fractal-server 2.3.5__py3-none-any.whl → 2.3.7__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.3.5"
+__VERSION__ = "2.3.7"

fractal_server/app/models/v2/task.py

@@ -1,5 +1,3 @@
-import json
-import logging
 from typing import Any
 from typing import Optional
 
@@ -41,53 +39,3 @@ class TaskV2(SQLModel, table=True):
 
     input_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
     output_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
-
-    @property
-    def default_args_non_parallel_from_args_schema(self) -> dict[str, Any]:
-        """
-        Extract default arguments from args_schema
-        """
-        # Return {} if there is no args_schema
-        if self.args_schema_non_parallel is None:
-            return {}
-        # Try to construct default_args
-        try:
-            default_args = {}
-            properties = self.args_schema_non_parallel["properties"]
-            for prop_name, prop_schema in properties.items():
-                default_value = prop_schema.get("default", None)
-                if default_value is not None:
-                    default_args[prop_name] = default_value
-            return default_args
-        except KeyError as e:
-            logging.warning(
-                "Cannot set default_args from args_schema_non_parallel="
-                f"{json.dumps(self.args_schema_non_parallel)}\n"
-                f"Original KeyError: {str(e)}"
-            )
-            return {}
-
-    @property
-    def default_args_parallel_from_args_schema(self) -> dict[str, Any]:
-        """
-        Extract default arguments from args_schema
-        """
-        # Return {} if there is no args_schema
-        if self.args_schema_parallel is None:
-            return {}
-        # Try to construct default_args
-        try:
-            default_args = {}
-            properties = self.args_schema_parallel["properties"]
-            for prop_name, prop_schema in properties.items():
-                default_value = prop_schema.get("default", None)
-                if default_value is not None:
-                    default_args[prop_name] = default_value
-            return default_args
-        except KeyError as e:
-            logging.warning(
-                "Cannot set default_args from args_schema_parallel="
-                f"{json.dumps(self.args_schema_parallel)}\n"
-                f"Original KeyError: {str(e)}"
-            )
-            return {}

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

@@ -422,6 +422,8 @@ async def _workflow_insert_task(
 
     # Get task from db, and extract default arguments via a Task property
     # method
+    # NOTE: this logic remains there for V1 tasks only. When we deprecate V1
+    # tasks, we can simplify this block
     if is_legacy_task is True:
         db_task = await db.get(Task, task_id)
         if db_task is None:
@@ -439,12 +441,8 @@ async def _workflow_insert_task(
             raise ValueError(f"TaskV2 {task_id} not found.")
         task_type = db_task.type
 
-        final_args_non_parallel = (
-            db_task.default_args_non_parallel_from_args_schema.copy()
-        )
-        final_args_parallel = (
-            db_task.default_args_parallel_from_args_schema.copy()
-        )
+        final_args_non_parallel = {}
+        final_args_parallel = {}
         final_meta_parallel = (db_task.meta_parallel or {}).copy()
         final_meta_non_parallel = (db_task.meta_non_parallel or {}).copy()
 

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

@@ -186,34 +186,17 @@ async def update_workflowtask(
                 default_args = (
                     db_wf_task.task_legacy.default_args_from_args_schema
                 )
+                actual_args = deepcopy(default_args)
+                if value is not None:
+                    for k, v in value.items():
+                        actual_args[k] = v
             else:
-                default_args = (
-                    db_wf_task.task.default_args_parallel_from_args_schema
-                )
-            # Override default_args with args value items
-            actual_args = deepcopy(default_args)
-            if value is not None:
-                for k, v in value.items():
-                    actual_args[k] = v
+                actual_args = deepcopy(value)
             if not actual_args:
                 actual_args = None
             setattr(db_wf_task, key, actual_args)
         elif key == "args_non_parallel":
-            # Get default arguments via a Task property method
-            if db_wf_task.is_legacy_task:
-                # This is only needed so that we don't have to modify the rest
-                # of this block, but legacy task cannot take any non-parallel
-                # args (see checks above).
-                default_args = {}
-            else:
-                default_args = deepcopy(
-                    db_wf_task.task.default_args_non_parallel_from_args_schema
-                )
-            # Override default_args with args value items
-            actual_args = default_args.copy()
-            if value is not None:
-                for k, v in value.items():
-                    actual_args[k] = v
+            actual_args = deepcopy(value)
             if not actual_args:
                 actual_args = None
             setattr(db_wf_task, key, actual_args)

fractal_server/app/runner/executors/slurm/ssh/_executor_wait_thread.py

@@ -7,6 +7,7 @@ from typing import Callable
 from cfut import FileWaitThread
 
 from ......logger import set_logger
+from fractal_server.app.runner.exceptions import JobExecutionError
 
 logger = set_logger(__name__)
 
@@ -48,6 +49,10 @@ class FractalSlurmWaitThread(FileWaitThread):
 
         This method is executed on the main thread.
         """
+        if self.shutdown:
+            error_msg = "Cannot call `wait` method after executor shutdown."
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
         with self.lock:
             self.active_job_ids.append(job_id)
 

fractal_server/app/runner/executors/slurm/ssh/executor.py

@@ -353,6 +353,12 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
             Future representing the execution of the current SLURM job.
         """
 
+        # Do not continue if auxiliary thread was shut down
+        if self.wait_thread.shutdown:
+            error_msg = "Cannot call `submit` method after executor shutdown"
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
+
         # Set defaults, if needed
         if slurm_config is None:
             slurm_config = get_default_slurm_config()
@@ -436,6 +442,12 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
 
         """
 
+        # Do not continue if auxiliary thread was shut down
+        if self.wait_thread.shutdown:
+            error_msg = "Cannot call `map` method after executor shutdown"
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
+
         def _result_or_cancel(fut):
             """
             This function is based on the Python Standard Library 3.11.
@@ -867,6 +879,14 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
             job: The `SlurmJob` object to submit.
         """
 
+        # Prevent calling sbatch if auxiliary thread was shut down
+        if self.wait_thread.shutdown:
+            error_msg = (
+                "Cannot call `_submit_job` method after executor shutdown"
+            )
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
+
         # Submit job to SLURM, and get jobid
         sbatch_command = f"sbatch --parsable {job.slurm_script_remote}"
         pre_submission_cmds = job.slurm_config.pre_submission_commands
@@ -1336,6 +1356,9 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         the self.wait_thread thread, see _completion.
         """
 
+        # Redudantly set thread shutdown attribute to True
+        self.wait_thread.shutdown = True
+
         logger.debug("Executor shutdown: start")
 
         # Handle all job futures

fractal_server/config.py

@@ -553,6 +553,11 @@ class Settings(BaseSettings):
     Whether to include the v1 API.
     """
 
+    FRACTAL_MAX_PIP_VERSION: str = "24.0"
+    """
+    Maximum value at which to update `pip` before performing task collection.
+    """
+
     ###########################################################################
     # BUSINESS LOGIC
     ###########################################################################

fractal_server/tasks/v2/_venv_pip.py

@@ -2,7 +2,9 @@ from pathlib import Path
 from typing import Optional
 
 from ..utils import COLLECTION_FREEZE_FILENAME
+from fractal_server.config import get_settings
 from fractal_server.logger import get_logger
+from fractal_server.syringe import Inject
 from fractal_server.tasks.v2._TaskCollectPip import _TaskCollectPip
 from fractal_server.tasks.v2.utils import get_python_interpreter_v2
 from fractal_server.utils import execute_command
@@ -24,6 +26,7 @@ async def _pip_install(
     Returns:
         The location of the package.
     """
+    settings = Inject(get_settings)
 
     logger = get_logger(logger_name)
 
@@ -41,7 +44,10 @@ async def _pip_install(
 
     await execute_command(
         cwd=venv_path,
-        command=f"{pip} install --upgrade pip",
+        command=(
+            f"{pip} install --upgrade "
+            f"'pip<={settings.FRACTAL_MAX_PIP_VERSION}'"
+        ),
         logger_name=logger_name,
     )
     await execute_command(

fractal_server/tasks/v2/background_operations_ssh.py

@@ -174,6 +174,10 @@ def background_collect_pip_ssh(
                     ("__PACKAGE__", task_pkg.package),
                     ("__PYTHON__", python_bin),
                     ("__INSTALL_STRING__", install_string),
+                    (
+                        "__FRACTAL_MAX_PIP_VERSION__",
+                        settings.FRACTAL_MAX_PIP_VERSION,
+                    ),
                 ]
 
                 common_args = dict(

fractal_server/tasks/v2/templates/_2_upgrade_pip.sh

@@ -14,7 +14,7 @@ VENVPYTHON=${PACKAGE_ENV_DIR}/bin/python
 
 # Upgrade pip
 write_log "START upgrade pip"
-"$VENVPYTHON" -m pip install pip --upgrade
+"$VENVPYTHON" -m pip install "pip<=__FRACTAL_MAX_PIP_VERSION__" --upgrade
 write_log "END   upgrade pip"
 echo
 

fractal_server/tasks/v2/templates/_4_pip_freeze.sh

@@ -12,4 +12,4 @@ PACKAGE_ENV_DIR=__PACKAGE_ENV_DIR__
 
 VENVPYTHON=${PACKAGE_ENV_DIR}/bin/python
 
-"$VENVPYTHON" -m pip freeze
+"$VENVPYTHON" -m pip freeze --all

{fractal_server-2.3.5.dist-info → fractal_server-2.3.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.3.5
+Version: 2.3.7
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -33,7 +33,7 @@ Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0) ; extra == "postgres-psycopg-bin
 Requires-Dist: pydantic (>=1.10.8,<2)
 Requires-Dist: python-dotenv (>=1.0.0,<2.0.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)
-Requires-Dist: sqlmodel (>=0.0.19,<0.0.20)
+Requires-Dist: sqlmodel (>=0.0.21,<0.0.22)
 Requires-Dist: uvicorn (>=0.29.0,<0.30.0)
 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

{fractal_server-2.3.5.dist-info → fractal_server-2.3.7.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=RqyrrNV86fgXA3ZGY013Ddl0XCyYA-YaiOneKISOYXc,22
+fractal_server/__init__.py,sha256=RnhDw1BSFncjEr_850CnTxRPd0CUQSmMtBKZ6CaNXg0,22
 fractal_server/__main__.py,sha256=CocbzZooX1UtGqPi55GcHGNxnrJXFg5tUU5b3wyFCyo,4958
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -18,7 +18,7 @@ fractal_server/app/models/v2/collection_state.py,sha256=nxb042i8tt8rCpmgbFJoBCYW
 fractal_server/app/models/v2/dataset.py,sha256=-7sxHEw4IIAvF_uSan7tA3o8hvoakBkQ0SRvqS2iOQU,1455
 fractal_server/app/models/v2/job.py,sha256=ypJmN-qspkKBGhBG7Mt-HypSQqcQ2EmB4Bzzb2-y550,1535
 fractal_server/app/models/v2/project.py,sha256=CRBnZ8QITNp6u1f5bMxvi1_mcvEfXpWyitsWB5f7gn8,759
-fractal_server/app/models/v2/task.py,sha256=9ZPhug3VWyeqgT8wQ9_8ZXQ2crSiiicRipxrxTslOso,3257
+fractal_server/app/models/v2/task.py,sha256=Esf2j9c-0pGYjdbb__Ptpdx7NCAKVxqbQMoza524miU,1286
 fractal_server/app/models/v2/workflow.py,sha256=YBgFGCziUgU0aJ5EM3Svu9W2c46AewZO9VBlFCHiSps,1069
 fractal_server/app/models/v2/workflowtask.py,sha256=3jEkObsSnlI05Pur_dSsXYdJxRqPL60Z7tK5-EJLOks,1532
 fractal_server/app/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -36,7 +36,7 @@ fractal_server/app/routes/api/v1/task_collection.py,sha256=82XBsJHlPiDPCbpLa-16o
 fractal_server/app/routes/api/v1/workflow.py,sha256=7r9IoIevg_rvYCrerMOsIsUabSOQatxdPCfLdkP0dRs,10942
 fractal_server/app/routes/api/v1/workflowtask.py,sha256=qcHQlzlSFf_k8gtId-mA3tnyzgSR7i1m7pvR4R86blE,5582
 fractal_server/app/routes/api/v2/__init__.py,sha256=JrPWfKIJy9btRCP-zw2nZwLpSdBxEKY5emuCuJbqG0s,1813
-fractal_server/app/routes/api/v2/_aux_functions.py,sha256=tYJr5EPaA0CVGp-Y4jottFJUVToWvjcSY6PJqN_d--s,14938
+fractal_server/app/routes/api/v2/_aux_functions.py,sha256=yeA0650pBk43M5ZQGpVQ17nH5D97NIGY-3tNNLQIW1M,14901
 fractal_server/app/routes/api/v2/dataset.py,sha256=_HjKNP9XsMGoqyubGdF2ZyeW7vXC3VdK_0_TaUxgIF0,8248
 fractal_server/app/routes/api/v2/images.py,sha256=4r_HblPWyuKSZSJZfn8mbDaLv1ncwZU0gWdKneZcNG4,7894
 fractal_server/app/routes/api/v2/job.py,sha256=RkIj7ANK-nkxUvcG9K2r4dFdPnvGomx7jdB6U9bqOVQ,5202
@@ -48,7 +48,7 @@ fractal_server/app/routes/api/v2/task_collection.py,sha256=BiZ5s6DwdQbM79s_dPivg
 fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=cvZorN_Xt57Rj-2JATRrdtSw6I_5befB0ua3FWh6hW4,5988
 fractal_server/app/routes/api/v2/task_legacy.py,sha256=P_VJv9v0yzFUBuS-DQHhMVSOe20ecGJJcFBqiiFciOM,1628
 fractal_server/app/routes/api/v2/workflow.py,sha256=2GlcYNjpvCdjwC_Kn7y0UP16B3pOLSNXBvIVsVDtDKM,11863
-fractal_server/app/routes/api/v2/workflowtask.py,sha256=l4eTD5IIun5cOdYzsxh3ajmnOISaSccYA_mVf15Cjtw,8802
+fractal_server/app/routes/api/v2/workflowtask.py,sha256=l_eQPniK1zR0u249bJj4c2hFlyDwsSJgsFR6hxJaOjs,8007
 fractal_server/app/routes/auth.py,sha256=Xv80iqdyfY3lyicYs2Y8B6zEDEnyUu_H6_6psYtv3R4,4885
 fractal_server/app/routes/aux/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/aux/_job.py,sha256=HUItNm0SZFAYsyL1rXSjBre1-rXSe6x51qH9KAQWS1w,1361
@@ -65,9 +65,9 @@ fractal_server/app/runner/executors/slurm/_batching.py,sha256=3mfeFuYm3UA4EXh4VW
 fractal_server/app/runner/executors/slurm/_slurm_config.py,sha256=iyhtDi1qveqq7I4S1tycVKsp3VfyocvBgGugYDpOzAs,16069
 fractal_server/app/runner/executors/slurm/remote.py,sha256=wLziIsGdSMiO-jIXM8x77JRK82g_2hx0iBKTiMghuIo,5852
 fractal_server/app/runner/executors/slurm/ssh/__init__.py,sha256=Cjn1rYvljddi96tAwS-qqGkNfOcfPzjChdaEZEObCcM,65
-fractal_server/app/runner/executors/slurm/ssh/_executor_wait_thread.py,sha256=jM4G-wiHynZhNERusVGLtDTepJDiYjCDloWZyflaMV0,3482
+fractal_server/app/runner/executors/slurm/ssh/_executor_wait_thread.py,sha256=bKo5Ja0IGxJWpPWyh9dN0AG-PwzTDZzD5LyaEHB3YU4,3742
 fractal_server/app/runner/executors/slurm/ssh/_slurm_job.py,sha256=rwlqZzoGo4SAb4nSlFjsQJdaCgfM1J6YGcjb8yYxlqc,4506
-fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=rfLEO6mN3sZvZYHqs3lmYvPYFGLmXyMPWl1Bg0mq-6k,56109
+fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=oCc5cLZoNmJ3ENV0VaYRiIKayVClKDoEnjgZjHU864Y,57052
 fractal_server/app/runner/executors/slurm/sudo/__init__.py,sha256=Cjn1rYvljddi96tAwS-qqGkNfOcfPzjChdaEZEObCcM,65
 fractal_server/app/runner/executors/slurm/sudo/_check_jobs_status.py,sha256=wAgwpVcr6JIslKHOuS0FhRa_6T1KCManyRJqA-fifzw,1909
 fractal_server/app/runner/executors/slurm/sudo/_executor_wait_thread.py,sha256=z5LlhaiqAb8pHsF1WwdzXN39C5anQmwjo1rSQgtRAYE,4422
@@ -139,7 +139,7 @@ fractal_server/app/schemas/v2/task_collection.py,sha256=8PG1bOqkfQqORMN0brWf6mHD
 fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
 fractal_server/app/schemas/v2/workflowtask.py,sha256=atVuVN4aXsVEOmSd-vyg-8_8OnPmqx-gT75rXcn_AlQ,6552
 fractal_server/app/security/__init__.py,sha256=2-QbwuR-nsuHM_uwKS_WzYvkhnuhO5jUv8UVROetyVk,11169
-fractal_server/config.py,sha256=KOa2jrsbx0H6zG2ItNZkLiKqbuOkV3aUYKFuIN3FIyE,24921
+fractal_server/config.py,sha256=-9x8grPTrM-rnztRAOlqHKuHCHWEg_-qnccU3kjuxbY,25058
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/gunicorn_fractal.py,sha256=2AOkgxu-oQ-XB578_voT0VuhmAXFTmb0c-nYn1XLy_Q,1231
 fractal_server/images/__init__.py,sha256=xO6jTLE4EZKO6cTDdJsBmK9cdeh9hFTaSbSuWgQg7y4,196
@@ -181,20 +181,20 @@ fractal_server/tasks/v1/get_collection_data.py,sha256=bi9tuApLgoKZNMIG1kR4GoKI9S
 fractal_server/tasks/v1/utils.py,sha256=J9oKys-82OehBxOon5wWl3CxjVBgYWeVEEyWGVFnreI,1759
 fractal_server/tasks/v2/_TaskCollectPip.py,sha256=kWQNMNZ8OEddkYhmhsk3E6ArcaD7qe4vsjYYx9vbrUg,4900
 fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/tasks/v2/_venv_pip.py,sha256=xm4XClWYbhXQRqDxYxM9cP7ZCnx-8b078fuVUL12D2M,6286
+fractal_server/tasks/v2/_venv_pip.py,sha256=6NCItfeWgO9BDnlfhoCfiUG5UCGGz_SJz4Mfn4Jg_nk,6489
 fractal_server/tasks/v2/background_operations.py,sha256=CQwQon5RKAXrjsN255Okh5dcT0R45axgqoPW3EB-v_Q,11527
-fractal_server/tasks/v2/background_operations_ssh.py,sha256=3TJp2NW2CJ9KlghWDEhTQ4HDZxmbrLHjb0OQJI3ALo0,13892
+fractal_server/tasks/v2/background_operations_ssh.py,sha256=wVnE6bubKsFqxsBFdyCcvW8nRr4kTGUiyt2OKQFIwrU,14050
 fractal_server/tasks/v2/endpoint_operations.py,sha256=gT38pl5TEH6WNWOtg4Itegt2lTJJI6YRa7fEj9Y4x2s,4226
 fractal_server/tasks/v2/templates/_1_create_venv.sh,sha256=5uW0ETYxl5xiQEXP107zgq8V_-vf3k5NzMMj1hSLjas,1015
-fractal_server/tasks/v2/templates/_2_upgrade_pip.sh,sha256=hVqwgWuNOxr6ck-0FklpcF0o7q-vQXQasYNNaPSxlKM,524
+fractal_server/tasks/v2/templates/_2_upgrade_pip.sh,sha256=ca5Yng6JgJYu-a4QrsIsatwUmrLdRWBKw7_VJrY7WLY,555
 fractal_server/tasks/v2/templates/_3_pip_install.sh,sha256=T9sabeB9iQzVZpLfuLkKGz9EpfHkUrJHKWO4HNij6yM,595
-fractal_server/tasks/v2/templates/_4_pip_freeze.sh,sha256=6BIOVYBPZmaaOuaDwNirt1iHWjj2oDjViUDvQaL_f6Y,268
+fractal_server/tasks/v2/templates/_4_pip_freeze.sh,sha256=qHdDKu1svXi1VQKGePciEJK4_uEKuwAvwaDCcGxSvNk,274
 fractal_server/tasks/v2/templates/_5_pip_show.sh,sha256=GrJ19uHYQxANEy9JaeNJZVTquY9c8Ww9eCdnC7eLVr0,1754
 fractal_server/tasks/v2/utils.py,sha256=JOyCacb6MNvrwfLNTyLwcz8y79J29YuJeJ2MK5kqXRM,1657
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
-fractal_server-2.3.5.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.3.5.dist-info/METADATA,sha256=dElt7KKeyH2IIRToMdsTiVKeIEww0ZsbFzlQcCskrKE,4425
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