.

fractal_server-2.9.2/fractal_server/migrations/versions/316140ff7ee1_remove_usersettings_cache_dir.py

@@ -0,0 +1,36 @@
+"""Remove UserSettings.cache_dir
+
+Revision ID: 316140ff7ee1
+Revises: d256a7379ab8
+Create Date: 2024-12-03 10:15:53.255958
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "316140ff7ee1"
+down_revision = "d256a7379ab8"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("user_settings", schema=None) as batch_op:
+        batch_op.drop_column("cache_dir")
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("user_settings", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "cache_dir", sa.VARCHAR(), autoincrement=False, nullable=True
+            )
+        )
+
+    # ### end Alembic commands ###

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/ssh/_fabric.py

@@ -366,10 +366,9 @@ class FractalSSH(object):
         Transfer a file via SSH
 
         Args:
-            local: Local path to file
-            remote: Target path on remote host
-            fractal_ssh: FractalSSH connection object with custom lock
-            logger_name: Name of the logger
+            local: Local path to file.
+            remote: Target path on remote host.
+            lock_timeout: Timeout for lock acquisition (overrides default).
         """
         try:
             self.logger.info(
@@ -407,10 +406,9 @@ class FractalSSH(object):
         Transfer a file via SSH
 
         Args:
-            local: Local path to file
-            remote: Target path on remote host
-            logger_name: Name of the logger
-            lock_timeout:
+            local: Local path to file.
+            remote: Target path on remote host.
+            lock_timeout: Timeout for lock acquisition (overrides default).
         """
         try:
             prefix = "[fetch_file] "
@@ -499,9 +497,9 @@ class FractalSSH(object):
         Open a remote file via SFTP and write it.
 
         Args:
-            path: Absolute path
-            contents: File contents
-            lock_timeout:
+            path: Absolute path of remote file.
+            content: Contents to be written to file.
+            lock_timeout: Timeout for lock acquisition (overrides default).
         """
         self.logger.info(f"START writing to remote file {path}.")
         actual_lock_timeout = self.default_lock_timeout

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/tasks/v2/ssh/_utils.py

@@ -24,7 +24,7 @@ def _customize_and_run_template(
     Args:
         template_filename: Filename of the template file (ends with ".sh").
         replacements: Dictionary of replacements.
-        script_dir: Local folder where the script will be placed.
+        script_dir_local: Local folder where the script will be placed.
         prefix: Prefix for the script filename.
         fractal_ssh: FractalSSH object
         script_dir_remote: Remote scripts directory

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/tasks/v2/utils_database.py

@@ -24,9 +24,12 @@ def create_db_tasks_and_update_task_group(
     Create a `TaskGroupV2` with N `TaskV2`s, and insert them into the database.
 
     Arguments:
-        task_group: ID of an existing TaskGroupV2 object.
-        task_list: A list of TaskCreateV2 objects to be inserted into the db.
-        db: A synchronous database session
+        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
+
+    Returns:
+        Updated `TaskGroupV2` object.
     """
     actual_task_list = [
         TaskV2(

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/tasks/v2/utils_python_interpreter.py

@@ -8,10 +8,10 @@ def get_python_interpreter_v2(
     python_version: Literal["3.9", "3.10", "3.11", "3.12"]
 ) -> str:
     """
-    Return the path to the python interpreter
+    Return the path to the Python interpreter
 
     Args:
-        version: Python version
+        python_version: Python version
 
     Raises:
         ValueError: If the python version requested is not available on the

{fractal_server-2.9.1 → fractal_server-2.9.2}/fractal_server/tasks/v2/utils_templates.py

@@ -19,9 +19,9 @@ def customize_template(
     Customize a bash-script template and write it to disk.
 
     Args:
-        template_filename:
-        templates_folder:
-        replacements:
+        template_name: Name of the template that will be customized.
+        replacements: List of replacements for template customization.
+        script_path: Local path where the customized template will be written.
     """
     # Read template
     template_path = TEMPLATES_DIR / template_name

{fractal_server-2.9.1 → fractal_server-2.9.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.9.1"
+version = "2.9.2"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Tommaso Comparin <tommaso.comparin@exact-lab.it>",
@@ -85,7 +85,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.9.1"
+current_version = "2.9.2"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.9.1/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.9.1"