fractal-server 2.0.0a12__py3-none-any.whl → 2.0.2__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.0.0a12"
+__VERSION__ = "2.0.2"

fractal_server/app/routes/api/v1/project.py

@@ -398,7 +398,7 @@ async def apply_workflow(
         user_email=user.email,
         input_dataset_dump=dict(
             **input_dataset.model_dump(
-                exclude={"resource_list", "timestamp_created"}
+                exclude={"resource_list", "history", "timestamp_created"}
             ),
             timestamp_created=_encode_as_utc(input_dataset.timestamp_created),
             resource_list=[
@@ -408,7 +408,7 @@ async def apply_workflow(
         ),
         output_dataset_dump=dict(
             **output_dataset.model_dump(
-                exclude={"resource_list", "timestamp_created"}
+                exclude={"resource_list", "history", "timestamp_created"}
             ),
             timestamp_created=_encode_as_utc(output_dataset.timestamp_created),
             resource_list=[

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

@@ -7,6 +7,7 @@ from fastapi import Depends
 from fastapi import HTTPException
 from fastapi import status
 
+from .....logger import set_logger
 from ....db import AsyncSession
 from ....db import get_async_db
 from ....models.v2 import JobV2
@@ -21,6 +22,8 @@ from fractal_server.app.runner.filenames import HISTORY_FILENAME
 
 router = APIRouter()
 
+logger = set_logger(__name__)
+
 
 @router.get(
     "/project/{project_id}/status/",
@@ -113,7 +116,22 @@ async def get_workflowtask_status(
 
         # The last workflow task that is included in the submitted job is also
         # the positional-last workflow task to be included in the response.
-        last_valid_wftask_id = workflow.task_list[end - 1]
+        try:
+            last_valid_wftask_id = workflow.task_list[end - 1].id
+        except IndexError as e:
+            logger.warning(
+                f"Handled IndexError in `get_workflowtask_status` ({str(e)})."
+            )
+            logger.warning(
+                "Additional information: "
+                f"{running_job.first_task_index=}; "
+                f"{running_job.last_task_index=}; "
+                f"{len(workflow.task_list)=}; "
+                f"{dataset_id=}; "
+                f"{workflow_id=}."
+            )
+            last_valid_wftask_id = None
+            logger.warning(f"Now setting {last_valid_wftask_id=}.")
 
         # Highest priority: Read status updates coming from the running-job
         # temporary file. Note: this file only contains information on

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

@@ -146,7 +146,9 @@ async def apply_workflow(
         workflow_id=workflow_id,
         user_email=user.email,
         dataset_dump=dict(
-            **dataset.model_dump(exclude={"timestamp_created"}),
+            **dataset.model_dump(
+                exclude={"images", "history", "timestamp_created"}
+            ),
             timestamp_created=_encode_as_utc(dataset.timestamp_created),
         ),
         workflow_dump=dict(

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

@@ -12,7 +12,7 @@ from pydantic.error_wrappers import ValidationError
 from sqlmodel import select
 
 from .....config import get_settings
-from .....logger import close_logger
+from .....logger import reset_logger_handlers
 from .....logger import set_logger
 from .....syringe import Inject
 from ....db import AsyncSession
@@ -196,7 +196,7 @@ async def collect_tasks_pip(
         "Task-collection endpoint: start background collection "
         "and return state"
     )
-    close_logger(logger)
+    reset_logger_handlers(logger)
     info = (
         "Collecting tasks in the background. "
         f"GET /task/collect/{state.id} to query collection status"
@@ -234,6 +234,6 @@ async def check_collection_status(
     if verbose and not data.log:
         data.log = get_collection_log(data.venv_path)
         state.data = data.sanitised_dict()
-    close_logger(logger)
+    reset_logger_handlers(logger)
     await db.close()
     return state

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

@@ -7,7 +7,7 @@ from fastapi import Response
 from fastapi import status
 from sqlmodel import select
 
-from .....logger import close_logger
+from .....logger import reset_logger_handlers
 from .....logger import set_logger
 from ....db import AsyncSession
 from ....db import get_async_db
@@ -259,7 +259,7 @@ async def export_worfklow(
                     "portable; re-importing this workflow may not work as "
                     "expected."
                 )
-    close_logger(logger)
+    reset_logger_handlers(logger)
 
     await db.close()
     return workflow

fractal_server/app/runner/v2/__init__.py

@@ -13,7 +13,7 @@ from typing import Optional
 from sqlalchemy.orm.attributes import flag_modified
 
 from ....config import get_settings
-from ....logger import close_logger
+from ....logger import reset_logger_handlers
 from ....logger import set_logger
 from ....syringe import Inject
 from ....utils import get_timestamp
@@ -332,5 +332,5 @@ async def submit_workflow(
         db_sync.merge(job)
         db_sync.commit()
     finally:
-        close_logger(logger)
+        reset_logger_handlers(logger)
         db_sync.close()

fractal_server/app/schemas/v2/dumps.py

@@ -70,14 +70,14 @@ class WorkflowTaskDumpV2(BaseModel):
         return values
 
 
-class WorkflowDumpV2(BaseModel):
+class WorkflowDumpV2(BaseModel, extra=Extra.forbid):
     id: int
     name: str
     project_id: int
     timestamp_created: str
 
 
-class DatasetDumpV2(BaseModel):
+class DatasetDumpV2(BaseModel, extra=Extra.forbid):
     id: int
     name: str
     project_id: int

fractal_server/config.py

@@ -441,9 +441,4 @@ class Settings(BaseSettings):
 
 
 def get_settings(settings=Settings()) -> Settings:
-    logging.debug("Fractal Settings:")
-    for key, value in settings.dict().items():
-        if any(s in key.upper() for s in ["PASSWORD", "SECRET"]):
-            value = "*****"
-        logging.debug(f"{key}: {value}")
     return settings

fractal_server/logger.py

@@ -125,3 +125,14 @@ def close_logger(logger: logging.Logger) -> None:
     """
     for handle in logger.handlers:
         handle.close()
+
+
+def reset_logger_handlers(logger: logging.Logger) -> None:
+    """
+    Close and remove all handlers associated to a `logging.Logger` object
+
+    Arguments:
+        logger: The actual logger
+    """
+    close_logger(logger)
+    logger.handlers.clear()

fractal_server/main.py

@@ -19,6 +19,8 @@ from fastapi import FastAPI
 
 from .app.security import _create_first_user
 from .config import get_settings
+from .logger import reset_logger_handlers
+from .logger import set_logger
 from .syringe import Inject
 
 
@@ -62,6 +64,14 @@ def check_settings() -> None:
     settings = Inject(get_settings)
     settings.check()
 
+    logger = set_logger("fractal_server_settings")
+    logger.debug("Fractal Settings:")
+    for key, value in settings.dict().items():
+        if any(s in key.upper() for s in ["PASSWORD", "SECRET"]):
+            value = "*****"
+        logger.debug(f"  {key}: {value}")
+    reset_logger_handlers(logger)
+
 
 async def __on_startup() -> None:
     """

fractal_server/tasks/v2/background_operations.py

@@ -20,8 +20,8 @@ from fractal_server.app.models.v2 import TaskV2
 from fractal_server.app.schemas.v2 import TaskCollectStatusV2
 from fractal_server.app.schemas.v2 import TaskCreateV2
 from fractal_server.app.schemas.v2 import TaskReadV2
-from fractal_server.logger import close_logger
 from fractal_server.logger import get_logger
+from fractal_server.logger import reset_logger_handlers
 from fractal_server.logger import set_logger
 from fractal_server.utils import execute_command
 
@@ -358,14 +358,14 @@ async def background_collect_pip(
             # Write last logs to file
             logger.debug("Task-collection status: OK")
             logger.info("Background task collection completed successfully")
-            close_logger(logger)
+            reset_logger_handlers(logger)
+
             db.close()
 
         except Exception as e:
             # Write last logs to file
             logger.debug("Task-collection status: fail")
             logger.info(f"Background collection failed. Original error: {e}")
-            close_logger(logger)
 
             # Update db
             data.status = "fail"
@@ -379,3 +379,5 @@ async def background_collect_pip(
             # Delete corrupted package dir
             logger.info(f"Now deleting temporary folder {venv_path}")
             shell_rmtree(venv_path)
+            logger.info("Temporary folder deleted")
+            reset_logger_handlers(logger)

{fractal_server-2.0.0a12.dist-info → fractal_server-2.0.2.dist-info}/METADATA

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.0.0a12
+Version: 2.0.2
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
-Author: Jacopo Nespolo
-Author-email: jacopo.nespolo@exact-lab.it
+Author: Tommaso Comparin
+Author-email: tommaso.comparin@exact-lab.it
 Requires-Python: >=3.9,<4.0
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3

{fractal_server-2.0.0a12.dist-info → fractal_server-2.0.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=n09kNau5UUJa9hzn0KtsMdH-0FpJzIry0v93FUKYRLg,25
+fractal_server/__init__.py,sha256=gs_vt2BGew5iMLZDjM9dN_UiSCo9swvJzExXe0z6N7w,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
@@ -30,7 +30,7 @@ fractal_server/app/routes/api/v1/__init__.py,sha256=Y2HQdG197J0a7DyQEE2jn53IfxD0
 fractal_server/app/routes/api/v1/_aux_functions.py,sha256=KoSefKiBXximu0df4fJ3l9bKsGaLO8rb3z6xhD8PWj4,11973
 fractal_server/app/routes/api/v1/dataset.py,sha256=HRE-8vPmVkeXf7WFYkI19mDtbY-iJZeJ7PmMiV0LMgY,16923
 fractal_server/app/routes/api/v1/job.py,sha256=NwXyhvvzdPDor0ts8Im__9-I0P1H943s4NXIRgaz7PM,5436
-fractal_server/app/routes/api/v1/project.py,sha256=4wlxcc-bR45bns6Yy0WyjA9Qv9eiMscATLZKjVhSd1k,15777
+fractal_server/app/routes/api/v1/project.py,sha256=tb1M2hhAKyHeToV0RwAQQx0ptIDeX6sEjM7dkfjCpXQ,15799
 fractal_server/app/routes/api/v1/task.py,sha256=udbKnenzc-Q10elYCVB9JmOPWATraa9tZi0AaByvWo0,6129
 fractal_server/app/routes/api/v1/task_collection.py,sha256=mFaYyCWtCPRqvs3j6zx_zaiDXn31Uzoa7UHZS-Lu_L0,8882
 fractal_server/app/routes/api/v1/workflow.py,sha256=7r9IoIevg_rvYCrerMOsIsUabSOQatxdPCfLdkP0dRs,10942
@@ -41,12 +41,12 @@ fractal_server/app/routes/api/v2/dataset.py,sha256=_HjKNP9XsMGoqyubGdF2ZyeW7vXC3
 fractal_server/app/routes/api/v2/images.py,sha256=4r_HblPWyuKSZSJZfn8mbDaLv1ncwZU0gWdKneZcNG4,7894
 fractal_server/app/routes/api/v2/job.py,sha256=BtaxErBDbLwjY2zgGD1I6eRpsffoMonifcS1CMEXmLU,5325
 fractal_server/app/routes/api/v2/project.py,sha256=qyvizYZ4aUFgF3tGdfp4z8AwWgfo19N_KbFEljfUaC8,5594
-fractal_server/app/routes/api/v2/status.py,sha256=3bqQejJ3TnIMan5wK6jr9sv4ypsQr9WWU8xqlvTgDCE,5739
-fractal_server/app/routes/api/v2/submit.py,sha256=lbPTZKemoRjypcpExi-Yz9fIiPdv9OIjFeUu9yuILA4,6889
+fractal_server/app/routes/api/v2/status.py,sha256=osLexiMOSqmYcEV-41tlrwt9ofyFbtRm5HmPS5BU0t4,6394
+fractal_server/app/routes/api/v2/submit.py,sha256=svI1Oa2zIxUEAomzRt7-M66xKC4Pb9NEGcXNrtN6b5g,6940
 fractal_server/app/routes/api/v2/task.py,sha256=gJ0LruSk-Q1iMw8ZOX8C0wrZ4S4DGlQTr_5SdJJud0Q,7130
-fractal_server/app/routes/api/v2/task_collection.py,sha256=wHkPkQKnvXEzidywuJqLe8QB_xjlHUqzPgsitXydNkU,8961
+fractal_server/app/routes/api/v2/task_collection.py,sha256=eN3NkZaZHkrqnLGRKE7Xd5mo0cHc8aK2lojCt26ErOQ,8988
 fractal_server/app/routes/api/v2/task_legacy.py,sha256=P_VJv9v0yzFUBuS-DQHhMVSOe20ecGJJcFBqiiFciOM,1628
-fractal_server/app/routes/api/v2/workflow.py,sha256=sw-1phO_rrmDAcWX9Zqb9M8SfrWF78-02AuLB1-D1PU,11845
+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/auth.py,sha256=Xv80iqdyfY3lyicYs2Y8B6zEDEnyUu_H6_6psYtv3R4,4885
 fractal_server/app/routes/aux/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -80,7 +80,7 @@ fractal_server/app/runner/v1/_slurm/_submit_setup.py,sha256=llTgSOCnCVMvm7Q0SoVp
 fractal_server/app/runner/v1/_slurm/get_slurm_config.py,sha256=6TLWQon8hSicsD7c3yXK4P9xeId0s_H3HOOeMUVGVss,5977
 fractal_server/app/runner/v1/common.py,sha256=_L-vjLnWato80VdlB_BFN4G8P4jSM07u-5cnl1T3S34,3294
 fractal_server/app/runner/v1/handle_failed_job.py,sha256=bHzScC_aIlU3q-bQxGW6rfWV4xbZ2tho_sktjsAs1no,4684
-fractal_server/app/runner/v2/__init__.py,sha256=RwIOSLCChMZWHix5QuUNRPtRwgf1UmFDk3YufRCTOoc,12482
+fractal_server/app/runner/v2/__init__.py,sha256=mnXlC69UBQVpEwEWH3ZbMSsrVLl1yCnROh8_WGnXKUk,12500
 fractal_server/app/runner/v2/_local/__init__.py,sha256=Q1s-DwXleUq6w1ZNv6tlh3tZv6cyBqxB_hMvZlqVYaM,5881
 fractal_server/app/runner/v2/_local/_local_config.py,sha256=lR0Js-l63mQUzN9hK0HkfdLsrTf-W6GHvPvbPC64amY,3630
 fractal_server/app/runner/v2/_local/_submit_setup.py,sha256=deagsLSy6A3ZHKaSDcQqrdvbQVM3i4kgyTcbVc0tC5U,1614
@@ -111,7 +111,7 @@ fractal_server/app/schemas/v1/task_collection.py,sha256=uvq9bcMaGD_qHsh7YtcpoSAk
 fractal_server/app/schemas/v1/workflow.py,sha256=tuOs5E5Q_ozA8if7YPZ07cQjzqB_QMkBS4u92qo4Ro0,4618
 fractal_server/app/schemas/v2/__init__.py,sha256=IssDWR6q_mgNkaAxfhSnEZZLZRZIqOsr9SM7RvN1IsY,1852
 fractal_server/app/schemas/v2/dataset.py,sha256=dLT52tV4dSf2HrFNak4vdQEn8PT_04IUrGnd2z-AXIU,2599
-fractal_server/app/schemas/v2/dumps.py,sha256=IpIT_2KxJd7qTgW2NllDknGeP7vBAJDfyz1I5p3TytU,2023
+fractal_server/app/schemas/v2/dumps.py,sha256=Qg7n0WNfqCV5DBFwfYIKP-OrBjyMZETnNZyoL-EqIco,2063
 fractal_server/app/schemas/v2/job.py,sha256=zfF9K3v4jWUJ7M482ta2CkqUJ4tVT4XfVt60p9IRhP0,3250
 fractal_server/app/schemas/v2/manifest.py,sha256=N37IWohcfO3_y2l8rVM0h_1nZq7m4Izxk9iL1vtwBJw,6243
 fractal_server/app/schemas/v2/project.py,sha256=u7S4B-bote1oGjzAGiZ-DuQIyeRAGqJsI71Tc1EtYE0,736
@@ -121,13 +121,13 @@ fractal_server/app/schemas/v2/task_collection.py,sha256=sY29NQfJrbjiidmVkVjSIH-2
 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=wxosoHc3mJYPCdPMyWnRD8w_2OgnKYp2aDkdmwrZh5k,11203
-fractal_server/config.py,sha256=CA8ASObADaME5chDiBXawAJZ3MvjTRpCKP0jvdYtSh8,15080
+fractal_server/config.py,sha256=2vw5M78aAogELsWut9X5sxxUz2lirNFpgqP6OynmKOQ,14859
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/images/__init__.py,sha256=xO6jTLE4EZKO6cTDdJsBmK9cdeh9hFTaSbSuWgQg7y4,196
 fractal_server/images/models.py,sha256=9ipU5h4N6ogBChoB-2vHoqtL0TXOHCv6kRR-fER3mkM,4167
 fractal_server/images/tools.py,sha256=gxeniYy4Z-cp_ToK2LHPJUTVVUUrdpogYdcBUvBuLiY,2209
-fractal_server/logger.py,sha256=95duXY8eSxf1HWg0CVn8SUGNzgJw9ZR0FlapDDF6WAY,3924
-fractal_server/main.py,sha256=7CpwPfCsHxBAo5fWuXPCsYOFCpbBI0F7Z0jsgCQdou8,3001
+fractal_server/logger.py,sha256=AuCmrwIydaFWpotMTM_tGRNJbExQO5fP8Xolo82Vdbg,4178
+fractal_server/main.py,sha256=u_MngsZWI-1uKrBpNDUYXKyLgaYodyAEw2dKZrIzS_U,3381
 fractal_server/migrations/README,sha256=4rQvyDfqodGhpJw74VYijRmgFP49ji5chyEemWGHsuw,59
 fractal_server/migrations/env.py,sha256=bsl0HGZpjhommztgcs7wQ94sJzI1Orgnij97K8P_uyo,2630
 fractal_server/migrations/script.py.mako,sha256=oMXw9LC3zRbinWWPPDgeZ4z9FJrV2zhRWiYdS5YgNbI,526
@@ -158,12 +158,12 @@ fractal_server/tasks/v1/background_operations.py,sha256=I-D4SaG56UMkoH7dNy5CzbEs
 fractal_server/tasks/v1/get_collection_data.py,sha256=bi9tuApLgoKZNMIG1kR4GoKI9S6Y040gFfNQapw4ikM,502
 fractal_server/tasks/v2/_TaskCollectPip.py,sha256=QeCqXDgOnMjk3diVlC5bgGEywyQjYFm5637Rke49vJY,3775
 fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/tasks/v2/background_operations.py,sha256=fUukEA-zFjUDhxgI3oO_Bvy7FinaYFaydciASOIbL3w,12842
+fractal_server/tasks/v2/background_operations.py,sha256=MAMBn6W2bhkdK59kfUGiD7a1G163exiYeJqqtj08Gv4,12922
 fractal_server/tasks/v2/get_collection_data.py,sha256=Qhf2T_aaqAfqu9_KpUSlXsS7EJoZQbEPEreHHa2jco8,502
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
-fractal_server-2.0.0a12.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.0.0a12.dist-info/METADATA,sha256=vBB1xO15zGGC1KMJRwj7xmVLHS0pF0BLTjVUusilAns,4201
-fractal_server-2.0.0a12.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-fractal_server-2.0.0a12.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.0.0a12.dist-info/RECORD,,
+fractal_server-2.0.2.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.0.2.dist-info/METADATA,sha256=ykUREKoZndksb0goOo27hM14j41SvTljFa5P7eR9zTU,4202
+fractal_server-2.0.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.0.2.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.0.2.dist-info/RECORD,,

{fractal_server-2.0.0a12.dist-info → fractal_server-2.0.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.8.1
+Generator: poetry-core 1.9.0
 Root-Is-Purelib: true
 Tag: py3-none-any