Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::DB::Biblio::pdf.3pm

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)