<commit_before>############################
# RED-I configuration file #
############################

# -------------------------------------------------------------------------------
# --- section_redcap
# -------------------------------------------------------------------------------
# The address for communicating with the REDCap server using API calls
# Required parameter
redcap_uri = http://localhost:8998/redcap/api/

# The token generated using REDCap web-interface to allow API calls
# 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
# -------------------------------------------------------------------------------
# smtp host details
# Required parameters
smtp_host_for_outbound_mail = smtp.example.org
smtp_port_for_outbound_mail = 25

# Option to specify whether to send email or not. Specify Y for yes and N for No
# Optional parameter
send_email = N

# Email of the report sender
# Required if send_email is set to Y
sender_email = please-do-not-reply<EMAIL>

# Email of the REDI report receiver.
# Required if send_email is set to Y
receiver_email = <EMAIL>

# Warning email options. Email of the sender
# Required parameter
redcap_support_sender_email = <EMAIL>

# Email of the receiver.
# for multiple addresses, put a space between each address.
# Required parameter
redcap_support_receiver_email = <EMAIL>

# This is an optional parameter used in the report email only
project = RED-I Sample Project

# name of the report file in xml format, which will be stored at this location.
# Optional parameter
report_file_path = report.xml

# name of the report file in html format, which will be stored at this location.
# Optional parameter
report_file_path2 = report.html
# --- /section_redi_emails
# -------------------------------------------------------------------------------


# -------------------------------------------------------------------------------
# --- redi_parsing_settings
# -------------------------------------------------------------------------------

# File name of the raw data xml located in the config folder.
# Required parameter
raw_xml_file = synthetic-lab-data.xml

# File name of the Form Events file located in the config folder.
# Required parameter
form_events_file = formEvents.xml

# File name of the Translation Table located in the config folder.
# Required parameter
translation_table_file = translationTable.xml

# File name of the research id to redcap id mapping xml file located in the config folder
# Required parameter
research_id_to_redcap_id = research_id_to_redcap_id_map.xml

# Required parameter
component_to_loinc_code_xml = clinical-component-to-loinc-code-example.xml

# Required parameter
replace_fields_in_raw_data_xml = replace_fields_in_raw_data.xml

# Optional parameter
input_date_format = %Y-%m-%d

# 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)
emr_sftp_server_hostname = hostname
emr_sftp_server_username = username
emr_sftp_server_password = password
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 = {}

# Set to "True" to include "rules" processing errors
# Optional parameter
include_rule_errors_in_report = False
# --- /section_rule_based_processing
# -------------------------------------------------------------------------------


# -------------------------------------------------------------------------------
# --- section_misc
# -------------------------------------------------------------------------------
# The SQLite database file path where we store md5 sums of the input files
# 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<commit_msg>Improve documentation in `config-example/settings.ini` Closes issue #63<commit_after>############################
# 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 = <PASSWORD>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 = <EMAIL>

# 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 = <EMAIL>

# 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 = <EMAIL>
redcap_support_receiver_email = <EMAIL>

# 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
# --- /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 = {}

# 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
{'fraction_non_alphanumeric': 0.2802941668059502, 'fraction_numerical': 0.0024235333444760153, 'mean_word_length': 1.7272105742935278, 'pattern_counts': {'":': 0, '<': 12, '<?xml version=': 0, '>': 13, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 24}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5079928', 'n_tokens_mistral': 2687, 'n_tokens_neox': 2604, 'n_words': 1120}