Elink 函数 returns HTTP 414 问题

Question

我正在 pubmed 中搜索术语并在 pubmed central 中查找相应的 ID。这是我的代码

Entrez.email = "Afsrtfgdsfg@bobxx.com"
batch_size = 10000

def idconv(idkeys):
    handle = Entrez.elink(db='pmc', dbfrom='pubmed', id=idkeys)
    return [each['LinkSetDb'][0]['Link'][0]['Id'] for each in Entrez.read(handle)]

def search(Term):
    handle = Entrez.esearch(db='pubmed', term=Term, retmax=100000000)
    record = Entrez.read(handle)
    idlist = record["IdList"]
    return idlist

mylist = search('"bacterial infections and mycoses"[MeSH Terms] AND pmc cc license[filter]AND ("review"[Publication Type]) AND "journal article"[Publication Type] NOT "letter"[Publication Type] NOT "comment"[Publication Type]')
print(len(idconv(mylist)))

我总是得到错误。

HTTP Error 414: Request-URI Too Large

我该如何解决这个问题？

Answer 1

我一次使用了 600 个块并得到了结果

from Bio import Entrez

Entrez.email = "Afsrtfgdsfg@bobxx.com"
batch_size = 10000
#['LinkSetDb'][0]['Link'][0]['Id']
def idconv(idkeys):
    res=[]
    for i in range(0, len(idkeys), 600):
        handle = Entrez.elink(db='pmc', dbfrom='pubmed', id=idkeys[i:i+600])
        for each in Entrez.read(handle):
            try:
                res.append(each['LinkSetDb'][0]['Link'][0]['Id'])
            except IndexError:
                pass
    return res

def search(Term):
    handle = Entrez.esearch(db='pubmed', term=Term, retmax=100000000)
    record = Entrez.read(handle)
    idlist = record["IdList"]
    return idlist

mylist = search('"bacterial infections and mycoses"[MeSH Terms] AND pmc cc license[filter]AND ("review"[Publication Type]) AND "journal article"[Publication Type] NOT "letter"[Publication Type] NOT "comment"[Publication Type]')
print(len(mylist))
print (len(idconv(mylist)))

Answer 2

Biopython 1.67（即将发布）应该通过在需要非常长的 HTTP GET URL 时切换到使用 HTTP POST 来解决这个问题。参见：

https://github.com/biopython/biopython/commit/674da1122593cdc492c3ae480c7c1b7db06343b7

同时，您可以尝试从源代码安装 Biopython 吗？

Elink 函数 returns HTTP 414 问题

Elink function returns HTTP 414 issue

python

biopython