我是 XML::Twig 的新手,我正在尝试解析 PubMed XML 2.0 最终摘要以放入 mySQL 数据库中。我已经走到这一步了:
#!/bin/perl -w
use strict;
use DBI;
use XML::Twig;
my $uid = "";
my $title = "";
my $sortpubdate = "";
my $sortfirstauthor = "";
my $dbh = DBI->connect ("DBI:mysql:medline:localhost:80",
"root", "mysql");
my $t= new XML::Twig( twig_roots => { 'DocumentSummary' => $uid => \&submit },
twig_handlers => { 'DocumentSummary/Title' => $title, 'DocumentSummary/SortPubDate' => $sortpubdate, 'DocumentSummary/SortFirstAuthor' => $sortfirstauthor});
$t->parsefile('20112.xml');
$dbh->disconnect();
exit;
sub submit
{ my $insert= $dbh->prepare( "INSERT INTO medline_citation (uid, title, sortpubdate, sortfirstauthor) VALUES (?, ?, ?, ?);");
$insert->bind_param( 1, $uid);
$insert->bind_param( 2, $title);
$insert->bind_param( 3, $sortpubdate);
$insert->bind_param( 4, $sortfirstauthor);
$insert->execute();
$t->purge;
}
但是 Perl 似乎由于某种原因停滞了。我这样做对吗?我正在尝试使用 twig_roots 来减少解析量,因为我只对几个字段感兴趣(这些是大文件)。
这是一个 XML 示例:
<DocumentSummary uid="22641317">
<PubDate>2012 Jun 1</PubDate>
<EPubDate></EPubDate>
<Source>Clin J Oncol Nurs</Source>
<Authors>
<Author>
<Name>Park SH</Name>
<AuthType>
Author
</AuthType>
<ClusterID>0</ClusterID>
</Author>
<Author>
<Name>Knobf MT</Name>
<AuthType>
Author
</AuthType>
<ClusterID>0</ClusterID>
</Author>
<Author>
<Name>Sutton KM</Name>
<AuthType>
Author
</AuthType>
<ClusterID>0</ClusterID>
</Author>
</Authors>
<LastAuthor>Sutton KM</LastAuthor>
<Title>Etiology, assessment, and management of aromatase inhibitor-related musculoskeletal symptoms.</Title>
<SortTitle>etiology assessment and management of aromatase inhibitor related musculoskeletal symptoms </SortTitle>
<Volume>16</Volume>
<Issue>3</Issue>
<Pages>260-6</Pages>
<Lang>
<string>eng</string>
</Lang>
<NlmUniqueID>9705336</NlmUniqueID>
<ISSN>1092-1095</ISSN>
<ESSN>1538-067X</ESSN>
<PubType>
<flag>Journal Article</flag>
</PubType>
<RecordStatus>
PubMed - in process
</RecordStatus>
<PubStatus>4</PubStatus>
<ArticleIds>
<ArticleId>
<IdType>pii</IdType>
<IdTypeN>4</IdTypeN>
<Value>N1750TW804546361</Value>
</ArticleId>
<ArticleId>
<IdType>doi</IdType>
<IdTypeN>3</IdTypeN>
<Value>10.1188/12.CJON.260-266</Value>
</ArticleId>
<ArticleId>
<IdType>pubmed</IdType>
<IdTypeN>1</IdTypeN>
<Value>22641317</Value>
</ArticleId>
<ArticleId>
<IdType>rid</IdType>
<IdTypeN>8</IdTypeN>
<Value>22641317</Value>
</ArticleId>
<ArticleId>
<IdType>eid</IdType>
<IdTypeN>8</IdTypeN>
<Value>22641317</Value>
</ArticleId>
</ArticleIds>
<History>
<PubMedPubDate>
<PubStatus>entrez</PubStatus>
<Date>2012/05/30 06:00</Date>
</PubMedPubDate>
<PubMedPubDate>
<PubStatus>pubmed</PubStatus>
<Date>2012/05/30 06:00</Date>
</PubMedPubDate>
<PubMedPubDate>
<PubStatus>medline</PubStatus>
<Date>2012/05/30 06:00</Date>
</PubMedPubDate>
</History>
<References>
</References>
<Attributes>
<flag>Has Abstract</flag>
</Attributes>
<PmcRefCount>0</PmcRefCount>
<FullJournalName>Clinical journal of oncology nursing</FullJournalName>
<ELocationID></ELocationID>
<ViewCount>0</ViewCount>
<DocType>citation</DocType>
<SrcContribList>
</SrcContribList>
<BookTitle></BookTitle>
<Medium></Medium>
<Edition></Edition>
<PublisherLocation></PublisherLocation>
<PublisherName></PublisherName>
<SrcDate></SrcDate>
<ReportNumber></ReportNumber>
<AvailableFromURL></AvailableFromURL>
<LocationLabel></LocationLabel>
<DocContribList>
</DocContribList>
<DocDate></DocDate>
<BookName></BookName>
<Chapter></Chapter>
<SortPubDate>2012/06/01 00:00</SortPubDate>
<SortFirstAuthor>Park SH</SortFirstAuthor>
</DocumentSummary>
谢谢!
最佳答案
我这样做的方法是为 DocumentSummary 使用一个处理程序,它提供数据库,然后清除记录。没有比这更花哨的了。
此外,我发现 DBIx::Simple,嗯,比原始 DBI 更易于使用,它负责为我准备和缓存语句:
#!/bin/perl
use strict;
use warnings;
use DBIx::Simple;
use XML::Twig;
my $db = DBIx::Simple->connect ("dbi:SQLite:dbname=t.db"); # replace by your DSN
my $t= XML::Twig->new( twig_roots => { DocumentSummary => \&submit },)
->parsefile('20112.xml');
$db->disconnect();
exit;
sub submit
{ my( $t, $summary)= @_;
my $insert= $db->query( "INSERT INTO medline_citation (uid, title, sortpubdate, sortfirstauthor) VALUES (?, ?, ?, ?);",
$summary->att( 'uid'),
map { $summary->field( $_) } ( qw( Title SortPubDate SortFirstAuthor))
);
$t->purge;
}
如果您想了解 map { $summary->field( $_) } ( qw( Title SortPubDate SortFirstAuthor))
,它只是一种更高级(恕我直言,更易于维护)的编写方式$summary->field('Title'),$summary->field('SortPubDate'),$summary->field('SortFirstAuthor')
关于mysql - 解析 PubMed XML 以提交到 mySQL 数据库 (XML::Twig),我们在Stack Overflow上找到一个类似的问题: https://stackoverflow.com/questions/10837564/