NAME

       bp_biofetch_genbank_proxy.pl - Caching BioFetch-compatible web proxy for GenBank

SYNOPSIS

         Install in cgi-bin directory of a Web server.  Stand back.

DESCRIPTION

       This CGI script acts as the server side of the BioFetch protocol as described in
       http://obda.open-bio.org/Specs/.  It provides two database access services, one for data source "genbank"
       (nucleotide entries) and the other for data source "genpep" (protein entries).

       This script works by forwarding its requests to NCBI's eutils script, which lives at
       https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi.  It then reformats the output according to the
       BioFetch format so the sequences can be processed and returned by the Bio::DB::BioFetch module.  Returned
       entries are temporarily cached on the Web server's file system, allowing frequently-accessed entries to
       be retrieved without another round trip to NCBI.

   INSTALLATION
       You must have the following installed in order to run this script:

          1) perl
          2) the perl modules LWP and Cache::FileCache
          3) a web server (Apache recommended)

       To install this script, copy it into the web server's cgi-bin directory.  You might want to shorten its
       name; "dbfetch" is recommended.

       There are several constants located at the top of the script that you may want to adjust.  These are:

       CACHE_LOCATION

       This is the location on the filesystem where the cached files will be located.  The default is
       /usr/tmp/dbfetch_cache.

       MAX_SIZE

       This is the maximum size that the cache can grow to.  When the cache exceeds this size older entries will
       be deleted automatically.  The default setting is 100,000,000 bytes (100 MB).

       EXPIRATION

       Entries that haven't been accessed in this length of time will be removed from the cache.  The default is
       1 week.

       PURGE

       This constant specifies how often the cache will be purged for older entries.  The default is 1 hour.

TESTING

       To see if this script is performing as expected, you may test it with this script:

        use Bio::DB::BioFetch;
        my $db = Bio::DB::BioFetch->new(-baseaddress=>'http://localhost/cgi-bin/dbfetch',
                                        -format     =>'genbank',
                                        -db         =>'genbank');
        my $seq = $db->get_Seq_by_id('DDU63596');
        print $seq->seq,"\n";

       This should print out a DNA sequence.

SEE ALSO

       Bio::DB::BioFetch, Bio::DB::Registry

AUTHOR

       Lincoln Stein, <lstein-at-cshl.org>

       Copyright (c) 2003 Cold Spring Harbor Laboratory

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl
       itself.  See DISCLAIMER.txt for disclaimers of warranty.

perl v5.36.0                                       2023-12-17                      BP_BIOFETCH_GENBANK_PROXY(1p)