# # install.packages("devtools")
# library(devtools)
# install_github('yikeshu0611/rs.driver')
# 安装R包
#install.packages('RSelenium')
#java -Dwebdriver.chrome.driver="chromedriver.exe" -jar selenium-server-standalone-4.0.0-alpha-2.jar -port 4444
# 加载R包
#library(devtools)
library(readxl)
library(RSelenium)
library(rvest)
library(xml2)
library(RS.Driver)
library(tidyverse)
name <- read_xlsx("example_tempelate.xlsx",sheet = 1)
RS.OpenChrome()
url <- c()
id<-name$`Compound Name`
for (i in id) {
  url <- c(url,paste('https://www.mzcloud.org/compound/Search?Query=',
                     i,sep = ''))
}
title <- c()
ID <- c()
for(i in 1:length(url)){
  RS.open_Url(url[i])
  Sys.sleep(2)
  title <- c(title,RS.get_Text('/html/body/div/div[2]/div/div//div[2]/div/div[2]/div/div[1]/a'))
  ID <- c(ID,RS.get_Text('/html/body/div/div[2]/div/div/div[*]/div[2]/div/div[2]/div/div[2]/p/span'))
}
df <- data.frame(title = title,ID=ID)
df<- filter(df,!duplicated(df$ID))
df1<-c()
for(i in 1:length(id)){
  df1 <- c(df1,df1<-df[id[i]==df$title,])
}
library(plyr)
df2 <-ldply(df1, data.frame)
colnames(df2)<-c('id','name')
df3<-data.frame(df2[df2$id=='title',])
df3.1<-data.frame(df2[df2$id=='ID',])
df4<-cbind(df3,df3.1)
df4<-df4[,c(2,4)]
colnames(df4)<-c('name','id')
df4_1<-gsub("ID: Reference","",df4$id)
df4_2<-cbind(df4,df4_1)
colnames(df4_2)<-c('name','id_1','id')
df4<-df4_2[,c(1,3)]
id2<-df4$id
url2<-c()
for (i in id2) {
  url2 <- c(url2,paste('https://www.mzcloud.org/compound/Reference/',
                     i,sep = ''))
}
RS.OpenChrome()
Key<-c()
SMILES<-c()
title<-c()
for(i in 1:length(url2)){
  RS.open_Url(url2[i])
  Sys.sleep(2.5)
  Key <- c(Key,RS.get_Text('/html/body/div/div[7]/div/div/table/tbody/tr[2]/td[2]'))
  SMILES<-c(SMILES,RS.get_Text('/html/body/div/div[7]/div/div/table/tbody/tr[3]/td[2]'))
  title <- c(title,RS.get_Text('/html/body/div/div[1]/div/h3'))
}
title_Key_SMILES <- data.frame(Compound_Name=title,
                               InChiKeys = Key,
                               SMILES=SMILES)
RS.OpenChrome()
Pubchem_ID<-c()
url3<-c()
for (i in length(Key)) {
  url3 <- c(url3,paste('https://pubchem.ncbi.nlm.nih.gov/#query=',
                       Key,sep = ''))
}
for(i in 1:length(Key)){
  RS.open_Url(url3[i])
  Sys.sleep(2.5)
  Pubchem_ID<-c(Pubchem_ID,RS.get_Text('/html/body/div[1]/div/div/main/div[2]/div[2]/div[3]/div/div/div/div[2]/ul/li/div/div/div[1]/div[2]/div[2]/div/span/a/span/span'))
}
Pubchem_ID <- data.frame(Pubchem_ID=Pubchem_ID)
total<-cbind(title_Key_SMILES,Pubchem_ID)