obojson parser requires optional fields to be present

[cmungall]

given:

{
  "graphs": [
    {
      "id": "test",
      "nodes": [
        {
          "id": "GO:0005773",
          "lbl": "vacuole",
          "meta": {
            "definition": {
              "val": "..."
            }
          }
        }
      ]
    }
  ]
}

pronto gives:

  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/pronto/parsers/obojson.py", line 19, in parse_from
    doc = fastobo.load_graph(handle).compact_ids()
ValueError: graphs[0].nodes[0].meta.definition: missing field `xrefs` at line 10 column 27

this can be fixed with inclusion of empty dicts and lists

{
  "graphs": [
      {
          
          "id": "test",
          "meta": {},
          "equivalentNodesSets": [],
          "logicalDefinitionAxioms": [],
          "domainRangeAxioms": [],
          "propertyChainAxioms": [],
          "nodes": [
              {
                  "id": "GO:0005773",
                  "lbl": "vacuole",
                  "meta": {
                      "definition": {
                          "val": "...",
                          "xrefs": []
                          
                      }
                  }
              }
          ]
      }
  ]
}

but this imposes a bit of a burden on lightweight producers

[althonos]

Hi @cmungall

I fixed the fastobo-graphs source, and will push a new release of fastobo-py later on. However, in the example you use, isn't the type attribute required for node objects? And if it isn't, how should the node be treated (default to class)?