Unable to load data to local cluster using harvester

[medcelerate]

We are attempting to launch our own instance of the meta-knowledgebase and are encountering issues loading data with the harvester. We successfully ran the make file however getting the errors below.

The first is a missing source parameter in the save_bulk for elastic search, we have modified our code to get past this error however now we are having issues with the data loader.

AttributeError: 'NoneType' object has no attribute 'find'
mutant
Traceback (most recent call last):
  File "harvester.py", line 287, in <module>
    main()
  File "harvester.py", line 267, in main
    silos[0].save_bulk(_check_dup(harvest_and_convert(args.genes)), source=h)
  File "/home/ec2-user/g2p-aggregator/harvester/silos/elastic_silo.py", line 129, in save_bulk
    request_timeout=120)
  File "/home/ec2-user/miniconda2/lib/python2.7/site-packages/elasticsearch/helpers/__init__.py", line 194, in bulk
    for ok, item in streaming_bulk(client, actions, **kwargs):
  File "/home/ec2-user/miniconda2/lib/python2.7/site-packages/elasticsearch/helpers/__init__.py", line 161, in streaming_bulk
    for bulk_actions in _chunk_actions(actions, chunk_size, max_chunk_bytes, client.transport.serializer):
  File "/home/ec2-user/miniconda2/lib/python2.7/site-packages/elasticsearch/helpers/__init__.py", line 55, in _chunk_actions
    for action, data in actions:
  File "/home/ec2-user/g2p-aggregator/harvester/silos/elastic_silo.py", line 128, in <genexpr>
    (d for d in _bulker(feature_association_generator)),
  File "/home/ec2-user/g2p-aggregator/harvester/silos/elastic_silo.py", line 118, in _bulker
    for feature_association in feature_association_generator:
  File "harvester.py", line 184, in _check_dup
    for feature_association in harvest:
  File "harvester.py", line 96, in harvest_and_convert
    for feature_association in harvester.harvest_and_convert(genes):
  File "/home/ec2-user/g2p-aggregator/harvester/cgi_biomarkers.py", line 253, in harvest_and_convert
    for feature_association in convert(evidence):
  File "/home/ec2-user/g2p-aggregator/harvester/cgi_biomarkers.py", line 194, in convert
    evidence['Association'])
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc2 in position 9: ordinal not in range(128)`