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.IX Title "BP_BIOFETCH_GENBANK_PROXY 1p"
.TH BP_BIOFETCH_GENBANK_PROXY 1p "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
bp_biofetch_genbank_proxy.pl \- Caching BioFetch\-compatible web proxy for GenBank
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  Install in cgi\-bin directory of a Web server.  Stand back.
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This \s-1CGI\s0 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 \*(L"genbank\*(R" (nucleotide
entries) and the other for data source \*(L"genpep\*(R" (protein entries).
.PP
This script works by forwarding its requests to \s-1NCBI\s0'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 \s-1NCBI.\s0
.SS "\s-1INSTALLATION\s0"
.IX Subsection "INSTALLATION"
You must have the following installed in order to run this script:
.PP
.Vb 3
\&   1) perl
\&   2) the perl modules LWP and Cache::FileCache
\&   3) a web server (Apache recommended)
.Ve
.PP
To install this script, copy it into the web server's cgi-bin
directory.  You might want to shorten its name; \*(L"dbfetch\*(R" is
recommended.
.PP
There are several constants located at the top of the script that you
may want to adjust.  These are:
.PP
\&\s-1CACHE_LOCATION\s0
.PP
This is the location on the filesystem where the cached files will be
located.  The default is /usr/tmp/dbfetch_cache.
.PP
\&\s-1MAX_SIZE\s0
.PP
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 \s-1MB\s0).
.PP
\&\s-1EXPIRATION\s0
.PP
Entries that haven't been accessed in this length of time will be
removed from the cache.  The default is 1 week.
.PP
\&\s-1PURGE\s0
.PP
This constant specifies how often the cache will be purged for older
entries.  The default is 1 hour.
.SH "TESTING"
.IX Header "TESTING"
To see if this script is performing as expected, you may test it with
this script:
.PP
.Vb 6
\& use Bio::DB::BioFetch;
\& my $db = Bio::DB::BioFetch\->new(\-baseaddress=>\*(Aqhttp://localhost/cgi\-bin/dbfetch\*(Aq,
\&                                 \-format     =>\*(Aqgenbank\*(Aq,
\&                                 \-db         =>\*(Aqgenbank\*(Aq);
\& my $seq = $db\->get_Seq_by_id(\*(AqDDU63596\*(Aq);
\& print $seq\->seq,"\en";
.Ve
.PP
This should print out a \s-1DNA\s0 sequence.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::DB::BioFetch, Bio::DB::Registry
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein, <lstein\-at\-cshl.org>
.PP
Copyright (c) 2003 Cold Spring Harbor Laboratory
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.