fractal-server 2.0.0a6__py3-none-any.whl → 2.0.0a8__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.0.0a6"
+__VERSION__ = "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/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/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/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/app/schemas/v2/dataset.py

@@ -12,6 +12,7 @@ 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):
@@ -50,6 +51,10 @@ class DatasetCreateV2(BaseModel, extra=Extra.forbid):
     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"))
 
 
@@ -83,4 +88,10 @@ class DatasetUpdateV2(BaseModel):
     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/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/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/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-2.0.0a6.dist-info → fractal_server-2.0.0a8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.0.0a6
+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-2.0.0a6.dist-info → fractal_server-2.0.0a8.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=5qWDQ_nyhHlAAd6zm7X6HCZpyfGaVJKhBA0qSF2KZfA,24
+fractal_server/__init__.py,sha256=K1rg40LWC0HcWGPng5LXrwtqh2Z-3XITlzdSqTIPpeQ,24
 fractal_server/__main__.py,sha256=CocbzZooX1UtGqPi55GcHGNxnrJXFg5tUU5b3wyFCyo,4958
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -36,8 +36,8 @@ fractal_server/app/routes/api/v1/workflow.py,sha256=ZObifWTPi100oRQ1wEER8Sgsr3Ne
 fractal_server/app/routes/api/v1/workflowtask.py,sha256=ox-DIIqYV4K35hCu86eGa2SHnR5IQml-I00UHEwnmHQ,5579
 fractal_server/app/routes/api/v2/__init__.py,sha256=x56HcY1uBNCgq4BRVj-0j6bAj6OsTN97RNDqY8NefJ8,1373
 fractal_server/app/routes/api/v2/_aux_functions.py,sha256=TCHf3aM-KQxaNJen10CGX1Da5IIra00xRF39FUTU698,14301
-fractal_server/app/routes/api/v2/dataset.py,sha256=qQi9jfT9YLu6DrRCPh280J3MoFWs9yMiejkCNaauCyQ,9680
-fractal_server/app/routes/api/v2/images.py,sha256=b1NM9Y0ocuRYRec-3UcVAizB0vFkmzPEHfObaoCnIMY,5956
+fractal_server/app/routes/api/v2/dataset.py,sha256=BmNKrhHUVoy0EuEYZpdocR_aG7U2tNuOpoAVimaGIBY,10008
+fractal_server/app/routes/api/v2/images.py,sha256=LX9-EYOGN4NHSARNXYGgSK4_vvAVFwzTiwVM5KuVukA,7589
 fractal_server/app/routes/api/v2/job.py,sha256=9mXaKCX_N3FXM0GIxdE49nWl_hJZ8CBLBIaMMhaCKOM,5334
 fractal_server/app/routes/api/v2/project.py,sha256=i9a19HAqE36N92G60ZYgObIP9nv-hR7Jt5nd9Dkhz1g,6024
 fractal_server/app/routes/api/v2/submit.py,sha256=iszII5CvWDEjGPTphBgH9FVS1pNb5m11Xc8xozGgjgI,6901
@@ -92,10 +92,10 @@ fractal_server/app/runner/v2/merge_outputs.py,sha256=IHuHqbKmk97K35BFvTrKVBs60z3
 fractal_server/app/runner/v2/runner.py,sha256=rBRehRDduGU0TUOkgQN6WbIGhDWZ6GOat4bv7IVB8cA,11784
 fractal_server/app/runner/v2/runner_functions.py,sha256=LfO1-FJF70_Qh78NQTCHJWyzyr011wvvtnzB6nTj5ZM,10087
 fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=Pp3hsj1i1t4ExDMcUBkQ27yEi7kjlvymY6q6eDiC8DM,3845
-fractal_server/app/runner/v2/task_interface.py,sha256=NJZUMHtEs5C3bFdXX42Kv1GMzQ7xPW2v5ZRxGNANOec,1410
+fractal_server/app/runner/v2/task_interface.py,sha256=TZLVJs6CNFo2lFhr-lsDxe585cEhRv48eA490LS9aqc,1746
 fractal_server/app/runner/v2/v1_compat.py,sha256=6UijuRYbB2ry2mM073u1fW4CSTeelB11lmoj_TOGtm4,511
 fractal_server/app/schemas/__init__.py,sha256=VL55f3CTFngXHYkOsFaLBEEkEEewEWI5ODlcGTI7cqA,157
-fractal_server/app/schemas/_validators.py,sha256=Pdff5plJJmoUTf_nZpMA24tZlFJb84EdRSnLwRZDxfE,3264
+fractal_server/app/schemas/_validators.py,sha256=1dTOYr1IZykrxuQSV2-zuEMZbKe_nGwrfS7iUrsh-sE,3461
 fractal_server/app/schemas/state.py,sha256=t4XM04aqxeluh8MfvD7LfEc-8-dOmUVluZHhLsfxxkc,692
 fractal_server/app/schemas/user.py,sha256=rE8WgBz-ceVUs0Sz2ZwcjUrSTZTnS0ys5SBtD2XD9r8,3113
 fractal_server/app/schemas/v1/__init__.py,sha256=gZLfkANl4YtZ7aV3PFoUj5w0m1-riQv9iRomJhZRLZo,2078
@@ -108,7 +108,7 @@ fractal_server/app/schemas/v1/task.py,sha256=7BxOZ_qoRQ8n3YbQpDvB7VMcxB5fSYQmR5R
 fractal_server/app/schemas/v1/task_collection.py,sha256=uvq9bcMaGD_qHsh7YtcpoSAkVAbw12eY4DocIO3MKOg,3057
 fractal_server/app/schemas/v1/workflow.py,sha256=tuOs5E5Q_ozA8if7YPZ07cQjzqB_QMkBS4u92qo4Ro0,4618
 fractal_server/app/schemas/v2/__init__.py,sha256=zlCYrplCWwnCL9-BYsExRMfVzhBy21IMBfdHPMgJZYk,1752
-fractal_server/app/schemas/v2/dataset.py,sha256=VSAB8np2TdZf_a2NJKkpBVJFDSs0IYpLan5RDzu6g3E,1757
+fractal_server/app/schemas/v2/dataset.py,sha256=V04_2bXgD12L53aW4_Ls8rnGLLgCaiVAFoAedx5of8Q,2086
 fractal_server/app/schemas/v2/dumps.py,sha256=Xen0OPf1Ax9i_7ItrAPvCk1OCNcUsnhlLRiyny89aLM,1997
 fractal_server/app/schemas/v2/job.py,sha256=zfF9K3v4jWUJ7M482ta2CkqUJ4tVT4XfVt60p9IRhP0,3250
 fractal_server/app/schemas/v2/manifest.py,sha256=N37IWohcfO3_y2l8rVM0h_1nZq7m4Izxk9iL1vtwBJw,6243
@@ -120,8 +120,8 @@ fractal_server/app/schemas/v2/workflowtask.py,sha256=vRyPca8smu6fzwd9gO1eOd3qdPL
 fractal_server/app/security/__init__.py,sha256=wxosoHc3mJYPCdPMyWnRD8w_2OgnKYp2aDkdmwrZh5k,11203
 fractal_server/config.py,sha256=CA8ASObADaME5chDiBXawAJZ3MvjTRpCKP0jvdYtSh8,15080
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
-fractal_server/images/__init__.py,sha256=KWLVMlWqTY85qq1VUpzaJi5Sl2VOYWEn0vIEiD-QZ5k,144
-fractal_server/images/models.py,sha256=hgDQf1-SsMJw504GFUufVETedPPEweCQxUhA2uDfdao,2904
+fractal_server/images/__init__.py,sha256=xO6jTLE4EZKO6cTDdJsBmK9cdeh9hFTaSbSuWgQg7y4,196
+fractal_server/images/models.py,sha256=9ipU5h4N6ogBChoB-2vHoqtL0TXOHCv6kRR-fER3mkM,4167
 fractal_server/images/tools.py,sha256=Q7jM60r_jq5bttrt1b4bU29n717RSUMMPbAbAkzWjgw,2234
 fractal_server/logger.py,sha256=95duXY8eSxf1HWg0CVn8SUGNzgJw9ZR0FlapDDF6WAY,3924
 fractal_server/main.py,sha256=7CpwPfCsHxBAo5fWuXPCsYOFCpbBI0F7Z0jsgCQdou8,3001
@@ -157,9 +157,10 @@ fractal_server/tasks/v2/_TaskCollectPip.py,sha256=QeCqXDgOnMjk3diVlC5bgGEywyQjYF
 fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/tasks/v2/background_operations.py,sha256=zr6j3uoWmCeW2EA9auxWNZ0sG3SHgSxUVTC1OpQXE3Y,12803
 fractal_server/tasks/v2/get_collection_data.py,sha256=Qhf2T_aaqAfqu9_KpUSlXsS7EJoZQbEPEreHHa2jco8,502
+fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
-fractal_server-2.0.0a6.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.0.0a6.dist-info/METADATA,sha256=VzuxOIkkB0Uv-MzjnyEf9Xu3xhQzJQUNCYROj_tVrwM,4204
-fractal_server-2.0.0a6.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-fractal_server-2.0.0a6.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.0.0a6.dist-info/RECORD,,
+fractal_server-2.0.0a8.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.0.0a8.dist-info/METADATA,sha256=sKsPtIdIowQ-avbzi1OajV7Qet2IIuHXM9duIYpxpyA,4204
+fractal_server-2.0.0a8.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+fractal_server-2.0.0a8.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.0.0a8.dist-info/RECORD,,