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  • R2-37-第二阶段第二次作业

    洪学志 发布于:2018.02.11

    一、

    library(DBI)

    library(RMySQL)

    con <- dbConnect(MySQL(),host="localhost",dbname="rdb",user="root",password="")

    dbSendQuery(con,'SET NAMES utf8') 

    dbGetInfo(con)  

    dbListTables(con)  

    dbRemoveTable(con,"test") 看老大的来练习

     二、

    library(DBI)

    library(RMySQL)

    con <- dbConnect(MySQL(),host="localhost",dbname="rdb",user="root",password="")

    dbSendQuery(con,'SET NAMES utf8')

    library(httr)

    totalNum=562

    pageSize=10

    totalPage=ceiling(totalNum/pageSize)

    currentPage=1

    term='(cell[TA]) AND 2017[DP]'

    usehistory='Y'

    querykey=''

    webenv=''

    postSearchUrl='https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'

    while(currentPage<=totalPage){

      retstart=(currentPage-1)*pageSize

      r <- POST(postSearchUrl, 

                body = list(

                  db='pubmed',

                  term=term,

                  retmode='json',

                  retstart=retstart,

                  retmax=pageSize,

                  usehistory=usehistory,

                  rettype='uilist'

                )

          )

      stop_for_status(r)

      data=content(r, "parsed", "application/json")

      esearchresult=data$esearchresult

      querykey=esearchresult$querykey

      webenv=esearchresult$webenv

      idlist =esearchresult$idlist

      n = length(idlist)

      pmid=c()

      i = 1

      while(i<=n){

        pmid=c(pmid, as.character(idlist[i][1]))

        i = i+1

      }

      article=data.frame('pmid'=pmid)

      dbWriteTable(con,"article",article,append=TRUE)

      currentPage = currentPage + 1

    }

    dbDisconnect(con)

    2-1.png

    三、

    library(RMySQL)

    library(xml2)

    library(httr)

    library(DBI)

    con <- dbConnect(MySQL(),host="localhost",dbname="rdb",user="root",password="")

    dbSendQuery(con,'SET NAMES utf8')

    rs <- dbSendQuery(con, "SELECT * FROM article WHERE isdone=0")

    while (!dbHasCompleted(rs)) {

      chunk <- dbFetch(rs, 10) 

      pmidStr=""

      i=1

      n=nrow(chunk)

      while(i<=n){

        pmidStr=paste(pmidStr,chunk[i,3],sep=",")

        i=i+1

      }

        pmidStr=substr(pmidStr,2,100000)

        postFetchUrl='https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'

      r2 <- POST(postFetchUrl, 

                 body = list(

                   db='pubmed',

                   id=pmidStr,

                   retmode='xml'

                 )

      )

      stop_for_status(r2)

      data2=content(r2, "parsed", "application/xml")

      article=xml_children(data2)

      count=length(article)

      cnt=1

      while(cnt<=count){

        title=xml_text(xml_find_first(article[cnt],".//ArticleTitle"))

        abstract=xml_text(xml_find_first(article[cnt],".//AbstractText"))

        pmid=xml_text(xml_find_first(article[cnt],".//PMID"))

        title=gsub("'","",title)

        abstract=gsub("'","",abstract)

        sql=paste("UPDATE article SET title='",title,"',abstract='",abstract,"',isdone=1"," where pmid='",pmid,"'",sep="")

        con2 <- dbConnect(MySQL(),host="localhost",dbname="rdb",user="root",password="")

        dbSendQuery(con2,'SET NAMES utf8')

        dbSendQuery(con2,sql)

        dbDisconnect(con2)

        cnt = cnt + 1

        Sys.sleep(1)

          }

    }

    3-1.png

    3-2.png

     

     
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