test_GeneBot.py 文件源码

def validate_all_human_genes():
    # runs all genes through the validator
    # and generates a log file

    coll = MongoClient().wikidata_src.mygene
    metadata_coll = MongoClient().wikidata_src.mygene_sources
    metadata = metadata_coll.find_one()
    doc_filter = {'taxid': 9606, 'entrezgene': {'$exists': True}}
    docs = coll.find(doc_filter)
    print("total number of records: {}".format(coll.find(doc_filter).count()))

    validate_type = 'eukaryotic'
    docs = HelperBot.validate_docs(docs, validate_type, 'P351')
    records = HelperBot.tag_mygene_docs(docs, metadata)

    _ = list(records)