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legumeinfo / microservices

A collection of microservices developed and maintained by the Legume Information System
https://legumeinfo.org/
Apache License 2.0
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chado flavor of redis_loading seems broken #602

Open adf-ncgr opened 1 year ago

adf-ncgr commented 1 year ago

when run without specifying --sequence_types I get:

File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/usr/local/lib/python3.11/site-packages/redis_loader/__main__.py", line 354, in <module>
    main()
  File "/usr/local/lib/python3.11/site-packages/redis_loader/__main__.py", line 350, in main
    args.command(loader, args)
  File "/usr/local/lib/python3.11/site-packages/redis_loader/__main__.py", line 22, in chado
    loadFromChado(
  File "/usr/local/lib/python3.11/site-packages/redis_loader/loaders/chado.py", line 202, in loadFromChado
    transferChromosomes(postgres_connection, redisearch_loader, uniquename, sequence_types)
  File "/usr/local/lib/python3.11/site-packages/redis_loader/loaders/chado.py", line 89, in transferChromosomes
    sequencetype_ids = [getCvterm(c, s, 'sequence') for s in sequence_types]
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/redis_loader/loaders/chado.py", line 89, in <listcomp>
    sequencetype_ids = [getCvterm(c, s, 'sequence') for s in sequence_types]
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/redis_loader/loaders/chado.py", line 60, in getCvterm
    raise Exception('Failed to retrieve the "' + name + '" cvterm entry')
Exception: Failed to retrieve the "c" cvterm entry
ERROR: 1

whereas if I specify --sequence_types it fails here: https://github.com/legumeinfo/microservices/blob/337835eff55b4e38aa2b235724d94e68d5c11710/redis_loader/redis_loader/loaders/chado.py#L108C1-L109C1 this line is throwing TypeError: expected str instance, int found

probably this is a good example of why @alancleary suggests https://github.com/legumeinfo/gcv-docker-compose/issues/6#issuecomment-1175562709