8000 handle broken links, add test by lukaspie · Pull Request #645 · FAIRmat-NFDI/pynxtools · GitHub
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handle broken links, add test #645

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Merged
merged 1 commit into from
May 26, 2025
Merged

handle broken links, add test #645

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5 changes: 5 additions & 0 deletions src/pynxtools/dataconverter/validation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -545,6 +545,7 @@ def _follow_link(
ValidationProblem.KeyToBeRemoved,
"key",
)
keys_to_remove.append(key_path)
del resolved_keys[key]
else:
resolved_keys[key] = current_keys
Expand Down Expand Up @@ -763,6 +764,10 @@ def is_documented(key: str, tree: NexusNode) -> bool:
if isinstance(mapping[key], dict) and "link" in mapping[key]:
resolved_link = _follow_link({key: mapping[key]}, "")

if key not in resolved_link:
# Link is broken and key will be removed; no need to check further
return False

is_mapping = isinstance(resolved_link[key], Mapping)

if node.type == "group" and not is_mapping:
Expand Down
36 changes: 36 additions & 0 deletions tests/dataconverter/test_validation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -816,6 +816,24 @@ def listify_template(data_dict: Template):
],
id="field-instead-of-named-group",
),
pytest.param(
alter_dict(
alter_dict(
TEMPLATE,
"/ENTRY[my_entry]/identified_calibration",
{"link": "/my_entry/some_group"},
),
"/ENTRY[my_entry]/NXODD_name[nxodd_name]/float_value",
{"link": "/my_entry/specified_group/some_field"},
),
[
"Broken link at /ENTRY[my_entry]/identified_calibration to /my_entry/some_group.",
"The key /ENTRY[my_entry]/identified_calibration will not be written.",
"Broken link at /ENTRY[my_entry]/NXODD_name[nxodd_name]/float_value to /my_entry/specified_group/some_field.",
"The key /ENTRY[my_entry]/NXODD_name[nxodd_name]/float_value will not be written.",
],
id="appdef-broken-links",
),
pytest.param(
alter_dict(
alter_dict(
Expand Down Expand Up @@ -850,6 +868,24 @@ def listify_template(data_dict: Template):
],
id="appdef-links-with-wrong-nexus-types",
),
pytest.param(
alter_dict(
alter_dict(
TEMPLATE,
"/ENTRY[my_entry]/SAMPLE[my_sample]",
{"link": "/my_entry/some_group"},
),
"/ENTRY[my_entry]/SAMPLE[my_sample2]/name",
{"link": "/my_entry/specified_group/some_field223"},
),
[
"Broken link at /ENTRY[my_entry]/SAMPLE[my_sample] to /my_entry/some_group.",
"The key /ENTRY[my_entry]/SAMPLE[my_sample] will not be written.",
"Broken link at /ENTRY[my_entry]/SAMPLE[my_sample2]/name to /my_entry/specified_group/some_field223.",
"The key /ENTRY[my_entry]/SAMPLE[my_sample2]/name will not be written.",
],
id="baseclass-broken-links",
),
pytest.param(
alter_dict(
alter_dict(
Expand Down
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