xml - Perl:从 XML 输出填充数组(通过 Eutils 的 PubMed UID)

Question

我正在尝试从 PubMed 的 Eutils 生成的 XML 输出构建一个 ID 数组。

Here is the code on GitHub .下面是具体的子程序。

解决这个问题的最佳方法是什么？

getUID($query);

sub getUID {

  # First, build the Eutils query
  my $utils = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils'; # Base URL for searches
  my $db = 'pubmed'; # Default to PubMed database; this may be changed.
  my $retmax = 10; # Get 10 results from Eutils

  my $esearch = $utils . '/esearch.fcgi?db=' . $db . '&retmax=' . $retmax . '&term=';

  my $esearch_result = get( $esearch . $query ); # Downloads the XML

  # Second, extract the UIDs
  $esearch_result =~ m(<Id>*</Id>);      

  print $esearch_result; # This should return a list of ID's (numbers), but doesn't.

}

PubMed XML 结果如下所示:

<?xml version="1.0" ?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd">
<eSearchResult><Count>2768671</Count><RetMax>10</RetMax><RetStart>0</RetStart><IdList>
<Id>23682407</Id>
<Id>23682406</Id>
<Id>23682388</Id>
<Id>23682359</Id>
<Id>23682336</Id>
<Id>23682331</Id>
<Id>23682325</Id>
<Id>23682320</Id>
<Id>23682315</Id>
<Id>23682311</Id>
</IdList><TranslationSet><Translation>     <From>cancer</From>     <To>"neoplasms"[MeSH Terms] OR "neoplasms"[All Fields] OR "cancer"[All Fields]</To>    </Translation></TranslationSet><TranslationStack>   <TermSet>    <Term>"neoplasms"[MeSH Terms]</Term>    <Field>MeSH Terms</Field>    <Count>2430901</Count>    <Explode>Y</Explode>   </TermSet>   <TermSet>    <Term>"neoplasms"[All Fields]</Term>    <Field>All Fields</Field>    <Count>1920766</Count>    <Explode>Y</Explode>   </TermSet>   <OP>OR</OP>   <TermSet>    <Term>"cancer"[All Fields]</Term>    <Field>All Fields</Field>    <Count>1192293</Count>    <Explode>Y</Explode>   </TermSet>   <OP>OR</OP>   <OP>GROUP</OP>  </TranslationStack><QueryTranslation>"neoplasms"[MeSH Terms] OR "neoplasms"[All Fields] OR "cancer"[All Fields]</QueryTranslation></eSearchResult>

Answer 1

如果您希望匹配返回一个字符串，您必须添加捕获括号。如果有多个匹配项，请使用 g 选项。将结果存储在数组中:

 my @matches = $esearch_result =~ m(<Id>(.*)</Id>)g;
 print "$_\n" for @matches;