Merge branch 'master' into py-647

.vscode/settings.json

@@ -4,7 +4,7 @@
     "editor.formatOnSave": true,
     "editor.tabSize": 4,
     "editor.codeActionsOnSave": {
-      "source.organizeImports": true,
+      "source.organizeImports": "explicit"
     },
     "editor.defaultFormatter": "ms-python.black-formatter"
   },

darwin/client.py

@@ -29,6 +29,17 @@
     Unauthorized,
     ValidationError,
 )
+from darwin.future.core.client import ClientCore, DarwinConfig
+from darwin.future.core.properties import create_property as create_property_future
+from darwin.future.core.properties import (
+    get_team_full_properties as get_team_full_properties_future,
+)
+from darwin.future.core.properties import (
+    get_team_properties as get_team_properties_future,
+)
+from darwin.future.core.properties import update_property as update_property_future
+from darwin.future.core.types.common import JSONDict
+from darwin.future.data_objects.properties import FullProperty
 from darwin.item import DatasetItem
 from darwin.utils import (
     get_response_content,
@@ -1474,3 +1485,40 @@ def api_v2(self) -> BackendV2:
         if not team:
             raise ValueError("No team was found.")
         return BackendV2(self, team.slug)
+
+    def get_team_properties(
+        self, team_slug: Optional[str] = None, include_property_values: bool = True
+    ) -> List[FullProperty]:
+        darwin_config = DarwinConfig.from_old(self.config)
+        future_client = ClientCore(darwin_config)
+
+        if not include_property_values:
+            return get_team_properties_future(
+                client=future_client,
+                team_slug=team_slug or self.default_team,
+            )
+
+        return get_team_full_properties_future(
+            client=future_client,
+            team_slug=team_slug or self.default_team,
+        )
+
+    def create_property(self, team_slug: Optional[str], params: Union[FullProperty, JSONDict]) -> FullProperty:
+        darwin_config = DarwinConfig.from_old(self.config)
+        future_client = ClientCore(darwin_config)
+
+        return create_property_future(
+            client=future_client,
+            team_slug=team_slug or self.default_team,
+            params=params,
+        )
+
+    def update_property(self, team_slug: Optional[str], params: Union[FullProperty, JSONDict]) -> FullProperty:
+        darwin_config = DarwinConfig.from_old(self.config)
+        future_client = ClientCore(darwin_config)
+
+        return update_property_future(
+            client=future_client,
+            team_slug=team_slug or self.default_team,
+            params=params,
+        )

darwin/dataset/local_dataset.py

@@ -506,7 +506,6 @@ def get_annotation_filepaths(
 
     if partition is None:
         return (str(e) for e in sorted(annotations_dir.glob("**/*.json")))
-
     if split_type == "random":
         split_filename = f"{split_type}_{partition}.txt"
     elif split_type == "stratified":

darwin/datatypes.py

@@ -22,6 +22,7 @@
 except ImportError:
     NDArray = Any  # type:ignore
 
+from darwin.future.data_objects.properties import SelectedProperty
 from darwin.path_utils import construct_full_path, is_properties_enabled, parse_metadata
 
 # Utility types
@@ -215,6 +216,9 @@ class Annotation:
     # The darwin ID of this annotation.
     id: Optional[str] = None
 
+    # Properties of this annotation.
+    properties: Optional[list[SelectedProperty]] = None
+
     def get_sub(self, annotation_type: str) -> Optional[SubAnnotation]:
         """
         Returns the first SubAnnotation that matches the given type.
@@ -269,6 +273,9 @@ class VideoAnnotation:
     # The darwin ID of this annotation.
     id: Optional[str] = None
 
+    # Properties of this annotation.
+    properties: Optional[list[SelectedProperty]] = None
+
     def get_data(
         self,
         only_keyframes: bool = True,
@@ -1272,6 +1279,7 @@ def make_video_annotation(
     segments: List[Segment],
     interpolated: bool,
     slot_names: List[str],
+    properties: Optional[list[SelectedProperty]] = None,
 ) -> VideoAnnotation:
     """
     Creates and returns a ``VideoAnnotation``.
@@ -1308,6 +1316,7 @@ def make_video_annotation(
         segments,
         interpolated,
         slot_names=slot_names or [],
+        properties=properties,
     )
 
 

darwin/exporter/formats/nifti.py

@@ -1,5 +1,6 @@
 import ast
 import json as native_json
+import re
 from dataclasses import dataclass
 from pathlib import Path
 from typing import Dict, Iterable, List, Optional, Tuple, Union
@@ -137,50 +138,28 @@ def check_for_error_and_return_imageid(
     image_id : str
 
     """
-    # check if all item slots have the correct file-extension
+    # Check if all item slots have the correct file-extension
     for slot in video_annotation.slots:
         for source_file in slot.source_files:
             filename = Path(source_file["file_name"])
-
-            try:
-                suffixes = filename.suffixes[-2:]
-            except IndexError:
-                suffixes = filename.suffixes
-            if len(suffixes) == 2:
-                if suffixes[0] == ".nii" and suffixes[1] == ".gz":
-                    image_id = str(filename).rstrip("".join(suffixes))
-                else:
-                    return create_error_message_json(
-                        "Two suffixes found but not ending in .nii.gz",
-                        output_dir,
-                        str(filename),
-                    )
-            elif len(suffixes) == 1:
-                if suffixes[0] == ".nii" or suffixes[0] == ".dcm":
-                    image_id = filename.stem
-                else:
-                    return create_error_message_json(
-                        "Misconfigured filename, not ending in .nii or .dcm. Are you sure this is medical data?",
-                        output_dir,
-                        str(filename),
-                    )
-            else:
+            if not (
+                filename.name.lower().endswith(".nii.gz")
+                or filename.name.lower().endswith(".nii")
+                or filename.name.lower().endswith(".dcm")
+            ):
                 return create_error_message_json(
-                    "You are trying to export to nifti. Filename should contain either .nii, .nii.gz or .dcm extension."
-                    "Are you sure this is medical data?",
+                    "Misconfigured filename, not ending in .nii, .nii.gz or .dcm. Are you sure this is medical data?",
                     output_dir,
                     str(filename),
                 )
 
     filename = Path(video_annotation.filename)
-    try:
-        suffixes = filename.suffixes[-2:]
-    except IndexError:
-        suffixes = filename.suffixes
-    if len(suffixes) == 2:
-        image_id = str(filename).rstrip("".join(suffixes))
-    elif len(suffixes) == 1:
-        image_id = str(filename.stem)
+    if filename.name.lower().endswith(".nii.gz"):
+        image_id = re.sub(r"(?i)\.nii\.gz$", "", str(filename))
+    elif filename.name.lower().endswith(".nii"):
+        image_id = re.sub(r"(?i)\.nii$", "", str(filename))
+    elif filename.name.lower().endswith(".dcm"):
+        image_id = re.sub(r"(?i)\.dcm$", "", str(filename))
     else:
         image_id = str(filename)
 

darwin/future/core/client.py

@@ -9,6 +9,7 @@
 from pydantic import BaseModel, root_validator, validator
 from requests.adapters import HTTPAdapter, Retry
 
+from darwin.config import Config as OldConfig
 from darwin.future.core.types.common import JSONType, QueryString
 from darwin.future.exceptions import (
     BadRequest,
@@ -121,6 +122,25 @@ def from_api_key_with_defaults(api_key: str) -> DarwinConfig:
             datasets_dir=DarwinConfig._default_config_path(),
         )
 
+    @staticmethod
+    def from_old(old_config: OldConfig) -> DarwinConfig:
+        teams = old_config.get("teams")
+        if not teams:
+            raise ValueError("No teams found in the old config")
+
+        default_team = old_config.get("global/default_team")
+        if not default_team:
+            default_team = list(teams.keys())[0]
+
+        return DarwinConfig(
+            api_key=teams[default_team]["api_key"],
+            api_endpoint=old_config.get("global/api_endpoint"),
+            base_url=old_config.get("global/base_url"),
+            default_team=default_team,
+            teams=teams,
+            datasets_dir=teams[default_team]["datasets_dir"],
+        )
+
     class Config:
         validate_assignment = True
 

darwin/future/core/properties/__init__.py

@@ -1,5 +1,7 @@
+from darwin.future.core.properties.create import create_property
 from darwin.future.core.properties.get import (
     get_property_by_id,
     get_team_full_properties,
     get_team_properties,
 )
+from darwin.future.core.properties.update import update_property, update_property_value

darwin/future/core/properties/create.py

@@ -0,0 +1,36 @@
+from typing import Optional, Union
+
+from pydantic import parse_obj_as
+
+from darwin.future.core.client import ClientCore
+from darwin.future.core.types.common import JSONDict
+from darwin.future.data_objects.properties import FullProperty
+
+
+def create_property(
+    client: ClientCore,
+    params: Union[FullProperty, JSONDict],
+    team_slug: Optional[str] = None,
+) -> FullProperty:
+    """
+    Creates a property for the specified team slug.
+
+    Parameters:
+        client (ClientCore): The client to use for the request.
+        team_slug (Optional[str]): The slug of the team to get. If not specified, the
+            default team from the client's config will be used.
+        params (Optional[JSONType]): The JSON data to use for the request.
+
+    Returns:
+        FullProperty: FullProperty object for the created property.
+
+    Raises:
+        HTTPError: If the response status code is not in the 200-299 range.
+    """
+    if not team_slug:
+        team_slug = client.config.default_team
+    if isinstance(params, FullProperty):
+        params = params.to_create_endpoint()
+    response = client.post(f"/v2/teams/{team_slug}/properties", data=params)
+    assert isinstance(response, dict)
+    return parse_obj_as(FullProperty, response)

darwin/future/core/properties/get.py

@@ -67,6 +67,6 @@ def get_property_by_id(
     """
     if not team_slug:
         team_slug = client.config.default_team
-    response = client.get(f"/v2/teams/{team_slug}/properties/{property_id}")
+    response = client.get(f"/v2/teams/{team_slug}/properties/{str(property_id)}")
     assert isinstance(response, dict)
     return parse_obj_as(FullProperty, response)

darwin/future/core/properties/update.py

@@ -0,0 +1,74 @@
+from typing import Optional, Union
+
+from pydantic import parse_obj_as
+
+from darwin.future.core.client import ClientCore
+from darwin.future.core.types.common import JSONDict
+from darwin.future.data_objects.properties import FullProperty, PropertyValue
+
+
+def update_property(
+    client: ClientCore,
+    params: Union[FullProperty, JSONDict],
+    team_slug: Optional[str] = None,
+) -> FullProperty:
+    """
+    Updates a property for the specified team slug.
+
+    Parameters:
+        client (ClientCore): The client to use for the request.
+        team_slug (Optional[str]): The slug of the team to get. If not specified, the
+            default team from the client's config will be used.
+        params (Optional[JSONType]): The JSON data to use for the request.
+
+    Returns:
+        FullProperty: FullProperty object for the created property.
+
+    Raises:
+        HTTPError: If the response status code is not in the 200-299 range.
+    """
+    if not team_slug:
+        team_slug = client.config.default_team
+    if isinstance(params, FullProperty):
+        id, params = params.to_update_endpoint()
+    else:
+        id = params.get("id")
+        del params["id"]
+    response = client.put(f"/v2/teams/{team_slug}/properties/{id}", data=params)
+    assert isinstance(response, dict)
+    return parse_obj_as(FullProperty, response)
+
+
+def update_property_value(
+    client: ClientCore,
+    params: Union[PropertyValue, JSONDict],
+    item_id: str,
+    team_slug: Optional[str] = None,
+) -> PropertyValue:
+    """
+    Updates a property value for the specified property id.
+
+    Parameters:
+        client (ClientCore): The client to use for the request.
+        team_slug (Optional[str]): The slug of the team to get. If not specified, the
+            default team from the client's config will be used.
+        params (Optional[JSONType]): The JSON data to use for the request.
+
+    Returns:
+        FullProperty: FullProperty object for the created property.
+
+    Raises:
+        HTTPError: If the response status code is not in the 200-299 range.
+    """
+    if not team_slug:
+        team_slug = client.config.default_team
+    if isinstance(params, PropertyValue):
+        id, params = params.to_update_endpoint()
+    else:
+        id = params.get("id")
+        del params["id"]
+    response = client.put(
+        f"/v2/teams/{team_slug}/properties/{item_id}/property_values/{id}", data=params
+    )
+    assert isinstance(response, dict)
+    return parse_obj_as(PropertyValue, response)

darwin/future/core/types/common.py

@@ -5,6 +5,7 @@
 from darwin.future.data_objects import validators as darwin_validators
 
 JSONType = Union[Dict[str, Any], List[Dict[str, Any]]]  # type: ignore
+JSONDict = Dict[str, Any]  # type: ignore
 
 
 class Implements_str(Protocol):