R-40 第二阶段第1次

barcaqiu 2018-01-23 11:21:35 阅读: 1293

> install.packages("jsonlite")

> install.packages("httr")

> library(httr)

> baseUrl="https://eutils.ncbi.nlm.nih.gov/"

> pubmedAction=list(base="entrez/eutils/index.fcgi",search="entrez/eutils/esearch.fcgi",fetch="entrez/eutils/efetch.fcgi",summary="entrez/eutils/esummary.fcgi")

> searchArticleParam=list(retstart=0,retmax=20,usehistory='Y',querykey='',webenv='',term='(cell[TA]) AND 2017[DP]',total_num=0,total_page=1, page_size=20, current_page=1)

> postSearchUrl=paste(baseUrl,pubmedAction$search,sep="")

> r <- POST(postSearchUrl, body = list(db='pubmed',term=searchArticleParam$term,retmode='json',retstart=searchArticleParam$retstart,retmax=searchArticleParam$retmax,usehistory=searchArticleParam$usehistory,rettype='uilist'))

> stop_for_status(r)

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

> esearchresult=data$esearchresult

> count = esearchresult$count

> print(count)

QQ截图20180123112108.png

 

> searchArticleParam$total_num=esearchresult$count

> searchArticleParam$querykey=esearchresult$querykey

> searchArticleParam$webenv=esearchresult$webenv

> pubmedidStr="29275861,29275860"

> postFetchUrl=paste(baseUrl,pubmedAction$fetch,sep="")

> r2 <- POST(postFetchUrl, body = list(db='pubmed',id=pubmedidStr,retmode='xml', usehistory=searchArticleParam$usehistory,querykey=searchArticleParam$querykey,webenv=searchArticleParam$webenv))

> stop_for_status(r2)

> install.packages("xml2")

> library(xml2)

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

> article=xml_children(data2)

> count=length(article)

> cnt=1

> while(cnt<=count){ 

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

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

+     print(xml_text(title))

+     print(xml_text(abstract))

+     cnt = cnt + 1

+ }

QQ截图20180123141828.png

好多地方都还没有搞明白,基本是借鉴原码的

 
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