############################ # RED-I configuration file # ############################ # ------------------------------------------------------------------------------- # --- section_redcap # ------------------------------------------------------------------------------- # The address for communicating with the REDCap server using API calls. # Note: The REDCap server administrator must enable the API access # from the "Applications->API" project menu. # Required parameter redcap_uri = http://localhost:8998/redcap/api/ # The token generated using REDCap server web-interface to allow API calls. # Note: The token is usually 32 chars long and should be never shared because # it can expose medical records. # Required parameter token = THIS_IS_THE_API_KEY # This flag allows to disable SSL certificate validation (! not a good idea) # when communicating with a REDCap server which does not have a certificate # or the certificate is self-signed # @see http://pycap.readthedocs.org/en/latest/api.html verify_ssl = True # --- /section_redcap # ------------------------------------------------------------------------------- # ------------------------------------------------------------------------------- # --- section_redi_emails # ------------------------------------------------------------------------------- # The application can be configured to send a report email with details about # how much data was transfered. If the application is run on a network where # there is a valid email server then the server host name and port can # be specified in the `smtp_*` parameters below. # Required parameters if `send_email` option is set to True smtp_host_for_outbound_mail = smtp.example.org smtp_port_for_outbound_mail = 25 # Use this option to enable/disable report email sending # Valid values are: Yes, No, Y, N # Optional parameter -- defaults to `No` if not specified send_email = N # If the report email is configured to be sent then this paramter # can be used to specify the email sender. # Required parameter if `send_email` parameter is set to `Yes` sender_email = please-do-not-reply@example.org # If the report email is configured to be sent then this paramter # can be used to specify a recipient. # Requiredparameter if `send_email` parameter is set to `Yes` receiver_email = me@example.org # During the execution of data transfer multiple error condition can be encountered. # If there is a specific person which needs to be notified please provide the # "redcap_support_*" parameters below # Required parameters redcap_support_sender_email = please-do-not-reply@example.com redcap_support_receiver_email = jdoe@example.com # Use this paramters to specify the name of the project in the report email. # Optional parameter project = RED-I Sample Project # Use this parameter to specify the file name for the report email stored in xml format. # Optional parameter report_file_path = report.xml # Use this parameter to specify the file name for the report email stored in html format. # Optional parameter report_file_path2 = report.html # Optional parameter used to choose sorting of the data # in the summary email by `lab_id` or by `redcap_id` is_sort_by_lab_id = Y # --- /section_redi_emails # ------------------------------------------------------------------------------- # ------------------------------------------------------------------------------- # --- redi_parsing_settings # ------------------------------------------------------------------------------- # Use this parameter to specify the RED-I file with data which needs # to be parsed and sent to REDCap. # Required parameter raw_xml_file = synthetic-lab-data.xml # Use this parameter to specify the config file describing the events # in the REDCap forms which are populated with data. # Required parameter form_events_file = formEvents.xml # Use this parameter to specify the config file translating # clinical components into REDCap fields. # Required parameter translation_table_file = translationTable.xml # Use this parameter to specify the config file translating # the person id into the corresponding person id in the REDCap database. # Required parameter research_id_to_redcap_id = research_id_to_redcap_id_map.xml # Use this parameter to specify the config file translating # a clinical component such as "WHITE BLOOD CELL COUNT" into # the proper loinc code such as "1577876". # Required parameter component_to_loinc_code_xml = clinical-component-to-loinc-code-example.xml # Use this parameter to specify the config file which # allows to replace some fields in the raw data file by other field names. # Required parameter replace_fields_in_raw_data_xml = replace_fields_in_raw_data.xml # Use this parameter to specify the format of dates in the input. # Optional parameter input_date_format = %Y-%m-%d # Use this parameter to specify the format of dates in the output. # Optional parameter output_date_format = %Y-%m-%d # --- /redi_parsing_settings # ------------------------------------------------------------------------------- # ------------------------------------------------------------------------------- # --- section_emrdata # ------------------------------------------------------------------------------- # The following parameters are required for getting EMR data # (i.e. required if -e command line argument is used) # Use this parameter to specify the address of the sftp host # from which EMR data will be retrieved emr_sftp_server_hostname = hostname # Use the two parameters below to specify the credentials # for accessing the sftp server where the EMR data is stored emr_sftp_server_username = username emr_sftp_server_password = password # Use the two parameters below to specify the folder and file name # on the sftp server where the EMR data is stored emr_sftp_project_name = tmp emr_data_file = output.csv # --- /section_emrdata # ------------------------------------------------------------------------------- # ------------------------------------------------------------------------------- # --- section_rule_based_processing # ------------------------------------------------------------------------------- # This is an optional dictionary which indicates that # custom code needs to be run to validate the data rules = {} preprocessors = {} # Set to "True" to include "rules" processing errors # Optional parameter include_rule_errors_in_report = False # --- /section_rule_based_processing # ------------------------------------------------------------------------------- # ------------------------------------------------------------------------------- # --- section_misc # ------------------------------------------------------------------------------- # Use this parameter to specify the SQLite database file path where we store # md5 sums of the input files. This allows to detect situations in which # the input file does not change for a long time. # Optional parameter. batch_info_database = redi.db # If the md5 sum of the input file does not change then generate a warning # after a specific number of days. # Optional parameter batch_warning_days = 13 # Optional parameter - TODO remove rate_limiter_value_in_redcap = 600 # --- /section_misc # -------------------------------------------------------------------------------