app-cookie.R

#
# Requires a json formatted cookie as "~/cookie/c" with this field: AWSELBAuthSessionCookie-0
#

library(shiny)
library(tidyverse)
library(httr)
library(jsonlite)
library(DT)


#if(file.exists("~/cookie/c")){ config=read_json("~/cookie/c")}

# Define UI for application that draws a histogram
ui <- fluidPage(


    # Application title
    titlePanel("NCPI FHIR and Monarch API Example"),

    # Sidebar with a slider input for number of bins 
    sidebarLayout(
        sidebarPanel(
            tabsetPanel(
                tabPanel("Participant",
                    textInput("participant_reference",
                              "Participant Reference:",
                              value = "Patient/546692"),
                    helpText("Particiant Information:"),
                    textOutput("patientID"),
                    textOutput("patientGender")
                ),
                tabPanel("Configuration",
                     helpText("Load a json config file containing:",
                              "AWSELBAuthSessionCookie-0 and server",
                              "with the cookie and FHIR base URL"),
                     fileInput("config.file", "Config File", accept = "application/json"),
                     textInput("cookie",
                               "Cookie Auth:",
                               value = ""),
                     textInput("server",
                               "Server Loc:",
                               value = "")
                     
                )
            )
        ),

        # Show a plot of the generated distribution
        mainPanel(
            h2("Monarch API Diseases"),
            DTOutput("found_diseases"),
            h2("Source HPO Terms"),
            DTOutput("hpo_terms"),
            h2("Source Conditions"),
            DTOutput("listed_conditions")
        )
    )
)

server <- function(input, output, session) {
    ## Configuration options
    observeEvent(input$config.file, {
        req(input$config.file)
        config=read_json(input$config.file$datapath)
        updateTextInput(session, "cookie",value = config$`AWSELBAuthSessionCookie-0`)
        updateTextInput(session, "server",value = config$server)
    })
    
    ## FHIR server helper functions
    #Create some reading functions to query the fhir server and extract resource responses. get_all() returns a list of resources returned by the query, extracting from Bundles and paging as necessary.
    
    c_get=function(request) {
        res=GET(paste0(input$server,request),add_headers(Cookie=sprintf("AWSELBAuthSessionCookie-0=%s",input$cookie), ContentType="application/json"))
        content(res,as="parsed",type="application/json")
    }
    get_all=function(request) {
        next_request=request
        all_content=list()
        while(next_request!="") {
            my_content=c_get(next_request)
            if(my_content$resourceType=="Bundle") {
                all_content=append(all_content,lapply(my_content$entry,function(x){x$resource}))
                next_request=strsplit(paste0(sapply(my_content$link,function(x){ifelse(x$relation=="next",x$url,"")}),collapse = ""),
                                      "?",fixed=T)[[1]][2]
                next_request=ifelse(is.na(next_request),"",paste0("?",next_request))
            }
            else {
                all_content=append(all_content,list(my_content))
                next_request=""
            }
        }
        all_content
    }
    
    ## Monarch API helper functions
    #These use the sim search endpoints documented here https://api.monarchinitiative.org/api to see what comes back. Does not currently support negated HPO ids.

    sim_search=function(hpo_ids) {
        searchURL="https://api.monarchinitiative.org/api/sim/search?is_feature_set=true&metric=phenodigm&limit=100&taxon=9606&id="
        request=paste0(hpo_ids,collapse = "&id=")
        res=GET(paste0(searchURL,request))
        content(res,as="parsed",type="application/json")
    }
    list_sim_results=function(sim_results) {
        data.frame(name=sapply(sim_results$matches,function(x){x$label}),
                   code=sapply(sim_results$matches,function(x){x$id}),
                   score=sapply(sim_results$matches,function(x){x$score}),
                   n_phenotypes=sapply(sim_results$matches,function(x){length(x$pairwise_match)}))
    }
    
    ## Create some reactive expressions for each step so the plots don't cause too many calls
    # Patient
    patientInput <- reactive({
        req(input$server)
        get_all(input$participant_reference)
    })
    patientID <- reactive({
        paste0("Patient/",patientInput()[[1]]$id)
    })
    # Gather Observations and create a nice table from the resources
    observations <- reactive({
        get_all(sprintf("Condition/?patient=%s&_profile:below=https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/phenotype",patientID()))
    })
    observationTable <- reactive({
        data.frame(name=sapply(observations(),function(x){ifelse(is.null(x$code$coding[[1]]$display),x$code$text,x$code$coding[[1]]$display)}),
                   code=sapply(observations(),function(x){ifelse(is.null(x$code$coding[[1]]$code),"NULL",x$code$coding[[1]]$code)}),
                   status=sapply(observations(),function(x){ifelse(is.null(x$verificationStatus$text),"NULL",x$verificationStatus$text)}))
    })
    #Gather Conditions and create a nice table from the resources
    conditions <- reactive({
        get_all(sprintf("Condition/?patient=%s&_profile:below=https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/disease",patientID()))
    })
    conditionTable <- reactive({
        data.frame(name=sapply(conditions(),function(x){ifelse(is.null(x$code$coding[[1]]$display),x$code$text,x$code$coding[[1]]$display)}),
                   code=sapply(conditions(),function(x){ifelse(is.null(x$code$coding[[1]]$code),"NULL",x$code$coding[[1]]$code)}),
                   status=sapply(conditions(),function(x){ifelse(is.null(x$verificationStatus$code$coding[[1]]$code),"NULL",x$verificationStatus$code$coding[[1]]$code)}))
    })
    
    #Request info from Monarch API on button press
    simMatches <- reactive({
        sim_search((filter(observationTable(),status=="Positive"))$code)
    })
    #Create table from API return
    simMatchTable <- reactive({
        list_sim_results(simMatches())
    })
    
    
    # Add the patient ID to the top of the output for clarity
    output$patientID <- renderText({
        patientID()
    })
    # Add the patient gender
    output$patientGender <- renderText({
        patientInput()[[1]]$gender
    })
    
    # Provide the table of HPO terms for reference
    output$hpo_terms <- renderDT( 
        datatable(observationTable() %>% arrange(desc(status)))
        )
    
    # Provide the list of Conditions for reference
    output$listed_conditions <- renderDT( 
        datatable(conditionTable() %>% arrange(desc(status)))
    )
    
    # Provide the list of potential matches
    output$found_diseases <- renderDT( 
        datatable(simMatchTable())
    )
    
}

# Run the application 
shinyApp(ui = ui, server = server)