fractal-server 2.0.1__py3-none-any.whl → 2.0.3__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.0.1"
+__VERSION__ = "2.0.3"

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={"images", "timestamp_created"}),
+            **dataset.model_dump(
+                exclude={"images", "history", "timestamp_created"}
+            ),
             timestamp_created=_encode_as_utc(dataset.timestamp_created),
         ),
         workflow_dump=dict(

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/data_migrations/2_0_3.py

@@ -0,0 +1,79 @@
+import logging
+
+from packaging.version import parse
+from sqlalchemy import select
+from sqlalchemy.orm.attributes import flag_modified
+
+import fractal_server
+from fractal_server.app.db import get_sync_db
+from fractal_server.app.models.v1 import ApplyWorkflow
+from fractal_server.app.models.v2 import JobV2
+from fractal_server.app.schemas.v1 import ApplyWorkflowReadV1
+from fractal_server.app.schemas.v2 import JobReadV2
+
+
+def fix_db():
+    logger = logging.getLogger("fix_db")
+    logger.warning("START execution of fix_db function")
+
+    # Check that this module matches with the current version
+    module_version = parse("2.0.3")
+    current_version = parse(fractal_server.__VERSION__)
+    if (
+        current_version.major != module_version.major
+        or current_version.minor != module_version.minor
+        or current_version.micro != module_version.micro
+    ):
+        raise RuntimeError(
+            f"{fractal_server.__VERSION__=} not matching with {__file__=}"
+        )
+
+    with next(get_sync_db()) as db:
+
+        # V1 jobs
+        stm = select(ApplyWorkflow)
+        jobs_v1 = db.execute(stm).scalars().all()
+        for job_v1 in sorted(jobs_v1, key=lambda x: x.id):
+            for KEY in ["history"]:
+                logger.warning(
+                    f"Now removing {KEY} from `input/output_dataset_dump`, "
+                    f"for appplyworkflow.id={job_v1.id}."
+                )
+                if KEY in job_v1.input_dataset_dump.keys():
+                    job_v1.input_dataset_dump.pop(KEY)
+                if KEY in job_v1.output_dataset_dump.keys():
+                    job_v1.output_dataset_dump.pop(KEY)
+            flag_modified(job_v1, "input_dataset_dump")
+            flag_modified(job_v1, "output_dataset_dump")
+            db.add(job_v1)
+            db.commit()
+            db.refresh(job_v1)
+            db.expunge(job_v1)
+            logger.warning(
+                f"Now validating applyworkflow.id={job_v1.id} with "
+                "ApplyWorkflowReadV1."
+            )
+            ApplyWorkflowReadV1(**job_v1.model_dump())
+
+        # V2 jobs
+        stm = select(JobV2)
+        jobs_v2 = db.execute(stm).scalars().all()
+        for job_v2 in sorted(jobs_v2, key=lambda x: x.id):
+            for KEY in ["history", "images"]:
+                logger.warning(
+                    f"Now removing {KEY} from `dataset_dump`, "
+                    f"for jobv2.id={job_v2.id}."
+                )
+                if KEY in job_v2.dataset_dump.keys():
+                    job_v2.dataset_dump.pop(KEY)
+            flag_modified(job_v2, "dataset_dump")
+            db.add(job_v2)
+            db.commit()
+            db.refresh(job_v2)
+            db.expunge(job_v2)
+            logger.warning(
+                f"Now validating jobv2.id={job_v2.id} with JobReadV2."
+            )
+            JobReadV2(**job_v2.model_dump())
+
+    logger.warning("END of execution of fix_db function")

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-2.0.1.dist-info → fractal_server-2.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.0.1
+Version: 2.0.3
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

{fractal_server-2.0.1.dist-info → fractal_server-2.0.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=JTWFDLKimtlT6mPcm6_e8XrP61UXaA7yz2ycXya7oVs,22
+fractal_server/__init__.py,sha256=y8qIfi3XJXZnIlvcM-yGdSqRCMQ2ceId2VN0yHXJBAI,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
@@ -41,8 +41,8 @@ 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=63nfaPr3rCiMXCITJ0TWBqqSuZdLrQ7vcfzJonU5nHk,6899
+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=eN3NkZaZHkrqnLGRKE7Xd5mo0cHc8aK2lojCt26ErOQ,8988
 fractal_server/app/routes/api/v2/task_legacy.py,sha256=P_VJv9v0yzFUBuS-DQHhMVSOe20ecGJJcFBqiiFciOM,1628
@@ -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 +121,14 @@ 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/2_0_3.py,sha256=7EhwLCZTk1yHD_dlU-HIf2uvx6jUIgfDaA5np27QEEM,2918
 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=AuCmrwIydaFWpotMTM_tGRNJbExQO5fP8Xolo82Vdbg,4178
-fractal_server/main.py,sha256=7CpwPfCsHxBAo5fWuXPCsYOFCpbBI0F7Z0jsgCQdou8,3001
+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
@@ -162,8 +163,8 @@ fractal_server/tasks/v2/background_operations.py,sha256=MAMBn6W2bhkdK59kfUGiD7a1
 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-2.0.1.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.0.1.dist-info/METADATA,sha256=P7zEZwNFrYKxiIHHc24m3XGNKnjrYiY7xabRv7vwz5A,4202
-fractal_server-2.0.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.0.1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.0.1.dist-info/RECORD,,
+fractal_server-2.0.3.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.0.3.dist-info/METADATA,sha256=DE7GliLouz0Eb5ar6MOL0eShI-bqrvx7jZi6RPavLtc,4202
+fractal_server-2.0.3.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.0.3.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.0.3.dist-info/RECORD,,