fractal-server 2.9.0a0__py3-none-any.whl → 2.9.0a2__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.9.0a0"
+__VERSION__ = "2.9.0a2"

fractal_server/app/db/__init__.py

@@ -2,17 +2,14 @@
 `db` module, loosely adapted from
 https://testdriven.io/blog/fastapi-sqlmodel/#async-sqlmodel
 """
-import sqlite3
 from typing import AsyncGenerator
 from typing import Generator
 
 from sqlalchemy import create_engine
-from sqlalchemy import event
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.ext.asyncio import create_async_engine
 from sqlalchemy.orm import Session as DBSyncSession
 from sqlalchemy.orm import sessionmaker
-from sqlalchemy.pool import StaticPool
 
 from ...config import get_settings
 from ...logger import set_logger
@@ -21,14 +18,6 @@ from ...syringe import Inject
 
 logger = set_logger(__name__)
 
-SQLITE_WARNING_MESSAGE = (
-    "SQLite is supported (supported version >=3.37, "
-    f"current {sqlite3.sqlite_version=}) "
-    "but discouraged in production. "
-    "Given its partial support for ForeignKey constraints, "
-    "database consistency cannot be guaranteed."
-)
-
 
 class DB:
     """
@@ -56,14 +45,7 @@ class DB:
         settings = Inject(get_settings)
         settings.check_db()
 
-        if settings.DB_ENGINE == "sqlite":
-            logger.warning(SQLITE_WARNING_MESSAGE)
-            # Set some sqlite-specific options
-            engine_kwargs_async = dict(poolclass=StaticPool)
-        else:
-            engine_kwargs_async = {
-                "pool_pre_ping": True,
-            }
+        engine_kwargs_async = {"pool_pre_ping": True}
 
         cls._engine_async = create_async_engine(
             settings.DATABASE_ASYNC_URL,
@@ -83,15 +65,7 @@ class DB:
         settings = Inject(get_settings)
         settings.check_db()
 
-        if settings.DB_ENGINE == "sqlite":
-            logger.warning(SQLITE_WARNING_MESSAGE)
-            # Set some sqlite-specific options
-            engine_kwargs_sync = dict(
-                poolclass=StaticPool,
-                connect_args={"check_same_thread": False},
-            )
-        else:
-            engine_kwargs_sync = {}
+        engine_kwargs_sync = {}
 
         cls._engine_sync = create_engine(
             settings.DATABASE_SYNC_URL,
@@ -107,13 +81,6 @@ class DB:
             future=True,
         )
 
-        @event.listens_for(cls._engine_sync, "connect")
-        def set_sqlite_pragma(dbapi_connection, connection_record):
-            if settings.DB_ENGINE == "sqlite":
-                cursor = dbapi_connection.cursor()
-                cursor.execute("PRAGMA journal_mode=WAL")
-                cursor.close()
-
     @classmethod
     async def get_async_db(cls) -> AsyncGenerator[AsyncSession, None]:
         """

fractal_server/app/models/v2/task_group.py

@@ -48,6 +48,10 @@ class TaskGroupV2(SQLModel, table=True):
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),
     )
+    timestamp_last_used: Optional[datetime] = Field(
+        default=None,
+        sa_column=Column(DateTime(timezone=True), nullable=True),
+    )
 
     @property
     def pip_install_string(self) -> str:

fractal_server/app/routes/api/v2/_aux_functions_tasks.py

@@ -221,27 +221,30 @@ async def _get_valid_user_group_id(
 
 
 async def _get_collection_task_group_activity_status_message(
-    task_group: TaskGroupV2, db: AsyncSession
+    task_group_id: int,
+    db: AsyncSession,
 ) -> str:
+
     res = await db.execute(
-        select(TaskGroupActivityV2).where(
-            TaskGroupActivityV2.taskgroupv2_id == task_group.id
-            and TaskGroupActivityV2.action == TaskGroupActivityActionV2.COLLECT
-        )
+        select(TaskGroupActivityV2)
+        .where(TaskGroupActivityV2.taskgroupv2_id == task_group_id)
+        .where(TaskGroupActivityV2.action == TaskGroupActivityActionV2.COLLECT)
     )
     task_group_activity_list = res.scalars().all()
     if len(task_group_activity_list) > 1:
         msg = (
-            "Expected one TaskGroupActivityV2 associated to TaskGroup "
-            f"{task_group.id}, found {len(task_group_activity_list)} "
-            f"(IDs: {[tga.id for tga in task_group_activity_list]}).\n"
+            "\nWarning: "
+            "Expected only one TaskGroupActivityV2 associated to TaskGroup "
+            f"{task_group_id}, found {len(task_group_activity_list)} "
+            f"(IDs: {[tga.id for tga in task_group_activity_list]})."
             "Warning: this should have not happened, please contact an admin."
         )
     elif len(task_group_activity_list) == 1:
         msg = (
-            "\nThere exists a task-group activity"
-            f"(ID={task_group_activity_list[0].id}) for "
-            f"such task group (ID={task_group.id}), with status "
+            "\nNote:"
+            "There exists another task-group collection "
+            f"(activity ID={task_group_activity_list[0].id}) for "
+            f"this task group (ID={task_group_id}), with status "
             f"'{task_group_activity_list[0].status}'."
         )
     else:
@@ -277,7 +280,7 @@ async def _verify_non_duplication_user_constraint(
                 ),
             )
         state_msg = await _get_collection_task_group_activity_status_message(
-            duplicate[0], db
+            duplicate[0].id, db
         )
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
@@ -319,7 +322,7 @@ async def _verify_non_duplication_group_constraint(
                 ),
             )
         state_msg = await _get_collection_task_group_activity_status_message(
-            duplicate[0], db
+            duplicate[0].id, db
         )
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,

fractal_server/app/routes/api/v2/submit.py

@@ -30,6 +30,7 @@ from ...aux.validate_user_settings import validate_user_settings
 from ._aux_functions import _get_dataset_check_owner
 from ._aux_functions import _get_workflow_check_owner
 from ._aux_functions import clean_app_job_list_v2
+from fractal_server.app.models import TaskGroupV2
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.api.v2._aux_functions_tasks import (
     _get_task_read_access,
@@ -61,6 +62,8 @@ async def apply_workflow(
     db: AsyncSession = Depends(get_async_db),
 ) -> Optional[JobReadV2]:
 
+    now = get_timestamp()
+
     # Remove non-submitted V2 jobs from the app state when the list grows
     # beyond a threshold
     settings = Inject(get_settings)
@@ -112,22 +115,23 @@ async def apply_workflow(
         )
 
     # Check that tasks have read-access and are `active`
+    used_task_group_ids = set()
     for wftask in workflow.task_list[
         first_task_index : last_task_index + 1  # noqa: E203
     ]:
-        await _get_task_read_access(
+        task = await _get_task_read_access(
             user_id=user.id,
             task_id=wftask.task_id,
             require_active=True,
             db=db,
         )
+        used_task_group_ids.add(task.taskgroupv2_id)
 
     # Validate user settings
     FRACTAL_RUNNER_BACKEND = settings.FRACTAL_RUNNER_BACKEND
     user_settings = await validate_user_settings(
         user=user, backend=FRACTAL_RUNNER_BACKEND, db=db
     )
-
     # Check that no other job with the same dataset_id is SUBMITTED
     stm = (
         select(JobV2)
@@ -184,8 +188,18 @@ async def apply_workflow(
     await db.commit()
     await db.refresh(job)
 
+    # Update TaskGroupV2.timestamp_last_used
+    res = await db.execute(
+        select(TaskGroupV2).where(TaskGroupV2.id.in_(used_task_group_ids))
+    )
+    used_task_groups = res.scalars().all()
+    for used_task_group in used_task_groups:
+        used_task_group.timestamp_last_used = now
+        db.add(used_task_group)
+    await db.commit()
+
     # Define server-side job directory
-    timestamp_string = get_timestamp().strftime("%Y%m%d_%H%M%S")
+    timestamp_string = now.strftime("%Y%m%d_%H%M%S")
     WORKFLOW_DIR_LOCAL = settings.FRACTAL_RUNNER_WORKING_BASE_DIR / (
         f"proj_v2_{project_id:07d}_wf_{workflow_id:07d}_job_{job.id:07d}"
         f"_{timestamp_string}"

fractal_server/app/routes/api/v2/task_collection.py

@@ -35,7 +35,7 @@ from fractal_server.app.schemas.v2 import (
 )
 from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.tasks.v2.local.collect import (
-    collect_package_local,
+    collect_local,
 )
 from fractal_server.tasks.v2.utils_package_names import _parse_wheel_filename
 from fractal_server.tasks.v2.utils_package_names import normalize_package_name
@@ -248,7 +248,7 @@ async def collect_tasks_pip(
         # SSH task collection
 
         from fractal_server.tasks.v2.ssh.collect import (
-            collect_package_ssh,
+            collect_ssh,
         )
 
         # User appropriate FractalSSH object
@@ -261,7 +261,7 @@ async def collect_tasks_pip(
         fractal_ssh = fractal_ssh_list.get(**ssh_credentials)
 
         background_tasks.add_task(
-            collect_package_ssh,
+            collect_ssh,
             task_group_id=task_group.id,
             task_group_activity_id=task_group_activity.id,
             fractal_ssh=fractal_ssh,
@@ -271,7 +271,7 @@ async def collect_tasks_pip(
     else:
         # Local task collection
         background_tasks.add_task(
-            collect_package_local,
+            collect_local,
             task_group_id=task_group.id,
             task_group_activity_id=task_group_activity.id,
         )

fractal_server/app/routes/aux/_timestamp.py

@@ -4,15 +4,10 @@ from datetime import timezone
 from fastapi import HTTPException
 from fastapi import status
 
-from fractal_server.config import get_settings
-from fractal_server.syringe import Inject
-
 
 def _convert_to_db_timestamp(dt: datetime) -> datetime:
     """
     This function takes a timezone-aware datetime and converts it to UTC.
-    If using SQLite, it also removes the timezone information in order to make
-    the datetime comparable with datetimes in the database.
     """
     if dt.tzinfo is None:
         raise HTTPException(
@@ -20,6 +15,4 @@ def _convert_to_db_timestamp(dt: datetime) -> datetime:
             detail=f"The timestamp provided has no timezone information: {dt}",
         )
     _dt = dt.astimezone(timezone.utc)
-    if Inject(get_settings).DB_ENGINE == "sqlite":
-        return _dt.replace(tzinfo=None)
     return _dt

fractal_server/app/schemas/_validators.py

@@ -108,8 +108,7 @@ def val_unique_list(attribute: str):
 def valutc(attribute: str):
     def val(timestamp: Optional[datetime]) -> Optional[datetime]:
         """
-        Replacing `tzinfo` with `timezone.utc` is just required by SQLite data.
-        If using Postgres, this function leaves the datetime exactly as it is.
+        Replace `tzinfo` with `timezone.utc`.
         """
         if timestamp is not None:
             return timestamp.replace(tzinfo=timezone.utc)

fractal_server/app/schemas/v2/task_group.py

@@ -1,6 +1,5 @@
 from datetime import datetime
 from enum import Enum
-from typing import Literal
 from typing import Optional
 
 from pydantic import BaseModel
@@ -74,7 +73,7 @@ class TaskGroupReadV2(BaseModel):
     user_id: int
     user_group_id: Optional[int] = None
 
-    origin: Literal["pypi", "wheel-file", "other"]
+    origin: TaskGroupV2OriginEnum
     pkg_name: str
     version: Optional[str] = None
     python_version: Optional[str] = None
@@ -90,6 +89,7 @@ class TaskGroupReadV2(BaseModel):
 
     active: bool
     timestamp_created: datetime
+    timestamp_last_used: Optional[datetime] = None
 
 
 class TaskGroupUpdateV2(BaseModel, extra=Extra.forbid):

fractal_server/config.py

@@ -16,7 +16,6 @@ import shutil
 import sys
 from os import environ
 from os import getenv
-from os.path import abspath
 from pathlib import Path
 from typing import Literal
 from typing import Optional
@@ -167,10 +166,6 @@ class Settings(BaseSettings):
     ###########################################################################
     # DATABASE
     ###########################################################################
-    DB_ENGINE: Literal["sqlite", "postgres-psycopg"] = "sqlite"
-    """
-    Database engine to use (supported: `sqlite`, `postgres-psycopg`).
-    """
     DB_ECHO: bool = False
     """
     If `True`, make database operations verbose.
@@ -196,44 +191,21 @@ class Settings(BaseSettings):
     Name of the PostgreSQL database to connect to.
     """
 
-    SQLITE_PATH: Optional[str]
-    """
-    File path where the SQLite database is located (or will be located).
-    """
-
     @property
     def DATABASE_ASYNC_URL(self) -> URL:
-        if self.DB_ENGINE == "postgres-psycopg":
-            url = URL.create(
-                drivername="postgresql+psycopg",
-                username=self.POSTGRES_USER,
-                password=self.POSTGRES_PASSWORD,
-                host=self.POSTGRES_HOST,
-                port=self.POSTGRES_PORT,
-                database=self.POSTGRES_DB,
-            )
-        else:
-            if not self.SQLITE_PATH:
-                raise FractalConfigurationError(
-                    "SQLITE_PATH path cannot be None"
-                )
-            sqlite_path = abspath(self.SQLITE_PATH)
-            url = URL.create(
-                drivername="sqlite+aiosqlite",
-                database=sqlite_path,
-            )
+        url = URL.create(
+            drivername="postgresql+psycopg",
+            username=self.POSTGRES_USER,
+            password=self.POSTGRES_PASSWORD,
+            host=self.POSTGRES_HOST,
+            port=self.POSTGRES_PORT,
+            database=self.POSTGRES_DB,
+        )
         return url
 
     @property
     def DATABASE_SYNC_URL(self):
-        if self.DB_ENGINE == "postgres-psycopg":
-            return self.DATABASE_ASYNC_URL.set(drivername="postgresql+psycopg")
-        else:
-            if not self.SQLITE_PATH:
-                raise FractalConfigurationError(
-                    "SQLITE_PATH path cannot be None"
-                )
-            return self.DATABASE_ASYNC_URL.set(drivername="sqlite")
+        return self.DATABASE_ASYNC_URL.set(drivername="postgresql+psycopg")
 
     ###########################################################################
     # FRACTAL SPECIFIC
@@ -533,25 +505,8 @@ class Settings(BaseSettings):
         """
         Checks that db environment variables are properly set.
         """
-        if self.DB_ENGINE == "postgres-psycopg":
-            if not self.POSTGRES_DB:
-                raise FractalConfigurationError(
-                    "POSTGRES_DB cannot be None when DB_ENGINE="
-                    "postgres-psycopg."
-                )
-
-            try:
-                import psycopg  # noqa: F401
-            except ModuleNotFoundError:
-                raise FractalConfigurationError(
-                    "DB engine is `postgres-psycopg` but `psycopg` is not "
-                    "available"
-                )
-        else:
-            if not self.SQLITE_PATH:
-                raise FractalConfigurationError(
-                    "SQLITE_PATH cannot be None when DB_ENGINE=sqlite."
-                )
+        if not self.POSTGRES_DB:
+            raise FractalConfigurationError("POSTGRES_DB cannot be None.")
 
     def check_runner(self) -> None:
 

fractal_server/migrations/versions/3082479ac4ea_taskgroup_activity_and_venv_info_to_.py

@@ -67,6 +67,13 @@ def upgrade() -> None:
         batch_op.add_column(
             sa.Column("venv_file_number", sa.Integer(), nullable=True)
         )
+        batch_op.add_column(
+            sa.Column(
+                "timestamp_last_used",
+                sa.DateTime(timezone=True),
+                nullable=True,
+            )
+        )
 
     # ### end Alembic commands ###
 
@@ -74,6 +81,7 @@ def upgrade() -> None:
 def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
     with op.batch_alter_table("taskgroupv2", schema=None) as batch_op:
+        batch_op.drop_column("timestamp_last_used")
         batch_op.drop_column("venv_file_number")
         batch_op.drop_column("venv_size_in_kB")
         batch_op.drop_column("pip_freeze")

fractal_server/ssh/_fabric.py

@@ -196,23 +196,57 @@ class FractalSSH(object):
         """
         Open the SSH connection and handle exceptions.
 
-        This function can be called from within other functions that use
-        `connection`, so that we can provide a meaningful error in case the
-        SSH connection cannot be opened.
+        This method should always be called at the beginning of background
+        operations that use FractalSSH, so that:
+
+        1. We try to restore unusable connections (e.g. due to closed socket).
+        2. We provide an informative error if connection cannot be established.
         """
-        if not self._connection.is_connected:
+        self.logger.debug(
+            f"[check_connection] {self._connection.is_connected=}"
+        )
+        if self._connection.is_connected:
+            # Even if the connection appears open, it could be broken for
+            # external reasons (e.g. the socket is closed because the SSH
+            # server was restarted). In these cases, we catch the error and
+            # try to re-open the connection.
             try:
-                with _acquire_lock_with_timeout(
-                    lock=self._lock,
-                    label="_connection.open",
-                    timeout=self.default_lock_timeout,
-                ):
-                    self._connection.open()
-            except Exception as e:
-                raise RuntimeError(
-                    f"Cannot open SSH connection. Original error:\n{str(e)}"
+                self.logger.info(
+                    "[check_connection] Run dummy command to check connection."
+                )
+                # Run both an SFTP and an SSH command, as they correspond to
+                # different sockets
+                self.remote_exists("/dummy/path/")
+                self.run_command(cmd="whoami")
+                self.logger.info(
+                    "[check_connection] SSH connection is already OK, exit."
+                )
+                return
+            except (OSError, EOFError) as e:
+                self.logger.warning(
+                    f"[check_connection] Detected error {str(e)}, re-open."
+                )
+        # Try opening the connection (if it was closed) or to re-open it (if
+        # an error happened).
+        try:
+            self.close()
+            with _acquire_lock_with_timeout(
+                lock=self._lock,
+                label="_connection.open",
+                timeout=self.default_lock_timeout,
+                logger_name=self.logger_name,
+            ):
+                self._connection.open()
+                self._connection.client.open_sftp()
+                self.logger.info(
+                    "[check_connection] SSH connection opened, exit."
                 )
 
+        except Exception as e:
+            raise RuntimeError(
+                f"Cannot open SSH connection. Original error:\n{str(e)}"
+            )
+
     def close(self) -> None:
         """
         Aggressively close `self._connection`.
@@ -228,9 +262,8 @@ class FractalSSH(object):
             timeout=self.default_lock_timeout,
         ):
             self._connection.close()
-
-        if self._connection.client is not None:
-            self._connection.client.close()
+            if self._connection.client is not None:
+                self._connection.client.close()
 
     def run_command(
         self,

fractal_server/tasks/v2/local/__init__.py

@@ -1,3 +1,3 @@
-from .collect import collect_package_local  # noqa
+from .collect import collect_local  # noqa
 from .deactivate import deactivate_local  # noqa
 from .reactivate import reactivate_local  # noqa

fractal_server/tasks/v2/local/collect.py

@@ -47,7 +47,7 @@ def _copy_wheel_file_local(task_group: TaskGroupV2) -> str:
     return dest
 
 
-def collect_package_local(
+def collect_local(
     *,
     task_group_activity_id: int,
     task_group_id: int,

fractal_server/tasks/v2/local/deactivate.py

@@ -12,6 +12,7 @@ from fractal_server.app.db import get_sync_db
 from fractal_server.app.models.v2 import TaskGroupActivityV2
 from fractal_server.app.models.v2 import TaskGroupV2
 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
 from fractal_server.logger import set_logger
 from fractal_server.tasks.utils import get_log_path
@@ -83,6 +84,7 @@ def deactivate_local(
 
                 activity.status = TaskGroupActivityStatusV2.ONGOING
                 activity = add_commit_refresh(obj=activity, db=db)
+
                 if task_group.pip_freeze is None:
                     logger.warning(
                         "Recreate pip-freeze information, since "
@@ -119,34 +121,80 @@ def deactivate_local(
                     task_group = add_commit_refresh(obj=task_group, db=db)
                     logger.info("Add pip freeze stdout to TaskGroupV2 - end")
 
-                if task_group.origin == "wheel" and (
-                    task_group.wheel_path is None
-                    or not Path(task_group.wheel_path).exists()
-                ):
+                # Handle some specific cases for wheel-file case
+                if task_group.origin == TaskGroupV2OriginEnum.WHEELFILE:
 
-                    logger.error(
-                        "Cannot find task_group wheel_path with "
-                        f"{task_group_id=} :\n"
-                        f"{task_group=}\n. Exit."
+                    logger.info(
+                        f"Handle specific cases for {task_group.origin=}."
                     )
-                    error_msg = f"{task_group.wheel_path} does not exist."
-                    logger.error(error_msg)
-                    fail_and_cleanup(
-                        task_group=task_group,
-                        task_group_activity=activity,
-                        logger_name=LOGGER_NAME,
-                        log_file_path=log_file_path,
-                        exception=FileNotFoundError(error_msg),
-                        db=db,
-                    )
-                    return
 
-                # At this point we are sure that venv_path
-                # wheel_path and pip_freeze exist
+                    # Blocking situation: `wheel_path` is not set or points
+                    # to a missing path
+                    if (
+                        task_group.wheel_path is None
+                        or not Path(task_group.wheel_path).exists()
+                    ):
+                        error_msg = (
+                            "Invalid wheel path for task group with "
+                            f"{task_group_id=}. {task_group.wheel_path=} is "
+                            "unset or does not exist."
+                        )
+                        logger.error(error_msg)
+                        fail_and_cleanup(
+                            task_group=task_group,
+                            task_group_activity=activity,
+                            logger_name=LOGGER_NAME,
+                            log_file_path=log_file_path,
+                            exception=FileNotFoundError(error_msg),
+                            db=db,
+                        )
+                        return
+
+                    # Recoverable situation: `wheel_path` was not yet copied
+                    # over to the correct server-side folder
+                    wheel_path_parent_dir = Path(task_group.wheel_path).parent
+                    if wheel_path_parent_dir != Path(task_group.path):
+                        logger.warning(
+                            f"{wheel_path_parent_dir.as_posix()} differs from "
+                            f"{task_group.path}. NOTE: this should only "
+                            "happen for task groups created before 2.9.0."
+                        )
+
+                        if task_group.wheel_path not in task_group.pip_freeze:
+                            raise ValueError(
+                                f"Cannot find {task_group.wheel_path=} in "
+                                "pip-freeze data. Exit."
+                            )
+
+                        logger.info(
+                            f"Now copy wheel file into {task_group.path}."
+                        )
+                        new_wheel_path = (
+                            Path(task_group.path)
+                            / Path(task_group.wheel_path).name
+                        ).as_posix()
+                        shutil.copy(task_group.wheel_path, new_wheel_path)
+                        logger.info(f"Copied wheel file to {new_wheel_path}.")
+
+                        task_group.wheel_path = new_wheel_path
+                        new_pip_freeze = task_group.pip_freeze.replace(
+                            task_group.wheel_path,
+                            new_wheel_path,
+                        )
+                        task_group.pip_freeze = new_pip_freeze
+                        task_group = add_commit_refresh(obj=task_group, db=db)
+                        logger.info(
+                            "Updated `wheel_path` and `pip_freeze` "
+                            "task-group attributes."
+                        )
+
+                # We now have all required information for reactivating the
+                # virtual environment at a later point
+                logger.info(f"Now removing {task_group.venv_path}.")
                 shutil.rmtree(task_group.venv_path)
-
-                activity.log = f"All good, {task_group.venv_path} removed."
+                logger.info(f"All good, {task_group.venv_path} removed.")
                 activity.status = TaskGroupActivityStatusV2.OK
+                activity.log = get_current_log(log_file_path)
                 activity.timestamp_ended = get_timestamp()
                 activity = add_commit_refresh(obj=activity, db=db)
 

fractal_server/tasks/v2/local/utils_local.py

@@ -1,5 +1,4 @@
 from pathlib import Path
-from typing import Optional
 
 from fractal_server.logger import get_logger
 from fractal_server.tasks.v2.utils_templates import customize_template
@@ -11,7 +10,7 @@ def _customize_and_run_template(
     replacements: list[tuple[str, str]],
     script_dir: str,
     logger_name: str,
-    prefix: Optional[int] = None,
+    prefix: int,
 ) -> str:
     """
     Customize one of the template bash scripts.
@@ -31,12 +30,7 @@ def _customize_and_run_template(
             f"Invalid {template_filename=} (it must end with '.sh')."
         )
 
-    template_filename_stripped = template_filename[:-3]
-
-    if prefix is not None:
-        script_filename = f"{prefix}{template_filename_stripped}"
-    else:
-        script_filename = template_filename_stripped
+    script_filename = f"{prefix}{template_filename}"
     script_path_local = Path(script_dir) / script_filename
     # Read template
     customize_template(
@@ -47,6 +41,5 @@ def _customize_and_run_template(
     cmd = f"bash {script_path_local}"
     logger.debug(f"Now run '{cmd}' ")
     stdout = execute_command_sync(command=cmd, logger_name=logger_name)
-    logger.debug(f"Standard output of '{cmd}':\n{stdout}")
     logger.debug(f"_customize_and_run_template {template_filename} - END")
     return stdout

fractal_server/tasks/v2/ssh/collect.py

@@ -63,8 +63,7 @@ def _customize_and_run_template(
         raise ValueError(
             f"Invalid {template_filename=} (it must end with '.sh')."
         )
-    template_filename_stripped = Path(template_filename).stem
-    script_filename = f"{prefix}{template_filename_stripped}"
+    script_filename = f"{prefix}_{template_filename}"
     script_path_local = Path(script_dir_local) / script_filename
 
     customize_template(
@@ -109,7 +108,7 @@ def _copy_wheel_file_ssh(
     return dest
 
 
-def collect_package_ssh(
+def collect_ssh(
     *,
     task_group_id: int,
     task_group_activity_id: int,

{fractal_server-2.9.0a0.dist-info → fractal_server-2.9.0a2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.9.0a0
+Version: 2.9.0a2
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -12,7 +12,6 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: aiosqlite (>=0.19.0,<0.20.0)
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
 Requires-Dist: bcrypt (==4.0.1)
 Requires-Dist: cloudpickle (>=3.0.0,<3.1.0)

{fractal_server-2.9.0a0.dist-info → fractal_server-2.9.0a2.dist-info}/RECORD

@@ -1,8 +1,8 @@
-fractal_server/__init__.py,sha256=nUyCW0fhiPHMc-u4jKcBUavNOA93MoQcsdShypf4ins,24
+fractal_server/__init__.py,sha256=d0Y48obcx61ZaWA7ZS1o1kdZRZ6sJMhUfuKDOT5xPKU,24
 fractal_server/__main__.py,sha256=dEkCfzLLQrIlxsGC-HBfoR-RBMWnJDgNrxYTyzmE9c0,6146
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/app/db/__init__.py,sha256=81rK9w1__Z6PJ5cEcChPVc-wI9YOK4fN--_5Opry0MQ,4119
+fractal_server/app/db/__init__.py,sha256=wup2wcOkyOh8Vd0Xm76PZn_naxeMqaL4eF8DHHXTGlI,2889
 fractal_server/app/models/__init__.py,sha256=aG7mf1zZbsgzDSp7GHEcZhdjHfW3TGPOLCI8MrvYhPw,500
 fractal_server/app/models/linkusergroup.py,sha256=LWTUfhH2uAnn_4moK7QdRUIHWtpw-hPZuW-5jClv_OE,610
 fractal_server/app/models/linkuserproject.py,sha256=eQaourbGRshvlMVlKzLYJKHEjfsW1CbWws9yW4eHXhA,567
@@ -20,7 +20,7 @@ fractal_server/app/models/v2/dataset.py,sha256=-7sxHEw4IIAvF_uSan7tA3o8hvoakBkQ0
 fractal_server/app/models/v2/job.py,sha256=ypJmN-qspkKBGhBG7Mt-HypSQqcQ2EmB4Bzzb2-y550,1535
 fractal_server/app/models/v2/project.py,sha256=rAHoh5KfYwIaW7rTX0_O0jvWmxEvfo1BafvmcXuSSRk,786
 fractal_server/app/models/v2/task.py,sha256=jebD28Pz8tGcsWCItxj6uKjcD8BMMnnU8dqYhvhEB6c,1520
-fractal_server/app/models/v2/task_group.py,sha256=X2Qlg-at2RcbvlWbpEMT3kZCk5WOVmJ6cOnKF-RDnQ0,3107
+fractal_server/app/models/v2/task_group.py,sha256=Lxtwxk6pfffM8IehqkFvhDuecSXnXqTWeUlf7Y78oss,3254
 fractal_server/app/models/v2/workflow.py,sha256=YBgFGCziUgU0aJ5EM3Svu9W2c46AewZO9VBlFCHiSps,1069
 fractal_server/app/models/v2/workflowtask.py,sha256=iDuJYk8kp4PNqGmbKRtGI7y-QsbjkNd_gDsbMzL4i-g,1274
 fractal_server/app/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -44,15 +44,15 @@ fractal_server/app/routes/api/v1/workflowtask.py,sha256=OYYConwJbmNULDw5I3T-UbSJ
 fractal_server/app/routes/api/v2/__init__.py,sha256=w4c9WzagaVV5d4TWBX5buu5ENk8jf3YftMQYmhavz9Q,2172
 fractal_server/app/routes/api/v2/_aux_functions.py,sha256=mb4R_qqFxeW0LAis2QJIIfVx8Sydv1jTYaRIMsMxnIk,11720
 fractal_server/app/routes/api/v2/_aux_functions_task_lifecycle.py,sha256=04-C7R8aWiXN9-rSTnZIqz7CAGcLm0y9bjIgJ2lHGZw,5332
-fractal_server/app/routes/api/v2/_aux_functions_tasks.py,sha256=kOoLy5a1YwgfSgsbnCVm_pc5DH6oiG0SU0k-pVDeOY0,10947
+fractal_server/app/routes/api/v2/_aux_functions_tasks.py,sha256=PuapLtvSk9yhBAsKNEp1w2oagOMr0YZTo247-CU3hdM,11008
 fractal_server/app/routes/api/v2/dataset.py,sha256=Y6uZz--YSEGgnPYu05rZ9sr1Ug08bNl2v1h3VeApBe8,9441
 fractal_server/app/routes/api/v2/images.py,sha256=JR1rR6qEs81nacjriOXAOBQjAbCXF4Ew7M7mkWdxBU0,7920
 fractal_server/app/routes/api/v2/job.py,sha256=Bga2Kz1OjvDIdxZObWaaXVhNIhC_5JKhKRjEH2_ayEE,5157
 fractal_server/app/routes/api/v2/project.py,sha256=eWYFJ7F2ZYQcpi-_n-rhPF-Q4gJhzYBsVGYFhHZZXAE,6653
 fractal_server/app/routes/api/v2/status.py,sha256=6N9DSZ4iFqbZImorWfEAPoyoFUgEruo4Hweqo0x0xXU,6435
-fractal_server/app/routes/api/v2/submit.py,sha256=tq-NGnUlpIcm_MRN47rJRHkRcIJ5HiL4Wj1wItJy3o8,8185
+fractal_server/app/routes/api/v2/submit.py,sha256=jqYix7X6dUJn8w6RWasu1lOFf7T_CcXQlpVY38njE24,8688
 fractal_server/app/routes/api/v2/task.py,sha256=K0ik33t7vL8BAK5S7fqyJDNdRK4stGqb_73bSa8tvPE,7159
-fractal_server/app/routes/api/v2/task_collection.py,sha256=1Jch0xRdcb--al6Oigk5fEMIOcIvNwa_aidFEHCd-FQ,9852
+fractal_server/app/routes/api/v2/task_collection.py,sha256=-DVhultvdI3Jh8Jq8W5np6Lnkh5oisjbKCwxFmwddmo,9820
 fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=cctW61-C2QYF2KXluS15lLhZJS_kt30Ca6UGLFO32z0,6207
 fractal_server/app/routes/api/v2/task_group.py,sha256=Ove7Vr3p8GKtskHANAZh8TWwOw8dfbFCN2UQFv6DhqM,8136
 fractal_server/app/routes/api/v2/task_group_lifecycle.py,sha256=UODAv1kk8qgT7wvcVKK6eRs-fEBw3T1pPwmT6VkkAn4,7404
@@ -71,7 +71,7 @@ fractal_server/app/routes/auth/users.py,sha256=FzKNoB-wD32AkVOj1Vi29lGGyOl8NSMCR
 fractal_server/app/routes/aux/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/aux/_job.py,sha256=q-RCiW17yXnZKAC_0La52RLvhqhxuvbgQJ2MlGXOj8A,702
 fractal_server/app/routes/aux/_runner.py,sha256=FdCVla5DxGAZ__aB7Z8dEJzD_RIeh5tftjrPyqkr8N8,895
-fractal_server/app/routes/aux/_timestamp.py,sha256=t3X1WQIGZVAf0snxZzUeOi9Gh4zQbxmiYPGc9NeuLHA,850
+fractal_server/app/routes/aux/_timestamp.py,sha256=MZenRoLfVSnYnL2Vkd8AsJJ9_mV8yDB6u7OumUFjFMM,530
 fractal_server/app/routes/aux/validate_user_settings.py,sha256=Y8eubau0julkwVYB5nA83nDtxh_7RU9Iq0zAhb_dXLA,2351
 fractal_server/app/runner/.gitignore,sha256=ytzN_oyHWXrGU7iFAtoHSTUbM6Rn6kG0Zkddg0xZk6s,16
 fractal_server/app/runner/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -134,7 +134,7 @@ fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=1fWvQ6YZUUnDhO
 fractal_server/app/runner/v2/task_interface.py,sha256=hT3p-bRGsLNAR_dNv_PYFoqzIF_EQtSsGwl38j1haYA,1824
 fractal_server/app/runner/versions.py,sha256=dSaPRWqmFPHjg20kTCHmi_dmGNcCETflDtDLronNanU,852
 fractal_server/app/schemas/__init__.py,sha256=stURAU_t3AOBaH0HSUbV-GKhlPKngnnIMoqWc3orFyI,135
-fractal_server/app/schemas/_validators.py,sha256=3YBteFMxrEE9DOYlIHvIMsUOWTPSHEZlDL7dUQzBQjs,3616
+fractal_server/app/schemas/_validators.py,sha256=Ft-Ueol_rFwGjEebKVK2bUELm7w7bFG8MOpTamlY8Fs,3503
 fractal_server/app/schemas/user.py,sha256=aUD8YAcfYTEO06TEUoTx4heVrXFiX7E2Mb8D2--4FsA,2130
 fractal_server/app/schemas/user_group.py,sha256=YwJvYgj-PI66LWy38CEd_FIZPsBV1_2N5zJPGFcFvBw,2143
 fractal_server/app/schemas/user_settings.py,sha256=TalISeEfCrtN8LgqbLx1Q8ZPoeiZnbksg5NYAVzkIqY,3527
@@ -157,12 +157,12 @@ fractal_server/app/schemas/v2/project.py,sha256=UXEA0UUUe0bFFOVLLmVtvDFLBO5vmD1J
 fractal_server/app/schemas/v2/status.py,sha256=SQaUpQkjFq5c5k5J4rOjNhuQaDOEg8lksPhkKmPU5VU,332
 fractal_server/app/schemas/v2/task.py,sha256=FFAbYwDlqowB8gVMdjFVPVHvAM0T89PYLixUth49xfQ,6870
 fractal_server/app/schemas/v2/task_collection.py,sha256=yHpCRxoj6tKqCiQfUjaTj8SfCn1ChD_P6okfEOzyUDE,6518
-fractal_server/app/schemas/v2/task_group.py,sha256=0eOjQ1PjvxxHQULX1f6gDGhm30BtKW6k5CcRaSUaQtg,3007
+fractal_server/app/schemas/v2/task_group.py,sha256=e4NwFuOmiO0afoZLVsI_XHIpD_o_QWDpzlI7ZoNAYwo,3014
 fractal_server/app/schemas/v2/workflow.py,sha256=HSNQSrBRdoBzh8Igr76FUWCAWvVzykrqmUv1vGv-8og,2026
 fractal_server/app/schemas/v2/workflowtask.py,sha256=vDdMktYbHeYBgB5OuWSv6wRPRXWqvetkeqQ7IC5YtfA,5751
 fractal_server/app/security/__init__.py,sha256=8Xd4GxumZgvxEH1Vli3ULehwdesEPiaAbtffJvAEgNo,12509
 fractal_server/app/user_settings.py,sha256=aZgQ3i0JkHfgwLGW1ee6Gzr1ae3IioFfJKKSsSS8Svk,1312
-fractal_server/config.py,sha256=-G1RvmaeSb6_wffUFuaAmhJV3u1q3HRpMLEfpGXBrz4,22797
+fractal_server/config.py,sha256=1MmVIbnztrFA0w2gYIjgJXg0bqVDsSeSEsMFimb4y74,21153
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/data_migrations/tools.py,sha256=LeMeASwYGtEqd-3wOLle6WARdTGAimoyMmRbbJl-hAM,572
 fractal_server/gunicorn_fractal.py,sha256=u6U01TLGlXgq1v8QmEpLih3QnsInZD7CqphgJ_GrGzc,1230
@@ -178,7 +178,7 @@ fractal_server/migrations/script.py.mako,sha256=oMXw9LC3zRbinWWPPDgeZ4z9FJrV2zhR
 fractal_server/migrations/versions/034a469ec2eb_task_groups.py,sha256=vrPhC8hfFu1c4HmLHNZyCuqEfecFD8-bWc49bXMNes0,6199
 fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_table.py,sha256=-BSS9AFTPcu3gYC-sYbawSy4MWQQx8TfMb5BW5EBKmQ,1450
 fractal_server/migrations/versions/19eca0dd47a9_user_settings_project_dir.py,sha256=Q1Gj1cJ0UrdLBJ5AXfFK9QpxTtmcv-4Z3NEGDnxOme4,961
-fractal_server/migrations/versions/3082479ac4ea_taskgroup_activity_and_venv_info_to_.py,sha256=oAqSwW9ilKm5x6Wez3JpJFU2-ls2_O8-j1R6KLEir08,3411
+fractal_server/migrations/versions/3082479ac4ea_taskgroup_activity_and_venv_info_to_.py,sha256=_wy9Yu2YfhpBffUsboAG9junlQ2jRR7qui9wbLvXp7w,3653
 fractal_server/migrations/versions/4c308bcaea2b_add_task_args_schema_and_task_args_.py,sha256=-wHe-fOffmYeAm0JXVl_lxZ7hhDkaEVqxgxpHkb_uL8,954
 fractal_server/migrations/versions/4cedeb448a53_workflowtask_foreign_keys_not_nullables.py,sha256=Mob8McGYAcmgvrseyyYOa54E6Gsgr-4SiGdC-r9O4_A,1157
 fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py,sha256=5ROUgcoZOdjf8kMt6cxuvPhzHmV6xaCxvZEbhUEyZM4,3271
@@ -202,7 +202,7 @@ fractal_server/migrations/versions/efa89c30e0a4_add_project_timestamp_created.py
 fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.py,sha256=9BwqUS9Gf7UW_KjrzHbtViC880qhD452KAytkHWWZyk,746
 fractal_server/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/ssh/__init__.py,sha256=sVUmzxf7_DuXG1xoLQ1_00fo5NPhi2LJipSmU5EAkPs,124
-fractal_server/ssh/_fabric.py,sha256=udbz8BsbToqf2J_JjSlGUgVQGcP0tY-TjG2plzPoGPM,20180
+fractal_server/ssh/_fabric.py,sha256=Nwsc5uU2BcOE7t1AFFpytKUsZHfbQxB0uKF5HD-dycA,21647
 fractal_server/string_tools.py,sha256=XtMNsr5R7GmgzmFi68zkKMedHs8vjGoVMMCXqWhIk9k,2568
 fractal_server/syringe.py,sha256=3qSMW3YaMKKnLdgnooAINOPxnCOxP7y2jeAQYB21Gdo,2786
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
@@ -214,13 +214,13 @@ fractal_server/tasks/v1/endpoint_operations.py,sha256=NQYvgh-_qEI9YhsLiulfOFPDac
 fractal_server/tasks/v1/get_collection_data.py,sha256=5C22jp356rCH5IIC0J57wOu-DCC_kp3B6p68JooN7IM,508
 fractal_server/tasks/v1/utils.py,sha256=HYFyNAyZofmf--mVgdwGC5TJpGShIWIDaS01yRr4HxM,1771
 fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/tasks/v2/local/__init__.py,sha256=taFip1YHvnsfTlReqwZsdo4EmIq7hlAl2WV1g3Vp_TY,149
-fractal_server/tasks/v2/local/collect.py,sha256=qUSKpI5h5qJjzwXtezEzzo9jIHfXR8mbWCgDCJ4Huyc,12207
-fractal_server/tasks/v2/local/deactivate.py,sha256=f3j-a5npujZ5lsCBI_f39bKR7n2n79iSprmgm7_FJYk,6437
+fractal_server/tasks/v2/local/__init__.py,sha256=9RVItnS7OyLsJOuJjWMCicaky4ASUPQEYD4SzDs0hOE,141
+fractal_server/tasks/v2/local/collect.py,sha256=kTgMDiOX9qVDncmrgieOfYE71jqFwBpDgO1cbD5ZQVQ,12199
+fractal_server/tasks/v2/local/deactivate.py,sha256=PyJm3PoQrYOBCm0F6p6xD7Gx9Tfnn_YZlXY-j3Fi6pM,8975
 fractal_server/tasks/v2/local/reactivate.py,sha256=eTSrEoZ54_6ExviozxRTgjNsrESG9PbQW-TiGqNMJcA,6117
-fractal_server/tasks/v2/local/utils_local.py,sha256=987EzL2BByPszoTc2dP-ucZigXp7fRdbBffeFGzbtPw,1785
+fractal_server/tasks/v2/local/utils_local.py,sha256=JHHiS_SvPLSezxGWSWslMhLEWmMp9PepnzePXV6r0e8,1521
 fractal_server/tasks/v2/ssh/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/tasks/v2/ssh/collect.py,sha256=IwsA8Xr0d6VXvajdFxwNIEB6jZ--hA1McEu6tydKq9E,15341
+fractal_server/tasks/v2/ssh/collect.py,sha256=j50euINjxGS4S5-aYTIWwV34xydKvT6W5P9Vxv5TMuk,15263
 fractal_server/tasks/v2/ssh/deactivate.py,sha256=fwBCtj-8I_8s8Zd-nyQX7YaTjoPOK1pn07Tznvjbv8Y,31
 fractal_server/tasks/v2/ssh/reactivate.py,sha256=0pqK-g5uyykCkLsjYDVr8QTEBrIB31XQXvi0MQfqv-w,31
 fractal_server/tasks/v2/templates/1_create_venv.sh,sha256=PK0jdHKtQpda1zULebBaVPORt4t6V17wa4N1ohcj5ac,548
@@ -237,8 +237,8 @@ fractal_server/tasks/v2/utils_templates.py,sha256=C5WLuY3uGG2s53OEL-__H35-fmSlgu
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=utvmBx8K9I8hRWFquxna2pBaOqe0JifDL_NVPmihEJI,3525
 fractal_server/zip_tools.py,sha256=xYpzBshysD2nmxkD5WLYqMzPYUcCRM3kYy-7n9bJL-U,4426
-fractal_server-2.9.0a0.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.9.0a0.dist-info/METADATA,sha256=6_oIEXxiAVbTAy9QvP753-1NvPXYmuWG-f-E4LMAQeo,4629
-fractal_server-2.9.0a0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.9.0a0.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.9.0a0.dist-info/RECORD,,
+fractal_server-2.9.0a2.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.9.0a2.dist-info/METADATA,sha256=Qk7nGzAcl_hZRCJp8pdCV2PQACAWwqOzTCH7nFW__pw,4585
+fractal_server-2.9.0a2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.9.0a2.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.9.0a2.dist-info/RECORD,,