Cli (#77)

* Add command line programs to collect metadata and export geojson

* Add command line programs to collect metadata and export geojson

* Update tests

* Fix tests and some warnings

* Cleanup

* Change CLI for json export

* Fix merge conflicts

* Add option to json export to filter for certain variables

src/ismn/cli.py

@@ -37,7 +37,7 @@ def collect_metadata(data_path, meta_path, parallel):
 
 @click.command("export_geojson", short_help="Export ISMN sensors to geojson.")
 @click.argument('data_path', type=click.STRING)
-@click.option('--file_out',
+@click.option('--file_out', '-o',
               type=click.STRING, default=None,
               help="Path to the json file that should be created. "
                    "If the file already exists it will be overwritten. "
@@ -49,7 +49,11 @@ def collect_metadata(data_path, meta_path, parallel):
                    "network, station, sensor, depth, timerange. \n "
                    "Or any sensor properties (also custom ones) that have a "
                    "value.")
-def export_geojson(data_path, file_out, field):
+@click.option('--variable', '-var', multiple=True,
+              help="To include only the metadata for a certain variable (e.g."
+                   "soil_moisture) pass the name here. This option is allowed"
+                   "multiple times.")
+def export_geojson(data_path, file_out, field, variable):
     """
     Calls
     Command line program to initialise ISMN metadata collection. THIS WILL
@@ -73,6 +77,8 @@ def export_geojson(data_path, file_out, field):
         file_out = os.path.join(ds.root.root_dir, 'ismn_sensors.json')
     os.makedirs(os.path.dirname(file_out), exist_ok=True)
     print(f"Exporting geojson to: {file_out}")
+    print(f"Include fields: {field}")
+    print(f"Filter for variables: {variable}")
 
     kwargs = {}
     field = [f.lower() for f in field]
@@ -84,6 +90,10 @@ def export_geojson(data_path, file_out, field):
             kwargs[opt] = False
 
     kwargs['extra_props'] = field if len(field) > 0 else None
+
+    if len(variable) > 0:
+        kwargs['filter_kwargs'] = {'variable': variable}
+
     ds.collection.export_geojson(file_out, **kwargs)
 
 @click.group(short_help="ISMN Command Line Programs.")

src/ismn/components.py

@@ -826,7 +826,7 @@ def export_citations(self, out_file=None):
 
     def export_geojson(self, path, network=True, station=True, sensor=False,
                        depth=True, timerange=True, extra_props=None,
-                       **filter_kwargs):
+                       filter_kwargs=None):
         """
         Filter sensors in collection and create geojson file containing all
         features.
@@ -850,8 +850,9 @@ def export_geojson(self, path, network=True, station=True, sensor=False,
             geojson file
             By default only depth_from and depth_to are included
             e.g. ['variable', 'frm_class'] etc.
-        filter_kwargs:
-            Keyword arguments to filter sensors in collection
+        filter_kwargs: dict, optional (default: None)
+            Keyword arguments to filter sensors in collection before extracting
+            metadata.
             see :func:`ismn.components.Sensor.eval`
         """
         extra_props = extra_props or []
@@ -860,6 +861,8 @@ def export_geojson(self, path, network=True, station=True, sensor=False,
             "features": [],
         }
 
+        filter_kwargs = filter_kwargs or dict()
+
         for nw, stat, sens in self.iter_sensors(**filter_kwargs):
             feature = {
                 "type": "Feature",

tests/test_cli.py

@@ -28,7 +28,9 @@ def test_cli_export_geojson():
                                 os.path.join(tempdir, "test.geojson"),
                                 "-f", "network",
                                 '-f', "timerange",
-                                "-f", "lc_2010"])
+                                "-f", "lc_2010",
+                                "-f", "variable",
+                                "-var", "soil_moisture"])
         assert result.exit_code == 0
         assert os.path.isfile(os.path.join(tempdir, "test.geojson"))
         with open(os.path.join(tempdir, "test.geojson"), "r") as f:
@@ -37,3 +39,5 @@ def test_cli_export_geojson():
             assert "timerange_from" in content[0]
             assert "timerange_to" in content[0]
             assert "lc_2010" in content[0]
+            assert 'soil_moisture' in content[0]
+            assert "precipitation" not in content[0]