fractal-server 2.0.0a12__tar.gz → 2.0.2__tar.gz

{fractal_server-2.0.0a12 → fractal_server-2.0.2}/PKG-INFO

@@ -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-2.0.2/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.0.2"

{fractal_server-2.0.0a12 → fractal_server-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-2.0.0a12 → fractal_server-2.0.2}/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-2.0.0a12 → fractal_server-2.0.2}/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-2.0.0a12 → fractal_server-2.0.2}/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-2.0.0a12 → fractal_server-2.0.2}/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-2.0.0a12 → fractal_server-2.0.2}/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-2.0.0a12 → fractal_server-2.0.2}/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-2.0.0a12 → fractal_server-2.0.2}/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-2.0.0a12 → fractal_server-2.0.2}/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-2.0.0a12 → fractal_server-2.0.2}/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-2.0.0a12 → fractal_server-2.0.2}/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 → fractal_server-2.0.2}/pyproject.toml

@@ -1,11 +1,12 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.0.0a12"
+version = "2.0.2"
 description = "Server component of the Fractal analytics platform"
 authors = [
-    "Jacopo Nespolo <jacopo.nespolo@exact-lab.it>",
-    "Marco Franzon <marco.franzon@exact-lab.it>",
     "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>",
 ]
 readme = "README.md"
 homepage = "https://github.com/fractal-analytics-platform/fractal-server"
@@ -86,7 +87,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.0.0a12"
+current_version = "2.0.2"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.0.0a12/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.0.0a12"