fractal-server 2.14.0a28__tar.gz → 2.14.0a30__tar.gz

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.14.0a28
+Version: 2.14.0a30
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin

fractal_server-2.14.0a30/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.14.0a30"

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/fractal_server/app/models/v2/history.py

@@ -27,6 +27,7 @@ class HistoryRun(SQLModel, table=True):
         default=None,
         ondelete="SET NULL",
     )
+    job_id: int = Field(foreign_key="jobv2.id")
 
     workflowtask_dump: dict[str, Any] = Field(
         sa_column=Column(JSONB, nullable=False),

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/fractal_server/app/routes/api/v2/verify_image_types.py

@@ -10,6 +10,7 @@ from fractal_server.app.db import AsyncSession
 from fractal_server.app.db import get_async_db
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.auth import current_active_user
+from fractal_server.images.tools import aggregate_types
 from fractal_server.images.tools import filter_image_list
 
 router = APIRouter()
@@ -42,12 +43,8 @@ async def verify_unique_types(
             type_filters=query.type_filters,
         )
 
-    # NOTE: see issue 2486
-    available_types = set(
-        _type for _img in filtered_images for _type in _img["types"].keys()
-    )
-
     # Get actual values for each available type
+    available_types = aggregate_types(filtered_images)
     values_per_type: dict[str, set] = {
         _type: set() for _type in available_types
     }

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/fractal_server/app/runner/v2/_local.py

@@ -15,6 +15,7 @@ def process_workflow(
     workflow: WorkflowV2,
     dataset: DatasetV2,
     workflow_dir_local: Path,
+    job_id: int,
     workflow_dir_remote: Optional[Path] = None,
     first_task_index: Optional[int] = None,
     last_task_index: Optional[int] = None,
@@ -75,6 +76,7 @@ def process_workflow(
                 first_task_index : (last_task_index + 1)
             ],
             dataset=dataset,
+            job_id=job_id,
             runner=runner,
             workflow_dir_local=workflow_dir_local,
             workflow_dir_remote=workflow_dir_local,

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/fractal_server/app/runner/v2/_slurm_ssh.py

@@ -38,6 +38,7 @@ def process_workflow(
     workflow: WorkflowV2,
     dataset: DatasetV2,
     workflow_dir_local: Path,
+    job_id: int,
     workflow_dir_remote: Optional[Path] = None,
     first_task_index: Optional[int] = None,
     last_task_index: Optional[int] = None,
@@ -87,6 +88,7 @@ def process_workflow(
                 first_task_index : (last_task_index + 1)
             ],
             dataset=dataset,
+            job_id=job_id,
             runner=runner,
             workflow_dir_local=workflow_dir_local,
             workflow_dir_remote=workflow_dir_remote,

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/fractal_server/app/runner/v2/_slurm_sudo.py

@@ -33,6 +33,7 @@ def process_workflow(
     workflow: WorkflowV2,
     dataset: DatasetV2,
     workflow_dir_local: Path,
+    job_id: int,
     workflow_dir_remote: Optional[Path] = None,
     first_task_index: Optional[int] = None,
     last_task_index: Optional[int] = None,
@@ -79,6 +80,7 @@ def process_workflow(
                 first_task_index : (last_task_index + 1)
             ],
             dataset=dataset,
+            job_id=job_id,
             runner=runner,
             workflow_dir_local=workflow_dir_local,
             workflow_dir_remote=workflow_dir_remote,

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/fractal_server/app/runner/v2/db_tools.py

@@ -8,9 +8,13 @@ from fractal_server.app.models.v2 import HistoryImageCache
 from fractal_server.app.models.v2 import HistoryRun
 from fractal_server.app.models.v2 import HistoryUnit
 from fractal_server.app.schemas.v2 import HistoryUnitStatus
+from fractal_server.logger import set_logger
+
 
 _CHUNK_SIZE = 2_000
 
+logger = set_logger(__name__)
+
 
 def update_status_of_history_run(
     *,
@@ -46,7 +50,12 @@ def bulk_update_status_of_history_unit(
     status: HistoryUnitStatus,
     db_sync: Session,
 ) -> None:
-    for ind in range(0, len(history_unit_ids), _CHUNK_SIZE):
+
+    len_history_unit_ids = len(history_unit_ids)
+    logger.debug(
+        f"[bulk_update_status_of_history_unit] {len_history_unit_ids=}."
+    )
+    for ind in range(0, len_history_unit_ids, _CHUNK_SIZE):
         db_sync.execute(
             update(HistoryUnit)
             .where(
@@ -85,10 +94,14 @@ def bulk_upsert_image_cache_fast(
             List of dictionaries for objects to be upsert-ed.
         db: A sync database session
     """
-    if len(list_upsert_objects) == 0:
+    len_list_upsert_objects = len(list_upsert_objects)
+
+    logger.debug(f"[bulk_upsert_image_cache_fast] {len_list_upsert_objects=}.")
+
+    if len_list_upsert_objects == 0:
         return None
 
-    for ind in range(0, len(list_upsert_objects), _CHUNK_SIZE):
+    for ind in range(0, len_list_upsert_objects, _CHUNK_SIZE):
         stmt = pg_insert(HistoryImageCache).values(
             list_upsert_objects[ind : ind + _CHUNK_SIZE]
         )

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/fractal_server/app/runner/v2/runner.py

@@ -42,6 +42,7 @@ def execute_tasks_v2(
     runner: BaseRunner,
     user_id: int,
     workflow_dir_local: Path,
+    job_id: int,
     workflow_dir_remote: Optional[Path] = None,
     logger_name: Optional[str] = None,
     get_runner_config: Callable[
@@ -119,6 +120,7 @@ def execute_tasks_v2(
             history_run = HistoryRun(
                 dataset_id=dataset.id,
                 workflowtask_id=wftask.id,
+                job_id=job_id,
                 workflowtask_dump=workflowtask_dump,
                 task_group_dump=task_group_dump,
                 num_available_images=num_available_images,
@@ -128,6 +130,10 @@ def execute_tasks_v2(
             db.commit()
             db.refresh(history_run)
             history_run_id = history_run.id
+            logger.debug(
+                "[execute_tasks_v2] Created `HistoryRun` with "
+                f"{history_run_id=}."
+            )
 
         # TASK EXECUTION (V2)
         if task.type in ["non_parallel", "converter_non_parallel"]:

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/fractal_server/app/runner/v2/runner_functions.py

@@ -187,6 +187,10 @@ def run_v2_task_non_parallel(
         db.add(history_unit)
         db.commit()
         db.refresh(history_unit)
+        logger.debug(
+            "[run_v2_task_non_parallel] Created `HistoryUnit` with "
+            f"{history_run_id=}."
+        )
         history_unit_id = history_unit.id
         bulk_upsert_image_cache_fast(
             db=db,
@@ -301,6 +305,10 @@ def run_v2_task_parallel(
     with next(get_sync_db()) as db:
         db.add_all(history_units)
         db.commit()
+        logger.debug(
+            f"[run_v2_task_non_parallel] Created {len(history_units)} "
+            "`HistoryUnit`s."
+        )
 
         for history_unit in history_units:
             db.refresh(history_unit)
@@ -419,6 +427,10 @@ def run_v2_task_compound(
         db.commit()
         db.refresh(history_unit)
         init_history_unit_id = history_unit.id
+        logger.debug(
+            "[run_v2_task_compound] Created `HistoryUnit` with "
+            f"{init_history_unit_id=}."
+        )
         # Create one `HistoryImageCache` for each input image
         bulk_upsert_image_cache_fast(
             db=db,
@@ -468,14 +480,6 @@ def run_v2_task_compound(
 
     num_tasks = 1 + len(parallelization_list)
 
-    # Mark the init-task `HistoryUnit` as "done"
-    with next(get_sync_db()) as db:
-        update_status_of_history_unit(
-            history_unit_id=init_history_unit_id,
-            status=HistoryUnitStatus.DONE,
-            db_sync=db,
-        )
-
     # 3/B: parallel part of a compound task
     _check_parallelization_list_size(parallelization_list)
 
@@ -536,6 +540,10 @@ def run_v2_task_compound(
         db.commit()
         for history_unit in history_units:
             db.refresh(history_unit)
+        logger.debug(
+            f"[run_v2_task_compound] Created {len(history_units)} "
+            "`HistoryUnit`s."
+        )
         history_unit_ids = [history_unit.id for history_unit in history_units]
 
     results, exceptions = runner.multisubmit(
@@ -585,7 +593,7 @@ def run_v2_task_compound(
         else:
             bulk_update_status_of_history_unit(
                 history_unit_ids=history_unit_ids,
-                status=HistoryUnitStatus.DONE,
+                status=HistoryUnitStatus.DONE + [init_history_unit_id],
                 db_sync=db,
             )
 

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/fractal_server/app/runner/v2/submit_workflow.py

@@ -282,6 +282,7 @@ def submit_workflow(
         process_workflow(
             workflow=workflow,
             dataset=dataset,
+            job_id=job_id,
             user_id=user_id,
             workflow_dir_local=WORKFLOW_DIR_LOCAL,
             workflow_dir_remote=WORKFLOW_DIR_REMOTE,

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/fractal_server/app/schemas/v2/history.py

@@ -45,6 +45,7 @@ class HistoryRunRead(BaseModel):
     id: int
     dataset_id: int
     workflowtask_id: Optional[int] = None
+    job_id: int
     workflowtask_dump: dict[str, Any]
     task_group_dump: dict[str, Any]
     timestamp_started: AwareDatetime

fractal_server-2.14.0a30/fractal_server/migrations/versions/c90a7c76e996_job_id_in_history_run.py

@@ -0,0 +1,41 @@
+"""job id in history run
+
+Revision ID: c90a7c76e996
+Revises: f37aceb45062
+Create Date: 2025-04-16 10:44:30.219309
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "c90a7c76e996"
+down_revision = "f37aceb45062"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("historyrun", schema=None) as batch_op:
+        batch_op.add_column(sa.Column("job_id", sa.Integer(), nullable=False))
+        batch_op.create_foreign_key(
+            batch_op.f("fk_historyrun_job_id_jobv2"),
+            "jobv2",
+            ["job_id"],
+            ["id"],
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("historyrun", schema=None) as batch_op:
+        batch_op.drop_constraint(
+            batch_op.f("fk_historyrun_job_id_jobv2"), type_="foreignkey"
+        )
+        batch_op.drop_column("job_id")
+
+    # ### end Alembic commands ###

{fractal_server-2.14.0a28 → fractal_server-2.14.0a30}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.14.0a28"
+version = "2.14.0a30"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -95,7 +95,7 @@ filterwarnings = [
 markers = ["container", "ssh"]
 
 [tool.bumpver]
-current_version = "2.14.0a28"
+current_version = "2.14.0a30"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.14.0a28/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.14.0a28"