EP-3981 Add #71 #114 references to vector cube todo's

openeo_driver/ProcessGraphDeserializer.py

@@ -521,7 +521,7 @@ def vector_buffer(args: Dict, env: EvalEnv) -> dict:
     input_crs = 'epsg:4326'
     buffer_resolution = 3
 
-    # TODO EP-3981 convert `geometry` to vector cube and move buffer logic to there
+    # TODO #114 EP-3981 convert `geometry` to vector cube and move buffer logic to there
     if isinstance(geometry, str):
         # TODO: assumption here that `geometry` is a path/url
         geoms = list(DelayedVector(geometry).geometries)
@@ -664,7 +664,7 @@ def chunk_polygon(args: dict, env: EvalEnv) -> DriverDataCube:
     data_cube = extract_arg(args, 'data')
 
     # Chunks parameter check.
-    # TODO EP-3981 normalize first to vector cube and simplify logic
+    # TODO #114 EP-3981 normalize first to vector cube and simplify logic
     if isinstance(chunks, DelayedVector):
         polygons = list(chunks.geometries)
         for p in polygons:
@@ -705,7 +705,7 @@ def fit_class_random_forest(args: dict, env: EvalEnv) -> DriverMlModel:
 
     predictors = extract_arg(args, 'predictors')
     if not isinstance(predictors, AggregatePolygonSpatialResult):
-        # TODO EP-3981 add support for real vector cubes.
+        # TODO #114 EP-3981 add support for real vector cubes.
         raise ProcessParameterInvalidException(
             parameter="predictors", process="fit_class_random_forest",
             reason=f"should be non-temporal vector-cube (got `{type(predictors)}`)."
@@ -716,7 +716,7 @@ def fit_class_random_forest(args: dict, env: EvalEnv) -> DriverMlModel:
             and target.get("type") == "FeatureCollection"
             and isinstance(target.get("features"), list)
     ):
-        # TODO EP-3981 vector cube support
+        # TODO #114 EP-3981 vector cube support
         raise ProcessParameterInvalidException(
             parameter="target", process="fit_class_random_forest",
             reason='only GeoJSON FeatureCollection is currently supported.',
@@ -949,7 +949,7 @@ def aggregate_spatial(args: dict, env: EvalEnv) -> DriverDataCube:
     target_dimension = args.get('target_dimension', None)
 
     geoms = extract_arg(args, 'geometries')
-    # TODO: convert all cases to DriverVectorCube first and just work with that
+    # TODO #114: convert all cases to DriverVectorCube first and just work with that
     if isinstance(geoms, DriverVectorCube):
         geoms = geoms
     elif isinstance(geoms, dict):
@@ -993,11 +993,11 @@ def mask_polygon(args: dict, env: EvalEnv) -> DriverDataCube:
     replacement = args.get('replacement', None)
     inside = args.get('inside', False)
 
-    # TODO: instead of if-elif-else chain: generically "cast" to VectorCube first (e.g. for wide input
+    # TODO #114: instead of if-elif-else chain: generically "cast" to VectorCube first (e.g. for wide input
     #       support: GeoJSON, WKT, ...) and then convert to MultiPolygon?
     if isinstance(mask, DelayedVector):
         # TODO: avoid reading DelayedVector twice due to dry-run?
-        # TODO EP-3981 embed DelayedVector in VectorCube implementation
+        # TODO #114 EP-3981 embed DelayedVector in VectorCube implementation
         polygon = shapely.ops.unary_union(list(mask.geometries))
     elif isinstance(mask, DriverVectorCube):
         polygon = mask.to_multipolygon()
@@ -1073,7 +1073,7 @@ def filter_spatial(args: Dict, env: EvalEnv) -> DriverDataCube:
     geometries = extract_arg(args, 'geometries')
 
     if not isinstance(geometries, dict):
-        # TODO: support DelayedVector
+        # TODO #114: support DriverDataCube
         raise NotImplementedError("filter_spatial only supports dict but got {g!r}".format(g=geometries))
 
     geometries = geojson_to_geometry(geometries)
@@ -1173,6 +1173,7 @@ def run_udf(args: dict, env: EvalEnv):
     if dry_run_tracer and isinstance(data, AggregatePolygonResult):
         return JSONResult({})
 
+    # TODO #114 add support for DriverVectorCube
     if isinstance(data, AggregatePolygonResult):
         pass
     if isinstance(data, (DelayedVector, dict)):
@@ -1346,15 +1347,15 @@ def apply_process(process_id: str, args: dict, namespace: Union[str, None], env:
         .returns("TODO", schema={"type": "object", "subtype": "vector-cube"})
 )
 def read_vector(args: Dict, env: EvalEnv) -> DelayedVector:
-    # TODO EP-3981: deprecated in favor of load_uploaded_files/load_external? https://github.com/Open-EO/openeo-processes/issues/322
+    # TODO #114 EP-3981: deprecated in favor of load_uploaded_files/load_external? https://github.com/Open-EO/openeo-processes/issues/322
     path = extract_arg(args, 'filename')
     return DelayedVector(path)
 
 
 @process_registry_100.add_function(spec=read_spec("openeo-processes/1.x/proposals/load_uploaded_files.json"))
 def load_uploaded_files(args: dict, env: EvalEnv) -> DriverVectorCube:
-    # TODO EP-3981 process name is still under discussion https://github.com/Open-EO/openeo-processes/issues/322
-    # TODO EP-3981 also other return types: raster data cube, array, ...
+    # TODO #114 EP-3981 process name is still under discussion https://github.com/Open-EO/openeo-processes/issues/322
+    # TODO also other return types: raster data cube, array, ...
     paths = extract_arg(args, 'paths', process_id="load_uploaded_files")
     format = extract_arg(args, 'format', process_id="load_uploaded_files")
     options = args.get("options", {})
@@ -1376,7 +1377,7 @@ def load_uploaded_files(args: dict, env: EvalEnv) -> DriverVectorCube:
         .returns("TODO", schema={"type": "object", "subtype": "vector-cube"})
 )
 def get_geometries(args: Dict, env: EvalEnv) -> Union[DelayedVector, dict]:
-    # TODO: standardize or deprecate this? EP-3981 https://github.com/Open-EO/openeo-processes/issues/322
+    # TODO: standardize or deprecate this? #114 EP-3981 https://github.com/Open-EO/openeo-processes/issues/322
     feature_collection = args.get('feature_collection', None)
     path = args.get('filename', None)
     if path is not None:

openeo_driver/datacube.py

@@ -156,7 +156,7 @@ class DriverVectorCube:
     DIM_GEOMETRIES = "geometries"
 
     def __init__(self, geometries: gpd.GeoDataFrame, cube: Optional[xarray.DataArray] = None):
-        # TODO EP-3981: consider other data containers (xarray) and lazy loading?
+        # TODO #114 EP-3981: lazy loading (like DelayedVector)?
         if cube is not None:
             if cube.dims[0] != self.DIM_GEOMETRIES:
                 log.error(f"First cube dim should be {self.DIM_GEOMETRIES!r} but got dims {cube.dims!r}")
@@ -176,9 +176,9 @@ def with_cube(self, cube: xarray.DataArray) -> "DriverVectorCube":
     def from_fiona(cls, paths: List[str], driver: str, options: dict):
         """Factory to load vector cube data using fiona/GeoPandas."""
         if len(paths) != 1:
-            # TODO EP-3981: support multiple paths
+            # TODO #114 EP-3981: support multiple paths
             raise FeatureUnsupportedException(message="Loading a vector cube from multiple files is not supported")
-        # TODO EP-3981: lazy loading like/with DelayedVector
+        # TODO #114 EP-3981: lazy loading like/with DelayedVector
         return cls(geometries=gpd.read_file(paths[0], driver=driver))
 
     def _as_geopandas_df(self) -> gpd.GeoDataFrame:

openeo_driver/delayed_vector.py

@@ -199,6 +199,7 @@ def _read_shapefile_crs(shp_path: str) -> pyproj.CRS:
 
     @staticmethod
     def _as_geometry_collection(feature_collection: Dict) -> Dict:
+        # TODO #71 #114 Deprecate/avoid usage of GeometryCollection
         geometries = (feature['geometry'] for feature in feature_collection['features'])
 
         return {

openeo_driver/dry_run.py

@@ -443,7 +443,7 @@ def aggregate_spatial(
             reducer: dict,
             target_dimension: str = "result",
     ) -> Union[AggregatePolygonResult, AggregatePolygonSpatialResult]:
-        # TODO EP-3981 normalize to vector cube instead of GeometryCollection
+        # TODO #71 #114 EP-3981 normalize to vector cube instead of GeometryCollection
         geometries, bbox = self._normalize_geometry(geometries)
         cube = self.filter_bbox(**bbox, operation="_weak_spatial_extent")
         cube._process(operation="aggregate_spatial", arguments={"geometries": geometries})
@@ -456,7 +456,7 @@ def _normalize_geometry(self, geometries) -> Tuple[Union[DriverVectorCube, Delay
         Helper to preprocess geometries (as used in aggregate_spatial and mask_polygon)
         and extract bbox (e.g. for filter_bbox)
         """
-        # TODO EP-3981 normalize to vector cube instead of GeometryCollection
+        # TODO #71 #114 EP-3981 normalize to vector cube instead of GeometryCollection
         if isinstance(geometries, DriverVectorCube):
             bbox = geometries.get_bounding_box()
         elif isinstance(geometries, dict):
@@ -478,7 +478,7 @@ def _normalize_geometry(self, geometries) -> Tuple[Union[DriverVectorCube, Delay
         bbox = dict(west=bbox[0], south=bbox[1], east=bbox[2], north=bbox[3], crs="EPSG:4326")
         return geometries, bbox
 
-    # TODO: this is a workaround until vectorcube is fully upgraded
+    # TODO: #114 this is a workaround until vectorcube is fully upgraded
     def raster_to_vector(self):
         return AggregatePolygonResult(timeseries={}, regions=None)
 
@@ -504,6 +504,7 @@ def reduce_dimension(self, reducer, dimension: str, context: Any, env: EvalEnv)
 
     def chunk_polygon(self, reducer, chunks: MultiPolygon, mask_value: float, env: EvalEnv, context={}) -> 'DryRunDataCube':
         polygons: List[Polygon] = chunks.geoms
+        # TODO #71 #114 Deprecate/avoid usage of GeometryCollection
         geometries, bbox = self._normalize_geometry(GeometryCollection(polygons))
         cube = self.filter_bbox(**bbox, operation="_weak_spatial_extent")
         return cube._process("chunk_polygon", arguments={"geometries": geometries})

openeo_driver/dummy/dummy_backend.py

@@ -219,7 +219,7 @@ def assert_polygon_sequence(geometries: Union[Sequence, BaseMultipartGeometry]):
             for g in geometries:
                 assert isinstance(g, Polygon) or isinstance(g, MultiPolygon)
 
-        # TODO EP-3981 normalize to vector cube and preserve original properties
+        # TODO #114 EP-3981 normalize to vector cube and preserve original properties
         if isinstance(geometries, DriverVectorCube):
             # Build dummy aggregation data cube
             dims = (DriverVectorCube.DIM_GEOMETRIES,)
@@ -239,7 +239,7 @@ def assert_polygon_sequence(geometries: Union[Sequence, BaseMultipartGeometry]):
             geometries = [geometry for geometry in DelayedVector(geometries).geometries]
             assert_polygon_sequence(geometries)
         elif isinstance(geometries, GeometryCollection):
-            # TODO EP-3981: GeometryCollection is deprecated
+            # TODO #71 #114 EP-3981: GeometryCollection is deprecated
             assert_polygon_sequence(geometries)
         elif isinstance(geometries, BaseGeometry):
             assert_polygon_sequence([geometries])
@@ -256,7 +256,7 @@ def assert_polygon_sequence(geometries: Union[Sequence, BaseMultipartGeometry]):
 
 
 class DummyAggregatePolygonSpatialResult(AggregatePolygonSpatialResult):
-    # TODO EP-3981 replace with proper VectorCube implementation
+    # TODO #114 EP-3981 replace with proper VectorCube implementation
 
     def __init__(self, cube: DummyDataCube, geometries: Iterable[BaseGeometry]):
         super().__init__(csv_dir="/dev/null", regions=geometries)

openeo_driver/save_result.py

@@ -199,7 +199,7 @@ class AggregatePolygonResult(JSONResult):  # TODO: if it supports NetCDF and CSV
 
     """
 
-    # TODO EP-3981 port this to proper vector cube support
+    # TODO #71 #114 EP-3981 port this to proper vector cube support
 
     def __init__(self, timeseries: dict, regions: GeometryCollection, metadata:CollectionMetadata=None):
         super().__init__(data=timeseries)
@@ -429,11 +429,10 @@ def to_covjson(self) -> dict:
         }
 
 
-
 class AggregatePolygonResultCSV(AggregatePolygonResult):
+    # TODO #71 #114 EP-3981 port this to proper vector cube support
 
-
-    def __init__(self, csv_dir, regions: GeometryCollection, metadata:CollectionMetadata=None):
+    def __init__(self, csv_dir, regions: GeometryCollection, metadata: CollectionMetadata = None):
 
         def _flatten_df(df):
             df.index = df.feature_index
@@ -464,7 +463,7 @@ class AggregatePolygonSpatialResult(SaveResult):
     """
     Container for result of `aggregate_polygon` process (aka "zonal stats") for a spatial layer.
     """
-    # TODO EP-3981 replace with proper VectorCube implementation
+    # TODO #71 #114 EP-3981 replace with proper VectorCube implementation
 
     DEFAULT_FORMAT = "JSON"
 
@@ -597,7 +596,7 @@ def to_save_result(data: Any, format: Optional[str] = None, options: Optional[di
     elif isinstance(data, DriverVectorCube):
         return VectorCubeResult(cube=data, format=format, options=options)
     elif isinstance(data, DelayedVector):
-        # TODO EP-3981 add vector cube support: keep features from feature collection
+        # TODO #114 EP-3981 add vector cube support: keep features from feature collection
         geojsons = [mapping(geometry) for geometry in data.geometries]
         return JSONResult(geojsons, format=format, options=options)
     elif isinstance(data, np.ndarray):

openeo_driver/utils.py

@@ -128,7 +128,7 @@ def smart_bool(value):
 
 def geojson_to_geometry(geojson: dict) -> shapely.geometry.base.BaseGeometry:
     """Convert GeoJSON object to shapely geometry object"""
-    # TODO EP-3981 standardize on using (FeatureCollection like) vector cubes  instead of GeometryCollection?
+    # TODO #71 #114 EP-3981 standardize on using (FeatureCollection like) vector cubes  instead of GeometryCollection?
     if geojson["type"] == "FeatureCollection":
         geojson = {
             'type': 'GeometryCollection',
@@ -147,6 +147,7 @@ def geojson_to_multipolygon(
     means dissolving overlapping polygons into one).
     """
     # TODO: option to also force conversion of Polygon to MultiPolygon?
+    # TODO: #71 #114 migrate/centralize all this kind of logic to vector cubes
     if geojson["type"] == "Feature":
         geojson = geojson["geometry"]