[med-svn] r1478 - trunk/community/infrastructure/getData

[smoe-guest at alioth.debian.org]

Author: smoe-guest
Date: 2008-02-27 14:55:14 +0000 (Wed, 27 Feb 2008)
New Revision: 1478

Added:
   trunk/community/infrastructure/getData/TODO
Modified:
   trunk/community/infrastructure/getData/getData
Log:
Added gene ontology, verbose option and Charles as co-author.


Added: trunk/community/infrastructure/getData/TODO
===================================================================
--- trunk/community/infrastructure/getData/TODO	                        (rev 0)
+++ trunk/community/infrastructure/getData/TODO	2008-02-27 14:55:14 UTC (rev 1478)
@@ -0,0 +1,12 @@
+getData - TODO
+==============
+
+
+* separate machinery from database descriptions
+* allow for Debian maintainers to install additional
+  database descriptions
+* come up with a set of standard use cases as a start
+* define Debian packages and/or applications that must
+  be installed prior to the execution of some scripts.
+
+-- Steffen <moeller at debian.org> Mon, 18 Feb 2008 13:46:48 +0100

Modified: trunk/community/infrastructure/getData/getData
===================================================================
--- trunk/community/infrastructure/getData/getData	2008-02-26 20:17:22 UTC (rev 1477)
+++ trunk/community/infrastructure/getData/getData	2008-02-27 14:55:14 UTC (rev 1478)
@@ -11,6 +11,7 @@
 # astronomy.
 
 # Copyright (c) 2008 Steffen Moeller <moeller at debian.org>
+# Copyright (c) 2008 Charles Plessy <debian-no-spam at plessy.org>
 # 
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
@@ -84,6 +85,11 @@
 
     Present a more detailed description in form of a man page.
 
+=item --verbose
+
+    Say one or two words more than required.
+
+
 =item --mirrordir <path>
 
     Specifies destination directory. The data will be mirrored to $mirrordir/$dbname/
@@ -116,7 +122,7 @@
 
 =head1 AUTHORS
 
-Steffen Moeller <moeller at debian.org>, ... and ?, from the Debian-Med packaging initiative.
+Steffen Moeller <moeller at debian.org>, Charles Plessy <debian-no-spam at plessy.org> ... and ?, from the Debian-Med packaging initiative.
 
 =cut
 
@@ -157,6 +163,11 @@
 
 #                    B  I  O  I  N  F  O  R  M  A  T  I  C  S
 
+	"gene.ontology.rdf" => {
+		name => "GeneOntology - RDF-formatted, terms only.",
+		source => "wget --mirror ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest/go_*-termdb.rdf-xml.gz"
+	},
+
 	"intact.psimitab" => {
 		name  => "IntACT Protein Interaction Database",
 		source => "wget --mirror ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip",
@@ -215,9 +226,10 @@
 #	}
 );
 
-my ($list,$help,$man)=(0,0,0);
+my ($list,$help,$man,$verbose)=(0,0,0,0);
 
-my %options=("mirrordir:s" => \$mirrordir, "list" => \$list, "help"=>\$help, "man"=>\$man);
+my %options=("mirrordir:s" => \$mirrordir, "list" => \$list,
+             "help"=>\$help, "man"=>\$man, "verbose"=>\$verbose);
 
 sub myhelp () {
     require "Pod/Usage.pm";
@@ -275,7 +287,7 @@
 		system($cmd) and die "Experienced problem.";
 	}
 	else {
-		print STDERR "$db: No post-download command defined.\n";
+		print STDERR "$db: No post-download command defined.\n" if $verbose;
 	}
 	chdir($d) or die "Could not change back to dir '$d'.\n";
 }