Merge pull request #127 from medizininformatik-initiative/release

Release

.gitignore

@@ -11,5 +11,4 @@ outputGlobal
 *.RData
 REDCap-app/html/redcap
 REDCap-app/html/redcapdocs
-REDCap-app/build/config/msmtprc
 REDCap-app/log

Dockerfile_R

@@ -27,7 +27,7 @@ RUN R CMD INSTALL --preclean --no-multiarch --with-keep.source R-kds2db/kds2db
 
 # db2frontend
 
-RUN apt-get install -y libsodium-dev
+RUN apt-get install -y libsodium-dev libsecret-1-0
 
 RUN /rocker_scripts/bin/install2.r redcapAPI dplyr
 

Install.md

@@ -0,0 +1,24 @@
+# Installationsanleitung bzw. Anleitung zur Einrichtung der INTERPOLAR IT Tools
+
+  * Checkout des INTERPOLAR Repositories \
+    ```git clone [email protected]:medizininformatik-initiative/INTERPOLAR.git```
+  * Wechsel in das geclonte Verzeichnis \
+    ```cd INTERPOLAR```
+  * den Branch 'release' auschecken \
+    ```git checkout release```
+  * Konfigurationsdateien aus den Vorlagen (Templates) erstellen
+    * Postgres-amts_db/template_env_amts_db_admin.password nach Postgres-amts_db/.env_amts_db_admin.password kopieren und ein Passwort-String einfügen. Dieses Passwort ist für den Admin-Nutzer der amts-Datenbank. \
+    ```cp Postgres-amts_db/template_env_amts_db_admin.password Postgres-amts_db/.env_amts_db_admin.password```
+    * REDCap-db/template_env-redcap-db kopieren nach REDCap-db/.env-redcap-db \
+    ```cp REDCap-db/template_env-redcap-db REDCap-db/.env-redcap-db```
+    * REDCap-db/template_env_redcap_db.password kopieren nach REDCap-db/.env_redcap_db.password und tragen Sie ein Passwort für den Nutzer der redcap Datenbank ein \
+    ```cp REDCap-db/template_env_redcap_db.password REDCap-db/.env_redcap_db.password```
+    * REDCap-db/template_env_redcap_db_root.password kopieren nach REDCap-db/.env_redcap_db_root.password und tragen Sie ein Passwort für den root-Nutzer der Datenbank ein \
+    ```cp REDCap-db/template_env_redcap_db_root.password REDCap-db/.env_redcap_db_root.password```
+  * Führen Sie die Anweisungen in [REDCap-app/Readme.md](REDCap-app/Readme.md) aus
+  * Führen Sie die Anweisungen in [REDCap-app/html/Readme.md](REDCap-app/html/Readme.md) aus
+  * Führen Sie docker-compose aus: \
+    ```docker-compose up```
+  * Die amts_db (Postges-Datenbank) erreichen Sie im Browser (PGAdmin) über die URL: [http://127.0.0.1:8089/](http://127.0.0.1:8089/)
+  * Das Frontend (REDCap) erreichen Sie im Browser über die URL: [http://127.0.0.1:8082/redcap](http://127.0.0.1:8082/redcap)
+

Postgres-amts_db/Readme.md

@@ -0,0 +1,4 @@
+# AMTS Datenbank (amts_db)
+
+Mit dem docker-compose wird ein PGAdmin zur Verfügung gestellt, welches unter der folgenden URL verfügbar ist: \
+[http://127.0.0.1:8089/](http://127.0.0.1:8089/)

Postgres-amts_db/postgresql.conf

@@ -816,7 +816,7 @@ default_text_search_config = 'pg_catalog.english'
 shared_preload_libraries = 'pg_cron'
 
 # optionally, specify the database in which the pg_cron background worker should run (defaults to postgres)
-cron.database_name = 'interpolar'
+cron.database_name = 'amts_db'
 
 # optionally, specify the timezone in which the pg_cron background worker should run (defaults to GMT). E.g:
 # cron.timezone = 'PRC'

R-dataprocessor/README.md

@@ -0,0 +1,7 @@
+### Data Processor
+
+Dies ist das Data Processor Modul, in dem sämtliche Umwandlungen von Daten erfolgen:
+
+* Validierung der FHIR Daten
+* Harmonisierung (Einheiten, Zeiten, ...)
+* Berechnung von Medication Related Problems (MRP)

R-dataprocessor/dataprocessor/.Rbuildignore

@@ -0,0 +1,3 @@
+^dataprocessor\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$

R-dataprocessor/dataprocessor/.gitignore

@@ -0,0 +1 @@
+.Rproj.user

R-dataprocessor/dataprocessor/DESCRIPTION

@@ -0,0 +1,16 @@
+Package: dataprocessor
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R: 
+    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: Apache License (>= 2)
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
+Imports: 
+    etlutils
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

R-dataprocessor/dataprocessor/LICENSE.md

@@ -0,0 +1,194 @@
+Apache License
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R-dataprocessor/dataprocessor/NAMESPACE

@@ -0,0 +1,2 @@
+# Generated by roxygen2: do not edit by hand
+

R-dataprocessor/dataprocessor/dataprocessor.Rproj

@@ -0,0 +1,22 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

R-dataprocessor/dataprocessor/tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(dataprocessor)
+
+test_check("dataprocessor")

R-dataprocessor/dataprocessor/tests/testthat/test-DUMMY-TEST.R

@@ -0,0 +1,4 @@
+# dummy test to fulfill all conditions for package install
+test_that("This is a dummy test and should be removed", {
+  expect_true(TRUE)
+})

R-db2frontend/StartDB2Frontend.R

@@ -1,8 +1,11 @@
-##########################################################################
+# chance the working directory to the main directory
+if (grepl('/db2frontend$', getwd())) setwd("../..")
+if (grepl('/R-db2frontend$', getwd())) setwd("../")
+
 # free memory
-##########################################################################
 rm(list = ls())
 
+library(etlutils)
 library(db2frontend)
 
 copyDB2Redcap()

R-db2frontend/db2frontend/R/dbDatatoREDCap.R

@@ -13,28 +13,13 @@
 #'
 initConstants <- function() {
   # Path to the module configuration TOML file
-  path2config_toml <- ifelse(interactive(), './R-db2frontend', '.')
-  path2config_toml <- paste0(path2config_toml, '/db2frontend_config.toml')
+  path2config_toml <- './R-db2frontend/db2frontend_config.toml'
   # Load module configuration settings
   etlutils::initConstants(path2config_toml)
-
   # Load database configuration settings
   etlutils::initConstants(PATH_TO_DB_CONFIG_TOML)
 }
 
-initConstants <- function() {
-  ###
-  # Read the module configuration toml file.
-  ###
-  path2config_toml <- ifelse(interactive(), './R-db2frontend', '.')
-  path2config_toml <- paste0(path2config_toml, '/db2frontend_config.toml')
-  etlutils::initConstants(path2config_toml)
-  ###
-  # Read the DB configuration toml file
-  ###
-  etlutils::initConstants(PATH_TO_DB_CONFIG_TOML)
-}
-
 #' Copy Database Content to REDCap
 #'
 #' This function retrieves data from the view or table in a database
@@ -60,6 +45,7 @@ initConstants <- function() {
 copyDB2Redcap <- function() {
   #get data from patient view / tabelle, schema _out
   initConstants()
+
   #establish connection to db
   dbcon <- etlutils::dbConnect(DB_DB2FRONTEND_USER, DB_DB2FRONTEND_PASSWORD, DB_GENERAL_NAME, DB_GENERAL_HOST,
                    DB_GENERAL_PORT, DB_DB2FRONTEND_SCHEMA_OUT)
@@ -70,7 +56,7 @@ copyDB2Redcap <- function() {
                               pat_gschlcht FROM patient")
 
   #connect to REDCap project
-  redcapcon <- redcapAPI::redcapConnection(url = url,token = token)
+  redcapcon <- redcapAPI::redcapConnection(url = REDCAP_URL, token = REDCAP_TOKEN)
 
   #send data to REDCap
   redcapAPI::importRecords(redcapcon, data = new_data, logfile = "log.txt")

R-db2frontend/db2frontend_config.toml

@@ -1,3 +1,10 @@
 [database]
 
 PATH_TO_DB_CONFIG_TOML = "./amts_db_config.toml"
+
+[redcap]
+
+# URL for the user's REDCap database API.
+REDCAP_URL = "http://redcap/redcap/api/"
+# REDCap API token
+REDCAP_TOKEN = "Fill with your REDCap API token"