fractal-server 2.0.0a5__tar.gz → 2.0.0a8__tar.gz

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.0.0a5
+Version: 2.0.0a8
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

fractal_server-2.0.0a8/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.0.0a8"

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/app/models/v2/dataset.py

@@ -28,7 +28,6 @@ class DatasetV2(SQLModel, table=True):
     history: list[dict[str, Any]] = Field(
         sa_column=Column(JSON, server_default="[]", nullable=False)
     )
-    read_only: bool = False
 
     timestamp_created: datetime = Field(
         default_factory=get_timestamp,

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/app/models/v2/project.py

@@ -16,7 +16,6 @@ class ProjectV2(SQLModel, table=True):
 
     id: Optional[int] = Field(default=None, primary_key=True)
     name: str
-    read_only: bool = False
     timestamp_created: datetime = Field(
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/app/routes/api/v2/dataset.py

@@ -134,6 +134,15 @@ async def update_dataset(
     )
     db_dataset = output["dataset"]
 
+    if (dataset_update.zarr_dir is not None) and (len(db_dataset.images) != 0):
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                "Cannot modify `zarr_dir` because the dataset has a non-empty "
+                "image list."
+            ),
+        )
+
     for key, value in dataset_update.dict(exclude_unset=True).items():
         setattr(db_dataset, key, value)
 

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/app/routes/api/v2/images.py

@@ -17,6 +17,8 @@ from fractal_server.app.security import current_active_user
 from fractal_server.app.security import User
 from fractal_server.images import Filters
 from fractal_server.images import SingleImage
+from fractal_server.images import SingleImageUpdate
+from fractal_server.images.tools import find_image_by_zarr_url
 from fractal_server.images.tools import match_filter
 
 router = APIRouter()
@@ -56,6 +58,15 @@ async def post_new_image(
     )
     dataset = output["dataset"]
 
+    if not new_image.zarr_url.startswith(dataset.zarr_dir):
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                "Cannot create image with zarr_url which is not relative to "
+                f"{dataset.zarr_dir}."
+            ),
+        )
+
     if new_image.zarr_url in dataset.image_zarr_urls:
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
@@ -213,3 +224,48 @@ async def delete_dataset_images(
     await db.commit()
 
     return Response(status_code=status.HTTP_204_NO_CONTENT)
+
+
+@router.patch(
+    "/project/{project_id}/dataset/{dataset_id}/images/",
+    response_model=SingleImage,
+    status_code=status.HTTP_200_OK,
+)
+async def patch_dataset_image(
+    project_id: int,
+    dataset_id: int,
+    image_update: SingleImageUpdate,
+    user: User = Depends(current_active_user),
+    db: AsyncSession = Depends(get_async_db),
+):
+    output = await _get_dataset_check_owner(
+        project_id=project_id,
+        dataset_id=dataset_id,
+        user_id=user.id,
+        db=db,
+    )
+    db_dataset = output["dataset"]
+
+    ret = find_image_by_zarr_url(
+        images=db_dataset.images, zarr_url=image_update.zarr_url
+    )
+    if ret is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=(
+                f"No image with zarr_url '{image_update.zarr_url}' in "
+                f"DatasetV2 {dataset_id}."
+            ),
+        )
+    index = ret["index"]
+
+    for key, value in image_update.dict(
+        exclude_none=True, exclude={"zarr_url"}
+    ).items():
+        db_dataset.images[index][key] = value
+
+    flag_modified(db_dataset, "images")
+
+    await db.commit()
+    await db.close()
+    return db_dataset.images[index]

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/app/routes/api/v2/submit.py

@@ -59,15 +59,6 @@ async def apply_workflow(
     project = output["project"]
     dataset = output["dataset"]
 
-    if dataset.read_only:
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                "Cannot apply workflow because dataset "
-                f"({dataset_id=}) is read_only."
-            ),
-        )
-
     workflow = await _get_workflow_check_owner(
         project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
     )

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/app/runner/v2/task_interface.py

@@ -2,9 +2,11 @@ from typing import Any
 
 from pydantic import BaseModel
 from pydantic import Field
+from pydantic import validator
 
 from ....images import SingleImageTaskOutput
 from fractal_server.images import Filters
+from fractal_server.urls import normalize_url
 
 
 class TaskOutput(BaseModel):
@@ -34,6 +36,10 @@ class TaskOutput(BaseModel):
                 msg = f"{msg}\n{duplicate}"
             raise ValueError(msg)
 
+    @validator("image_list_removals")
+    def normalize_paths(cls, v: list[str]) -> list[str]:
+        return [normalize_url(zarr_url) for zarr_url in v]
+
 
 class InitArgsModel(BaseModel):
     class Config:
@@ -42,6 +48,10 @@ class InitArgsModel(BaseModel):
     zarr_url: str
     init_args: dict[str, Any] = Field(default_factory=dict)
 
+    @validator("zarr_url")
+    def normalize_path(cls, v: str) -> str:
+        return normalize_url(v)
+
 
 class InitTaskOutput(BaseModel):
     class Config:

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/app/schemas/_validators.py

@@ -2,6 +2,7 @@ import os
 from datetime import datetime
 from datetime import timezone
 from typing import Any
+from typing import Optional
 
 
 def valstr(attribute: str, accept_none: bool = False):
@@ -12,7 +13,7 @@ def valstr(attribute: str, accept_none: bool = False):
     If `accept_none`, the validator also accepts `None`.
     """
 
-    def val(string: str):
+    def val(string: Optional[str]) -> Optional[str]:
         if string is None:
             if accept_none:
                 return string
@@ -29,7 +30,7 @@ def valstr(attribute: str, accept_none: bool = False):
 
 
 def valdictkeys(attribute: str):
-    def val(d: dict[str, Any]):
+    def val(d: Optional[dict[str, Any]]) -> Optional[dict[str, Any]]:
         """
         Apply valstr to every key of the dictionary, and fail if there are
         identical keys.
@@ -55,7 +56,7 @@ def valint(attribute: str, min_val: int = 1):
     database entry) is greater or equal to min_val.
     """
 
-    def val(integer: int):
+    def val(integer: Optional[int]) -> Optional[int]:
         if integer is None:
             raise ValueError(f"Integer attribute '{attribute}' cannot be None")
         if integer < min_val:
@@ -73,7 +74,7 @@ def val_absolute_path(attribute: str):
     Check that a string attribute is an absolute path
     """
 
-    def val(string: str):
+    def val(string: Optional[str]) -> str:
         if string is None:
             raise ValueError(f"String attribute '{attribute}' cannot be None")
         s = string.strip()
@@ -90,7 +91,7 @@ def val_absolute_path(attribute: str):
 
 
 def val_unique_list(attribute: str):
-    def val(must_be_unique: list):
+    def val(must_be_unique: Optional[list]) -> Optional[list]:
         if must_be_unique is not None:
             if len(set(must_be_unique)) != len(must_be_unique):
                 raise ValueError(f"`{attribute}` list has repetitions")
@@ -100,7 +101,7 @@ def val_unique_list(attribute: str):
 
 
 def valutc(attribute: str):
-    def val(timestamp: datetime):
+    def val(timestamp: Optional[datetime]) -> Optional[datetime]:
         """
         Replacing `tzinfo` with `timezone.utc` is just required by SQLite data.
         If using Postgres, this function leaves the datetime exactly as it is.

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/app/schemas/v2/dataset.py

@@ -8,10 +8,11 @@ from pydantic import validator
 
 from .._validators import valstr
 from .._validators import valutc
-from ..v1.project import ProjectReadV1
 from .dumps import WorkflowTaskDumpV2
+from .project import ProjectReadV2
 from .workflowtask import WorkflowTaskStatusTypeV2
 from fractal_server.images import Filters
+from fractal_server.urls import normalize_url
 
 
 class _DatasetHistoryItemV2(BaseModel):
@@ -45,12 +46,15 @@ class DatasetCreateV2(BaseModel, extra=Extra.forbid):
 
     name: str
 
-    read_only: bool = False
     zarr_dir: str
 
     filters: Filters = Field(default_factory=Filters)
 
     # Validators
+    @validator("zarr_dir")
+    def normalize_zarr_dir(cls, v: str) -> str:
+        return normalize_url(v)
+
     _name = validator("name", allow_reuse=True)(valstr("name"))
 
 
@@ -60,10 +64,9 @@ class DatasetReadV2(BaseModel):
     name: str
 
     project_id: int
-    project: ProjectReadV1
+    project: ProjectReadV2
 
     history: list[_DatasetHistoryItemV2]
-    read_only: bool
 
     timestamp_created: datetime
 
@@ -81,9 +84,14 @@ class DatasetUpdateV2(BaseModel):
         extra = "forbid"
 
     name: Optional[str]
-    read_only: Optional[bool]
     zarr_dir: Optional[str]
     filters: Optional[Filters]
 
     # Validators
+    @validator("zarr_dir")
+    def normalize_zarr_dir(cls, v: Optional[str]) -> Optional[str]:
+        if v is not None:
+            return normalize_url(v)
+        return v
+
     _name = validator("name", allow_reuse=True)(valstr("name"))

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/app/schemas/v2/dumps.py

@@ -22,7 +22,6 @@ class ProjectDumpV2(BaseModel, extra=Extra.forbid):
 
     id: int
     name: str
-    read_only: bool
     timestamp_created: str
 
 
@@ -80,7 +79,6 @@ class DatasetDumpV2(BaseModel):
     id: int
     name: str
     project_id: int
-    read_only: bool
     timestamp_created: str
 
     zarr_dir: str

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/app/schemas/v2/project.py

@@ -12,7 +12,6 @@ from .._validators import valutc
 class ProjectCreateV2(BaseModel, extra=Extra.forbid):
 
     name: str
-    read_only: bool = False
     # Validators
     _name = validator("name", allow_reuse=True)(valstr("name"))
 
@@ -21,7 +20,6 @@ class ProjectReadV2(BaseModel):
 
     id: int
     name: str
-    read_only: bool
     timestamp_created: datetime
     # Validators
     _timestamp_created = validator("timestamp_created", allow_reuse=True)(
@@ -32,6 +30,5 @@ class ProjectReadV2(BaseModel):
 class ProjectUpdateV2(BaseModel):
 
     name: Optional[str]
-    read_only: Optional[bool]
     # Validators
     _name = validator("name", allow_reuse=True)(valstr("name"))

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/app/schemas/v2/workflow.py

@@ -7,7 +7,7 @@ from pydantic import validator
 
 from .._validators import valstr
 from .._validators import valutc
-from ..v1.project import ProjectReadV1
+from .project import ProjectReadV2
 from .workflowtask import WorkflowTaskExportV2
 from .workflowtask import WorkflowTaskImportV2
 from .workflowtask import WorkflowTaskReadV2
@@ -27,7 +27,7 @@ class WorkflowReadV2(BaseModel):
     name: str
     project_id: int
     task_list: list[WorkflowTaskReadV2]
-    project: ProjectReadV1
+    project: ProjectReadV2
     timestamp_created: datetime
 
     _timestamp_created = validator("timestamp_created", allow_reuse=True)(

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/images/__init__.py

@@ -1,3 +1,4 @@
 from .models import Filters  # noqa: F401
 from .models import SingleImage  # noqa: F401
 from .models import SingleImageTaskOutput  # noqa: F401
+from .models import SingleImageUpdate  # noqa: F401

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/fractal_server/images/models.py

@@ -7,6 +7,7 @@ from pydantic import Field
 from pydantic import validator
 
 from fractal_server.app.schemas._validators import valdictkeys
+from fractal_server.urls import normalize_url
 
 
 class SingleImageBase(BaseModel):
@@ -32,6 +33,15 @@ class SingleImageBase(BaseModel):
     )
     _types = validator("types", allow_reuse=True)(valdictkeys("types"))
 
+    @validator("zarr_url")
+    def normalize_zarr_url(cls, v: str) -> str:
+        return normalize_url(v)
+
+    @validator("origin")
+    def normalize_orig(cls, v: Optional[str]) -> Optional[str]:
+        if v is not None:
+            return normalize_url(v)
+
 
 class SingleImageTaskOutput(SingleImageBase):
     """
@@ -70,6 +80,35 @@ class SingleImage(SingleImageBase):
         return v
 
 
+class SingleImageUpdate(BaseModel):
+    zarr_url: str
+    attributes: Optional[dict[str, Any]]
+    types: Optional[dict[str, bool]]
+
+    @validator("zarr_url")
+    def normalize_zarr_url(cls, v: str) -> str:
+        return normalize_url(v)
+
+    @validator("attributes")
+    def validate_attributes(
+        cls, v: dict[str, Any]
+    ) -> dict[str, Union[int, float, str, bool]]:
+        if v is not None:
+            # validate keys
+            valdictkeys("attributes")(v)
+            # validate values
+            for key, value in v.items():
+                if not isinstance(value, (int, float, str, bool)):
+                    raise ValueError(
+                        f"SingleImageUpdate.attributes[{key}] must be a scalar"
+                        " (int, float, str or bool). "
+                        f"Given {value} ({type(value)})"
+                    )
+        return v
+
+    _types = validator("types", allow_reuse=True)(valdictkeys("types"))
+
+
 class Filters(BaseModel):
     attributes: dict[str, Any] = Field(default_factory=dict)
     types: dict[str, bool] = Field(default_factory=dict)

fractal_server-2.0.0a5/fractal_server/migrations/versions/d71e732236cd_v2.py → fractal_server-2.0.0a8/fractal_server/migrations/versions/80e12e1bc4fd_v2.py

@@ -1,8 +1,8 @@
-"""v2
+"""V2
 
-Revision ID: d71e732236cd
+Revision ID: 80e12e1bc4fd
 Revises: 9fd26a2b0de4
-Create Date: 2024-04-05 11:09:17.639183
+Create Date: 2024-04-12 10:13:58.085788
 
 """
 import sqlalchemy as sa
@@ -11,7 +11,7 @@ from alembic import op
 
 
 # revision identifiers, used by Alembic.
-revision = "d71e732236cd"
+revision = "80e12e1bc4fd"
 down_revision = "9fd26a2b0de4"
 branch_labels = None
 depends_on = None
@@ -23,7 +23,6 @@ def upgrade() -> None:
         "projectv2",
         sa.Column("id", sa.Integer(), nullable=False),
         sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
-        sa.Column("read_only", sa.Boolean(), nullable=False),
         sa.Column(
             "timestamp_created", sa.DateTime(timezone=True), nullable=False
         ),
@@ -81,7 +80,6 @@ def upgrade() -> None:
         sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
         sa.Column("project_id", sa.Integer(), nullable=False),
         sa.Column("history", sa.JSON(), server_default="[]", nullable=False),
-        sa.Column("read_only", sa.Boolean(), nullable=False),
         sa.Column(
             "timestamp_created", sa.DateTime(timezone=True), nullable=False
         ),

fractal_server-2.0.0a8/fractal_server/urls.py

@@ -0,0 +1,13 @@
+from os.path import normpath
+
+
+def normalize_url(url: str) -> str:
+    if url.startswith("/"):
+        return normpath(url)
+    elif url.startswith("s3"):
+        # It would be better to have a NotImplementedError
+        # but Pydantic Validation + FastAPI require
+        # ValueError, TypeError or AssertionError
+        raise ValueError("S3 handling not implemented yet")
+    else:
+        raise ValueError("URLs must begin with '/' or 's3'.")

{fractal_server-2.0.0a5 → fractal_server-2.0.0a8}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.0.0a5"
+version = "2.0.0a8"
 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 = "2.0.0a5"
+current_version = "2.0.0a8"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.0.0a5/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.0.0a5"