fractal-server 2.18.4__tar.gz → 2.18.6__tar.gz

{fractal_server-2.18.4 → fractal_server-2.18.6}/PKG-INFO

@@ -1,26 +1,26 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.18.4
+Version: 2.18.6
 Summary: Backend component of the Fractal analytics platform
 Author: Tommaso Comparin, Marco Franzon, Yuri Chiucconi, Jacopo Nespolo
 Author-email: Tommaso Comparin <tommaso.comparin@exact-lab.it>, Marco Franzon <marco.franzon@exact-lab.it>, Yuri Chiucconi <yuri.chiucconi@exact-lab.it>, Jacopo Nespolo <jacopo.nespolo@exact-lab.it>
 License-Expression: BSD-3-Clause
 License-File: LICENSE
-Requires-Dist: fastapi>=0.120.0,<0.121.0
-Requires-Dist: sqlmodel==0.0.27
+Requires-Dist: fastapi>=0.128.0,<0.129.0
+Requires-Dist: sqlmodel==0.0.31
 Requires-Dist: sqlalchemy[asyncio]>=2.0.23,<2.1
 Requires-Dist: fastapi-users[oauth]>=15,<16
 Requires-Dist: alembic>=1.13.1,<2.0.0
-Requires-Dist: uvicorn>=0.38.0,<0.39.0
+Requires-Dist: uvicorn>=0.40.0,<0.41.0
 Requires-Dist: uvicorn-worker==0.4.0
 Requires-Dist: pydantic>=2.12.0,<2.13.0
-Requires-Dist: pydantic-settings==2.11.0
+Requires-Dist: pydantic-settings==2.12.0
 Requires-Dist: packaging>=25.0.0,<26.0.0
 Requires-Dist: fabric>=3.2.2,<3.3.0
 Requires-Dist: gunicorn>=23.0,<24.0
 Requires-Dist: psycopg[binary]>=3.1.0,<4.0.0
 Requires-Dist: tomli-w>=1.2.0,<1.3.0
-Requires-Python: >=3.11, <3.15
+Requires-Python: >=3.12, <3.15
 Project-URL: changelog, https://github.com/fractal-analytics-platform/fractal-server/blob/main/CHANGELOG.md
 Project-URL: documentation, https://fractal-analytics-platform.github.io/fractal-server
 Project-URL: homepage, https://github.com/fractal-analytics-platform/fractal-server

fractal_server-2.18.6/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.18.6"

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/db/__init__.py

@@ -54,7 +54,6 @@ class DB:
             cls._engine_async,
             class_=AsyncSession,
             expire_on_commit=False,
-            future=True,
         )
 
     @classmethod
@@ -68,12 +67,7 @@ class DB:
             pool_pre_ping=True,
         )
 
-        cls._sync_session_maker = sessionmaker(
-            bind=cls._engine_sync,
-            autocommit=False,
-            autoflush=False,
-            future=True,
-        )
+        cls._sync_session_maker = sessionmaker(cls._engine_sync)
 
     @classmethod
     async def get_async_db(cls) -> AsyncGenerator[AsyncSession, None]:

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/routes/admin/v2/job.py

@@ -176,7 +176,6 @@ async def view_single_job(
             status_code=status.HTTP_404_NOT_FOUND,
             detail=f"Job {job_id} not found",
         )
-    await db.close()
 
     if show_tmp_logs and (job.status == JobStatusType.SUBMITTED):
         try:
@@ -249,7 +248,6 @@ async def update_job(
 
     await db.commit()
     await db.refresh(job)
-    await db.close()
     return job
 
 

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/routes/api/v2/images.py

@@ -274,5 +274,4 @@ async def patch_dataset_image(
     flag_modified(db_dataset, "images")
 
     await db.commit()
-    await db.close()
     return db_dataset.images[index]

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/routes/api/v2/job.py

@@ -59,7 +59,6 @@ async def get_user_jobs(
     )
     res = await db.execute(stm)
     job_list = res.scalars().all()
-    await db.close()
     if not log:
         for job in job_list:
             setattr(job, "log", None)
@@ -152,7 +151,6 @@ async def read_job(
         db=db,
     )
     job = output["job"]
-    await db.close()
 
     if show_tmp_logs and (job.status == JobStatusType.SUBMITTED):
         try:
@@ -222,7 +220,6 @@ async def get_job_list(
         .order_by(JobV2.start_timestamp.desc())
     )
     job_list = res.scalars().all()
-    await db.close()
     if not log:
         for job in job_list:
             setattr(job, "log", None)

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/routes/api/v2/project.py

@@ -47,7 +47,6 @@ async def get_list_project(
     )
     res = await db.execute(stm)
     project_list = res.scalars().all()
-    await db.close()
     return project_list
 
 
@@ -107,7 +106,6 @@ async def read_project(
         required_permissions=ProjectPermissions.READ,
         db=db,
     )
-    await db.close()
     return project
 
 
@@ -136,7 +134,6 @@ async def update_project(
 
     await db.commit()
     await db.refresh(project)
-    await db.close()
     return project
 
 

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/routes/api/v2/task.py

@@ -77,7 +77,6 @@ async def get_list_task(
     stm = stm.order_by(TaskV2.id)
     res = await db.execute(stm)
     task_list = list(res.scalars().all())
-    await db.close()
     if args_schema is False:
         for task in task_list:
             setattr(task, "args_schema_parallel", None)
@@ -133,7 +132,6 @@ async def patch_task(
 
     await db.commit()
     await db.refresh(db_task)
-    await db.close()
     return db_task
 
 
@@ -216,7 +214,6 @@ async def create_task(
     db.add(db_task_group)
     await db.commit()
     await db.refresh(db_task)
-    await db.close()
 
     return db_task
 

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/routes/api/v2/task_group.py

@@ -163,6 +163,7 @@ async def get_task_group_list(
     if args_schema is False:
         for taskgroup in task_groups:
             for task in taskgroup.task_list:
+                db.expunge(task)  # See issue 3101
                 setattr(task, "args_schema_non_parallel", None)
                 setattr(task, "args_schema_parallel", None)
 

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/routes/api/v2/workflow.py

@@ -89,7 +89,6 @@ async def create_workflow(
     db.add(db_workflow)
     await db.commit()
     await db.refresh(db_workflow)
-    await db.close()
     return db_workflow
 
 
@@ -189,7 +188,6 @@ async def update_workflow(
 
     await db.commit()
     await db.refresh(workflow)
-    await db.close()
 
     wftask_list_with_warnings = await _add_warnings_to_workflow_tasks(
         wftask_list=workflow.task_list, user_id=user.id, db=db

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/routes/api/v2/workflowtask.py

@@ -202,7 +202,6 @@ async def update_workflowtask(
 
     await db.commit()
     await db.refresh(db_wf_task)
-    await db.close()
 
     return db_wf_task
 

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/routes/auth/oauth.py

@@ -1,3 +1,5 @@
+from typing import override
+
 from fastapi import APIRouter
 from httpx_oauth.clients.github import GitHubOAuth2
 from httpx_oauth.clients.google import GoogleOAuth2
@@ -25,7 +27,7 @@ class FractalOpenID(OpenID):
         super().__init__(**kwargs)
         self.email_claim = email_claim
 
-    # TODO-requires-py312: add `@override` decorator
+    @override
     async def get_id_email(self, token: str) -> tuple[str, str | None]:
         """
         Identical to the parent-class method (httpx-oauth version 0.16.1),

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/routes/auth/viewer_paths.py

@@ -23,9 +23,12 @@ async def get_current_user_allowed_viewer_paths(
 ) -> list[str]:
     """
     Returns the allowed viewer paths for current user.
-    """
-    authorized_paths = current_user.project_dirs.copy()
 
+    NOTE: `include_shared_projects` is an obsolete query-parameter name,
+    because it does not make a difference between owners/guests. A better
+    naming would be e.g. `include_zarr_dirs`, but it would require a fix
+    in `fractal-web` as well.
+    """
     if include_shared_projects:
         res = await db.execute(
             select(DatasetV2.zarr_dir)
@@ -36,8 +39,9 @@ async def get_current_user_allowed_viewer_paths(
             .where(LinkUserProjectV2.user_id == current_user.id)
             .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
-        # common elements, and then this list may have non-unique items.
-
-    return authorized_paths
+        authorized_zarr_dirs = list(res.unique().scalars().all())
+        # Note that `project_dirs` and the `authorized_zarr_dirs` may have some
+        # common elements, and then the response may include non-unique items.
+        return current_user.project_dirs + authorized_zarr_dirs
+    else:
+        return current_user.project_dirs

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/app/security/signup_email.py

@@ -13,7 +13,7 @@ def send_fractal_email_or_log_failure(
     subject: str,
     msg: str,
     email_settings: PublicEmailSettings | None,
-):
+) -> None:
     """
     Send an email using the specified settings, or log about failure.
     """
@@ -22,6 +22,7 @@ def send_fractal_email_or_log_failure(
         logger.error(
             f"Cannot send email with {subject=}, because {email_settings=}."
         )
+        return
 
     try:
         logger.info(f"START sending email with {subject=}.")

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/images/tools.py

@@ -117,7 +117,7 @@ def merge_type_filters(
                 f"`{task_input_types}` (from task) "
                 f"and `{wftask_type_filters}` (from workflowtask)."
             )
-    merged_dict = task_input_types
+    merged_dict = task_input_types.copy()
     merged_dict.update(wftask_type_filters)
     return merged_dict
 

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/runner/executors/local/runner.py

@@ -3,6 +3,7 @@ from concurrent.futures import Future
 from concurrent.futures import ThreadPoolExecutor
 from pathlib import Path
 from typing import Any
+from typing import override
 
 from fractal_server.app.db import get_sync_db
 from fractal_server.app.models import Profile
@@ -91,6 +92,7 @@ class LocalRunner(BaseRunner):
         )
         return self.executor.__exit__(exc_type, exc_val, exc_tb)
 
+    @override
     def submit(
         self,
         *,

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/runner/executors/slurm_ssh/runner.py

@@ -1,5 +1,6 @@
 import time
 from pathlib import Path
+from typing import override
 
 from fractal_server.app.models import Profile
 from fractal_server.app.models import Resource
@@ -64,9 +65,11 @@ class SlurmSSHRunner(BaseSlurmRunner):
             slurm_account=slurm_account,
         )
 
+    @override
     def _mkdir_local_folder(self, folder: str) -> None:
         Path(folder).mkdir(parents=True)
 
+    @override
     def _mkdir_remote_folder(self, folder: str):
         self.fractal_ssh.mkdir(
             folder=folder,
@@ -169,6 +172,7 @@ class SlurmSSHRunner(BaseSlurmRunner):
         t_1 = time.perf_counter()
         logger.info(f"[_fetch_artifacts] End - elapsed={t_1 - t_0:.3f} s")
 
+    @override
     def _run_remote_cmd(self, cmd: str) -> str:
         stdout = self.fractal_ssh.run_command(cmd=cmd)
         return stdout
@@ -232,6 +236,7 @@ class SlurmSSHRunner(BaseSlurmRunner):
 
         logger.debug("[_send_many_job_inputs] END.")
 
+    @override
     def run_squeue(self, *, job_ids: list[str]) -> str:
         """
         Run `squeue` for a set of SLURM job IDs.

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/runner/executors/slurm_sudo/runner.py

@@ -4,6 +4,7 @@ import shlex
 import subprocess  # nosec
 from concurrent.futures import ThreadPoolExecutor
 from pathlib import Path
+from typing import override
 
 from fractal_server.app.models import Profile
 from fractal_server.app.models import Resource
@@ -85,11 +86,13 @@ class SlurmSudoRunner(BaseSlurmRunner):
             slurm_account=slurm_account,
         )
 
+    @override
     def _mkdir_local_folder(self, folder: str) -> None:
         original_umask = os.umask(0)
         Path(folder).mkdir(parents=True, mode=0o755)
         os.umask(original_umask)
 
+    @override
     def _mkdir_remote_folder(self, folder: str) -> None:
         _mkdir_as_user(folder=folder, user=self.slurm_user)
 
@@ -164,6 +167,7 @@ class SlurmSudoRunner(BaseSlurmRunner):
             )
         logger.debug("[_fetch_artifacts] END.")
 
+    @override
     def _run_remote_cmd(self, cmd: str) -> str:
         res = _run_command_as_user(
             cmd=cmd,
@@ -172,6 +176,7 @@ class SlurmSudoRunner(BaseSlurmRunner):
         )
         return res.stdout
 
+    @override
     def run_squeue(self, *, job_ids: list[str]) -> str:
         """
         Run `squeue` for a set of SLURM job IDs.

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/runner/v2/runner.py

@@ -473,7 +473,6 @@ def execute_tasks(
             )
 
             db.commit()
-            db.close()  # NOTE: this is needed, but the reason is unclear
 
             # Store the SLURM error in the job database
             job_db = db.get(JobV2, job_id)

{fractal_server-2.18.4 → fractal_server-2.18.6}/fractal_server/runner/v2/submit_workflow.py

@@ -76,7 +76,6 @@ def fail_job(
     job.log = log_msg
     db.merge(job)
     db.commit()
-    db.close()
     return
 
 

{fractal_server-2.18.4 → fractal_server-2.18.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.18.4"
+version = "2.18.6"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -12,17 +12,17 @@ readme = "README.md"
 license = "BSD-3-Clause"
 license-files = ["LICENSE"]
 
-requires-python = ">=3.11,<3.15"
+requires-python = ">=3.12,<3.15"
 dependencies = [
-    "fastapi >= 0.120.0, <0.121.0",
-    "sqlmodel == 0.0.27",
+    "fastapi >= 0.128.0, <0.129.0",
+    "sqlmodel == 0.0.31",
     "sqlalchemy[asyncio] >=2.0.23,<2.1",
     "fastapi-users[oauth] >=15,<16",
     "alembic >=1.13.1, <2.0.0",
-    "uvicorn >= 0.38.0, <0.39.0",
+    "uvicorn >= 0.40.0, <0.41.0",
     "uvicorn-worker == 0.4.0",
     "pydantic >=2.12.0,<2.13.0",
-    "pydantic-settings ==2.11.0",
+    "pydantic-settings ==2.12.0",
     "packaging >= 25.0.0, <26.0.0",
     "fabric >= 3.2.2, <3.3.0",
     "gunicorn >=23.0,<24.0",
@@ -49,9 +49,8 @@ dev = [
     "pytest-asyncio >= 1.2.0,<1.3.0",
     "bumpver >=2024.0",
     "pre-commit ==4.2.0",
-    "coverage[toml]>=7.12.0,<7.13.0",
+    "coverage>=7.12.0,<7.13.0",
     "pytest-docker >=3.2.0,<3.3.0",
-    "mypy >= 1.9",
     "pytest-subprocess >=1.5.0,<1.6.0",
     "a2wsgi >=1.10.0,<1.11.0",
     "jinja2 >=3.1.3,<3.1.4",
@@ -94,7 +93,7 @@ filterwarnings = [
 markers = ["container", "ssh", "fails_on_macos", "oauth"]
 
 [tool.bumpver]
-current_version = "2.18.4"
+current_version = "2.18.6"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.18.4/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.18.4"