Merged with dev conflicts in requirements and gitignore

RShinyApps/.Rproj.user/shared/notebooks/paths

@@ -1,45 +1,3 @@
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/ChangePoint/server.R="03DE5832"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/ChangePoint/ui.R="D84E3A25"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/Dash/server.R="A1CDDFAF"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/Dash/ui.R="E47E3ADA"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/DynPRR/server.R="5C121CA5"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/DynPRR/ui.R="4B61A081"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/LrTest/../sharedscripts/getters.R="A95D52A5"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/LrTest/LRT.R="D8AE1FE7"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/LrTest/server.R="CA392995"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/LrTest/ui.R="CBEAE387"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/LrTest_E/LRTE.R="7E025976"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/LrTest_E/server.R="6AABA9B1"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/LrTest_E/ui.R="CA267492"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/QuickViewDrug/server.R="EF5EDF9D"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/QuickViewDrugEvent/../sharedscripts/getters.R="777682F1"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/QuickViewDrugEvent/server.R="841B9C06"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/QuickViewDrugEvent/ui.R="C7E05880"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/RR_D/../sharedscripts/getters.R="544AF445"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/RR_D/../sharedscripts/prr2.R="00C6AFE3"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/RR_D/server.R="2CB1106D"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/RR_D/sourcedir.R="4317EA8E"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/RR_D/ui.R="17A5EAF9"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/RR_E/helperfunctions.r="D483CB5E"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/RR_E/server.R="3E5D96C1"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/RR_E/sourcedir.R="11C9DC07"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/RR_E/ui.R="FFC9D141"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/ReportView/server.R="E6F4461F"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/ReportView/ui.R="8FD03CFD"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/buildshinyapps.R="123E2675"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/sharedscripts/getters.R="7BBECBFF"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/sharedscripts/helpfunctions.r="C63F4D59"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/sharedscripts/jstats.R="90B4B871"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/sharedscripts/mongoQueries.R="6A4AC89C"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/sharedscripts/prr2.R="C4C9F43A"
-C:/Users/sdimitsaki/Desktop/PVClinical/pvclinical-dashboard/RShinyApps/sharedscripts/serverhelpers.R="983D2B8B"
-C:/Users/sdimitsaki/Documents/Cell-cell interaction/scConn.R="BA033D45"
-C:/Users/sdimitsaki/Downloads/CytoTalk_package_v3.1.0/CytoTalk_package_v3.1.0/RunCytoTalk_Example_StepByStep.R="BC1C39B4"
-C:/Users/sdimitsaki/Downloads/Revigo (2).R="6B7CC7C1"
-C:/Users/sdimitsaki/Downloads/Revigo (3).R="496482A0"
-C:/Users/sdimitsaki/Downloads/Revigo (4) LMM severity cluster 1.R="FBDC0B7E"
-C:/Users/sdimitsaki/Downloads/Revigo (4).R="353DEC4C"
-C:/Users/sdimitsaki/Downloads/Revigo (5).R="50991A29"
-C:/Users/sdimitsaki/Downloads/Revigo ICL analysis (1).R="30FCD087"
-C:/Users/sdimitsaki/Downloads/Revigo.R="4CFA6610"
-C:/Users/sdimitsaki/Downloads/_similar.R="6A5BE386"
+C:/Users/dimst/Desktop/pvclinical-Rshiny/PVClinical_main/pvclinical-dashboard/RShinyApps/DynPRR/server.R="63AFE394"
+C:/Users/dimst/Desktop/pvclinical-Rshiny/PVClinical_main/pvclinical-dashboard/RShinyApps/DynPRR/ui.R="256D0C05"
+C:/Users/dimst/Desktop/pvclinical-Rshiny/PVClinical_main/pvclinical-dashboard/RShinyApps/DynPRR/www/datatablesEnglish.json="DDD02526"

RShinyApps/DynPRR/server.R

@@ -1325,7 +1325,7 @@ geturlquery <- reactive({
   # q$t1<-"A02BC01"
   # q$t2<-"10021015"
   # q$hash <- "ksjdhfksdhfhsk"
-  # q$concomitant<-FALSE
+  # q$concomitant<-TRUE
   updateSelectizeInput(session, inputId = "v1", selected = q$drugvar)
   updateTextInput(session, "t1", value=q$term1)
   updateTextInput(session,"t2", value=q$term2) 
@@ -1387,6 +1387,11 @@ output$About <- renderUI({
   HTML(stri_enc_toutf8(i18n()$t("About")))
 
 })
+output$toDate <- renderUI({ 
+  HTML(stri_enc_toutf8(i18n()$t("to")))
+
+})
+
 output$DataReference <- renderUI({ 
   HTML(stri_enc_toutf8(i18n()$t("Data Reference")))
 
@@ -1424,7 +1429,7 @@ output$infoprrplot<-renderUI({
   addPopover(session=session, id="infoprrplot", title="Proportional Reporting Ratio", 
              content=paste(i18n()$t("prr explanation"),"<br><br>",i18n()$t("dynprr explanation")), placement = "left",
              trigger = "hover", options = list(html = "true"))
-  return(HTML('<button type="button" class="btn btn-info">i</button>'))
+  return(HTML('<button type="button" class="btn btn-info" style="background-color:#2A3F54; color:#FFFFFF; border-color:#2A3F54;">i</button>'))
 })
 
 output$sourceInDataReport<-renderUI({

RShinyApps/DynPRR/ui.R

@@ -4,6 +4,7 @@ library(shinycssloaders)
 source('sourcedir.R')
 library(shinyalert)
 library(DT)
+library(shiny.i18n)
 
 options(encoding = 'UTF-8')
 
@@ -65,7 +66,7 @@ shinyUI(fluidPage(includeCSS("../sharedscripts/custom.css"),
                  fluidRow( useShinyjs(),
                  style="margin-bottom: 0.3rem",
                  column(width=2, dateInput("date1", "", value = '1989-6-30') ),
-                 column(width=1, p("to"),
+                 column(width=1, uiOutput('toDate'),
                         style="margin-top: 2.45rem; text-align: center;"),
                  column(width=2, dateInput("date2", "", value = Sys.Date()) ),
 

RShinyApps/DynPRR/www/datatablesGreek.json

@@ -18,7 +18,8 @@
 		"sFirst":    "Πρώτη",
 		"sPrevious": "Προηγούμενη",
 		"sNext":     "Επόμενη",
-		"sLast":     "Τελευταία"
+		"sLast":     "Τελευταία",
+		"to": "έως"
 	},
 	"oAria": {
 		"sSortAscending":  ": ενεργοποιήστε για αύξουσα ταξινόμηση της στήλης",

RShinyApps/QuickViewDrug/server.R

@@ -1,4 +1,4 @@
-1require(shiny)
+require(shiny)
 
 require(shinyBS)
 
@@ -946,8 +946,8 @@ shinyServer(function(input, output, session) {
 
   geturlquery <- reactive({
     q <- parseQueryString(session$clientData$url_search)
-    print("userexact")
-    print(q$useexact)
+    # print("userexact")
+    # print(q$useexact)
 
     updateSelectizeInput(session, inputId = "v1", selected = q$drugvar)
     updateTextInput(session, "t1", value=q$term1)

RShinyApps/ReportView/server.R

@@ -212,24 +212,24 @@ observeEvent( input$searchID, {
   if (q$concomitant == FALSE){
     if (q$v1 == 'patient.reaction.reactionmeddrapt') {
       con <- mongo("dict_fda", url = mongoConnection())
-      eventQuery <- SearchEventReports(q$t1, startdate = '1998-01-01', enddate = Sys.Date())
+      eventQuery <- SearchEventReports(q$t1, startdate = input$date1, enddate = input$date2)
       ids <- con$aggregate(eventQuery)
       con$disconnect()
     } else if (q$v2 == 'patient.reaction.reactionmeddrapt'){
       con <- mongo("dict_fda", url = mongoConnection())
-      drugeventQuery <- SearchDrugEventReports(q$t1,q$t2, startdate = '1998-01-01', enddate = Sys.Date(), q$dename)
+      drugeventQuery <- SearchDrugEventReports(q$t1,q$t2, startdate = input$date1, enddate = input$date2, q$dename)
       ids <- con$aggregate(drugeventQuery)
       con$disconnect()
     } else {
       con <- mongo("dict_fda", url = mongoConnection())
-      drugQuery <- SearchDrugReports(q$t1, startdate = '1998-01-01', enddate = Sys.Date(),q$dename)
+      drugQuery <- SearchDrugReports(q$t1, startdate = input$date1, enddate = input$date2,q$dename)
       ids <- con$aggregate(drugQuery)
       con$disconnect()
     }
 
     id_vector <- unlist(list(ids$safetyreportid))
     search_val$skip <- match(input$searchID, id_vector) + 1
-
+    
     myskip <- getskip()
     mydf <- getfullquery()
     numrecs <- mydf$df.total
@@ -242,6 +242,8 @@ observeEvent( input$searchID, {
     if (v1[2] == "patient.reaction.reactionmeddrapt"){
       t1[2] = q$ename
     }
+    t1[3] <- paste0('[', input$date1, '+TO+', input$date2, ']')
+    v1[3] <- 'receiptdate'
     myurl <- buildURL(v1, t1, limit = 1000, count = 'safetyreportid.exact')
     ids <-  fda_fetch_p(session, myurl)
     id_vector <- unlist(list(ids$results$term))
@@ -250,7 +252,7 @@ observeEvent( input$searchID, {
     mydf <- getfullquery()
     numrecs <- mydf$df.meta$results$total 
   }
-  # browser()
+
   maxlim <- min(getopenfdamaxrecords(), numrecs)
   updateSliderInput( session, 'skip', value= min(myskip+2, maxlim), min=1, step= 1, max=maxlim)
 
@@ -379,23 +381,25 @@ getquery <- reactive({
   if (v1[2] == "patient.reaction.reactionmeddrapt"){
     t1[2] = q$ename
   }
+  t1[3] <- paste0('[', input$date1, '+TO+', input$date2, ']')
+  v1[3] <- 'receiptdate'
   myurl <- buildURL(v1, t1,  limit=1, skip=getskip())
   # browser()
 
   if (q$concomitant == FALSE){
     if (q$v1 == 'patient.reaction.reactionmeddrapt') {
       con <- mongo("dict_fda", url = mongoConnection())
-      eventQuery <- SearchEventReports(q$t1, startdate = '1998-01-01', enddate = Sys.Date())
+      eventQuery <- SearchEventReports(q$t1, startdate = input$date1, enddate = input$date2)
       ids <- con$aggregate(eventQuery)
       con$disconnect()
     } else if (q$v2 == 'patient.reaction.reactionmeddrapt'){
       con <- mongo("dict_fda", url = mongoConnection())
-      drugeventQuery <- SearchDrugEventReports(q$t1,q$t2,startdate = '1998-01-01', enddate = Sys.Date(), q$dename)
+      drugeventQuery <- SearchDrugEventReports(q$t1,q$t2,startdate = input$date1, enddate = input$date2, q$dename)
       ids <- con$aggregate(drugeventQuery)
       con$disconnect()
     } else {
       con <- mongo("dict_fda", url = mongoConnection())
-      drugQuery <- SearchDrugReports(q$t1, startdate = '1998-01-01', enddate = Sys.Date(), q$dename)
+      drugQuery <- SearchDrugReports(q$t1, startdate = input$date1, enddate = input$date2, q$dename)
       ids <- con$aggregate(drugQuery)
       con$disconnect()
     }
@@ -458,23 +462,25 @@ getfullquery <- reactive({
   if (v1[2] == "patient.reaction.reactionmeddrapt"){
     t1[2] = q$ename
   }
+  t1[3] <- paste0('[', input$date1, '+TO+', input$date2, ']')
+  v1[3] <- 'receiptdate'
   myurl <- buildURL(v1, t1, limit=1)
 
 
   if (q$concomitant == FALSE){
     if (q$v1 == 'patient.reaction.reactionmeddrapt') {
       con <- mongo("dict_fda", url = mongoConnection())
-      eventQuery <- SearchEventReports(q$t1, startdate = '1998-01-01', enddate = Sys.Date())
+      eventQuery <- SearchEventReports(q$t1, startdate = input$date1, enddate = input$date2)
       ids <- con$aggregate(eventQuery)
       con$disconnect()
     } else if (q$v2 == 'patient.reaction.reactionmeddrapt'){
       con <- mongo("dict_fda", url = mongoConnection())
-      drugeventQuery <- SearchDrugEventReports(q$t1,q$t2, startdate = '1998-01-01', enddate = Sys.Date(), q$dename)
+      drugeventQuery <- SearchDrugEventReports(q$t1,q$t2, startdate = input$date1, enddate = input$date2, q$dename)
       ids <- con$aggregate(drugeventQuery)
       con$disconnect()
     } else {
       con <- mongo("dict_fda", url = mongoConnection())
-      drugQuery <- SearchDrugReports(q$t1, startdate = '1998-01-01', enddate = Sys.Date(), q$dename)
+      drugQuery <- SearchDrugReports(q$t1, startdate = input$date1, enddate = input$date2, q$dename)
       ids <- con$aggregate(drugQuery)
       con$disconnect()
     }
@@ -1387,11 +1393,32 @@ output$downloadAllData <- downloadHandler(
     if (v1[2] == "patient.reaction.reactionmeddrapt"){
       t1[2] = q$ename
     }
-    myurl <- buildURL(v1, t1, limit=100)
+    t1[3] <- paste0('[', input$date1, '+TO+', input$date2, ']')
+    v1[3] <- 'receiptdate'
+
+    # if (q$v1 == 'patient.reaction.reactionmeddrapt') {
+    #   con <- mongo("dict_fda", url = mongoConnection())
+    #   eventQuery <- SearchEventReports(q$t1, startdate = '1998-01-01', enddate = Sys.Date())
+    #   ids <- con$aggregate(eventQuery)
+    #   con$disconnect()
+    # } else if (q$v2 == 'patient.reaction.reactionmeddrapt'){
+    #   con <- mongo("dict_fda", url = mongoConnection())
+    #   drugeventQuery <- SearchDrugEventReports(q$t1,q$t2, startdate = '1998-01-01', enddate = Sys.Date(), q$dename)
+    #   ids <- con$aggregate(drugeventQuery)
+    #   con$disconnect()
+    # } else {
+    #   con <- mongo("dict_fda", url = mongoConnection())
+    #   drugQuery <- SearchDrugReports(q$t1, startdate = '1998-01-01', enddate = Sys.Date(),q$dename)
+    #   ids <- con$aggregate(drugQuery)
+    #   con$disconnect()
+    # }
+
+
+    myurl <- buildURL(v1, t1, limit=1000)
     mydf <- fda_fetch_p(session, myurl)
 
     df <- mydf
-
+    # browser()
     if ( is.data.frame(mydf$results$patient) )
     {
       mydf <- (mydf$results$patient)    
@@ -1633,14 +1660,18 @@ output$applinks <- renderText({
   return( makeapplinks(  getcururl() )  )
 })
 
+output$toDate <- renderUI({ 
+  HTML(stri_enc_toutf8(i18n()$t("to")))
+
+})
 
 geturlquery <- reactive({
    q <- parseQueryString(session$clientData$url_search)
    # q<-NULL
    # q$v1<-"patient.drug.openfda.generic_name"
    # q$v2<-"patient.reaction.reactionmeddrapt"
-   # # q$t1<-"Omeprazole"
-   # # q$t2<-"Hypokalaemia"
+   # q$t1<-"Omeprazole"
+   # q$t2<-"Hypokalaemia"
    # q$t1<-"A02BC01"
    # q$t2<-"10012378"
    # q$hash <- "ksjdhfksdhfhsk"

RShinyApps/ReportView/ui.R

@@ -87,11 +87,21 @@ shinyUI(fluidPage(includeCSS("../sharedscripts/custom.css"),
                            #   img(src='l_openFDA.png', align='bottom')),
                            #renderDates()
                     ),
-                    column(width=8,
+
+                    column(width=8, 
                            titlePanel(
                              textOutput("paneltitle"),
                              "")) 
                     , id='titlerow'),
+                  fluidRow(useShinyjs(),
+                           style="margin-bottom: 0.3rem; float: center;",
+                           column(width=2, dateInput("date1", "", value = '1989-6-30') ),
+                           column(width=1, uiOutput('toDate'),
+                                  style="margin-top: 2.45rem; text-align: center;"),
+                           column(width=2, dateInput("date2", "", value = Sys.Date()) ),
+
+                  ),
+
 #                   img(src='l_openFDA.png'),
 #   titlePanel("Report Browser"),
 #   fluidRow(
@@ -147,11 +157,11 @@ shinyUI(fluidPage(includeCSS("../sharedscripts/custom.css"),
     , id='sliderrow'),
 fluidRow(column(width=2, downloadButton( 'downloadData', 'Download report', 
                                          block=TRUE) ),
-         style= " margin-bottom: 0.3rem; float:right;",
+         style= " margin-bottom: 0.3rem; float:right; color: #fffff",
          ),
 fluidRow(column(width=2, downloadButton( 'downloadAllData', 'Download all reports', 
                                          block=TRUE) ),
-         style= " margin-bottom: 0.3rem; float:right;",
+         style= " margin-bottom: 0.3rem; float:right; color: #fffff",
 ),
 fluidRow(useShinyjs(),
          hidden(column(width=3,

RShinyApps/sharedscripts/custom.css

@@ -21,6 +21,17 @@ body{
    width:500px!important;
 }
 
+.action-button {
+   background-color:#2A3F54;
+   border-color: :#2A3F54;
+  color: #FFFFFF;
+}
+
+.btn-info {
+  background-color:#2A3F54;
+   border-color: :#2A3F54;
+  color: #FFFFFF;
+}
 
 /* Tooltip on top */
  .tooltip-arrow {
@@ -46,6 +57,14 @@ a {
   margin-top:40px;
   /*height:280px!important;*/
 }
+.loader {
+  background:#2A3F54;
+  color:#2A3F54;
+}
+
+.paneltitle {
+  font-size: 25px;
+}
 
 #cpmeanplot img{
   /*padding-right:20px;

gentelella/app/apps.py

@@ -20,7 +20,7 @@ class AppConfig(AppConfig):
     def ready(self):
         knw = KnowledgeGraphWrapper()
         knw.cache_drugs()
-        # knw.cache_conditions()
+        knw.cache_conditions()
 
         domains = ["drug", "condition"]