CLI: Filter cutoffs from JSON file for family cutoffs set (#132)

Currently the `family cutoffs set` command requires that the JSON file
that contains the cutoffs _only_ has the cutoff keys specified for each
element. This is because the cutoffs are validated by the
`RecommendedCutoffMixin.validate_cutoffs()` method, which doesn't allow
for extraneous keys.

However, the  `.json`  file could have been adapted by the user from e.g. the
SSSP `metadata.json` or some other dictionary that also contains other keys.
As long as the cutoff keys are defined, we shouldn't raise an error just because
there are other keys present.

Here we first filter the data loaded from the JSON file for the cutoffs,
before passing the dictionary to the `set_cutoffs` method.

src/aiida_pseudo/cli/family.py

@@ -85,8 +85,17 @@ def cmd_family_cutoffs_set(family, cutoffs, stringency, unit):  # noqa: D301
     except ValueError as exception:
         raise click.BadParameter(f'`{cutoffs.name}` contains invalid JSON: {exception}', param_hint='CUTOFFS')
 
+    cutoffs_dict = {}
+    for element, values in data.items():
+        try:
+            cutoffs_dict[element] = {'cutoff_wfc': values['cutoff_wfc'], 'cutoff_rho': values['cutoff_rho']}
+        except KeyError as exception:
+            raise click.BadParameter(
+                f'`{cutoffs.name}` is missing cutoffs for element `{element}`: {exception}', param_hint='CUTOFFS'
+            ) from exception
+
     try:
-        family.set_cutoffs(data, stringency, unit=unit)
+        family.set_cutoffs(cutoffs_dict, stringency, unit=unit)
     except ValueError as exception:
         raise click.BadParameter(f'`{cutoffs.name}` contains invalid cutoffs: {exception}', param_hint='CUTOFFS')
 

tests/cli/test_family.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 # pylint: disable=unused-argument,redefined-outer-name
 """Tests for the command `aiida-pseudo family`."""
+from copy import deepcopy
 import json
 
 from aiida.orm import Group
@@ -31,13 +32,15 @@ def test_family_cutoffs_set(run_cli_command, get_pseudo_family, generate_cutoffs
     assert "Error: Missing option '-s' / '--stringency'" in result.output
     assert sorted(family.get_cutoff_stringencies()) == sorted(['low', 'normal'])
 
-    # Invalid cutoffs structure
-    filepath.write_text(json.dumps({'Ar': {'cutoff_rho': 300}}))
+    # Missing cutoffs
+    high_cutoffs = deepcopy(cutoffs_dict['high'])
+    high_cutoffs['Ar'].pop('cutoff_wfc')
+    filepath.write_text(json.dumps(high_cutoffs))
     result = run_cli_command(cmd_family_cutoffs_set, [family.label, str(filepath), '-s', 'high'], raises=True)
-    assert 'Error: Invalid value for CUTOFFS:' in result.output
+    assert 'Error: Invalid value for CUTOFFS: ' in result.output
     assert sorted(family.get_cutoff_stringencies()) == sorted(['low', 'normal'])
 
-    # Set correct stringency
+    # Set the high stringency
     stringency = 'high'
     filepath.write_text(json.dumps(cutoffs_dict['high']))
     result = run_cli_command(cmd_family_cutoffs_set, [family.label, str(filepath), '-s', stringency])
@@ -46,6 +49,16 @@ def test_family_cutoffs_set(run_cli_command, get_pseudo_family, generate_cutoffs
     assert sorted(family.get_cutoff_stringencies()) == sorted(['low', 'normal', 'high'])
     assert family.get_cutoffs(stringency) == cutoffs_dict[stringency]
 
+    # Additional keys in the cutoffs should be accepted and simply ignored
+    stringency = 'invalid'
+    high_cutoffs = deepcopy(cutoffs_dict['high'])
+    high_cutoffs['Ar']['GME'] = 'moon'
+    filepath.write_text(json.dumps(high_cutoffs))
+    result = run_cli_command(cmd_family_cutoffs_set, [family.label, str(filepath), '-s', stringency])
+    assert 'Success: set cutoffs for' in result.output
+    assert sorted(family.get_cutoff_stringencies()) == sorted(['low', 'normal', 'high', stringency])
+    assert family.get_cutoffs(stringency) == cutoffs_dict['high']
+
 
 @pytest.mark.usefixtures('clear_db')
 def test_family_cutoffs_set_unit(run_cli_command, get_pseudo_family, generate_cutoffs, tmp_path):