fractal-server 2.17.2__py3-none-any.whl → 2.18.0__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.17.2"
+__VERSION__ = "2.18.0"

fractal_server/__main__.py

@@ -167,7 +167,8 @@ def init_db_data(
             "`--admin-pwd` and `--admin-project-dir`. Exit."
         )
         sys.exit(1)
-    if admin_password and admin_email:
+
+    if admin_email:
         asyncio.run(
             _create_first_user(
                 email=admin_email,

fractal_server/app/models/linkuserproject.py

@@ -1,5 +1,11 @@
+from sqlmodel import BOOLEAN
+from sqlmodel import CheckConstraint
+from sqlmodel import Column
 from sqlmodel import Field
+from sqlmodel import Index
 from sqlmodel import SQLModel
+from sqlmodel import String
+from sqlmodel import column
 
 
 class LinkUserProjectV2(SQLModel, table=True):
@@ -11,3 +17,37 @@ class LinkUserProjectV2(SQLModel, table=True):
         foreign_key="projectv2.id", primary_key=True, ondelete="CASCADE"
     )
     user_id: int = Field(foreign_key="user_oauth.id", primary_key=True)
+
+    # TODO-2.18.1 drop server_default
+    is_owner: bool = Field(
+        sa_column=Column(BOOLEAN, server_default="true", nullable=False)
+    )
+    # TODO-2.18.1 drop server_default
+    is_verified: bool = Field(
+        sa_column=Column(BOOLEAN, server_default="true", nullable=False)
+    )
+    # TODO-2.18.1 drop server_default
+    permissions: str = Field(
+        sa_column=Column(String, server_default="'rwx'", nullable=False)
+    )
+
+    __table_args__ = (
+        Index(
+            "ix_linkuserprojectv2_one_owner_per_project",
+            "project_id",
+            unique=True,
+            postgresql_where=column("is_owner").is_(True),
+        ),
+        CheckConstraint(
+            "NOT (is_owner AND NOT is_verified)",
+            name="owner_is_verified",
+        ),
+        CheckConstraint(
+            "NOT (is_owner AND permissions <> 'rwx')",
+            name="owner_full_permissions",
+        ),
+        CheckConstraint(
+            "permissions IN ('r', 'rw', 'rwx')",
+            name="valid_permissions",
+        ),
+    )

fractal_server/app/models/security.py

@@ -6,7 +6,6 @@ from pydantic import EmailStr
 from sqlalchemy import Column
 from sqlalchemy import String
 from sqlalchemy.dialects.postgresql import ARRAY
-from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
 from sqlmodel import Field
 from sqlmodel import Relationship
@@ -113,7 +112,13 @@ class UserOAuth(SQLModel, table=True):
         ondelete="RESTRICT",
     )
 
-    project_dir: str
+    # TODO-2.18.1: drop `project_dir`
+    project_dir: str | None = Field(default=None, nullable=True)
+    # TODO-2.18.1: `project_dirs: list[str] = Field(min_length=1)`
+    project_dirs: list[str] = Field(
+        sa_column=Column(ARRAY(String), nullable=False, server_default="{}"),
+    )
+
     slurm_accounts: list[str] = Field(
         sa_column=Column(ARRAY(String), server_default="{}"),
     )
@@ -135,6 +140,3 @@ class UserGroup(SQLModel, table=True):
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),
     )
-    viewer_paths: list[str] = Field(
-        sa_column=Column(JSONB, server_default="[]", nullable=False)
-    )

fractal_server/app/models/v2/job.py

@@ -6,9 +6,11 @@ from sqlalchemy import Column
 from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
 from sqlmodel import Field
+from sqlmodel import Index
 from sqlmodel import SQLModel
+from sqlmodel import text
 
-from fractal_server.app.schemas.v2 import JobStatusTypeV2
+from fractal_server.app.schemas.v2 import JobStatusType
 from fractal_server.utils import get_timestamp
 
 
@@ -56,7 +58,7 @@ class JobV2(SQLModel, table=True):
     end_timestamp: datetime | None = Field(
         default=None, sa_column=Column(DateTime(timezone=True))
     )
-    status: str = JobStatusTypeV2.SUBMITTED
+    status: str = JobStatusType.SUBMITTED
     log: str | None = None
     executor_error_log: str | None = None
 
@@ -66,3 +68,12 @@ class JobV2(SQLModel, table=True):
     type_filters: dict[str, bool] = Field(
         sa_column=Column(JSONB, nullable=False, server_default="{}")
     )
+
+    __table_args__ = (
+        Index(
+            "ix_jobv2_one_submitted_job_per_dataset",
+            "dataset_id",
+            unique=True,
+            postgresql_where=text(f"status = '{JobStatusType.SUBMITTED}'"),
+        ),
+    )

fractal_server/app/models/v2/resource.py

@@ -5,6 +5,7 @@ from typing import Self
 from sqlalchemy import Column
 from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
+from sqlmodel import BOOLEAN
 from sqlmodel import CheckConstraint
 from sqlmodel import Field
 from sqlmodel import SQLModel
@@ -43,6 +44,18 @@ class Resource(SQLModel, table=True):
     Address for ssh connections, when `type="slurm_ssh"`.
     """
 
+    prevent_new_submissions: bool = Field(
+        sa_column=Column(
+            BOOLEAN,
+            server_default="false",
+            nullable=False,
+        ),
+    )
+    """
+    When set to true: Prevent new job submissions and stop execution of
+    ongoing jobs as soon as the current task is complete.
+    """
+
     jobs_local_dir: str
     """
     Base local folder for job subfolders (containing artifacts and logs).

fractal_server/app/routes/admin/v2/__init__.py

@@ -9,19 +9,19 @@ from .impersonate import router as impersonate_router
 from .job import router as job_router
 from .profile import router as profile_router
 from .resource import router as resource_router
+from .sharing import router as sharing_router
 from .task import router as task_router
 from .task_group import router as task_group_router
 from .task_group_lifecycle import router as task_group_lifecycle_router
 
-router_admin_v2 = APIRouter()
+router_admin = APIRouter()
 
-router_admin_v2.include_router(accounting_router, prefix="/accounting")
-router_admin_v2.include_router(job_router, prefix="/job")
-router_admin_v2.include_router(task_router, prefix="/task")
-router_admin_v2.include_router(task_group_router, prefix="/task-group")
-router_admin_v2.include_router(
-    task_group_lifecycle_router, prefix="/task-group"
-)
-router_admin_v2.include_router(impersonate_router, prefix="/impersonate")
-router_admin_v2.include_router(resource_router, prefix="/resource")
-router_admin_v2.include_router(profile_router, prefix="/profile")
+router_admin.include_router(accounting_router, prefix="/accounting")
+router_admin.include_router(job_router, prefix="/job")
+router_admin.include_router(task_router, prefix="/task")
+router_admin.include_router(task_group_router, prefix="/task-group")
+router_admin.include_router(task_group_lifecycle_router, prefix="/task-group")
+router_admin.include_router(impersonate_router, prefix="/impersonate")
+router_admin.include_router(resource_router, prefix="/resource")
+router_admin.include_router(profile_router, prefix="/profile")
+router_admin.include_router(sharing_router, prefix="/linkuserproject")

fractal_server/app/routes/admin/v2/accounting.py

@@ -67,11 +67,11 @@ async def query_accounting(
     res = await db.execute(stm)
     records = res.scalars().all()
 
-    return PaginationResponse[AccountingRecordRead](
+    return dict(
         total_count=total_count,
         page_size=page_size,
         current_page=page,
-        items=[record.model_dump() for record in records],
+        items=records,
     )
 
 

fractal_server/app/routes/admin/v2/job.py

@@ -24,9 +24,9 @@ from fractal_server.app.routes.pagination import PaginationRequest
 from fractal_server.app.routes.pagination import PaginationResponse
 from fractal_server.app.routes.pagination import get_pagination_params
 from fractal_server.app.schemas.v2 import HistoryUnitStatus
-from fractal_server.app.schemas.v2 import JobReadV2
-from fractal_server.app.schemas.v2 import JobStatusTypeV2
-from fractal_server.app.schemas.v2 import JobUpdateV2
+from fractal_server.app.schemas.v2 import JobRead
+from fractal_server.app.schemas.v2 import JobStatusType
+from fractal_server.app.schemas.v2 import JobUpdate
 from fractal_server.runner.filenames import WORKFLOW_LOG_FILENAME
 from fractal_server.utils import get_timestamp
 from fractal_server.zip_tools import _zip_folder_to_byte_stream_iterator
@@ -34,14 +34,14 @@ from fractal_server.zip_tools import _zip_folder_to_byte_stream_iterator
 router = APIRouter()
 
 
-@router.get("/", response_model=PaginationResponse[JobReadV2])
+@router.get("/", response_model=PaginationResponse[JobRead])
 async def view_job(
     id: int | None = None,
     user_id: int | None = None,
     project_id: int | None = None,
     dataset_id: int | None = None,
     workflow_id: int | None = None,
-    status: JobStatusTypeV2 | None = None,
+    status: JobStatusType | None = None,
     start_timestamp_min: AwareDatetime | None = None,
     start_timestamp_max: AwareDatetime | None = None,
     end_timestamp_min: AwareDatetime | None = None,
@@ -50,12 +50,13 @@ async def view_job(
     pagination: PaginationRequest = Depends(get_pagination_params),
     user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
-) -> PaginationResponse[JobReadV2]:
+) -> PaginationResponse[JobRead]:
     """
     Query `JobV2` table.
 
     Args:
         id: If not `None`, select a given `applyworkflow.id`.
+        user_id:
         project_id: If not `None`, select a given `applyworkflow.project_id`.
         dataset_id: If not `None`, select a given
             `applyworkflow.input_dataset_id`.
@@ -84,12 +85,22 @@ async def view_job(
         stm = stm.where(JobV2.id == id)
         stm_count = stm_count.where(JobV2.id == id)
     if user_id is not None:
-        stm = stm.join(
-            LinkUserProjectV2, LinkUserProjectV2.project_id == JobV2.project_id
-        ).where(LinkUserProjectV2.user_id == user_id)
-        stm_count = stm_count.join(
-            LinkUserProjectV2, LinkUserProjectV2.project_id == JobV2.project_id
-        ).where(LinkUserProjectV2.user_id == user_id)
+        stm = (
+            stm.join(
+                LinkUserProjectV2,
+                LinkUserProjectV2.project_id == JobV2.project_id,
+            )
+            .where(LinkUserProjectV2.user_id == user_id)
+            .where(LinkUserProjectV2.is_owner.is_(True))
+        )
+        stm_count = (
+            stm_count.join(
+                LinkUserProjectV2,
+                LinkUserProjectV2.project_id == JobV2.project_id,
+            )
+            .where(LinkUserProjectV2.user_id == user_id)
+            .where(LinkUserProjectV2.is_owner.is_(True))
+        )
     if project_id is not None:
         stm = stm.where(JobV2.project_id == project_id)
         stm_count = stm_count.where(JobV2.project_id == project_id)
@@ -135,21 +146,21 @@ async def view_job(
         for job in job_list:
             setattr(job, "log", None)
 
-    return PaginationResponse[JobReadV2](
+    return dict(
         total_count=total_count,
         page_size=page_size,
         current_page=page,
-        items=[job.model_dump() for job in job_list],
+        items=job_list,
     )
 
 
-@router.get("/{job_id}/", response_model=JobReadV2)
+@router.get("/{job_id}/", response_model=JobRead)
 async def view_single_job(
     job_id: int,
     show_tmp_logs: bool = False,
     user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
-) -> JobReadV2:
+) -> JobRead:
     job = await db.get(JobV2, job_id)
     if not job:
         raise HTTPException(
@@ -158,7 +169,7 @@ async def view_single_job(
         )
     await db.close()
 
-    if show_tmp_logs and (job.status == JobStatusTypeV2.SUBMITTED):
+    if show_tmp_logs and (job.status == JobStatusType.SUBMITTED):
         try:
             with open(f"{job.working_dir}/{WORKFLOW_LOG_FILENAME}") as f:
                 job.log = f.read()
@@ -168,13 +179,13 @@ async def view_single_job(
     return job
 
 
-@router.patch("/{job_id}/", response_model=JobReadV2)
+@router.patch("/{job_id}/", response_model=JobRead)
 async def update_job(
-    job_update: JobUpdateV2,
+    job_update: JobUpdate,
     job_id: int,
     user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
-) -> JobReadV2 | None:
+) -> JobRead | None:
     """
     Change the status of an existing job.
 
@@ -187,13 +198,13 @@ async def update_job(
             status_code=status.HTTP_404_NOT_FOUND,
             detail=f"Job {job_id} not found",
         )
-    if job.status != JobStatusTypeV2.SUBMITTED:
+    if job.status != JobStatusType.SUBMITTED:
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
             detail=f"Job {job_id} has status {job.status=} != 'submitted'.",
         )
 
-    if job_update.status != JobStatusTypeV2.FAILED:
+    if job_update.status != JobStatusType.FAILED:
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
             detail=f"Cannot set job status to {job_update.status}",
@@ -206,7 +217,7 @@ async def update_job(
         job,
         "log",
         f"{job.log or ''}\nThis job was manually marked as "
-        f"'{JobStatusTypeV2.FAILED}' by an admin ({timestamp.isoformat()}).",
+        f"'{JobStatusType.FAILED}' by an admin ({timestamp.isoformat()}).",
     )
 
     res = await db.execute(

fractal_server/app/routes/admin/v2/sharing.py

@@ -0,0 +1,103 @@
+from fastapi import APIRouter
+from fastapi import Depends
+from sqlalchemy import func
+from sqlmodel import select
+
+from fractal_server.app.db import AsyncSession
+from fractal_server.app.db import get_async_db
+from fractal_server.app.models import LinkUserProjectV2
+from fractal_server.app.models import UserOAuth
+from fractal_server.app.models.v2 import ProjectV2
+from fractal_server.app.routes.auth import current_superuser_act
+from fractal_server.app.routes.pagination import PaginationRequest
+from fractal_server.app.routes.pagination import PaginationResponse
+from fractal_server.app.routes.pagination import get_pagination_params
+from fractal_server.app.schemas.v2 import LinkUserProjectRead
+
+router = APIRouter()
+
+
+@router.get("/", response_model=PaginationResponse[LinkUserProjectRead])
+async def view_link_user_project(
+    # User info
+    user_id: int | None = None,
+    # Project info
+    project_id: int | None = None,
+    project_name: str | None = None,
+    # Permissions
+    is_owner: bool | None = None,
+    is_verified: bool | None = None,
+    # -----
+    pagination: PaginationRequest = Depends(get_pagination_params),
+    superuser: UserOAuth = Depends(current_superuser_act),
+    db: AsyncSession = Depends(get_async_db),
+) -> PaginationResponse[LinkUserProjectRead]:
+    page = pagination.page
+    page_size = pagination.page_size
+
+    stm = (
+        select(
+            LinkUserProjectV2,
+            UserOAuth.email,
+            ProjectV2.name,
+        )
+        .join(UserOAuth, UserOAuth.id == LinkUserProjectV2.user_id)
+        .join(ProjectV2, ProjectV2.id == LinkUserProjectV2.project_id)
+        .order_by(UserOAuth.email, ProjectV2.name)
+    )
+    stm_count = (
+        select(func.count())
+        .select_from(LinkUserProjectV2)
+        .join(UserOAuth, UserOAuth.id == LinkUserProjectV2.user_id)
+        .join(ProjectV2, ProjectV2.id == LinkUserProjectV2.project_id)
+    )
+
+    if project_id is not None:
+        stm = stm.where(LinkUserProjectV2.project_id == project_id)
+        stm_count = stm_count.where(LinkUserProjectV2.project_id == project_id)
+    if project_name is not None:
+        stm = stm.where(ProjectV2.name.icontains(project_name))
+        stm_count = stm_count.where(ProjectV2.name.icontains(project_name))
+    if user_id is not None:
+        stm = stm.where(LinkUserProjectV2.user_id == user_id)
+        stm_count = stm_count.where(LinkUserProjectV2.user_id == user_id)
+    if is_owner is not None:
+        stm = stm.where(LinkUserProjectV2.is_owner == is_owner)
+        stm_count = stm_count.where(LinkUserProjectV2.is_owner == is_owner)
+    if is_verified is not None:
+        stm = stm.where(LinkUserProjectV2.is_verified == is_verified)
+        stm_count = stm_count.where(
+            LinkUserProjectV2.is_verified == is_verified
+        )
+
+    res_total_count = await db.execute(stm_count)
+
+    total_count = res_total_count.scalar()
+    if page_size is None:
+        page_size = total_count
+    else:
+        stm = stm.offset((page - 1) * page_size).limit(page_size)
+
+    res = await db.execute(stm)
+    items = res.all()
+
+    return PaginationResponse[LinkUserProjectRead](
+        total_count=total_count,
+        page_size=page_size,
+        current_page=page,
+        items=[
+            dict(
+                # User info
+                user_id=linkuserproject.user_id,
+                user_email=user_email,
+                # Project info
+                project_id=linkuserproject.project_id,
+                project_name=project_name,
+                # Permissions
+                is_verified=linkuserproject.is_verified,
+                is_owner=linkuserproject.is_owner,
+                permissions=linkuserproject.permissions,
+            )
+            for linkuserproject, user_email, project_name in items
+        ],
+    )

fractal_server/app/routes/admin/v2/task.py

@@ -23,7 +23,7 @@ from fractal_server.app.schemas.v2.task import TaskType
 router = APIRouter()
 
 
-class TaskV2Minimal(BaseModel):
+class TaskMinimal(BaseModel):
     id: int
     name: str
     type: str
@@ -39,7 +39,7 @@ class ProjectUser(BaseModel):
     email: EmailStr
 
 
-class TaskV2Relationship(BaseModel):
+class TaskRelationship(BaseModel):
     workflow_id: int
     workflow_name: str
     project_id: int
@@ -47,12 +47,12 @@ class TaskV2Relationship(BaseModel):
     project_users: list[ProjectUser] = Field(default_factory=list)
 
 
-class TaskV2Info(BaseModel):
-    task: TaskV2Minimal
-    relationships: list[TaskV2Relationship]
+class TaskInfo(BaseModel):
+    task: TaskMinimal
+    relationships: list[TaskRelationship]
 
 
-@router.get("/", response_model=PaginationResponse[TaskV2Info])
+@router.get("/", response_model=PaginationResponse[TaskInfo])
 async def query_tasks(
     id: int | None = None,
     source: str | None = None,
@@ -66,7 +66,7 @@ async def query_tasks(
     pagination: PaginationRequest = Depends(get_pagination_params),
     user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
-) -> PaginationResponse[TaskV2Info]:
+) -> PaginationResponse[TaskInfo]:
     """
     Query `TaskV2` and get information about related workflows and projects.
     """
@@ -148,6 +148,7 @@ async def query_tasks(
                     LinkUserProjectV2.user_id == UserOAuth.id,
                 )
                 .where(LinkUserProjectV2.project_id == project_id)
+                .where(LinkUserProjectV2.is_owner.is_(True))
             )
             project_users[project_id] = [
                 ProjectUser(id=p_user[0], email=p_user[1])
@@ -169,7 +170,7 @@ async def query_tasks(
                 ],
             )
         )
-    return PaginationResponse[TaskV2Info](
+    return dict(
         total_count=total_count,
         page_size=page_size,
         current_page=page,