Sendu Bala
and 1 contributors

NAME

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

SYNOPSIS

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');

DESCRIPTION

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.

FEEDBACK

Mailing Lists

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

Reporting Bugs

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/

AUTHOR

Allen Day <allenday@ucla.edu>

COPYRIGHT

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.

DISCLAIMER

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

BUGS AND LIMITATIONS

  • Of course, you'll need access to the sites hosting the PDFs to download them.

    = item *

    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.

SEE ALSO

 Pub Med Help
 http://eutils.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html

 Entrez Utilities
 http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

APPENDIX

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

 Usage   : my $obj = new Bio::Biblio (-access => 'pdf' ...);
           (_initialize is internally called from this constructor)
 Returns : 1 on success
 Args    : none

This is an actual new() method (except for the real object creation and its blessing which is done in the parent class Bio::Root::Root in method _create_object).

Note that this method is called always as an object method (never as a class method) - and that the object who calls this method may already be partly initiated (from Bio::Biblio::new method); so if you need to do some tricks with the 'class invocation' you need to change Bio::Biblio::new method, not this one.

get_next

  Title   : get_next
  Usage   : $xml = $biblio->get_next();
  Function: return next record as xml
  Returns : an xml string
  Args    : none

find

  Title   : find
  Usage   : $biblio = $biblio->find(1234);
  Function: perform a PubMed query by PubMed ID
  Returns : a reference to the object on which the method was called
  Args    : a PubMed ID

exists

  Title   : exists
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

destroy

  Title   : destroy
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

get_vocabulary_names

  Title   : get_vocabulary_names
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : empty arrayref
  Args    : none

contains

  Title   : contains
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

get_entry_description

  Title   : get_entry_description
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

get_all_values

  Title   : get_all_values
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

get_all_entries

  Title   : get_all_entries
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

Internal methods unrelated to Bio::DB::BiblioI

depth()

 Usage   : $obj->depth($newval)
 Function: track link recursion depth
 Example : 
 Returns : value of depth (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

max_depth()

 Usage   : $obj->max_depth($newval)
 Function: how far should link recursion go?
 Example : 
 Returns : value of max_depth (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

ua()

 Usage   : $obj->ua($newval)
 Function: holds an LWP::UserAgent instance
 Example : 
 Returns : value of ua (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

pdf()

 Usage   : $obj->pdf($newval)
 Function: holds pdf data
 Example : 
 Returns : value of pdf (a scalar)
 Args    : on set, new value (a scalar or undef, optional)