Release/1.0.1

.devcontainer/dev_container.dockerfile

@@ -5,25 +5,21 @@ FROM ${BASE_URL}
 USER root
 
 # We'll be running as a non-root user in a container and may want root permissions
-RUN apt update && apt -y install nano ssh sudo && apt clean
-
-# Install setup tools and dependencies
-WORKDIR /app
-COPY . /app
-RUN pip install --upgrade pip setuptools && pip install .[dev] 
+RUN apt update && apt -y install --no-install-recommends nano ssh sudo && apt clean
 
 # Set up user to match the host OS (https://stackoverflow.com/a/78621662/415551)
 ARG HOST_USER
 ARG HOST_UID
 ARG HOST_GID
 
-RUN addgroup --gid ${HOST_GID} ${HOST_USER} \
-    && adduser --gecos "" --disabled-password --uid ${HOST_UID} --gid ${HOST_GID} ${HOST_USER} \
-    && usermod -aG sudo ${HOST_USER} \
+RUN addgroup --gid "${HOST_GID}" "${HOST_USER}" \
+    && adduser --gecos "" --disabled-password --uid "${HOST_UID}" --gid "${HOST_GID}" "${HOST_USER}" \
+    && usermod -aG sudo "${HOST_USER}" \
     && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
 
 ENV HOME /home/${HOST_USER}
 ENV TMPDIR=/tmp
 WORKDIR /home/${HOST_USER}
 
 USER ${HOST_USER}
+ENV PATH "/home/${HOST_USER}/.local/bin:$PATH"

.devcontainer/devcontainer.json

@@ -39,11 +39,11 @@
 				]
 			}
 		}
-	}
+	},
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.
 	// "forwardPorts": [],
 	// Uncomment the next line to run commands after the container is created.
-	// "postCreateCommand": "cat /etc/os-release",
+	"postCreateCommand": "pip install --upgrade pip setuptools && pip install --no-cache-dir -e .[dev]"
 	// Configure tool-specific properties.
 	// "customizations": {},
 	// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.

CHANGELOG.md

@@ -1,4 +1,14 @@
 # Changelog
+## 1.0.1
+### Introduction
+Address SonarQube findings and fix coordinate retrieval for layers.
+
+### Maintenance
+* Addressed SonarQube findings.
+
+### Bugfixes
+* Fixed layer coordinate retrieval to allow multiple coordinates in a list to be combined together.
+
 ## 1.0.0
 Summary release of all features since inception.
 

example/app.py

@@ -110,13 +110,13 @@ def api_home(endpoint):
 
 
 # add in some other endpoints.
-@app.route("/")
+@app.route("/", methods=["GET"])
 def home():
     return """This is an example OGC flask app.
     See <a href="/ogc_full"> FULL </a> and <a href="/ogc"> PARTIAL </a> endpoints."""
 
 
-@app.route("/layers/<layer>")
+@app.route("/layers/<layer>", methods=["GET"])
 def check_layers(layer):
     match_object = re.match("[a-zA-Z0-9]+", layer)
 

ogc/edr/edr_api.py

@@ -7,7 +7,7 @@
 from functools import wraps
 from http import HTTPStatus
 from datetime import datetime, timezone
-from typing import Tuple, List, Dict, Any, Union, Callable
+from typing import Tuple, List, Dict, Any, Callable
 
 from traitlets import TraitError
 from ogc import podpac as pogc
@@ -328,12 +328,12 @@ def get_collection_edr_query(
         return pygeoedr.get_collection_edr_query(api, request, dataset, instance, query_type, location_id)
 
     @staticmethod
-    def _temporal_extents(times: List[Union[np.datetime64, datetime]], trs: str | None) -> Dict[str, Any]:
+    def _temporal_extents(times: List[np.datetime64 | datetime], trs: str | None) -> Dict[str, Any]:
         """Get the temporal extents for the provided times and reference system.
 
         Parameters
         ----------
-        times : List[Union[np.datetime64, datetime]]
+        times : List[np.datetime64 | datetime]
             Times used to create the temporal extent.
         trs : str | None
             The reference system for the times.

ogc/edr/test/conftest.py

@@ -62,7 +62,7 @@ def set_env_vars():
     importlib.reload(settings)
 
 
-@pytest.fixture()
+@pytest.fixture
 def layers() -> List[pogc.Layer]:
     """List of test layers.
 
@@ -74,7 +74,7 @@ def layers() -> List[pogc.Layer]:
     return [layer1, layer2]
 
 
-@pytest.fixture()
+@pytest.fixture
 def layers_no_instance() -> List[pogc.Layer]:
     """List of test layers without instances.
 
@@ -86,7 +86,7 @@ def layers_no_instance() -> List[pogc.Layer]:
     return [layer3]
 
 
-@pytest.fixture()
+@pytest.fixture
 def single_layer_cube_args() -> Dict[str, Any]:
     """Dictionary of valid request arguments that align to a single test layer cube request.
 
@@ -104,7 +104,7 @@ def single_layer_cube_args() -> Dict[str, Any]:
     }
 
 
-@pytest.fixture()
+@pytest.fixture
 def single_layer_cube_args_internal() -> Dict[str, Any]:
     """Dictionary of valid arguments that align to a single test layer request with internal pygeoapi keys.
 
@@ -123,7 +123,7 @@ def single_layer_cube_args_internal() -> Dict[str, Any]:
     }
 
 
-@pytest.fixture()
+@pytest.fixture
 def single_layer_cube_args_no_instance_internal() -> Dict[str, Any]:
     """Dictionary of valid arguments that align to a single non-instance test layer request with internal pygeoapi keys.
 

ogc/edr/test/test_edr_routes.py

@@ -372,12 +372,13 @@ def test_edr_routes_collection_query_invalid_bbox(layers: List[pogc.Layer], sing
     single_layer_cube_args["bbox"] = "invalid"
     request = mock_request(single_layer_cube_args)
     edr_routes = EdrRoutes(layers=layers)
+    instance = next(iter(layers[0].time_instances()))
 
     with pytest.raises(EDRException) as exception_info:
         edr_routes.collection_query(
             request,
             collection_id=layers[0].group,
-            instance_id=next(iter(layers[0].time_instances())),
+            instance_id=instance,
             query_type="cube",
         )
 

ogc/podpac.py

@@ -4,7 +4,7 @@
 
 import ogc
 import podpac
-from podpac.core.coordinates import Coordinates
+from podpac.core.coordinates import Coordinates, union, merge_dims
 import traitlets as tl
 from typing import List
 from matplotlib import pyplot as plt
@@ -80,27 +80,50 @@ def time_instances(self) -> List[str]:
     def get_coordinates(self) -> Coordinates | None:
         """Retrieve the coordinates from the node.
 
+        This enforces that all coordinates implement unstacked latitude and longitude dimensions.
+
         Returns
         -------
         Coordinates | None
             Coordinates from the node or None if not found.
+
+        Raises
+        ------
+        ValueError
+            If any coordinates do not have unstacked latitude and longitude dimensions.
         """
         if self.node is None:
             return None
 
+        output_coordinates_list = []
+        shared_dims = ["lat", "lon"]
         coordinates_list = self.node.find_coordinates()
-        dimension_set = set()
-        coordinates = None
 
-        for coords in coordinates_list:
-            dimension_set.update(coords.udims)
-            if coordinates is None or len(coords.udims) > len(coordinates.udims):
-                coordinates = coords
+        if len(coordinates_list) == 0:
+            return None
+
+        # Verify all coordinates define unstacked latitude and longitude
+        if not all(dim in coordinates.dims for coordinates in coordinates_list for dim in shared_dims):
+            raise ValueError("Invalid dimensions for coordinate retrieval.")
+
+        # Only use one source for shared coordinates
+        shared_coordinates_source = coordinates_list[0]
+        for dim in shared_dims:
+            output_coordinates_list.append(
+                Coordinates(
+                    [shared_coordinates_source[dim].coordinates],
+                    dims=[dim],
+                    crs=shared_coordinates_source.crs,
+                )
+            )
 
-        if coordinates is not None and not all(dim in coordinates.udims for dim in dimension_set):
-            raise ValueError("Not all node coordinate dimensions contained in the layer coordinates.")
+        # Use all sources for remaining dimensions, removing duplicates and enforce matching CRS
+        remaining_coords = union(
+            [coords.drop(shared_dims).transform(shared_coordinates_source.crs) for coords in coordinates_list]
+        )
+        output_coordinates_list.append(remaining_coords)
 
-        return coordinates
+        return merge_dims(output_coordinates_list)
 
     def get_units(self) -> str | None:
         """Retrieve the units from the node.

ogc/test/test_core.py

@@ -227,16 +227,16 @@ def test_ogc_core_handle_wms_kv_get_capabilities_hierachical_layers():
     root = lxml.etree.fromstring(response.encode("utf-8"))
 
     layers = root.xpath(f".//{capability}/{layer}/{title}/text()")
-    assert {ogc.service_group_title} == set(layers)
+    assert set(layers) == {ogc.service_group_title}
 
     layers = root.xpath(f".//{capability}/{layer}/{layer}/{title}/text()")
-    assert {layer_root.title, layer_nested.group_path[0]} == set(layers)
+    assert set(layers) == {layer_root.title, layer_nested.group_path[0]}
 
     layers = root.xpath(f".//{capability}/{layer}/{layer}/{layer}/{title}/text()")
-    assert {layer_nested.group_path[1]} == set(layers)
+    assert set(layers) == {layer_nested.group_path[1]}
 
     layers = root.xpath(f".//{capability}/{layer}/{layer}/{layer}/{layer}/{title}/text()")
-    assert {layer_nested.title} == set(layers)
+    assert set(layers) == {layer_nested.title}
 
 
 def test_ogc_core_handle_wms_kv_get_capabilities_invalid_service():

ogc/test/test_input_security.py

@@ -32,7 +32,7 @@ def client():
     ogc_instance = core.OGC(layers=[layer])
     app = servers.FlaskServer(__name__, ogcs=[ogc_instance])
     app.config["TESTING"] = True
-    yield app.test_client()
+    return app.test_client()
 
 
 # ---------------------------------------------------------------------------

ogc/test/test_input_validation.py

@@ -11,7 +11,7 @@
 from ogc import servers
 from ogc import settings
 from ogc import podpac as pogc
-from ogc.settings import EDR_TIME_INSTANCE_DIMENSION
+from ogc.settings import EDR_TIME_INSTANCE_DIMENSION, crs_84_uri_format
 
 lat = np.linspace(90, -90, 11)
 lon = np.linspace(-180, 180, 21)
@@ -73,7 +73,7 @@ def client():
     """
     Create a test client for the Flask server.
 
-    Yields
+    Returns
     ------
     client : FlaskClient
         A test client for the Flask server.
@@ -84,7 +84,7 @@ def client():
     # Create a FlaskServer instance
     app = servers.FlaskServer(__name__, ogcs=[ogc])
     app.config.update({"TESTING": True})
-    yield app.test_client()
+    return app.test_client()
 
 
 def make_valid_ogc_wms_get_capabilities_args() -> dict:
@@ -332,7 +332,7 @@ def make_valid_ogc_edr_static_cube_args(layer: str) -> dict:
     return {
         "f": "CoverageJSON",
         "bbox": "-180,-90,180,90",
-        "crs": "http://www.opengis.net/def/crs/OGC/1.3/CRS84",
+        "crs": crs_84_uri_format,
         "parameter-name": layer,
         "resolution-x": 512,
         "resolution-y": 512,
@@ -355,7 +355,7 @@ def make_valid_ogc_edr_static_area_args(layer: str) -> dict:
     return {
         "f": "CoverageJSON",
         "coords": "POLYGON((-180 90, -180 -90, 180 -90, 180 90, -180 90))",
-        "crs": "http://www.opengis.net/def/crs/OGC/1.3/CRS84",
+        "crs": crs_84_uri_format,
         "parameter-name": layer,
         "resolution-x": 512,
         "resolution-y": 512,
@@ -378,7 +378,7 @@ def make_valid_ogc_edr_static_position_args(layer: str) -> dict:
     return {
         "f": "CoverageJSON",
         "coords": "POINT(40 50)",
-        "crs": "http://www.opengis.net/def/crs/OGC/1.3/CRS84",
+        "crs": crs_84_uri_format,
         "parameter-name": layer,
     }
 
@@ -401,7 +401,7 @@ def make_valid_ogc_edr_instance_cube_args(layer: str, time: str) -> dict:
     return {
         "f": "CoverageJSON",
         "bbox": "-180,-90,180,90",
-        "crs": "http://www.opengis.net/def/crs/OGC/1.3/CRS84",
+        "crs": crs_84_uri_format,
         "datetime": time,
         "parameter-name": layer,
         "resolution-x": 512,
@@ -427,7 +427,7 @@ def make_valid_ogc_edr_instance_area_args(layer: str, time: str) -> dict:
     return {
         "f": "CoverageJSON",
         "coords": "POLYGON((-180 90, -180 -90, 180 -90, 180 90, -180 90))",
-        "crs": "http://www.opengis.net/def/crs/OGC/1.3/CRS84",
+        "crs": crs_84_uri_format,
         "datetime": time,
         "parameter-name": layer,
         "resolution-x": 512,
@@ -453,7 +453,7 @@ def make_valid_ogc_edr_instance_position_args(layer: str, time: str) -> dict:
     return {
         "f": "CoverageJSON",
         "coords": "POINT(40 50)",
-        "crs": "http://www.opengis.net/def/crs/OGC/1.3/CRS84",
+        "crs": crs_84_uri_format,
         "datetime": time,
         "parameter-name": layer,
     }