fractal-server 2.0.0a10__tar.gz → 2.0.0a11__tar.gz

{fractal_server-2.0.0a10 → fractal_server-2.0.0a11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.0.0a10
+Version: 2.0.0a11
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

fractal_server-2.0.0a11/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.0.0a11"

{fractal_server-2.0.0a10 → fractal_server-2.0.0a11}/fractal_server/app/models/__init__.py

@@ -2,6 +2,5 @@
 `models` module
 """
 from .security import *  # noqa: F401, F403
-from .state import State  # noqa: F401
 from .v1 import *  # noqa: F401, F403
 from .v2 import *  # noqa: F401, F403

{fractal_server-2.0.0a10 → fractal_server-2.0.0a11}/fractal_server/app/models/v1/__init__.py

@@ -6,6 +6,7 @@ from .dataset import Resource  # noqa: F401
 from .job import ApplyWorkflow  # noqa: F403, F401
 from .job import JobStatusTypeV1  # noqa: F401, F403
 from .project import Project  # noqa: F403, F401
+from .state import State  # noqa: F403, F401
 from .task import Task  # noqa: F403, F401
 from .workflow import Workflow  # noqa: F401, F403
 from .workflow import WorkflowTask  # noqa: F401, F403

{fractal_server-2.0.0a10/fractal_server/app/models → fractal_server-2.0.0a11/fractal_server/app/models/v1}/state.py

@@ -8,8 +8,8 @@ from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import SQLModel
 
-from ...utils import get_timestamp
-from ..schemas.v1 import _StateBase
+from ....utils import get_timestamp
+from ...schemas.v1 import _StateBase
 
 
 class State(_StateBase, SQLModel, table=True):

{fractal_server-2.0.0a10 → fractal_server-2.0.0a11}/fractal_server/app/models/v2/__init__.py

@@ -2,6 +2,7 @@
 v2 `models` module
 """
 from ..linkuserproject import LinkUserProjectV2
+from .collection_state import CollectionStateV2
 from .dataset import DatasetV2
 from .job import JobV2
 from .project import ProjectV2
@@ -14,6 +15,7 @@ __all__ = [
     "DatasetV2",
     "JobV2",
     "ProjectV2",
+    "CollectionStateV2",
     "TaskV2",
     "WorkflowTaskV2",
     "WorkflowV2",

fractal_server-2.0.0a11/fractal_server/app/models/v2/collection_state.py

@@ -0,0 +1,21 @@
+from datetime import datetime
+from typing import Any
+from typing import Optional
+
+from sqlalchemy import Column
+from sqlalchemy.types import DateTime
+from sqlalchemy.types import JSON
+from sqlmodel import Field
+from sqlmodel import SQLModel
+
+from ....utils import get_timestamp
+
+
+class CollectionStateV2(SQLModel, table=True):
+
+    id: Optional[int] = Field(default=None, primary_key=True)
+    data: dict[str, Any] = Field(sa_column=Column(JSON), default={})
+    timestamp: datetime = Field(
+        default_factory=get_timestamp,
+        sa_column=Column(DateTime(timezone=True)),
+    )

{fractal_server-2.0.0a10 → fractal_server-2.0.0a11}/fractal_server/app/models/v2/job.py

@@ -9,7 +9,7 @@ from sqlmodel import Field
 from sqlmodel import SQLModel
 
 from ....utils import get_timestamp
-from ...schemas.v1 import JobStatusTypeV1
+from ...schemas.v2 import JobStatusTypeV2
 
 
 class JobV2(SQLModel, table=True):
@@ -47,5 +47,5 @@ class JobV2(SQLModel, table=True):
     end_timestamp: Optional[datetime] = Field(
         default=None, sa_column=Column(DateTime(timezone=True))
     )
-    status: str = JobStatusTypeV1.SUBMITTED
+    status: str = JobStatusTypeV2.SUBMITTED
     log: Optional[str] = None

{fractal_server-2.0.0a10 → fractal_server-2.0.0a11}/fractal_server/app/routes/admin/v2.py

@@ -20,13 +20,13 @@ from ....syringe import Inject
 from ....utils import get_timestamp
 from ...db import AsyncSession
 from ...db import get_async_db
-from ...models import JobStatusTypeV1
 from ...models.security import UserOAuth as User
 from ...models.v1 import Task
 from ...models.v2 import JobV2
 from ...models.v2 import ProjectV2
 from ...runner.filenames import WORKFLOW_LOG_FILENAME
 from ...schemas.v2 import JobReadV2
+from ...schemas.v2 import JobStatusTypeV2
 from ...schemas.v2 import JobUpdateV2
 from ...schemas.v2 import ProjectReadV2
 from ...security import current_active_superuser
@@ -90,7 +90,7 @@ async def view_job(
     project_id: Optional[int] = None,
     dataset_id: Optional[int] = None,
     workflow_id: Optional[int] = None,
-    status: Optional[JobStatusTypeV1] = None,
+    status: Optional[JobStatusTypeV2] = None,
     start_timestamp_min: Optional[datetime] = None,
     start_timestamp_max: Optional[datetime] = None,
     end_timestamp_min: Optional[datetime] = None,
@@ -175,7 +175,7 @@ async def view_single_job(
         )
     await db.close()
 
-    if show_tmp_logs and (job.status == JobStatusTypeV1.SUBMITTED):
+    if show_tmp_logs and (job.status == JobStatusTypeV2.SUBMITTED):
         try:
             with open(f"{job.working_dir}/{WORKFLOW_LOG_FILENAME}", "r") as f:
                 job.log = f.read()
@@ -208,7 +208,7 @@ async def update_job(
             detail=f"Job {job_id} not found",
         )
 
-    if job_update.status != JobStatusTypeV1.FAILED:
+    if job_update.status != JobStatusTypeV2.FAILED:
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
             detail=f"Cannot set job status to {job_update.status}",

{fractal_server-2.0.0a10 → fractal_server-2.0.0a11}/fractal_server/app/routes/api/v2/_aux_functions.py

@@ -21,7 +21,7 @@ from ....models.v2 import ProjectV2
 from ....models.v2 import TaskV2
 from ....models.v2 import WorkflowTaskV2
 from ....models.v2 import WorkflowV2
-from ....schemas.v1 import JobStatusTypeV1
+from ....schemas.v2 import JobStatusTypeV2
 from ....security import User
 from fractal_server.images import Filters
 
@@ -384,7 +384,7 @@ def _get_submitted_jobs_statement() -> SelectOfScalar:
         A sqlmodel statement that selects all `Job`s with
         `Job.status` equal to `submitted`.
     """
-    stm = select(JobV2).where(JobV2.status == JobStatusTypeV1.SUBMITTED)
+    stm = select(JobV2).where(JobV2.status == JobStatusTypeV2.SUBMITTED)
     return stm
 
 

{fractal_server-2.0.0a10 → fractal_server-2.0.0a11}/fractal_server/app/routes/api/v2/task_collection.py

@@ -17,7 +17,7 @@ from .....logger import set_logger
 from .....syringe import Inject
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models import State
+from ....models import CollectionStateV2
 from ....models.v2 import TaskV2
 from ....schemas import StateRead
 from ....schemas.v2 import TaskCollectPipV2
@@ -151,7 +151,7 @@ async def collect_tasks_pip(
                 ),
             )
         task_collect_status.info = "Already installed"
-        state = State(data=task_collect_status.sanitised_dict())
+        state = CollectionStateV2(data=task_collect_status.sanitised_dict())
         response.status_code == status.HTTP_200_OK
         await db.close()
         return state
@@ -181,7 +181,7 @@ async def collect_tasks_pip(
     # Create State object (after casting venv_path to string)
     collection_status_dict = collection_status.dict()
     collection_status_dict["venv_path"] = str(collection_status.venv_path)
-    state = State(data=collection_status_dict)
+    state = CollectionStateV2(data=collection_status_dict)
     db.add(state)
     await db.commit()
     await db.refresh(state)
@@ -220,7 +220,7 @@ async def check_collection_status(
     """
     logger = set_logger(logger_name="check_collection_status")
     logger.debug(f"Querying state for state.id={state_id}")
-    state = await db.get(State, state_id)
+    state = await db.get(CollectionStateV2, state_id)
     if not state:
         await db.close()
         raise HTTPException(

{fractal_server-2.0.0a10 → fractal_server-2.0.0a11}/fractal_server/app/routes/api/v2/workflowtask.py

@@ -46,6 +46,11 @@ async def create_workflowtask(
 
     if new_task.is_legacy_task is True:
         task = await db.get(Task, task_id)
+        if not task:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"Task {task_id} not found.",
+            )
         if not task.is_v2_compatible:
             raise HTTPException(
                 status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
@@ -53,16 +58,11 @@ async def create_workflowtask(
             )
     else:
         task = await db.get(TaskV2, task_id)
-
-    if not task:
-        if new_task.is_legacy_task:
-            error = f"Task {task_id} not found."
-        else:
-            error = f"TaskV2 {task_id} not found."
-
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail=error
-        )
+        if not task:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"TaskV2 {task_id} not found.",
+            )
 
     if new_task.is_legacy_task is True or task.type == "parallel":
         if (

fractal_server-2.0.0a10/fractal_server/migrations/versions/80e12e1bc4fd_v2.py → fractal_server-2.0.0a11/fractal_server/migrations/versions/5bf02391cfef_v2.py

@@ -1,8 +1,8 @@
-"""V2
+"""v2
 
-Revision ID: 80e12e1bc4fd
+Revision ID: 5bf02391cfef
 Revises: 9fd26a2b0de4
-Create Date: 2024-04-12 10:13:58.085788
+Create Date: 2024-04-18 10:35:19.067833
 
 """
 import sqlalchemy as sa
@@ -11,7 +11,7 @@ from alembic import op
 
 
 # revision identifiers, used by Alembic.
-revision = "80e12e1bc4fd"
+revision = "5bf02391cfef"
 down_revision = "9fd26a2b0de4"
 branch_labels = None
 depends_on = None
@@ -19,6 +19,13 @@ depends_on = None
 
 def upgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "collectionstatev2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("data", sa.JSON(), nullable=True),
+        sa.Column("timestamp", sa.DateTime(timezone=True), nullable=True),
+        sa.PrimaryKeyConstraint("id"),
+    )
     op.create_table(
         "projectv2",
         sa.Column("id", sa.Integer(), nullable=False),
@@ -234,4 +241,5 @@ def downgrade() -> None:
     op.drop_table("datasetv2")
     op.drop_table("taskv2")
     op.drop_table("projectv2")
+    op.drop_table("collectionstatev2")
     # ### end Alembic commands ###

{fractal_server-2.0.0a10 → fractal_server-2.0.0a11}/fractal_server/tasks/v2/background_operations.py

@@ -15,7 +15,7 @@ from ..utils import slugify_task_name
 from ._TaskCollectPip import _TaskCollectPip
 from fractal_server.app.db import DBSyncSession
 from fractal_server.app.db import get_sync_db
-from fractal_server.app.models import State
+from fractal_server.app.models.v2 import CollectionStateV2
 from fractal_server.app.models.v2 import TaskV2
 from fractal_server.app.schemas.v2 import TaskCollectStatusV2
 from fractal_server.app.schemas.v2 import TaskCreateV2
@@ -313,7 +313,7 @@ async def background_collect_pip(
         logger.debug(f"{key}: {value}")
 
     with next(get_sync_db()) as db:
-        state: State = db.get(State, state_id)
+        state: CollectionStateV2 = db.get(CollectionStateV2, state_id)
         data = TaskCollectStatusV2(**state.data)
         data.info = None
 

{fractal_server-2.0.0a10 → fractal_server-2.0.0a11}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.0.0a10"
+version = "2.0.0a11"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Jacopo Nespolo <jacopo.nespolo@exact-lab.it>",
@@ -86,7 +86,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.0.0a10"
+current_version = "2.0.0a11"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.0.0a10/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.0.0a10"