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cancerDHC / ccdh-terminology-service

CCDH Terminology and Mapping Service
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Bugfix: GDC Importer: TypeError: Values of type <class 'rdflib.term.URIRef'> are not supported #117

Closed joeflack4 closed 2 years ago

joeflack4 commented 2 years ago

When deploying, we received this new error:

INFO:ccdh.importers.importer:Processed attributes: 335
INFO:ccdh.importers.importer:Importing CRDC-H model -- completed
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/local/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/app/ccdh/importers/importer.py", line 218, in <module>
    Importer.import_all()
  File "/app/ccdh/importers/importer.py", line 213, in import_all
    Importer(neo4j_graph()).import_ncit_mapping(GdcImporter.read_ncit_mappings(), 'GDC')
  File "/app/ccdh/importers/importer.py", line 135, in import_ncit_mapping
    self.graph.run(query, **params)
  File "/usr/local/lib/python3.8/site-packages/py2neo/database.py", line 405, in run
    return self.auto().run(cypher, parameters, **kwparameters)
  File "/usr/local/lib/python3.8/site-packages/py2neo/database.py", line 989, in run
    result = self._connector.auto_run(cypher, parameters,
  File "/usr/local/lib/python3.8/site-packages/py2neo/client/__init__.py", line 1340, in auto_run
    return cx.auto_run(cypher, parameters, graph_name=graph_name, readonly=readonly)
  File "/usr/local/lib/python3.8/site-packages/py2neo/client/bolt.py", line 861, in auto_run
    return self._run(graph_name, cypher, parameters or {},
  File "/usr/local/lib/python3.8/site-packages/py2neo/client/bolt.py", line 923, in _run
    response = self.append_message(0x10, cypher, parameters, extra or {})
  File "/usr/local/lib/python3.8/site-packages/py2neo/client/bolt.py", line 726, in append_message
    self.write_message(tag, fields)
  File "/usr/local/lib/python3.8/site-packages/py2neo/client/bolt.py", line 701, in write_message
    self._writer.write_message(tag, fields)
  File "/usr/local/lib/python3.8/site-packages/py2neo/client/bolt.py", line 240, in write_message
    packer.pack(field)
  File "/usr/local/lib/python3.8/site-packages/interchange/packstream.py", line 151, in pack
    self._pack_dict(value)
  File "/usr/local/lib/python3.8/site-packages/interchange/packstream.py", line 285, in _pack_dict
    self.pack(item)
  File "/usr/local/lib/python3.8/site-packages/interchange/packstream.py", line 200, in pack
    raise TypeError("Values of type %s are not supported" % type(value))
TypeError: Values of type <class 'rdflib.term.URIRef'> are not supported
root@c8daa42a6522:/app#
joeflack4 commented 2 years ago

Fixed in: https://github.com/cancerDHC/ccdh-terminology-service/commit/50c62d1dcd3261fa54a11e2510eccbe1e4100508