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ImperialCollegeLondon / safedata_validator

Python tools to validate and publish datasets using the safedata metadata format.
https://safedata-validator.readthedocs.io/
MIT License
2 stars 4 forks source link

Handle missing XML configuration in dataset publication. #166

Closed davidorme closed 2 months ago

davidorme commented 2 months ago

The current publication workflow breaks when the XML configuration is missing and the XML file creation is requested. 

safedata_zenodo publish_dataset Hardwick_microclimate_2ndOrder.json Hardwick_microclimate_2ndOrder.xlsx -e Microclimate1319.Rdata  Microclimate1319.csv -n 51399
- Configuring Resources
    - Configuring resources from site_path: /etc/xdg/safedata_validator/safedata_validator.cfg
    - Validating gazetteer: /srv/safedata_validator/gazetteer.geojson
    - Validating location aliases: /srv/safedata_validator/location_aliases.csv
    - Validating GBIF database: /srv/safedata_validator/gbif_backbone_2023-08-28.sqlite
    - Validating NCBI database: /srv/safedata_validator/ncbi_taxonomy_2024-02-01.sqlite
    - Validating project database: /srv/safedata_validator/safe_projects_complete.csv
Preparing new version of deposit 51399
 - Removing outdated files: BaitShapefile.zip, Test_format_good_all_features.xlsx, BaitImages.zip, 51399_GEMINI.xml
 - Uploading new or updated files: Hardwick_microclimate_2ndOrder.xlsx, Microclimate1319.Rdata, Microclimate1319.csv
Deposit created: 80969
Traceback (most recent call last):
  File "/home/validate/.local/bin/safedata_zenodo", line 8, in <module>
    sys.exit(_safedata_zenodo_cli())
  File "/home/validate/.local/lib/python3.10/site-packages/safedata_validator/entry_points.py", line 992, in _safedata_zenodo_cli
    publish_id, publish_url = publish_dataset(
  File "/home/validate/.local/lib/python3.10/site-packages/safedata_validator/zenodo.py", line 1084, in publish_dataset
    xml_content = generate_inspire_xml(
  File "/home/validate/.local/lib/python3.10/site-packages/safedata_validator/zenodo.py", line 915, in generate_inspire_xml
    xml = template.render(context_dict)
  File "/home/validate/.local/lib/python3.10/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/home/validate/.local/lib/python3.10/site-packages/jinja2/environment.py", line 939, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/home/validate/.local/lib/python3.10/site-packages/safedata_validator/templates/gemini_xml_template.xml", line 264, in top-level template code
    {% for topic in topicCategories %}
TypeError: 'NoneType' object is not iterable

This should fail elegantly.