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是否有用于填写在线表格的 R 函数？

分类：编程问答

如何解决是否有用于填写在线表格的 R 函数？

我正在尝试填写在线 form 并抓取结果。 使用 Rselenium 我可以为一行填充数据：

    library(RSelenium)
    library(xml2)
    library(tidyverse)
    library(rvest)
    
    
    
    # Start Selenium Server --------------------------------------------------------
    
    # https://docs.ropensci.org/RSelenium/articles/basics.html#connecting-to-a-selenium-server-1
    # https://www.akipredictor.com/en/aki_predictor/
    
    rD <- rsDriver(browser="firefox",port=4545L,verbose=F)
    remDr <- rD[["client"]]
    
    # form ------------------------------------------------------------------
    remDr$navigate('https://www.akipredictor.com/en/aki_predictor/')
    remDr$findElement(using = "name",value = "agree_to_legal_terms")$clickElement()
    
    #Pre-admission information
    webElemAge <- remDr$findElement(using = "name",value = "age")
    webElemAge$sendKeystoElement(list("70"))
    webElemBaselinesCreat <- remDr$findElement(using = "name",value = "baseline_screat")
    webElemBaselinesCreat$sendKeystoElement(list("1"))
    webElemIsDiabetic <- remDr$findElement(using = "name",value = "is_diabetic")
    webElemIsDiabetic$sendKeystoElement(list("Yes"))
    webElemIsElectiveAdmited <- remDr$findElement(using = "name",value = "is_elective_admitted")
    webElemIsElectiveAdmited$sendKeystoElement(list("Unplanned admission"))
    webElemTypeOfSurgery <- remDr$findElement(using = "name",value = "type_of_surgery")
    webElemTypeOfSurgery$sendKeystoElement(list("Transplant surgery"))
    
    # ICU admission information
    remDr$findElement(using = "name",value = "show_admission")$clickElement()
    webElemBloodglucose <- remDr$findElement(using = "name",value = "blood_glucose")
    webElemBloodglucose$sendKeystoElement(list("200"))
    webElemHasSUSPECTedSepsis <- remDr$findElement(using = "name",value = "has_SUSPECTed_sepsis")
    webElemHasSUSPECTedSepsis$sendKeystoElement(list("Yes"))
    webElemHDSupport <- remDr$findElement(using = "name",value = "hd_support")
    webElemHDSupport$sendKeystoElement(list("Pharmacological"))
    # Day 1 information
    remDr$findElement(using = "name",value = "show_day1")$clickElement()
    webElemCreatinineD1 <- remDr$findElement(using = "name",value = "creatinine_d1")
    webElemCreatinineD1$sendKeystoElement(list("1.2"))
    webElemApacheIID1 <- remDr$findElement(using = "name",value = "apacheII_d1")
    webElemApacheIID1$sendKeystoElement(list("30"))
    webElemmaxLactateD1 <- remDr$findElement(using = "name",value = "max_lactate_d1")
    webElemmaxLactateD1$sendKeystoElement(list("10"))
    webElemBilirrubinD1 <- remDr$findElement(using = "name",value = "bilirubin_d1")
    webElemBilirrubinD1$sendKeystoElement(list("2"))
    webElemHoursOfICUStay <- remDr$findElement(using = "name",value = "hours_of_icu_stay")
    webElemHoursOfICUStay$sendKeystoElement(list("24"))
    remDr$findElement(using = "name",value = "predict_day1_dev")$clickElement()
    
    # extract HTML -----------------
    Sys.sleep(5) # give the page time to fully load
    html <- remDr$getPageSource()[[1]]
    
    results <- read_html(html) %>% # parse HTML
      html_nodes("div") %>% # extract node"
      .[12] %>%
      .[[1]] %>%
      html_text() # string
    
    results <- results %>%
      str_replace_all("\n","") %>%
      str_replace_all(" ","") %>%
      str_replace_all("RiskofdevelopingAKIduringthefirstweekofICUstay","") %>%
      str_replace_all("AdvancedoptionsChoosetheclassificationthresholdClickonthequestionmarkforadditionalexplanationSincethepredictedriskisabovethechosenclassificationthreshold,thepatientisclassifiedasdevelopingAKIwithinthefirstweekofICUstay.DependingontheintendeduSEOftheAKIpredictor,theusermaychoosetoadapttheclassificationthreshold,andevaluatetheeffectonthestatisticsbelow.Thedefaultclassificationthresholdof14.5maximizedbothsensitivityandspecificityinthestudieddatabase.Sensitivity:63.8%specificity:81.9%PPV:38.0%NPV:92.8%ΔNetbenefitNone:6.8%ΔNetbenefitAll:6.4%Atthechosenclassificationthreshold,AKIpredictorcorrectlyidentifies63.8%ofthepatientswhodevelopedAKIinthestudieddatabaseAtthechosenclassificationthreshold,AKIpredictorcorrectlyidentifies81.9%ofthepatientswhodidnotdevelopAKIinthestudieddatabaseInthestudieddatabase,38.0%ofthepatientswhodevelopedAKIhadapredictedriskabovethechosenclassificationthresholdInthestudieddatabase,92.8%ofthepatientswhodidnotdevelopAKIhadapredictedriskbelowthechosenclassificationthresholdAtthechosenclassificationthreshold,AKIpredictorincreasesthepercentageofcorrectlyidentifiedAKIby6.8%inthestudieddatabase,withoutincreasingfalseclassifications,ascomparedtoconsideringnopatientwilldevelopAKI.OnlyuseaclassificationthresholdthatresultsinaΔNetbenefitNone>0Atthechosenclassificationthreshold,AKIpredictordecreasesthepercentageofmisclassifiedAKIby6.4%inthestudieddatabase,whilekeepingthesamenumberofcorrectclassifications,ascomparedtoconsideringallpatientswilldevelopAKIOnlyuseaclassificationthresholdthatresultsinaΔNetbenefitAll>0Clickonthestatisticsfordetails","")
    
    results
    
    
    remDr$close()

我需要使用数据框中的数据执行相同的过程。我尝试了以下代码：

    rD <- rsDriver(browser="firefox",port=4560L,verbose=F)
    remDr <- rD[["client"]]
    remDr$navigate('https://www.akipredictor.com/en/aki_predictor/')
    
    
    
    scrape.AKIpredictor <- function(age,baselinesCreat,IsDiabetic,IsElectiveAdmited,TypeOfSurgery,glucose,SUSPECTedSepsis,HDSupport,CreatinineD1,ApacheIID1,MaxLactateD1,BilirrubinD1,HoursOfICUStay) {
      
      remDr$findElement(using = "name",value = "agree_to_legal_terms")$clickElement()
    
      #Pre-admission information
      webElemAge <- remDr$findElement(using = "name",value = "age")
      webElemAge$sendKeystoElement(list(age))
      webElemBaselinesCreat <- remDr$findElement(using = "name",value = "baseline_screat")
      webElemBaselinesCreat$sendKeystoElement(list(baselinesCreat))
      webElemIsDiabetic <- remDr$findElement(using = "name",value = "is_diabetic")
      webElemIsDiabetic$sendKeystoElement(list(IsDiabetic))
      webElemIsElectiveAdmited <- remDr$findElement(using = "name",value = "is_elective_admitted")
      webElemIsElectiveAdmited$sendKeystoElement(list(IsElectiveAdmited))
      webElemTypeOfSurgery <- remDr$findElement(using = "name",value = "type_of_surgery")
      webElemTypeOfSurgery$sendKeystoElement(list(TypeOfSurgery))
      
      # ICU admission information
      remDr$findElement(using = "name",value = "show_admission")$clickElement()
      webElemBloodglucose <- remDr$findElement(using = "name",value = "blood_glucose")
      webElemBloodglucose$sendKeystoElement(list(glucose))
      webElemHasSUSPECTedSepsis <- remDr$findElement(using = "name",value = "has_SUSPECTed_sepsis")
      webElemHasSUSPECTedSepsis$sendKeystoElement(list(SUSPECTedSepsis))
      webElemHDSupport <- remDr$findElement(using = "name",value = "hd_support")
      webElemHDSupport$sendKeystoElement(list(HDSupport))
      
      # Day 1 information
      remDr$findElement(using = "name",value = "show_day1")$clickElement()
      webElemCreatinineD1 <- remDr$findElement(using = "name",value = "creatinine_d1")
      webElemCreatinineD1$sendKeystoElement(list(CreatinineD1))
      webElemApacheIID1 <- remDr$findElement(using = "name",value = "apacheII_d1")
      webElemApacheIID1$sendKeystoElement(list(ApacheIID1))
      webElemmaxLactateD1 <- remDr$findElement(using = "name",value = "max_lactate_d1")
      webElemmaxLactateD1$sendKeystoElement(list(MaxLactateD1))
      webElemBilirrubinD1 <- remDr$findElement(using = "name",value = "bilirubin_d1")
      webElemBilirrubinD1$sendKeystoElement(list(BilirrubinD1))
      webElemHoursOfICUStay <- remDr$findElement(using = "name",value = "hours_of_icu_stay")
      webElemHoursOfICUStay$sendKeystoElement(list(HoursOfICUStay))
      remDr$findElement(using = "name",value = "predict_day1_dev")$clickElement()
      
      Sys.sleep(5) # give the page time to fully load
      html <- remDr$getPageSource()[[1]]
      
      results <- read_html(html) %>% # parse HTML
        html_nodes("div") %>% # extract node"
        .[12] %>%
        .[[1]] %>%
        html_text() # string
      
      results <- results %>% #trim trim trim
        str_replace_all("\n","") %>%
        str_replace_all(" ","") %>%
        str_replace_all("RiskofdevelopingAKIduringthefirstweekofICUstay","") %>%
        str_replace_all("AdvancedoptionsChoosetheclassificationthresholdClickonthequestionmarkforadditionalexplanationSincethepredictedriskisabovethechosenclassificationthreshold,"")
      
      remDr$findElement(using = "name",value = "empty_form")$clickElement()
      
      
      return(results)
        
    }
    
    #data frame
    age <- c(50,70,80)
    baselinesCreat <- c(1,1.5,1.1)
    IsDiabetic <- c("Yes","No","Yes")
    IsElectiveAdmited <- c("Planned admission","Unplanned admission","Planned admission")
    TypeOfSurgery <- c("Transplant surgery","Cardiovascular surgery (non transplant)","Abdominal surgery")
    glucose <- c(200,180,140)
    SUSPECTedSepsis <- c("Yes","Yes")
    HDSupport <- c("None","Mechanical","Pharmacological")
    CreatinineD1 <- c(1.1,1.6,1.2)
    ApacheIID1 <- c(30,40,10)
    MaxLactateD1 <-c(10,15,5)
    BilirrubinD1 <- c(2,3,4)
    HoursOfICUStay <- c(24,24,24)
    
    data <- data.frame(age,HoursOfICUStay)
    
    scrape.AKIpredictor(data$age,data$baselinesCreat,data$IsDiabetic,data$IsElectiveAdmited,data$TypeOfSurgery,data$glucose,data$SUSPECTedSepsis,data$HDSupport,data$CreatinineD1,data$ApacheIID1,data$MaxLactateD1,data$BilirrubinD1,data$HoursOfICUStay)

但是我收到以下错误：

处理命令时发生未知的服务器端错误。

使用 for 循环尝试了以下代码

remDr$navigate('https://www.akipredictor.com/en/aki_predictor/')
remDr$findElement(using = "name",value = "agree_to_legal_terms")$clickElement()

Sys.sleep(10)
#Set start,end and steps
for(row in 1:nrow(data)) {
  #Pre-admission information
  webElemAge <- remDr$findElement(using = "name",value = "age")
  webElemAge$sendKeystoElement(list(data[row,"age"]))
  webElemBaselinesCreat <- remDr$findElement(using = "name",value = "baseline_screat")
  webElemBaselinesCreat$sendKeystoElement(list(data[row,"baselinesCreat"]))
  webElemIsDiabetic <- remDr$findElement(using = "name",value = "is_diabetic")
  webElemIsDiabetic$sendKeystoElement(list(data[row,"IsDiabetic"]))
  webElemIsElectiveAdmited <- remDr$findElement(using = "name",value = "is_elective_admitted")
  webElemIsElectiveAdmited$sendKeystoElement(list(data[row,"IsElectiveAdmited"]))
  webElemTypeOfSurgery <- remDr$findElement(using = "name",value = "type_of_surgery")
  webElemTypeOfSurgery$sendKeystoElement( list(data[row,"TypeOfSurgery"]))
  
  # ICU admission information
  remDr$findElement(using = "name",value = "show_admission")$clickElement()
  Sys.sleep(5)
  webElemBloodglucose <- remDr$findElement(using = "name",value = "blood_glucose")
  webElemBloodglucose$sendKeystoElement(list(data[row,"glucose"]))
  webElemHasSUSPECTedSepsis <- remDr$findElement(using = "name",value = "has_SUSPECTed_sepsis")
  webElemHasSUSPECTedSepsis$sendKeystoElement(list(data[row,"SUSPECTedSepsis"]))
  webElemHDSupport <- remDr$findElement(using = "name",value = "hd_support")
  webElemHDSupport$sendKeystoElement(list(data[row,"HDSupport"]))
  
  # Day 1 information
  remDr$findElement(using = "name",value = "show_day1")$clickElement()
  Sys.sleep(5)
  webElemCreatinineD1 <- remDr$findElement(using = "name",value = "creatinine_d1")
  webElemCreatinineD1$sendKeystoElement(list(data[row,"CreatinineD1"]))
  webElemApacheIID1 <- remDr$findElement(using = "name",value = "apacheII_d1")
  webElemApacheIID1$sendKeystoElement(list(data[row,"ApacheIID1"]))
  webElemmaxLactateD1 <- remDr$findElement(using = "name",value = "max_lactate_d1")
  webElemmaxLactateD1$sendKeystoElement(list(data[row,"MaxLactateD1"]))
  webElemBilirrubinD1 <- remDr$findElement(using = "name",value = "bilirubin_d1")
  webElemBilirrubinD1$sendKeystoElement(list(data[row,"BilirrubinD1"]))
  webElemHoursOfICUStay <- remDr$findElement(using = "name",value = "hours_of_icu_stay")
  webElemHoursOfICUStay$sendKeystoElement(list(data[row,"HoursOfICUStay"]))
  remDr$findElement(using = "name",value = "predict_day1_dev")$clickElement()

  Sys.sleep(5) # give the page time to fully load
  html <- remDr$getPageSource()[[1]]
  
  results <- read_html(html) %>% # parse HTML
    html_nodes("div") %>% # extract node"
    .[12] %>%
    .[[1]] %>%
    html_text() # string
  
  results[row,] <- results %>% #trim trim trim
    str_replace_all("\n","") %>%
    str_replace_all(" ","") %>%
    str_replace_all("RiskofdevelopingAKIduringthefirstweekofICUstay","") %>%
    str_replace_all("AdvancedoptionsChoosetheclassificationthresholdClickonthequestionmarkforadditionalexplanationSincethepredictedriskisabovethechosenclassificationthreshold,"")
  
  remDr$findElement(using = "name",value = "empty_form")$clickElement()
  
  results
}

这给了我以下错误：

Selenium 消息：类 java.lang.Long 不能转换为类 java.lang.CharSequence（java.lang.Long 和 java.lang.CharSequence 位于加载程序 'bootstrap' 的模块 java.base 中）

解决方法

Rselenium 只接受字符串，使用 for 循环解决了问题。

library(RSelenium)
library(xml2)
library(tidyverse)
library(rvest)

age <- c(50,70,80)
baselineSCreat <- c(1,1.5,1.1)
IsDiabetic <- c("Yes","No","Yes")
IsElectiveAdmited <- c("Planned admission","Unplanned admission","Planned admission")
TypeOfSurgery <- c("Transplant surgery","Cardiovascular surgery (non transplant)","Abdominal surgery")
Glucose <- c(200,180,140)
SuspectedSepsis <- c("Yes","Yes")
HDSupport <- c("None","Mechanical","Pharmacological")
CreatinineD1 <- c(1.1,1.6,1.2)
ApacheIID1 <- c(30,40,10)
MaxLactateD1 <-c(10,15,5)
BilirrubinD1 <- c(2,3,4)
HoursOfICUStay <- c(24,24,24)

data <- data.frame(age,baselineSCreat,IsDiabetic,IsElectiveAdmited,TypeOfSurgery,Glucose,SuspectedSepsis,HDSupport,CreatinineD1,ApacheIID1,MaxLactateD1,BilirrubinD1,HoursOfICUStay)

data <- sapply(data,as.character)

rD <- rsDriver(browser="firefox",port=4560L,verbose=F)
remDr <- rD[["client"]]

remDr$navigate('https://www.akipredictor.com/en/aki_predictor/')
remDr$findElement(using = "name",value = "agree_to_legal_terms")$clickElement()

output <- matrix(ncol=1,nrow=nrow(data))

Sys.sleep(5)
#Set start,end and steps
for(row in 1:nrow(data)) {
  #Pre-admission information
  webElemAge <- remDr$findElement(using = "name",value = "age")
  webElemAge$sendKeysToElement(list(data[row,"age"]))
  webElemBaselineSCreat <- remDr$findElement(using = "name",value = "baseline_screat")
  webElemBaselineSCreat$sendKeysToElement(list(data[row,"baselineSCreat"]))
  webElemIsDiabetic <- remDr$findElement(using = "name",value = "is_diabetic")
  webElemIsDiabetic$sendKeysToElement(list(data[row,"IsDiabetic"]))
  webElemIsElectiveAdmited <- remDr$findElement(using = "name",value = "is_elective_admitted")
  webElemIsElectiveAdmited$sendKeysToElement(list(data[row,"IsElectiveAdmited"]))
  webElemTypeOfSurgery <- remDr$findElement(using = "name",value = "type_of_surgery")
  webElemTypeOfSurgery$sendKeysToElement( list(data[row,"TypeOfSurgery"]))
  
  # ICU admission information
  remDr$findElement(using = "name",value = "show_admission")$clickElement()
  Sys.sleep(1)
  webElemBloodGlucose <- remDr$findElement(using = "name",value = "blood_glucose")
  webElemBloodGlucose$sendKeysToElement(list(data[row,"Glucose"]))
  webElemHasSuspectedSepsis <- remDr$findElement(using = "name",value = "has_suspected_sepsis")
  webElemHasSuspectedSepsis$sendKeysToElement(list(data[row,"SuspectedSepsis"]))
  webElemHDSupport <- remDr$findElement(using = "name",value = "hd_support")
  webElemHDSupport$sendKeysToElement(list(data[row,"HDSupport"]))
  
  # Day 1 information
  remDr$findElement(using = "name",value = "show_day1")$clickElement()
  Sys.sleep(1)
  webElemCreatinineD1 <- remDr$findElement(using = "name",value = "creatinine_d1")
  webElemCreatinineD1$sendKeysToElement(list(data[row,"CreatinineD1"]))
  webElemApacheIID1 <- remDr$findElement(using = "name",value = "apacheII_d1")
  webElemApacheIID1$sendKeysToElement(list(data[row,"ApacheIID1"]))
  webElemMaxLactateD1 <- remDr$findElement(using = "name",value = "max_lactate_d1")
  webElemMaxLactateD1$sendKeysToElement(list(data[row,"MaxLactateD1"]))
  webElemBilirrubinD1 <- remDr$findElement(using = "name",value = "bilirubin_d1")
  webElemBilirrubinD1$sendKeysToElement(list(data[row,"BilirrubinD1"]))
  webElemHoursOfICUStay <- remDr$findElement(using = "name",value = "hours_of_icu_stay")
  webElemHoursOfICUStay$sendKeysToElement(list(data[row,"HoursOfICUStay"]))
  remDr$findElement(using = "name",value = "predict_day1_dev")$clickElement()

  Sys.sleep(1) # give the page time to fully load
  html <- remDr$getPageSource()[[1]]
  
  output[row,] <- read_html(html) %>% # parse HTML
    html_nodes("div") %>% # extract node"
    .[12] %>%
    .[[1]] %>%
    html_text() # string
  
  output[row,] <- output[row,] %>% #trim trim trim
    str_replace_all("\n","") %>%
    str_replace_all(" ","") %>%
    str_replace_all("RiskofdevelopingAKIduringthefirstweekofICUstay","") %>%
    str_replace_all("AdvancedoptionsChoosetheclassificationthresholdClickonthequestionmarkforadditionalexplanationSincethepredictedriskisabovethechosenclassificationthreshold,thepatientisclassifiedasdevelopingAKIwithinthefirstweekofICUstay.DependingontheintendeduseoftheAKIpredictor,theusermaychoosetoadapttheclassificationthreshold,andevaluatetheeffectonthestatisticsbelow.Thedefaultclassificationthresholdof14.5maximizedbothsensitivityandspecificityinthestudieddatabase.Sensitivity:63.8%Specificity:81.9%PPV:38.0%NPV:92.8%ΔNetbenefitNone:6.8%ΔNetbenefitAll:6.4%Atthechosenclassificationthreshold,AKIpredictorcorrectlyidentifies63.8%ofthepatientswhodevelopedAKIinthestudieddatabaseAtthechosenclassificationthreshold,AKIpredictorcorrectlyidentifies81.9%ofthepatientswhodidnotdevelopAKIinthestudieddatabaseInthestudieddatabase,38.0%ofthepatientswhodevelopedAKIhadapredictedriskabovethechosenclassificationthresholdInthestudieddatabase,92.8%ofthepatientswhodidnotdevelopAKIhadapredictedriskbelowthechosenclassificationthresholdAtthechosenclassificationthreshold,AKIpredictorincreasesthepercentageofcorrectlyidentifiedAKIby6.8%inthestudieddatabase,withoutincreasingfalseclassifications,ascomparedtoconsideringnopatientwilldevelopAKI.OnlyuseaclassificationthresholdthatresultsinaΔNetbenefitNone>0Atthechosenclassificationthreshold,AKIpredictordecreasesthepercentageofmisclassifiedAKIby6.4%inthestudieddatabase,whilekeepingthesamenumberofcorrectclassifications,ascomparedtoconsideringallpatientswilldevelopAKIOnlyuseaclassificationthresholdthatresultsinaΔNetbenefitAll>0Clickonthestatisticsfordetails","")


  remDr$findElement(using = "name",value = "empty_form")$clickElement()
  
}

output

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