Merge pull request #48 from davemfish/bugfix/PGP-requirement-and-tests

Bump Pygeoprocessing requirement, and a couple other fixes

requirements.txt

@@ -8,6 +8,6 @@ GDAL
 frictionless
 numpy
 platformdirs
-pygeoprocessing>=2.4.3
+pygeoprocessing>=2.4.5
 pyyaml
 requests

src/geometamaker/config.py

@@ -8,14 +8,13 @@
 
 LOGGER = logging.getLogger(__name__)
 
-DEFAULT_CONFIG_PATH = os.path.join(
-    platformdirs.user_config_dir(), 'geometamaker_profile.yml')
+CONFIG_FILENAME = 'geometamaker_profile.yml'
 
 
 class Config(object):
     """Encapsulates user-settings such as a metadata Profile."""
 
-    def __init__(self, config_path=DEFAULT_CONFIG_PATH):
+    def __init__(self, config_path=None):
         """Load a Profile from a config file.
 
         Use a default user profile if none given.
@@ -24,7 +23,11 @@ def __init__(self, config_path=DEFAULT_CONFIG_PATH):
             config_path (str): path to a local yaml file
 
         """
-        self.config_path = config_path
+        if config_path is None:
+            self.config_path = os.path.join(
+                platformdirs.user_config_dir(), CONFIG_FILENAME)
+        else:
+            self.config_path = config_path
         self.profile = models.Profile()
 
         try:

src/geometamaker/geometamaker.py

@@ -85,19 +85,20 @@ def _vsi_path(filepath, scheme):
     return filepath
 
 
-def _wkt_to_epsg_string(wkt_string):
+def _wkt_to_epsg_units_string(wkt_string):
     crs_string = 'unknown'
+    units_string = 'unknown'
     try:
         srs = osr.SpatialReference(wkt_string)
         srs.AutoIdentifyEPSG()
         crs_string = (
             f"{srs.GetAttrValue('AUTHORITY', 0)}:"
-            f"{srs.GetAttrValue('AUTHORITY', 1)}; "
-            f"Units:{srs.GetAttrValue('UNITS')}")
+            f"{srs.GetAttrValue('AUTHORITY', 1)}")
+        units_string = srs.GetAttrValue('UNIT', 0)
     except RuntimeError:
         LOGGER.warning(
             f'{wkt_string} cannot be interpreted as a coordinate reference system')
-    return crs_string
+    return crs_string, units_string
 
 
 def detect_file_type(filepath, scheme):
@@ -230,12 +231,13 @@ def describe_vector(source_dataset_path, scheme):
     description['schema'] = models.TableSchema(fields=fields)
 
     info = pygeoprocessing.get_vector_info(source_dataset_path)
-    epsg_string = _wkt_to_epsg_string(info['projection_wkt'])
-    spatial = {
-        'bounding_box': models.BoundingBox(*info['bounding_box']),
-        'crs': epsg_string
-    }
-    description['spatial'] = models.SpatialSchema(**spatial)
+    bbox = models.BoundingBox(*info['bounding_box'])
+    epsg_string, units_string = _wkt_to_epsg_units_string(
+        info['projection_wkt'])
+    description['spatial'] = models.SpatialSchema(
+        bounding_box=bbox,
+        crs=epsg_string,
+        crs_units=units_string)
     description['sources'] = info['file_list']
     return description
 
@@ -269,10 +271,12 @@ def describe_raster(source_dataset_path, scheme):
     # Some values of raster info are numpy types, which the
     # yaml dumper doesn't know how to represent.
     bbox = models.BoundingBox(*[float(x) for x in info['bounding_box']])
-    epsg_string = _wkt_to_epsg_string(info['projection_wkt'])
+    epsg_string, units_string = _wkt_to_epsg_units_string(
+        info['projection_wkt'])
     description['spatial'] = models.SpatialSchema(
         bounding_box=bbox,
-        crs=epsg_string)
+        crs=epsg_string,
+        crs_units=units_string)
     description['sources'] = info['file_list']
     return description
 
@@ -391,6 +395,6 @@ def describe(source_dataset_path, profile=None):
     # Or less common, ValueError if it exists but is incompatible
     except (FileNotFoundError, ValueError):
         resource = RESOURCE_MODELS[resource_type](**description)
-        resource = resource.replace(user_profile)
 
+    resource = resource.replace(user_profile)
     return resource

src/geometamaker/models.py

@@ -41,6 +41,7 @@ class SpatialSchema:
 
     bounding_box: BoundingBox
     crs: str
+    crs_units: str
 
 
 @dataclass
@@ -247,6 +248,9 @@ class Profile(BaseMetadata):
 
     """
 
+    def __post_init__(self):
+        super().__post_init__()
+
     @classmethod
     def load(cls, filepath):
         """Load metadata document from a yaml file.
@@ -323,6 +327,7 @@ class Resource(BaseMetadata):
     url: str = ''
 
     def __post_init__(self):
+        super().__post_init__()
         self.metadata_path = f'{self.path}.yml'
         self.metadata_version: str = f'geometamaker.{geometamaker.__version__}'
         self.path = self.path.replace('\\', '/')

tests/test_geometamaker.py

@@ -213,11 +213,15 @@ def test_describe_raster(self):
         import geometamaker
 
         datasource_path = os.path.join(self.workspace_dir, 'raster.tif')
-        create_raster(numpy.int16, datasource_path)
+        create_raster(numpy.int16, datasource_path, projection_epsg=4326)
 
         resource = geometamaker.describe(datasource_path)
         self.assertTrue(isinstance(
             resource.spatial, geometamaker.models.SpatialSchema))
+        self.assertRegex(
+            resource.spatial.crs, r'EPSG:[0-9]*')
+        self.assertEqual(
+            resource.spatial.crs_units, 'degree')
 
         resource.write()
         self.assertTrue(os.path.exists(f'{datasource_path}.yml'))
@@ -496,6 +500,27 @@ def test_preexisting_doc_new_fields(self):
         field2 = new_resource.get_field_description(field2_name)
         self.assertEqual(field2.type, 'String')
 
+    def test_preexisting_metadata_document_new_profile(self):
+        """Test ammending an existing Metadata document with a profile."""
+        import geometamaker
+
+        title = 'Title'
+        datasource_path = os.path.join(self.workspace_dir, 'raster.tif')
+        create_raster(numpy.int16, datasource_path)
+        resource = geometamaker.describe(datasource_path)
+        resource.set_title(title)
+        resource.set_contact(individual_name='alice')
+        resource.write()
+
+        profile = geometamaker.Profile()
+        profile.set_contact(individual_name='bob')
+        new_resource = geometamaker.describe(datasource_path, profile=profile)
+
+        self.assertEqual(
+            new_resource.get_title(), title)
+        self.assertEqual(
+            new_resource.contact.individual_name, 'bob')
+
     def test_preexisting_incompatible_doc(self):
         """Test when yaml file not created by geometamaker already exists."""
         import geometamaker
@@ -561,7 +586,6 @@ def test_user_configuration(self, mock_user_config_dir):
         """Test existing config populates resource."""
         mock_user_config_dir.return_value = self.workspace_dir
         import geometamaker
-        from geometamaker import models
 
         contact = {
             'individual_name': 'bob'
@@ -570,7 +594,7 @@ def test_user_configuration(self, mock_user_config_dir):
             'title': 'CC-BY-4'
         }
 
-        profile = models.Profile()
+        profile = geometamaker.Profile()
         profile.set_contact(**contact)
         profile.set_license(**license)
 
@@ -655,7 +679,10 @@ def test_invalid_config(self, mock_user_config_dir):
         mock_user_config_dir.return_value = self.workspace_dir
         import geometamaker.config
 
-        with open(geometamaker.config.DEFAULT_CONFIG_PATH, 'w') as file:
+        config_path = os.path.join(
+            geometamaker.config.platformdirs.user_config_dir(),
+            geometamaker.config.CONFIG_FILENAME)
+        with open(config_path, 'w') as file:
             file.write(yaml.dump({'bad': 'data'}))
 
         config = geometamaker.config.Config()
@@ -668,10 +695,12 @@ def test_delete_config(self, mock_user_config_dir):
         mock_user_config_dir.return_value = self.workspace_dir
         import geometamaker.config
 
-        with open(geometamaker.config.DEFAULT_CONFIG_PATH, 'w') as file:
+        config_path = os.path.join(
+            geometamaker.config.platformdirs.user_config_dir(),
+            geometamaker.config.CONFIG_FILENAME)
+        with open(config_path, 'w') as file:
             file.write(yaml.dump({'bad': 'data'}))
 
         config = geometamaker.config.Config()
         config.delete()
-        self.assertFalse(
-            os.path.exists(geometamaker.config.DEFAULT_CONFIG_PATH))
+        self.assertFalse(os.path.exists(config_path))