pdf documentation.

Bio::DB::Biblio::pdf - Fetch PDF for a PubMed ID

Privates (from "my" definitions)

%visit = ()

Data::Dumper

WWW::Mechanize

base qw ( Bio::Biblio Bio::DB::BiblioI )

Do not use this object directly, it is recommended to access it and use
it through the Bio::Biblio module:

  use Bio::Biblio;
  my $biblio = new Bio::Biblio (-access => 'pdf');

This object contains the real implementation of a Bibliographic Query
Service as defined in Bio::DB::BiblioI.
Bio::DB::BiblioI is not implemented as documented in the interface,
particularly the find() method, which is not compatible with PubMed's
query language.

sub _initialize {

    my ($self, @args) = @_;

    #pdf doesn't need this code, but it doesn't hurt to leave it here... -ad

    # make a hashtable from @args
    my %param = @args;
    @param { map { lc $_ } keys %param } = values %param; # lowercase keys

    $self->max_depth(3);
    $self->depth(0);
    $self->ua( WWW::Mechanize->new());
    $self->ua->agent_alias('Linux Mozilla');

    #now override with passed hash

    # copy all @args into this object (overwriting what may already be
    # there) - changing '-key' into '_key'
    my $new_key;
    foreach my $key (keys %param) {
      ($new_key = $key) =~ s/^-/_/;
      $self->{ $new_key } = $param { $key };
    }

    #AOK
    return 1;

}

sub get_next {

  my $self = shift;

  return $self->pdf();

  return;

}

sub find {

  my ($self,$id) = @_;

  $self->{pdf} = undef;
  $self->_process_pubmed_html($id);

}

sub exists {

  return;

}

sub destroy {

  return;

}

sub get_vocabulary_names {

  return [];

}

sub contains {

  return;

}

sub get_entry_description {

  return;

}

sub get_all_values {

  return;

}

sub get_all_entries {

  return;

}

sub depth {

  my($self,$val) = @_;
  $self->{'depth'} = $val if defined($val);
  return $self->{'depth'};

}

sub max_depth {

  my($self,$val) = @_;
  $self->{'max_depth'} = $val if defined($val);
  return $self->{'max_depth'};

}

sub ua {

  my($self,$val) = @_;
  $self->{'ua'} = $val if defined($val);
  return $self->{'ua'};

}

sub _process_pubmed_html {

  my ($self,$id) = @_;

  $self->ua->get( ABSTRACT_BASE . $id );
  my $page = $self->ua->content();

  #here is the treasure
  $page =~ m|<!---- Pager -- \(page header\) -- end ------>.+?<SPAN><a href="(.+?)" onClick="window.open|s;

  if( ! defined($1) ) {
    return;
  }

  $self->ua->follow_link( url => $1 );

  #uncomment this to do site crawl -- old style
  #$self->_crawl();

  my $pdf_url = $self->guess_pdf_url($self->ua->uri);
  $self->throw( "didn't recognize pattern in '".$self->ua->uri."', please patch module" ) unless $pdf_url;
  $self->ua->get( $pdf_url );
  my $content = $self->ua->content();
  $self->pdf( $content );

}

sub guess_pdf_url {

  my($self,$url) = @_;

  #cancer research
  if( $url =~ m!^(.+?)/cgi/content/full/(\d+)/(\d+)/(\d+)/?$! ) {
    return qq($1/cgi/reprint/$2/$3/$4.pdf);
  }
  #nature
  #http://www.nature.com/cgi-taf/DynaPage.taf?file=/onc/journal/v18/n27/abs/1202776a.html&dynoptions=doi1108513968
  #http://www.nature.com/cgi-taf/DynaPage.taf?file=/onc/journal/v18/n27/full/1202776a.html&filetype=pdf
  elsif( $url =~ m!^(.+?cgi-taf/DynaPage.taf.+?)/journal/(.+?)/abs/(.+?\.html)! ) {
    return qq($1/journal/$2/full/$3\&filetype=pdf);
  }
  #science direct
  #these pages contain some unpredictable md5 bullshit, so we need to parse the page
  #http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VPM-480CTTS-5&_coverDate=04%2F30%2F2003&_alid=247076467&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6210&_sort=d&view=c&_acct=C000059605&_version=1&_urlVersion=0&_userid=4423&md5=8054dea49e32e98a6b30b206ea47fbfe
  #http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VPM-480CTTS-5-5&_cdi=6210&_user=4423&_orig=search&_coverDate=04%2F30%2F2003&_qd=1&_sk=999779997&view=c&wchp=dGLbVtz-zSkzV&md5=5b04979d84dab066be5cde52fd2affa7&ie=/sdarticle.pdf
  elsif( $url =~ m!^(.+?science\?_ob=)ArticleURL(.+?)$! ) {
    my $link = $self->ua->find_link( text_regex => qr/PDF \(.+?\)/s );
    return unless $link;
    return $link->url_abs();
  }
  #genome biology
  #http://genomebiology.com/2003/4/7/R43
  #http://genomebiology.com/content/pdf/gb-2003-4-7-r43.pdf
  elsif( $url =~ m!^(.+?genomebiology.com)/(\d+)/(\d+)/(\d+)/(.+?)/?$! ) {
    my $file = lc(sprintf("gb-%d-%d-%d-%s.pdf",$2,$3,$4,$5));
    return qq($1/content/pdf/$file);
  }
  #wiley interscience
  #http://www3.interscience.wiley.com/cgi-bin/abstract/91013753/ABSTRACT
  #http://www3.interscience.wiley.com/cgi-bin/fulltext/91013753/PDFSTART
  #http://download.interscience.wiley.com/cgi-bin/fulltext?ID=96515300&PLACEBO=IE.pdf&mode=pdf
  elsif( $url =~ m!^(.+?/cgi-bin)/abstract/(\d+?)/ABSTRACT$! ) {
    $self->ua->get( qq($1/fulltext/$2/PDFSTART) );
    my $link = $self->ua->find_link( url_regex => qr/fulltext/ );
    return unless $link;
    return $link->url_abs();
  }
  #nar, bioinformatics
  #http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D258
  #http://nar.oupjournals.org/cgi/reprint/32/suppl_1/D258.pdf
  elsif( $url =~ m!^(.+?oupjournals.org/cgi)/reprint/(.+?)$! ) {
    return qq($1/reprint/$2.pdf);
  }
  elsif( $url =~ m!^(.+?oupjournals.org/cgi)/content/full/(.+?)$! ) {
    return qq($1/reprint/$2.pdf);
  }

  #plos
  #http://biology.plosjournals.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0020009
  #http://www.plosbiology.org/archive/1545-7885/2/1/pdf/10.1371_journal.pbio.0020009-S.pdf
  elsif( $url =~ m!^http://[^.]+?\.plos! ) {
    my $link = $self->ua->find_link( text_regex => qr/^Screen/s );
    return unless $link;
    return $link->url_abs();
  }
  #bmc bioinformatics
  #http://www.biomedcentral.com/1471-2105/2/7
  #http://www.biomedcentral.com/content/pdf/1471-2105-2-7.pdf
  elsif( $url =~ m!^(.+?biomedcentral.+?)/(\d+\-\d+)/(\d+)/(\d+)/?$! ) {
    my $file = lc(sprintf("%s-%d-%d.pdf",$2,$3,$4));
    return qq($1/content/pdf/$file);
  }


warn $url;
  return;

}

sub pdf {

  my($self,$val) = @_;
  $self->{'pdf'} = $val if defined($val);
  return $self->{'pdf'};

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  http://bugzilla.open-bio.org/

Allen Day <allenday@ucla.edu>

Copyright (c) 2004 Allen Day, University of California, Los Angeles.
This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.

This software is provided "as is" without warranty of any kind.

Of course, you'll need access to the sites hosting the PDFs to download
them.
If you're having problems retrieving PDF from a site you have access to,
you might try adjusting the max_depth() attribute. It is default set to 3,
and affects how many links deep will be recursively followed in page
fetches to try to find your PDF.

The main documentation details are to be found in
Bio::DB::BiblioI.
Here is the rest of the object methods. Interface methods first,
followed by internal methods.

_initialize	Description	Code
get_next	Description	Code
find	Description	Code
exists	Description	Code
destroy	Description	Code
get_vocabulary_names	Description	Code
contains	Description	Code
get_entry_description	Description	Code
get_all_values	Description	Code
get_all_entries	Description	Code
depth	Description	Code
max_depth	Description	Code
ua	Description	Code
_process_pubmed_html	No description	Code
guess_pdf_url	No description	Code
pdf	Description	Code