fractal-server 2.18.0a9__tar.gz → 2.18.2__tar.gz

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.18.0a9
+Version: 2.18.2
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE

fractal_server-2.18.2/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.18.2"

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/app/models/linkuserproject.py

@@ -1,10 +1,7 @@
-from sqlmodel import BOOLEAN
 from sqlmodel import CheckConstraint
-from sqlmodel import Column
 from sqlmodel import Field
 from sqlmodel import Index
 from sqlmodel import SQLModel
-from sqlmodel import String
 from sqlmodel import column
 
 
@@ -18,18 +15,9 @@ class LinkUserProjectV2(SQLModel, table=True):
     )
     user_id: int = Field(foreign_key="user_oauth.id", primary_key=True)
 
-    # TODO-2.18.1 drop server_default
-    is_owner: bool = Field(
-        sa_column=Column(BOOLEAN, server_default="true", nullable=False)
-    )
-    # TODO-2.18.1 drop server_default
-    is_verified: bool = Field(
-        sa_column=Column(BOOLEAN, server_default="true", nullable=False)
-    )
-    # TODO-2.18.1 drop server_default
-    permissions: str = Field(
-        sa_column=Column(String, server_default="'rwx'", nullable=False)
-    )
+    is_owner: bool
+    is_verified: bool
+    permissions: str
 
     __table_args__ = (
         Index(

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/app/models/security.py

@@ -75,8 +75,8 @@ class UserOAuth(SQLModel, table=True):
         profile_id:
             Foreign key linking the user to a `Profile`. If this is unset,
             the user has no access to the `/api/v2/` endpoints.
-        project_dir:
-            Absolute path of the user's project directory. This is used (A) as
+        project_dirs:
+            Absolute paths of the user's project directory. This is used (A) as
             a default base folder for the `zarr_dir` of new datasets (where
             the output Zarr are located), and (B) as a folder which is included
             by default in the paths that a user is allowed to stream (if the
@@ -112,11 +112,8 @@ class UserOAuth(SQLModel, table=True):
         ondelete="RESTRICT",
     )
 
-    # TODO-2.18.1: drop `project_dir`
-    project_dir: str | None = Field(default=None, nullable=True)
-    # TODO-2.18.1: `project_dirs: list[str] = Field(min_length=1)`
     project_dirs: list[str] = Field(
-        sa_column=Column(ARRAY(String), nullable=False, server_default="{}"),
+        sa_column=Column(ARRAY(String), nullable=False),
     )
 
     slurm_accounts: list[str] = Field(

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/app/models/v2/task_group.py

@@ -71,8 +71,6 @@ class TaskGroupV2(SQLModel, table=True):
     )
     env_info: str | None = None
     venv_path: str | None = None
-    venv_size_in_kB: int | None = None
-    venv_file_number: int | None = None
 
     active: bool = True
     timestamp_created: datetime = Field(

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/app/routes/api/v2/_aux_functions_history.py

@@ -19,6 +19,7 @@ from fractal_server.app.routes.api.v2._aux_functions import _get_workflow_or_404
 from fractal_server.app.routes.api.v2._aux_functions import (
     _get_workflowtask_or_404,
 )
+from fractal_server.app.schemas.v2.job import JobStatusType
 from fractal_server.app.schemas.v2.sharing import ProjectPermissions
 from fractal_server.logger import set_logger
 from fractal_server.zip_tools import _read_single_file_from_zip
@@ -70,6 +71,7 @@ def read_log_file(
     dataset_id: int,
     logfile: str,
     job_working_dir: str,
+    job_status: JobStatusType,
 ) -> str:
     """
     Returns the contents of a Job's log file, either directly from the working
@@ -93,12 +95,18 @@ def read_log_file(
             return _read_single_file_from_zip(
                 file_path=relative_logfile, archive_path=archive_path
             )
-
         else:
-            logger.error(
-                f"Error while retrieving logs for {logfile=} and "
-                f"{archive_path=}: both files do not exist."
-            )
+            match job_status:
+                case JobStatusType.SUBMITTED:
+                    logger.info(
+                        f"Neither {logfile=} nor {archive_path=} exist "
+                        "(for submitted job)."
+                    )
+                case _:
+                    logger.warning(
+                        f"Error while retrieving logs for {logfile=} and "
+                        f"{archive_path=}."
+                    )
             return (
                 f"Logs for task '{task_name}' in dataset "
                 f"{dataset_id} are not available."

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/app/routes/api/v2/history.py

@@ -458,11 +458,11 @@ async def get_image_log(
 
     # Get job.working_dir
     res = await db.execute(
-        select(JobV2.working_dir)
+        select(JobV2.working_dir, JobV2.status)
         .join(HistoryRun, HistoryRun.job_id == JobV2.id)
         .where(HistoryRun.id == history_unit.history_run_id)
     )
-    job_working_dir = res.scalar_one_or_none()
+    job_working_dir, job_status = res.one()
 
     # Get log or placeholder text
     log = read_log_file(
@@ -470,6 +470,7 @@ async def get_image_log(
         task_name=wftask.task.name,
         dataset_id=request_data.dataset_id,
         job_working_dir=job_working_dir,
+        job_status=job_status,
     )
     return JSONResponse(content=log)
 
@@ -525,6 +526,7 @@ async def get_history_unit_log(
         task_name=wftask.task.name,
         dataset_id=dataset_id,
         job_working_dir=job.working_dir,
+        job_status=job.status,
     )
     return JSONResponse(content=log)
 

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/app/routes/api/v2/job.py

@@ -54,7 +54,8 @@ async def get_user_jobs(
             LinkUserProjectV2, LinkUserProjectV2.project_id == JobV2.project_id
         )
         .where(LinkUserProjectV2.user_id == user.id)
-        .where(LinkUserProjectV2.is_owner.is_(True))
+        .where(LinkUserProjectV2.is_verified.is_(True))
+        .order_by(JobV2.start_timestamp.desc())
     )
     res = await db.execute(stm)
     job_list = res.scalars().all()
@@ -86,8 +87,11 @@ async def get_workflow_jobs(
         required_permissions=ProjectPermissions.READ,
         db=db,
     )
-    stm = select(JobV2).where(JobV2.workflow_id == workflow_id)
-    res = await db.execute(stm)
+    res = await db.execute(
+        select(JobV2)
+        .where(JobV2.workflow_id == workflow_id)
+        .order_by(JobV2.start_timestamp.desc())
+    )
     job_list = res.scalars().all()
     return job_list
 
@@ -212,8 +216,11 @@ async def get_job_list(
         db=db,
     )
 
-    stm = select(JobV2).where(JobV2.project_id == project.id)
-    res = await db.execute(stm)
+    res = await db.execute(
+        select(JobV2)
+        .where(JobV2.project_id == project.id)
+        .order_by(JobV2.start_timestamp.desc())
+    )
     job_list = res.scalars().all()
     await db.close()
     if not log:

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/app/routes/auth/_aux_auth.py

@@ -228,6 +228,7 @@ async def _check_project_dirs_update(
                 LinkUserProjectV2.project_id == ProjectV2.id,
             )
             .where(LinkUserProjectV2.user_id == user_id)
+            .where(LinkUserProjectV2.is_verified.is_(True))
             .where(
                 or_(
                     *[

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/app/routes/auth/viewer_paths.py

@@ -34,7 +34,7 @@ async def get_current_user_allowed_viewer_paths(
                 LinkUserProjectV2, LinkUserProjectV2.project_id == ProjectV2.id
             )
             .where(LinkUserProjectV2.user_id == current_user.id)
-            .where(LinkUserProjectV2.is_owner.is_(False))
+            .where(LinkUserProjectV2.is_verified.is_(True))
         )
         authorized_paths.extend(res.unique().scalars().all())
         # Note that `project_dirs` and the `db.execute` result may have some

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/app/schemas/v2/task_group.py

@@ -84,9 +84,6 @@ class TaskGroupRead(BaseModel):
     pinned_package_versions_pre: dict[str, str] = Field(default_factory=dict)
     pinned_package_versions_post: dict[str, str] = Field(default_factory=dict)
 
-    venv_size_in_kB: int | None = None
-    venv_file_number: int | None = None
-
     active: bool
     timestamp_created: AwareDatetime
     timestamp_last_used: AwareDatetime

fractal_server-2.18.2/fractal_server/migrations/versions/068496367952_drop_taskgroup_venv_size_and_files_.py

@@ -0,0 +1,48 @@
+"""Drop TaskGroup venv size and files number
+
+Revision ID: 068496367952
+Revises: b7477cc98f45
+Create Date: 2025-12-10 15:24:47.720796
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "068496367952"
+down_revision = "b7477cc98f45"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("taskgroupv2", schema=None) as batch_op:
+        batch_op.drop_column("venv_size_in_kB")
+        batch_op.drop_column("venv_file_number")
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("taskgroupv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "venv_file_number",
+                sa.INTEGER(),
+                autoincrement=False,
+                nullable=True,
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "venv_size_in_kB",
+                sa.INTEGER(),
+                autoincrement=False,
+                nullable=True,
+            )
+        )
+
+    # ### end Alembic commands ###

fractal_server-2.18.2/fractal_server/migrations/versions/b7477cc98f45_2_18_1.py

@@ -0,0 +1,50 @@
+"""2.18.1
+
+Revision ID: b7477cc98f45
+Revises: 88270f589c9b
+Create Date: 2025-12-04 14:07:27.954252
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "b7477cc98f45"
+down_revision = "88270f589c9b"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("user_oauth", schema=None) as batch_op:
+        batch_op.drop_column("project_dir")
+
+        # ### end Alembic commands ###
+
+        batch_op.alter_column("project_dirs", server_default=None)
+
+    with op.batch_alter_table("linkuserprojectv2", schema=None) as batch_op:
+        batch_op.alter_column("is_owner", server_default=None)
+        batch_op.alter_column("is_verified", server_default=None)
+        batch_op.alter_column("permissions", server_default=None)
+
+
+def downgrade() -> None:
+    with op.batch_alter_table("linkuserprojectv2", schema=None) as batch_op:
+        batch_op.alter_column("permissions", server_default="rwx")
+        batch_op.alter_column("is_verified", server_default="true")
+        batch_op.alter_column("is_owner", server_default="true")
+
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("user_oauth", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "project_dir", sa.VARCHAR(), autoincrement=False, nullable=True
+            )
+        )
+
+        # ### end Alembic commands ###
+
+        batch_op.alter_column("project_dirs", server_default="{}")

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/tasks/v2/local/collect.py

@@ -174,15 +174,6 @@ def collect_local(
                 activity.log = get_current_log(log_file_path)
                 activity = add_commit_refresh(obj=activity, db=db)
 
-                # Run script 5
-                venv_info = _customize_and_run_template(
-                    template_filename="5_get_venv_size_and_file_number.sh",
-                    **common_args,
-                )
-                venv_size, venv_file_number = venv_info.split()
-                activity.log = get_current_log(log_file_path)
-                activity = add_commit_refresh(obj=activity, db=db)
-
                 pkg_attrs = parse_script_pip_show_stdout(stdout)
                 for key, value in pkg_attrs.items():
                     logger.debug(f"Parsed from pip-show: {key}={value}")
@@ -241,18 +232,10 @@ def collect_local(
                 logger.info("create_db_tasks_and_update_task_group - end")
 
                 # Update task_group data
-                logger.info(
-                    "Add env_info, venv_size and venv_file_number "
-                    "to TaskGroupV2 - start"
-                )
+                logger.info("Add env_info to TaskGroupV2 - start")
                 task_group.env_info = pip_freeze_stdout
-                task_group.venv_size_in_kB = int(venv_size)
-                task_group.venv_file_number = int(venv_file_number)
                 task_group = add_commit_refresh(obj=task_group, db=db)
-                logger.info(
-                    "Add env_info, venv_size and venv_file_number "
-                    "to TaskGroupV2 - end"
-                )
+                logger.info("Add env_info to TaskGroupV2 - end")
 
                 # Finalize (write metadata to DB)
                 logger.info("finalising - START")

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/tasks/v2/local/collect_pixi.py

@@ -175,8 +175,6 @@ def collect_local_pixi(
                 # Parse stdout
                 parsed_output = parse_collect_stdout(stdout)
                 package_root = parsed_output["package_root"]
-                venv_size = parsed_output["venv_size"]
-                venv_file_number = parsed_output["venv_file_number"]
                 project_python_wrapper = parsed_output["project_python_wrapper"]
 
                 # Make task folder 755
@@ -220,23 +218,15 @@ def collect_local_pixi(
                 logger.info("create_db_tasks_and_update_task_group - end")
 
                 # Update task_group data
-                logger.info(
-                    "Add env_info, venv_size and venv_file_number "
-                    "to TaskGroupV2 - start"
-                )
+                logger.info("Add env_info to TaskGroupV2 - start")
                 with Path(source_dir, "pixi.lock").open() as f:
                     pixi_lock_contents = f.read()
 
                 # NOTE: see issue 2626 about whether to keep `pixi.lock` files
                 # in the database
                 task_group.env_info = pixi_lock_contents
-                task_group.venv_size_in_kB = int(venv_size)
-                task_group.venv_file_number = int(venv_file_number)
                 task_group = add_commit_refresh(obj=task_group, db=db)
-                logger.info(
-                    "Add env_info, venv_size and venv_file_number "
-                    "to TaskGroupV2 - end"
-                )
+                logger.info("Add env_info to TaskGroupV2 - end")
 
                 # Finalize (write metadata to DB)
                 logger.info("finalising - START")

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/tasks/v2/local/reactivate.py

@@ -121,7 +121,7 @@ def reactivate_local(
 
                 logger.debug("start - install from pip freeze")
                 _customize_and_run_template(
-                    template_filename="6_pip_install_from_freeze.sh",
+                    template_filename="5_pip_install_from_freeze.sh",
                     **common_args,
                 )
                 logger.debug("end - install from pip freeze")

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/tasks/v2/ssh/collect.py

@@ -211,15 +211,6 @@ def collect_ssh(
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 
-                    # Run script 5
-                    venv_info = _customize_and_run_template(
-                        template_filename="5_get_venv_size_and_file_number.sh",
-                        **common_args,
-                    )
-                    venv_size, venv_file_number = venv_info.split()
-                    activity.log = get_current_log(log_file_path)
-                    activity = add_commit_refresh(obj=activity, db=db)
-
                     pkg_attrs = parse_script_pip_show_stdout(stdout)
 
                     for key, value in pkg_attrs.items():
@@ -275,18 +266,10 @@ def collect_ssh(
                     logger.info("create_db_tasks_and_update_task_group - end")
 
                     # Update task_group data
-                    logger.info(
-                        "Add env_info, venv_size and venv_file_number "
-                        "to TaskGroupV2 - start"
-                    )
+                    logger.info("Add env_info to TaskGroupV2 - start")
                     task_group.env_info = pip_freeze_stdout
-                    task_group.venv_size_in_kB = int(venv_size)
-                    task_group.venv_file_number = int(venv_file_number)
                     task_group = add_commit_refresh(obj=task_group, db=db)
-                    logger.info(
-                        "Add env_info, venv_size and venv_file_number "
-                        "to TaskGroupV2 - end"
-                    )
+                    logger.info("Add env_info to TaskGroupV2 - end")
 
                     # Finalize (write metadata to DB)
                     logger.info("finalising - START")

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/tasks/v2/ssh/collect_pixi.py

@@ -266,8 +266,6 @@ def collect_ssh_pixi(
                     # Parse stdout
                     parsed_output = parse_collect_stdout(stdout)
                     package_root_remote = parsed_output["package_root"]
-                    venv_size = parsed_output["venv_size"]
-                    venv_file_number = parsed_output["venv_file_number"]
                     project_python_wrapper = parsed_output[
                         "project_python_wrapper"
                     ]
@@ -312,18 +310,10 @@ def collect_ssh_pixi(
                     )
 
                     # Update task_group data
-                    logger.info(
-                        "Add env_info, venv_size and venv_file_number "
-                        "to TaskGroupV2 - start"
-                    )
+                    logger.info("Add env_info to TaskGroupV2 - start")
                     task_group.env_info = pixi_lock_contents
-                    task_group.venv_size_in_kB = int(venv_size)
-                    task_group.venv_file_number = int(venv_file_number)
                     task_group = add_commit_refresh(obj=task_group, db=db)
-                    logger.info(
-                        "Add env_info, venv_size and venv_file_number "
-                        "to TaskGroupV2 - end"
-                    )
+                    logger.info("Add env_info to TaskGroupV2 - end")
 
                     # Finalize (write metadata to DB)
                     logger.info("finalising - START")

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/tasks/v2/ssh/reactivate.py

@@ -167,7 +167,7 @@ def reactivate_ssh(
 
                     logger.info("start - install from pip freeze")
                     _customize_and_run_template(
-                        template_filename="6_pip_install_from_freeze.sh",
+                        template_filename="5_pip_install_from_freeze.sh",
                         **common_args,
                     )
                     logger.info("end - install from pip freeze")

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/tasks/v2/templates/pixi_3_post_install.sh

@@ -66,12 +66,6 @@ PACKAGE_FOLDER=$(bash "${FIND_PACKAGE_FOLDER_SCRIPT}")
 write_log "Package folder: ${PACKAGE_FOLDER}"
 echo
 
-ENV_DISK_USAGE=$(du -sk "${PACKAGE_DIR}" | cut -f1)
-ENV_FILE_NUMBER=$(find "${PACKAGE_DIR}" -type f | wc -l)
-write_log "Disk usage: ${ENV_DISK_USAGE}"
-write_log "Number of files: ${ENV_FILE_NUMBER}"
-echo
-
 TIME_END=$(date +%s)
 write_log "Elapsed: $((TIME_END - TIME_START)) seconds"
 write_log "All ok, exit."

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/fractal_server/tasks/v2/utils_pixi.py

@@ -12,8 +12,6 @@ SOURCE_DIR_NAME = "source_dir"
 
 class ParsedOutput(TypedDict):
     package_root: str
-    venv_size: str
-    venv_file_number: str
     project_python_wrapper: str
 
 
@@ -23,8 +21,6 @@ def parse_collect_stdout(stdout: str) -> ParsedOutput:
     """
     searches = [
         ("Package folder:", "package_root"),
-        ("Disk usage:", "venv_size"),
-        ("Number of files:", "venv_file_number"),
         ("Project Python wrapper:", "project_python_wrapper"),
     ]
     stdout_lines = stdout.splitlines()

{fractal_server-2.18.0a9 → fractal_server-2.18.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.18.0a9"
+version = "2.18.2"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -95,7 +95,7 @@ filterwarnings = [
 markers = ["container", "ssh", "fails_on_macos", "oauth"]
 
 [tool.bumpver]
-current_version = "2.18.0a9"
+current_version = "2.18.2"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.18.0a9/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.18.0a9"

fractal_server-2.18.0a9/fractal_server/data_migrations/2_18_0.py

@@ -1,30 +0,0 @@
-import logging
-import sys
-from os.path import normpath
-
-from sqlalchemy.orm.attributes import flag_modified
-from sqlmodel import select
-
-from fractal_server.app.db import get_sync_db
-from fractal_server.app.models import UserOAuth
-
-logging.basicConfig(level=logging.INFO)
-
-
-def fix_db():
-    logging.info("START - fix db")
-
-    with next(get_sync_db()) as db:
-        res = db.execute(select(UserOAuth).order_by(UserOAuth.email))
-        user_list = res.scalars().unique().all()
-
-        for user in user_list:
-            logging.info(f"Now handling user {user.email}.")
-            if user.project_dirs != []:
-                sys.exit(f"Non empty `project_dirs` for User[{user.id}]")
-            user.project_dirs.append(normpath(user.project_dir))
-            flag_modified(user, "project_dirs")
-
-        db.commit()
-
-    logging.info("END - fix db")

fractal_server-2.18.0a9/fractal_server/tasks/v2/templates/5_get_venv_size_and_file_number.sh

@@ -1,12 +0,0 @@
-#!/bin/bash
-
-set -e
-
-# Variables to be filled within fractal-server
-PACKAGE_ENV_DIR=__PACKAGE_ENV_DIR__
-
-# Find memory usage and file number
-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"