semehr_process_settings.json

{
  "env": {
    "java_home": "",
    "gcp_home": "",
    "gate_home": "",
    "yodie_path": "",
    "ukb_home": ""
  },
  "yodie": {
    "os": "win",
    "gcp_run_path": "",
    "input_doc_file_path": "",
    "thread_num": "40",
    "memory": "30g",
    "config_xml_path": "",
    "output_file_path": "",
    "output_destination": "sql",
    "output_dbconn_setting_file": "..dbconn.json..",
    "output_table": "..[kconnect_annotations]..",
    "output_concept_filter_file": "..retain_concepts.txt..",
    "input_source": "sql",
    "input_dbconn_setting_file": "..dbconn.json.."
  },
  "semehr": {
    "es_doc_url": "",
    "full_text_doc_id": "",
    "full_text_doc_date": "",
    "full_text_index": "",
    "full_text_doc_type": "",
    "full_text_patient_field": "",
    "full_text_text_field": "",
    "es_host": "",
    "index": "",
    "concept_index": "ctx_concept_index",
    "concept_doc_type": "ctx_concept",
    "entity_doc_type": "patient"
  },
  "doc_copy":{
    "thread_num": "10",
    "es_host": "",
    "src_index": "",
    "src_doc_type": "",
    "dest_index": "",
    "dest_doc_type": ""
  },
  "new_docs":{
    "sql_query": "select docid from ...",
    "dbconn_setting_file": "..dbconn.json.."
  },
  "action_trans":{
    "cohort_name": "",
    "dbconn_setting_file": "",
    "sql_cohort_doc_template": "",
    "sql_doc_anns_template": "",
    "sql_doc_content_template": "",
    "sql_action_trans_update_template": "",
    "action_trans_model_file": ""
  },
  "job":{
    "load_docs": "no",
    "copy_docs": "no",
    "yodie": "yes",
    "semehr-concept": "no",
    "semehr-patients": "no",
    "action_trans": "no",
    "job_id": "camcris",
    "job_status_file_path": "..semehr-runtime.."
  }
}