initial commit; development of new shiny dqa tool

.gitignore

+/*
+/*/
+
+*.log
+
+!/.gitignore
+!/README.md
+!/FAQ.md
+!/docker/
+/docker/addfolder/
+!/DQA_Tool/
+!/DQA_Tool/app/
+/DQA_Tool/app/_settings/
+.Rproj.user
+*.Rproj
+.RData
+.Rhistory
\ No newline at end of file

DQA_Tool/app.R

+library(shiny)
+library(shinyjs)
+library(shinydashboard)
+library(shinyFiles)
+library(DT)
+library(data.table)
+library(ggplot2)
+library(config)
+library(jsonlite)
+library(RPostgres)
+
+# app entrypoint here
+shinyAppDir("app")
\ No newline at end of file

DQA_Tool/app/_utilities/SQL_i2b2.JSON

+{
+  "dt_patient.db": ["SELECT\n\tpatient_num       AS    patient_id, \n  birth_date::date  AS    birth_date, \n  sex_cd            AS    gender, \n  zip_cd            AS    zip_code\nFROM\n\ti2b2miracum.patient_dimension\nORDER BY \n\tpatient_num;"],
+  "dt_visit.db": ["SELECT\n\tpatient_num       AS    patient_id,\n  encounter_num     AS    encounter_id, \n  start_date::date  AS    encounter_start_date, \n  end_date::date    AS    encounter_end_date\nFROM\n  i2b2miracum.visit_dimension\nORDER BY \n  patient_num;"],
+  "dt_aitaa.db": ["SELECT \n  encounter_num     AS    encounter_id, \n  nval_num          AS    age\nFROM \n  i2b2miracum.observation_fact\nWHERE \n  concept_cd LIKE 'FALL:AITAA'\nGROUP BY\n\tencounter_num, patient_num, concept_cd, nval_num\nORDER BY\n  encounter_num;"],
+  "dt_aijaa.db": ["SELECT \n  encounter_num     AS    encounter_id, \n  nval_num          AS    age\nFROM \n  i2b2miracum.observation_fact\nWHERE \n  concept_cd LIKE 'FALL:AIJAA'\nGROUP BY\n\tencounter_num, patient_num, concept_cd, nval_num\nORDER BY\n  encounter_num;"],
+  "dt_aufnan.db": ["SELECT\n\tencounter_num     AS    encounter_id, \n  concept_cd        AS    admission_occasion\nFROM \n  i2b2miracum.observation_fact\nWHERE \n  concept_cd LIKE 'AUFNAN%'\nORDER BY \n  encounter_num;"],
+  "dt_aufngr.db": ["SELECT \n  encounter_num     AS    encounter_id, \n  concept_cd        AS    admission_reason\nFROM \n  i2b2miracum.observation_fact\nWHERE \n  concept_cd LIKE 'AUFNGR%'\nORDER BY \n  encounter_num;"],
+  "dt_entlgr.db": ["SELECT \n  encounter_num     AS    encounter_id, \n  concept_cd        AS    discharge_reason\nFROM \n  i2b2miracum.observation_fact\nWHERE \n  concept_cd LIKE 'ENTLGR%'\nORDER BY \n  encounter_num;"],
+  "dt_beatmst.db": ["SELECT \n  encounter_num     AS    encounter_id, \n  nval_num          AS    ventilation_hours\nFROM \n\ti2b2miracum.observation_fact \nWHERE \n\tconcept_cd LIKE 'FALL:BEATMST'\nORDER BY \n\tencounter_num;"],
+  "dt_icd.db": ["SELECT \n  encounter_num     AS    encounter_id, \n  concept_cd        AS    icd_code,\n\tmodifier_cd       AS    diagnosis_type\nFROM \n  i2b2miracum.observation_fact\nWHERE \n  concept_cd LIKE 'ICD%'\nORDER BY\n  encounter_num;"],
+  "dt_ops.db": ["SELECT \n  encounter_num     AS    encounter_id, \n  concept_cd        AS    ops_code,\n  start_date::date  AS    ops_date\nFROM \n  i2b2miracum.observation_fact\nWHERE \n  concept_cd LIKE 'OPS%'\nORDER BY\n  encounter_num;"],
+  "dt_fab.db": ["SELECT \n  encounter_num     AS    encounter_id, \n  tval_char         AS    department,\n  start_date::date  AS    department_start_date, \n  end_date::date    AS    department_end_date\nFROM \n\ti2b2miracum.observation_fact\nWHERE \n\tconcept_cd LIKE 'FACHABT%'\nORDER BY\n\tencounter_num;"],
+  "dt_pl_c5x.db": ["SELECT \n  ob.encounter_num    AS    encounter_id, \n  ob.patient_num      AS    patient_id,\n  ob.concept_cd       AS    icd_code,\n  pa.sex_cd           AS    gender,\n  regexp_matches(ob.concept_cd, 'ICD10:C5[1-8]', 'g') AS regex\nFROM \n  i2b2miracum.observation_fact AS ob\nLEFT OUTER JOIN \n  i2b2miracum.patient_dimension AS pa ON ob.patient_num = pa.patient_num\nORDER BY\n  ob.encounter_num;"],
+  "dt_pl_c6x.db": ["SELECT \n  ob.encounter_num    AS    encounter_id, \n  ob.patient_num      AS    patient_id,\n  ob.concept_cd       AS    icd_code,\n  pa.sex_cd           AS    gender,\n  regexp_matches(ob.concept_cd, 'ICD10:C6[0-3]', 'g') AS regex\nFROM \n  i2b2miracum.observation_fact AS ob\nLEFT OUTER JOIN \n  i2b2miracum.patient_dimension AS pa ON ob.patient_num = pa.patient_num\nORDER BY\n  ob.encounter_num;"],
+  "dt_pl_05xx.db": ["SELECT \n  ob.encounter_num    AS    encounter_id, \n  ob.patient_num      AS    patient_id,\n  ob.concept_cd       AS    admission_reason,\n  pa.sex_cd           AS    gender,\n  regexp_matches(ob.concept_cd, 'AUFNGR:05', 'g') AS regex\nFROM \n  i2b2miracum.observation_fact AS ob\nLEFT OUTER JOIN \n  i2b2miracum.patient_dimension AS pa ON ob.patient_num = pa.patient_num\nORDER BY\n  ob.encounter_num;"],
+  "dt_pl_o0099.db": ["SELECT \n  ob.encounter_num    AS    encounter_id, \n  ob.patient_num      AS    patient_id,\n  ob.concept_cd       AS    icd_code,\n  pa.sex_cd           AS    gender,\n  regexp_matches(ob.concept_cd, 'ICD10:O[0-9]', 'g') AS regex\nFROM \n  i2b2miracum.observation_fact AS ob\nLEFT OUTER JOIN \n  i2b2miracum.patient_dimension AS pa ON ob.patient_num = pa.patient_num\nORDER BY\n  ob.encounter_num;"]
+}
\ No newline at end of file

DQA_Tool/app/_utilities/SQL_omop.JSON

+{
+  "dt_patient.db": ["SELECT\n  per.person_id       AS    patient_id, \n  per.year_of_birth   AS    birth_date,\n  per.month_of_birth  AS    birth_month,\n  con.concept_code    AS    gender, \n  loc.zip             AS    zip_code\nFROM\n\tp21_cdm.person AS per\nLEFT OUTER JOIN \n\tp21_cdm.location AS loc ON \n\tper.location_id = loc.location_id\nLEFT OUTER JOIN \n\tp21_cdm.concept AS con ON \n\tper.gender_concept_id = con.concept_id\nORDER BY \n\tper.person_id;"],
+  "dt_visit.db": ["SELECT\n  person_id               AS    patient_id, \n  visit_occurrence_id     AS    encounter_id, \n  visit_start_date::DATE  AS    encounter_start_date, \n  visit_end_date::DATE    AS    encounter_end_date\nFROM \n\tp21_cdm.visit_occurrence\nORDER BY \n\tperson_id;"],
+  "dt_aitaa.db": ["SELECT \n  obs.visit_occurrence_id AS    encounter_id, \n  obs.value_as_number     AS    age\nFROM \n  p21_cdm.observation AS obs\nWHERE \n  obs.observation_concept_id = 4265453 AND\n  obs.unit_concept_id = 8512\nORDER BY\n  obs.visit_occurrence_id;"],
+  "dt_aijaa.db": ["SELECT \n  obs.visit_occurrence_id AS    encounter_id, \n  obs.value_as_number     AS    age\nFROM \n  p21_cdm.observation AS obs\nWHERE \n  obs.observation_concept_id = 4265453 AND\n  obs.unit_concept_id = 9448\nORDER BY\n  obs.visit_occurrence_id;"],
+  "dt_aufnan.db": ["SELECT \n  obs.visit_occurrence_id AS    encounter_id, \n  obs.value_as_string     AS    admission_occasion\nFROM \n  p21_cdm.observation AS obs\nWHERE \n  obs.observation_concept_id IN (4079617, 4164916, 4138807, 4123917, 4164916, 4216316, 4146925, 4194310) AND \n  obs.observation_type_concept_id = 43542355\nORDER BY\n  obs.visit_occurrence_id;"],
+  "dt_aufngr.db": ["SELECT \n  obs.visit_occurrence_id AS    encounter_id, \n  obs.value_as_string     AS    admission_reason\nFROM \n  p21_cdm.observation AS obs\nWHERE \n  obs.observation_concept_id IN (4214577, 4010105, 4123929, 4235698, 4214577, 4216316, 4213258, 4180080) AND \n  obs.observation_type_concept_id = 43542355\nORDER BY\n  obs.visit_occurrence_id;"],
+  "dt_entlgr.db": ["SELECT \n  obs.visit_occurrence_id AS    encounter_id, \n  obs.value_as_string     AS    discharge_reason\nFROM \n  p21_cdm.observation AS obs\nWHERE \n  obs.observation_concept_id IN (4082735, 4203130, 4021968, 4147710, 4216643, 4139566, 4143443, 4127600, 45878214, 4084686, 4213258, 4084500) AND\n  obs.observation_type_concept_id = 38000280\nORDER BY\n  obs.visit_occurrence_id;"],
+  "dt_beatmst.db": ["SELECT \n  obs.visit_occurrence_id AS    encounter_id, \n  obs.value_as_number     AS    ventilation_hours\nFROM \n  p21_cdm.observation AS obs\nWHERE \n  obs.observation_concept_id = 4108449\nORDER BY\n  obs.visit_occurrence_id;"],
+  "dt_icd.db": ["SELECT\n  cond.visit_occurrence_id\t      AS \t\tencounter_id,\n  cond.condition_concept_id\t      AS \t\tsnowmed,\n  icd.source_code\t\t\t            AS\t\ticd_code,\n  cond.condition_type_concept_id  AS    diagnosis_type\nFROM\n(SELECT \n  DISTINCT\n  source_code,\n  target_concept_id\nFROM\n  p21_cdm.source_to_concept_map\nWHERE\n  source_vocabulary_id='ICD10GM') AS icd\nJOIN \n  p21_cdm.condition_occurrence AS cond ON\n  cond.condition_concept_id = icd.target_concept_id\nWHERE\n  cond.condition_type_concept_id IN (44786627, 44786629)\n  AND cond.condition_type_concept_id != 0\nORDER BY \n  cond.visit_occurrence_id;"],
+  "dt_ops.db": ["SELECT \n  visit_occurrence_id\t\t  AS\t\tencounter_id,\n  procedure_concept_id\t\tAS\t\tsnowmed,\n  procedure_source_value\tAS\t\tops_code,\n  procedure_date::date \t\tAS \t\tops_date\nFROM\n  p21_cdm.procedure_occurrence\nORDER BY \n  visit_occurrence_id;"],
+  "dt_fab.db": ["SELECT \n  visit_occurrence_id\t\tAS \t\tencounter_id,\n  care_site_id\t\t\t\t  AS\t\tdepartment\nFROM \n  p21_cdm.visit_occurrence;"],
+  "dt_pl_c5x.db": ["SELECT \n  cond.visit_occurrence_id\t\tAS \t\tencounter_id,\n  cond.person_id\t\t\t\t      AS \t\tpatient_id,\n  icd.source_code\t\t\t\t      AS \t\ticd_code,\n  con.concept_code  \t\t\t    AS\t  gender\nFROM\n(SELECT\n  DISTINCT\n  source_code,\n  target_concept_id,\n  regexp_matches(source_code, 'C5[1-8]', 'g')\nFROM\n  p21_cdm.source_to_concept_map\nWHERE\n  source_vocabulary_id='ICD10GM'\nORDER BY \n  source_code) AS icd\nJOIN \n  p21_cdm.condition_occurrence AS cond ON\n  cond.condition_concept_id = icd.target_concept_id\nLEFT OUTER JOIN \n  p21_cdm.person AS per ON \n  cond.person_id = per.person_id\nLEFT OUTER JOIN \n  p21_cdm.concept AS con ON \n  per.gender_concept_id = con.concept_id\nORDER BY \n  cond.visit_occurrence_id;"],
+  "dt_pl_c6x.db": ["SELECT \n  cond.visit_occurrence_id\t\tAS \t\tencounter_id,\n  cond.person_id\t\t\t\t      AS \t\tpatient_id,\n  icd.source_code\t\t\t\t      AS \t\ticd_code,\n  con.concept_code  \t\t\t    AS\t  gender\nFROM\n(SELECT\n  DISTINCT\n  source_code,\n  target_concept_id,\n  regexp_matches(source_code, 'C6[0-3]', 'g')\nFROM\n  p21_cdm.source_to_concept_map\nWHERE\n  source_vocabulary_id='ICD10GM'\nORDER BY \n  source_code) AS icd\nJOIN \n  p21_cdm.condition_occurrence AS cond ON\n  cond.condition_concept_id = icd.target_concept_id\nLEFT OUTER JOIN \n  p21_cdm.person AS per ON \n  cond.person_id = per.person_id\nLEFT OUTER JOIN \n  p21_cdm.concept AS con ON \n  per.gender_concept_id = con.concept_id\nORDER BY \n  cond.visit_occurrence_id;"],
+  "dt_pl_05xx.db": ["SELECT \n  obs.visit_occurrence_id\t\t  AS \t\t  encounter_id,\n  obs.person_id\t\t\t\t\t      AS \t\t  patient_id,\n  obs.value_as_string     \t\tAS    \tadmission_reason,\n  obs.observation_concept_id\tAS \t\t  snowmed,\n  con.concept_code  \t\t\t    AS\t    gender\nFROM \n  p21_cdm.observation AS obs\nLEFT OUTER JOIN \n  p21_cdm.person AS per ON \n  obs.person_id = per.person_id\nLEFT OUTER JOIN \n  p21_cdm.concept AS con ON \n  per.gender_concept_id = con.concept_id\nWHERE \n  obs.observation_concept_id = 4214577 AND\n  obs.observation_type_concept_id = 43542355\nORDER BY\n  obs.visit_occurrence_id;"],
+  "dt_pl_o0099.db": ["SELECT \n  cond.visit_occurrence_id\t\tAS \t\tencounter_id,\n  cond.person_id\t\t\t\t      AS \t\tpatient_id,\n  icd.source_code\t\t\t\t      AS \t\ticd_code,\n  con.concept_code  \t\t\t    AS\t  gender\nFROM\n(SELECT\n  DISTINCT\n  source_code,\n  target_concept_id,\n  regexp_matches(source_code, 'O[0-9]', 'g')\nFROM\n  p21_cdm.source_to_concept_map\nWHERE\n  source_vocabulary_id='ICD10GM'\nORDER BY \n  source_code) AS icd\nJOIN \n  p21_cdm.condition_occurrence AS cond ON\n  cond.condition_concept_id = icd.target_concept_id\nLEFT OUTER JOIN \n  p21_cdm.person AS per ON \n  cond.person_id = per.person_id\nLEFT OUTER JOIN \n  p21_cdm.concept AS con ON \n  per.gender_concept_id = con.concept_id\nORDER BY \n  cond.visit_occurrence_id;"]
+}
\ No newline at end of file

DQA_Tool/app/_utilities/functions.R

+# get db_settings
+getDBsettings <- function(input, rv){
+  rv$tab <- data.table("keys" = character(), "value" = character())
+  # create description of column selections
+  vec <- c("dbname", "host", "port", "user", "password")
+  selections <- c("config_targetdb_dbname", "config_targetdb_hostname", "config_targetdb_port", "config_targetdb_user", "config_targetdb_password")
+  
+  lapply(1:length(vec), function(g) {
+    rv$tab <- rbind(rv$tab, cbind("keys" = vec[g], "value" = eval(parse(text=paste0("input$", selections[g])))))
+  })
+  
+  # if one column is selected multiple times
+  if ("" %in% rv$tab[,value] || any(rv$tab[,grepl("\\s", value)])){
+    showModal(modalDialog(
+      title = "Invalid values",
+      "No empty strings or spaces allowed in database configurations"
+    ))
+    return(NULL)
+    
+  } else {
+    print(rv$tab)
+    outlist <- lapply(setNames(vec, vec), function(g){
+      rv$tab[keys==g,value]
+    })
+    return(outlist)
+  }
+}
+
+# test db connection
+testDBcon <- function(rv){
+  drv <- RPostgres::Postgres()
+  tryCatch({
+    rv$db_con <- dbConnect(
+      drv = drv,
+      dbname = rv$db_settings$dbname,
+      host = rv$db_settings$host,
+      port = rv$db_settings$port,
+      user = rv$db_settings$user,
+      password = rv$db_settings$password
+    )
+    
+    print(RPostgres::dbGetInfo(rv$db_con))
+  }, error = function(e){
+    showModal(modalDialog(
+      title = "Error occured during testing database connection",
+      "An error occured during the test of the database connection. Please check your settings and try again."
+    ))
+    rv$db_con <- NULL
+    cat("\nDB connection error\n")
+  })
+}
+
+fireSQL <- function(rv, jsonobj){
+  withProgress(
+    message = paste0("Getting ", jsonobj, " data from server"), value = 0, {
+    # avoid sql-injection
+    # https://db.rstudio.com/best-practices/run-queries-safely/
+    sql <- DBI::sqlInterpolate(rv$db_con, rv$sql[[jsonobj]])
+    incProgress(1/1, detail = "... working hard to get data ...")
+    # get data
+    rv$data_objects[[jsonobj]] <- paste0("rv$", jsonobj)
+    return(data.table(dbGetQuery(rv$db_con, sql), stringsAsFactors = TRUE))
+  })
+}
\ No newline at end of file

DQA_Tool/app/_utilities/settings_default.yml

+default:
+  i2b2:
+    dbname: "i2b2"
+    host: "i2b2-pg"
+    port: 5432
+    user: "i2b2"
+    password: "demouser"
+  omop:
+    dbname: "OHDSI"
+    host: "omop-pg"
+    port: 5432
+    user: "ohdsi_admin_user"
+    password: "admin1"
+    
\ No newline at end of file

DQA_Tool/app/global.R

+# assign global variable here
\ No newline at end of file

DQA_Tool/app/reset.js

+shinyjs.reset = function() {
+    console.log("Entered shinyjs.reset");
+    //location.reload();
+    history.go(0);
+  };
\ No newline at end of file

DQA_Tool/app/server.R

+shinyServer(function(input, output, session) {
+
+    # if you want to source any files with functions, do it inside the server-function, so the information will not be shared across sessions
+    source("./_utilities/functions.R", encoding = "UTF-8")
+    
+    # define reactive values here
+    rv <- reactiveValues(
+        file = NULL,
+        db_settings = NULL,
+        db_con = NULL,
+        db_getdata = FALSE,
+        data_objects = list()
+    )
+    
+    
+    
+    ########################
+    # tab_config
+    ########################
+    # observe source file directory
+    observe({
+        shinyDirChoose(input, "config_sourcedir_in", updateFreq = 0, session = session, defaultPath = "", roots = c(home="/home/"), defaultRoot = "home")
+        
+        output$config_sourcedir_out <- reactive({
+            roots = c(home="/home/")
+            sourcefiledir <- parseDirPath(roots, input$config_sourcedir_in)
+            paste(sourcefiledir)
+        })
+    })
+    
+    # observe target database configuration
+    observeEvent(input$config_targetdb_rad, {
+        print(input$config_targetdb_rad)
+        
+        # if "./_utilities/settings.yml" not present, read default settings list here and populate textInputs
+        if (!file.exists(paste0("./_settings/settings_", input$config_targetdb_rad, ".JSON"))){
+            cat("\nReading default settings\n")
+            rv$db_settings <- config::get(input$config_targetdb_rad, file = "./_utilities/settings_default.yml")
+            
+            showModal(modalDialog(
+                "Loading default configuration", 
+                title = "Loading default database configuration")
+            )
+        } else {
+            rv$db_settings <- fromJSON(paste0("./_settings/settings_", input$config_targetdb_rad, ".JSON"))
+        }
+        
+        updateTextInput(session, "config_targetdb_dbname", value = rv$db_settings$dbname)
+        updateTextInput(session, "config_targetdb_hostname", value = rv$db_settings$host)
+        updateTextInput(session, "config_targetdb_port", value = rv$db_settings$port)
+        updateTextInput(session, "config_targetdb_user", value = rv$db_settings$user)
+        updateTextInput(session, "config_targetdb_password", value = rv$db_settings$password)
+    })
+    
+    # observe saving of settings
+    observeEvent(input$config_targetdb_save_btn,{
+        rv$db_settings <- getDBsettings(input, rv)
+            
+        if (!is.null(rv$db_settings)){
+            print(rv$db_settings)
+            
+            if (!dir.exists("./_settings/")){
+                dir.create("./_settings/")
+            }
+            
+            writeLines(toJSON(rv$db_settings,
+                              pretty = T,
+                              auto_unbox = F),
+                       paste0("./_settings/settings_", input$config_targetdb_rad, ".JSON"))
+        }
+    })
+    
+    # test db-connection
+    observeEvent(input$config_targetdb_test_btn, {
+        rv$db_settings <- getDBsettings(input, rv)
+        
+        if (!is.null(rv$db_settings)){
+            
+            testDBcon(rv)
+        
+            if (!is.null(rv$db_con)){
+                cat("\nDB connection successfully established\n")
+                showModal(modalDialog(
+                    title = "Database connection successfully tested",
+                    "The database connection has been successfully established and tested."
+                ))
+            }
+            
+            # workaround to tell ui, that db_connection is there
+            output$dbConnection <- reactive({
+                if (!is.null(rv$db_con)){
+                    shinyjs::hide("dash_instruction")
+                    return(TRUE)
+                } else {
+                    shinyjs::show("dash_instruction")
+                    return(FALSE)
+                }
+            })
+            outputOptions(output, 'dbConnection', suspendWhenHidden=FALSE)
+        }
+    })
+    
+    # load sql statements
+    observe({
+        req(rv$db_con)
+        
+        if (is.null(rv$sql)){
+            if (input$config_targetdb_rad == "i2b2"){
+                rv$sql <- fromJSON("./_utilities/SQL_i2b2.JSON")
+            } else if (input$config_targetdb_rad == "omop"){
+                rv$sql <- fromJSON("./_utilities/SQL_omop.JSON")
+            }
+        }
+    })
+    
+    
+    ########################
+    # tab_dashboard
+    ########################
+    output$dash_instruction <- renderText({
+        paste0("Please configure and test your database connection in the settings tab.\nThen return here in order to load the data.")
+    })
+    
+    observeEvent(input$dash_load_btn, {
+        testDBcon(rv)
+        
+        if (!is.null(rv$sql)){
+            rv$db_getdata <- TRUE
+            
+            output$menu <- renderMenu({
+                sidebarMenu(
+                    menuItem("Raw data", tabName = "tab_rawdata1", icon = icon("table"))
+                )
+            })
+            updateTabItems(session, "tabs", "tab_rawdata1")
+            
+            output$rawdata1_uiout <- renderUI({
+                selectInput("rawdata1_sel", "Data object", rv$data_objects, multiple=TRUE, selectize=FALSE)
+            })
+            
+            shinyjs::disable("dash_load_btn")
+            
+        } else {
+            cat("\nSQL not loaded yet\n")
+        }
+    })
+    
+    # TODO overview: count encounter ids, count begleitlieger, count patient ids
+    
+    ########################
+    # tab_rawdata1
+    ########################
+    # dt_patient.db
+    observe({
+        req(rv$db_getdata)
+        vec <- c("dt_patient.db", "dt_visit.db", "dt_aitaa.db", "dt_aijaa.db",
+                 "dt_aufnan.db", "dt_aufngr.db", "dt_entlgr.db", "dt_beatmst.db",
+                 "dt_icd.db", "dt_ops.db", "dt_fab.db",
+                 "dt_pl_c5x.db", "dt_pl_c6x.db", "dt_pl_05xx.db", "dt_pl_o0099.db")
+        
+        for (i in vec){
+            if (is.null(eval(parse(text=paste0("rv$", i))))){
+                rv[[i]] <- fireSQL(rv, i)
+            }
+        }
+        invisible(gc())
+        rv$db_getdata <- FALSE
+    })
+    
+    observeEvent(input$rawdata1_sel, {
+        output$rawdata1_table <- DT::renderDataTable({
+            DT::datatable(eval(parse(text= input$rawdata1_sel)), options = list(scrollX = TRUE, pageLength = 20))
+        })
+    })
+})

DQA_Tool/app/ui.R

+shinyUI(dashboardPage(skin = "black",
+
+    # Application title
+    dashboardHeader(title = "Shiny DQA Tool"),
+
+    dashboardSidebar(
+
+        # Include shinyjs in the UI Sidebar
+        shinyjs::useShinyjs(), 
+        
+        #Sidebar Panel
+        sidebarMenu(id = "tabs",
+                    menuItem("Dashboard", tabName = "tab_dashboard", icon = icon("file")),
+                    sidebarMenuOutput("menu"),
+                    menuItem("Settings", tabName = "tab_config", icon = icon("file"))
+        )),
+    
+    dashboardBody(
+
+        # Include shinyjs in the UI Body
+        shinyjs::useShinyjs(),
+
+        # js reset function 
+        # https://stackoverflow.com/questions/25062422/restart-shiny-session
+        extendShinyjs(script = "reset.js", functions = "reset"), # Add the js code to the page
+
+        tabItems(
+            tabItem(tabName = "tab_dashboard",
+                    fluidRow(
+                        box(title = "Overview",
+                            verbatimTextOutput("dash_instruction"),
+                            conditionalPanel(
+                                condition = "output.dbConnection",
+                                actionButton("dash_load_btn", "Load data")
+                            ),
+                            width = 6
+                        )
+                    )
+            ),
+            
+            tabItem(tabName = "tab_config",
+                    fluidRow(
+                        box(
+                            title = "Target Database Configuration",
+                            radioButtons(inputId = "config_targetdb_rad", 
+                                         label = "Pleas select the target database",
+                                         choices = list("i2b2" = "i2b2", 
+                                                        "OMOP" = "omop"), 
+                                         selected = NULL, 
+                                         inline = TRUE),
+                            textInput("config_targetdb_dbname", label = "Database name"),
+                            textInput("config_targetdb_hostname", label = "Host name"),
+                            textInput("config_targetdb_port", label = "Port"),
+                            textInput("config_targetdb_user", label = "Username"),
+                            textInput("config_targetdb_password", label = "Password"),
+                            div(class = "row", style = "text-align: center;",
+                                actionButton("config_targetdb_save_btn", "Save settings"),
+                                actionButton("config_targetdb_test_btn", "Test connection")),
+                            width = 6
+                        ),
+                        
+                        box(title = "Source File Directory",
+                            div(class = "row",
+                                div(class="col-sm-4", shinyDirButton("config_sourcedir_in", 
+                                                                     "Source Dir", 
+                                                                     "Please select the source file directory", 
+                                                                     buttonType = "default", 
+                                                                     class = NULL, 
+                                                                     icon = NULL, 
+                                                                     style = NULL)),
+                                div(class = "col-sm-8", verbatimTextOutput("config_sourcedir_out"))
+                            ),
+                            width = 6
+                        )
+                    )
+            ), 
+            
+            tabItem(tabName = "tab_rawdata1",
+                    fluidRow(
+                        box(title = "Select data",
+                            uiOutput("rawdata1_uiout"),
+                            width = 4
+                        ),
+                        box(
+                            title = "Raw data",
+                            dataTableOutput("rawdata1_table"),
+                            width = 8
+                        )
+                    )
+            )
+        )
+    )
+))

README.md

+# docker-shiny_baser
+
+- this is a basic Shiny container  
+
+- put your Shiny app to the folder "shiny_app"
+
+- add your required R packages to the Dockerfile before building the image 
+
+- to build your image:
+```
+cd ./docker/
+chmod +x build_image.sh
+./build_image.sh
+```
+
+# More Infos:
+- about Shiny: https://www.rstudio.com/products/shiny/  
+- RStudio and Shiny are trademarks of RStudio, Inc.  

docker/Dockerfile

+FROM ubuntu:18.04
+
+# set environment variable to supress user interaction
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    apt-utils \ 
+    dialog \
+    dirmngr \
+    gdebi-core \
+    gpg-agent \
+    less \
+    libcurl4-openssl-dev \
+    libssh-dev \
+    libssl-dev \
+    locales \
+    nano \
+    software-properties-common \
+    ssh \
+    sudo \
+    tar \
+    unzip \
+    vim \
+    wget \
+    xtail
+
+RUN apt-get clean
+
+RUN locale-gen en_US.utf8 \
+    && /usr/sbin/update-locale LANG=en_US.UTF-8
+ENV LANG=en_US.UTF-8
+
+# add user + password
+# https://stackoverflow.com/questions/2150882/how-to-automatically-add-user-account-and-password-with-a-bash-script
+RUN useradd -ms /bin/bash user
+RUN echo user:password | chpasswd 
+
+# Add R apt repository for latest R
+# https://cran.r-project.org/bin/linux/ubuntu/
+RUN gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9 | sudo apt-key add -
+RUN add-apt-repository "deb http://cran.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran35/"
+
+# install basic R packages
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    r-base-dev \
+    pandoc \
+    pandoc-citeproc \
+    libcairo2-dev \
+    libxt-dev \
+    libsasl2-dev \
+    libxml2-dev \
+    libgmp3-dev \
+    libpq-dev \
+    libffi-dev \
+    libmpfr-dev \
+    libgsl-dev \
+    libglu1-mesa-dev \
+    texinfo \
+    unixodbc-dev
+
+RUN apt-get clean && apt-get autoclean
+
+
+# install opensource shiny server
+# https://www.rstudio.com/products/shiny/download-server/
+# https://github.com/rocker-org/shiny/blob/master/Dockerfile
+RUN wget --no-verbose https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION -O "version.txt" && \
+    VERSION=$(cat version.txt)  && \
+    wget --no-verbose "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
+    gdebi -n ss-latest.deb && \
+    rm -f version.txt ss-latest.deb
+
+# install necessary r-packages
+ARG p_base="shiny \
+    shinyjs \
+    shinydashboard \
+    shinyWidgets \
+    DT \
+    data.table \
+    ggplot2"
+ARG p_add="RPostgres"
+
+RUN for package in $p_base; do \
+    R -q -e "p <- \"$package\"; if (isFALSE(p %in% installed.packages()[,\"Package\"])){; cat(paste(\"Installing package:\", p, \"\n\n\")); install.packages(p, repos = \"https://ftp.fau.de/cran/\", quiet=T);} else {;cat(paste(\"Package\", p, \"is already installed\n\n\"));}"; \
+    done
+RUN for package in $p_add; do \
+    R -q -e "p <- \"$package\"; if (isFALSE(p %in% installed.packages()[,\"Package\"])){; cat(paste(\"Installing package:\", p, \"\n\n\")); install.packages(p, repos = \"https://ftp.fau.de/cran/\", quiet=T);} else {;cat(paste(\"Package\", p, \"is already installed\n\n\"));}"; \
+    done
+
+# server configuration
+ADD shiny-server.conf /etc/shiny-server/shiny-server.conf
+
+# copy app
+ADD addfolder /srv/shiny-server/
+
+# fix permissions
+RUN chown -R shiny:shiny /srv/shiny-server/
+
+
+# add log-script
+ADD show-log.sh /
+RUN chmod +x show-log.sh
+
+# make app available at port 3838
+EXPOSE 3838
+
+# copy server script
+# https://github.com/rocker-org/shiny/blob/master/shiny-server.sh
+ADD shiny-server.sh /usr/bin/shiny-server.sh 
+RUN cd /usr/bin/ && chmod +x shiny-server.sh 
+
+CMD ["/usr/bin/shiny-server.sh"]

docker/build_image.sh

+#!/bin/bash
+
+mkdir -p addfolder/
+cp -R ../shiny_app/* addfolder/
+
+docker build -f Dockerfile -t dqa-shiny-web-app .
+
+rm -rf addfolder/

docker/docker-compose.yml

+version: '3'
+
+services:
+  shiny:
+    container_name: dqa-app
+    image: dqa-shiny-web-app
+    restart: unless-stopped
+    ports:
+    - "3838:3838"
+    networks:
+    - shiny_app_net
+
+networks:
+  shiny_app_net: 
\ No newline at end of file

docker/shiny-server.conf

+# https://docs.rstudio.com/shiny-server/#server-management
+
+# Define the user we should use when spawning R Shiny processes
+run_as shiny;
+
+# Define a top-level server which will listen on a port
+server {
+  # Instruct this server to listen on port 3838
+  listen 3838;
+
+  # Define the location available at the base URL
+  location / {
+
+    # Run this location in 'site_dir' mode, which hosts the entire directory
+    # tree at '/srv/shiny-server'
+    site_dir /srv/shiny-server;
+    
+    # Define where we should put the log files for this location
+    log_dir /var/log/shiny-server;
+    
+    # Should we list the contents of a (non-Shiny-App) directory when the user 
+    # visits the corresponding URL?
+    directory_index on;
+  }
+}
\ No newline at end of file

docker/shiny-server.sh

+#!/bin/sh
+
+# Make sure the directory for individual app logs exists
+mkdir -p /var/log/shiny-server
+chown shiny.shiny /var/log/shiny-server
+
+if [ "$APPLICATION_LOGS_TO_STDOUT" = "false" ];
+then
+    exec shiny-server 2>&1
+else
+    # start shiny server in detached mode
+    exec shiny-server 2>&1 &
+
+    # push the "real" application logs to stdout with xtail
+    exec xtail /var/log/shiny-server/
+fi
\ No newline at end of file

docker/show-log.sh

+#!/bin/bash
+
+cd /var/log/shiny-server/
+tail -f shiny*.log
\ No newline at end of file