JSON dump problem

[bedroesb]

When I try to dump with ISA JSON using:

from isatools.isajson import ISAJSONEncoder
json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': '))

I get following error:

2019-05-21 11:43:28,237 [ERROR]: brapi_to_isa.py(<module>:424) >> 'str' object has no attribute 'term'
Traceback (most recent call last):
  File "brapi_to_isa.py", line 422, in <module>
    main(arg=SERVER)
  File "brapi_to_isa.py", line 373, in main
    json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': '))
  File "/usr/lib/python3.6/json/__init__.py", line 238, in dumps
    **kw).encode(obj)
  File "/usr/lib/python3.6/json/encoder.py", line 201, in encode
    chunks = list(chunks)
  File "/usr/lib/python3.6/json/encoder.py", line 437, in _iterencode
    o = _default(o)
  File "/usr/local/lib/python3.6/dist-packages/isatools/isajson.py", line 1832, in default
    "studies": list(map(lambda x: get_study(x), o.studies))
  File "/usr/local/lib/python3.6/dist-packages/isatools/isajson.py", line 1832, in <lambda>
    "studies": list(map(lambda x: get_study(x), o.studies))
  File "/usr/local/lib/python3.6/dist-packages/isatools/isajson.py", line 1775, in get_study
    "assays": list(map(lambda x: get_assay(x), o.assays))
  File "/usr/local/lib/python3.6/dist-packages/isatools/isajson.py", line 1775, in <lambda>
    "assays": list(map(lambda x: get_assay(x), o.assays))
  File "/usr/local/lib/python3.6/dist-packages/isatools/isajson.py", line 1798, in get_assay
    "characteristicCategories": get_characteristic_categories(o.characteristic_categories),
  File "/usr/local/lib/python3.6/dist-packages/isatools/isajson.py", line 1780, in get_characteristic_categories
    return list(map(lambda x: get_characteristic_category(x), o))
  File "/usr/local/lib/python3.6/dist-packages/isatools/isajson.py", line 1780, in <lambda>
    return list(map(lambda x: get_characteristic_category(x), o))
  File "/usr/local/lib/python3.6/dist-packages/isatools/isajson.py", line 1663, in get_characteristic_category
    "characteristicType": get_ontology_annotation(o)
  File "/usr/local/lib/python3.6/dist-packages/isatools/isajson.py", line 1568, in get_ontology_annotation
    "annotationValue": o.term,
AttributeError: 'str' object has no attribute 'term'

The isatab.dump instead works flawless on the given dataset.

[Zigur]

I will add a test where we create an investigation with characteristic_category set as a string, and see whether serialising this to JSON triggers an error.

Potential problematic line: https://github.com/ISA-tools/isa-api/blob/master/isatools/model.py#L2706

[Zigur]

Verify if a test takes care of this issue