From d8245a8bd7b77af4cdb72418346e52d8834e94a6 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Wed, 12 Dec 2007 00:42:08 +0000
Subject: [PATCH]  * Add --invalidate-state option to specifically invalidate a
 state

git-svn-id: file:///srv/svn/function2gene/trunk@21 a0738b58-4706-0410-8799-fb830574a030
---
 bin/function2gene | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/bin/function2gene b/bin/function2gene
index ed9a38c..c407047 100755
--- a/bin/function2gene
+++ b/bin/function2gene
@@ -28,6 +28,7 @@ use Storable;
   --results directory to store results in
   --database databases to search
   --restart-at mode to start searching at
+  --invalidate-state state to invalidate
   --debug, -d debugging level (Default 0)
   --help, -h display this help
   --man, -m display manual
@@ -59,6 +60,14 @@ If you need to restart the process at a particular state (which has
 already been completed) specify this option. Valid values are get,
 parse, or combine.
 
+=item B<--invalidate-state>
+
+This is a more powerful version of --restart-at, which can
+specifically invalidate a certain method,database,keyword combination.
+
+For example, you can request that the keyword foo be retreived again
+from ncbi using --invalidate-state 'get,ncbi,foo'
+
 =item B<--debug, -d>
 
 Debug verbosity. (Default 0)
@@ -99,10 +108,12 @@ my %options = (databases       => [],
 	       help            => 0,
 	       man             => 0,
 	       results         => '',
+	       invalidate_state => [],
 	       );
 
 GetOptions(\%options,'keywords=s@','databases=s@',
 	   'restart_at|restart-at=s','results=s',
+	   'invalidate_state|invalidate-state=s@',
 	   'debug|d+','help|h|?','man|m');
 
 pod2usage() if $options{help};
@@ -206,6 +217,24 @@ if (exists $options{restart_at} and length $options{restart_at}) {
      }
 }
 
+if (exists $options{invalidate_state}) {
+     for my $invalidate_state (@{$options{invalidate_state}}) {
+	  my ($method,$database,$keyword) = split /,/, $invalidate_state;
+	  if (not exists $state{done_keywords}{$method}) {
+	       print STDERR "Method '$method' does not exist, and cannot be invalidated\n";
+	  }
+	  elsif (not exists $state{done_keywords}{$method}{$database}) {
+	       print STDERR "Database '$database' does not exist for method '$method', and cannot be invalidated\n";
+	  }
+	  elsif (not exists $state{done_keywords}{$method}{$database}{$keyword}) {
+	       print STDERR "Keyword '$keyword' does not exist for database '$database' and method '$method', and cannot be invalidated\n";
+	  }
+	  else {
+	       delete $state{done_keywords}{$method}{$database}{$keyword};
+	  }
+     }
+}
+
 # now we need to figure out what has to happen
 # for each keyword, we check to see if we've got results, parsed
 # results, and combined it. If not, we queue up those actions.
-- 
2.39.2