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dataprocessor_config.toml
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##################################################
# Project Definition for module dataprocessor #
##################################################
###
# VERBOSE LEVELS
###
# VL_00_NOTHING = 0
# VL_10_MAIN_INFO = 1
# VL_20_OUTER_SCRIPTS = 2
# VL_30_INNER_SCRIPTS = 3
# VL_40_INNER_SCRIPTS_INFOS = 4
# VL_50_TABLES = 5
# VL_60_ALL_TABLES = 6
# VL_70_DOWNLOAD = 7
# VL_80_COI_PROCESSING = 8
# VL_90_FHIR_RESPONSE = 9
VERBOSE = 10 # Retrieval / analysis verbose level
# Set true if every sourcing of the 00_Main file should create result
# directories in the otuputGlobal and otuputLocal directores with a timestamp
# suffix. If false then every run will write in the same subdirectory without
# a timestamp. The default behaviour should write in subdirectories with only
# the project name (false) or in or in a subdirectory with the project name
# and the suffix '_timestamp'. (true)
USE_TIMESTAMP_AS_RESULT_DIR_SUFFIX = false
# Maximum of saved cds2db result folders in outputLocal and outputGlobal
MAX_DIR_COUNT = 5
[debug]
###################
# FOR DEBUG ONLY: #
###################
# Activate this date to run the analysis for a spectific date. If it is not set,
# then time now will be taken.
# This date must match the data in the database. Only Encounters whose start
# date is before this date and whose end date is not set or is after this date
# are loaded from the database.
#DEBUG_ENCOUNTER_DATETIME = "2020-07-31 21:25:00"
[analyse]
# In the patient table of the frontend, the patient ID should be displayed, which
# can be used to search for further information on the patient in other systems.
# This is normally specified as one of several possible identifiers for a FHIR
# patient resource. To select the correct one, a string as a grep pattern can be
# specified here for the 'system' entry of the Identifier, 'type/coding/system'
# and/or the 'type/coding/code' of the Identifier, via which the correct one
# can be found.
# These patterns are regular expressions for R
# (see https://hypebright.nl/index.php/en/2020/05/25/ultimate-cheatsheet-for-regex-in-r-2/).
# Exception: If a variable is commented out or the empty string "" then the filter
# on this FHIR expression is deactivated. The same result can be achieved by passing
# ".*" as the pattern, which means "any characters any number of times".
# If the filter result on a single Patient resoruce will provide more than one
# Identifier, then they are written one after the other, separated by semicolons.
#
# acceppts every system:
FRONTEND_DISPLAYED_PATIENT_FHIR_IDENTIFIER_SYSTEM = ".*"
# Accepts only type/coding/sytem with the exact value 'http://terminology.hl7.org/CodeSystem/v2-0203'
# this system is the binded system for the clinical information system patient ID.
# FRONTEND_DISPLAYED_PATIENT_FHIR_IDENTIFIER_TYPE_SYSTEM = "^http://terminology.hl7.org/CodeSystem/v2-0203$"
# alternative variant to accept every value in 'type/coding/system':
FRONTEND_DISPLAYED_PATIENT_FHIR_IDENTIFIER_TYPE_SYSTEM = ""
# Accepts only type/coding/code with the exact value 'MR'. This value means
# 'medical record number' in the system http://terminology.hl7.org/CodeSystem/v2-0203
# and is the recommended code for the patient ID in the hospital (if the variable
# is commented out then every value will be accepted). To match the start and end of the exact
# value, use caret (^) and dollar ($) symbols.
#FRONTEND_DISPLAYED_PATIENT_FHIR_IDENTIFIER_TYPE_CODE = "^MR$"
# Only Encounters that have one of the entries specified here as a class attribute are displayed
# in the frontend. This match must be exact, i.e. no patterns may be specified here.
# This can be used to ensure that, for example, no outpatient Encounters are displayed even though
# they have not yet ended.
FRONTEND_DISPLAYED_ENCOUNTER_CLASS = ["IMP"]
# Additional filter with which all encounters are filtered out for which the following filters do
# not apply. This can be used if, for example, the "Fachabteilungskontakt" do not have a partof
# relationship with the "Einrichtungskontakt" and can therefore only be removed using this filter.
# Same for the "Versorgungsstellenkontakt".
# An Encounter will be accepted, if at least one condition is fulfilled (OR connected). A condition
# defines which expressions of the Encounter should have which value. The values can be defined as
# grep patterns. Multilpe subconditions can be connected by '+' (logcal AND). All Patterns are Case
# INSENSITIVE!
#FRONTEND_DISPLAYED_ENCOUNTER_FILTER = [
# "enc_type_code = 'einrichtungskontakt' + enc_type_display = 'Einrichtungskontakt'",
# "enc_type_system = 'http://fhir.de/CodeSystem/Kontaktebene'"
# ]
# The codes for height, weight and BMI can be customised here. If several codes
# can occur, these must be entered in the respective list separated by spaces.
OBSERVATION_BODY_WEIGHT_SYSTEM = "http://loinc.org"
OBSERVATION_BODY_WEIGHT_CODES = "3142-7 29463-7"
OBSERVATION_BODY_HEIGHT_SYSTEM = "http://loinc.org"
OBSERVATION_BODY_HEIGHT_CODES = "8302-2"
OBSERVATION_BMI_SYSTEM = "http://loinc.org"
OBSERVATION_BMI_CODES = "39156-5"
[database]
PATH_TO_DB_CONFIG_TOML = "./cds_hub_db_config.toml"