add do it all script to call other modules

git-svn-id: file:///srv/svn/function2gene/trunk@3 a0738b58-4706-0410-8799-fb830574a030

diff --git a/bin/do_it_all b/bin/do_it_all
new file mode 100755 (executable)
index 0000000..b85356d
--- /dev/null
+++ b/bin/do_it_all
@@ -0,0 +1,240 @@
+#! /usr/bin/perl
+# do_it_all, is part of the gene search suite and is released
+# under the terms of the GPL version 2, or any later version, at your
+# option. See the file README and COPYING for more information.
+# Copyright 2007 by Don Armstrong <don@donarmstrong.com>.
+# $Id: perl_script 495 2006-08-10 08:02:01Z don $
+
+
+use warnings;
+use strict;
+
+use Getopt::Long;
+use Pod::Usage;
+
+use Storable;
+
+=head1 NAME
+
+do_it_all - Call out to each of the search modules to search for each
+of the terms
+
+=head1 SYNOPSIS
+
+ do_it_all --keywords keywords.txt --results gene_search_results
+
+ Options:
+  --keywords newline delineated list of keywords to search for
+  --results directory to store results in
+  --database databases to search
+  --restart-at mode to start searching at
+  --debug, -d debugging level (Default 0)
+  --help, -h display this help
+  --man, -m display manual
+
+=head1 OPTIONS
+
+=over
+
+=item B<--keywords>
+
+A file which contains a newline delinated list of keywords to search
+for. Can be specified multiple times. Lines starting with # or ; are
+ignored.
+
+=item B<--results>
+
+Directory in which to store results; also stores the current state of
+the system
+
+=item B<--database>
+
+Databases to search, can be specified multiple times. [Defaults to
+NCBI, GeneCards and Harvester, the only currently supported
+databases.]
+
+=item B<--restart-at>
+
+If you need to restart the process at a particular state (which has
+already been completed) specify this option.
+
+=item B<--debug, -d>
+
+Debug verbosity. (Default 0)
+
+=item B<--help, -h>
+
+Display brief useage information.
+
+=item B<--man, -m>
+
+Display this manual.
+
+=back
+
+=head1 EXAMPLES
+
+
+=cut
+
+
+use vars qw($DEBUG);
+
+my %options = (databases       => [],
+              keywords        => [],
+              debug           => 0,
+              help            => 0,
+              man             => 0,
+              directory       => '',
+              );
+
+GetOptions(\%options,'keywords=s@','databases=s@',
+          'restart_at|restart-at=s',
+          'debug|d+','help|h|?','man|m');
+
+pod2usage() if $options{help};
+pod2usage({verbose=>2}) if $options{man};
+
+my $ERRORS='';
+
+$ERRORS.="restart-at must be one of get, parse or combine\n" if
+     exists $options{restart_at} and $options{restart_at} !~ /^(?:get|parse|combine)$/;
+
+$ERRORS.="unknown database(s)" if
+     @{$options{databases}} and
+     grep {$_ !~ /^(?:ncbi|genecards|harvester)$/i} @{$options{databases}};
+
+if (not length $options{directory}) {
+     $ERRORS.="directory not specified";
+}
+elsif (not -d $options{directory} or not -w $options{directory}) {
+     $ERRORS.="directory $options{directory} does not exist or is not writeable";
+}
+
+pod2usage($ERRORS) if length $ERRORS;
+
+if (not @{$options{databases}}) {
+     $options{databases} = [qw(ncbi genecards harvester)]
+}
+
+$DEBUG = $options{debug};
+
+# There are three states for our engine
+# Getting results
+# Parsing them
+# Combining results
+
+# first, check to see if the state in the result directory exists
+
+my %state;
+
+if (-e "$options{directory}/do_it_all_state") {
+     ADVISE("Using existing state information");
+     my $state_fh = IO::File->new("$options{directory}/do_it_all_state",'r') or die
+         "Unable to open state file for reading: $!";
+     local $/;
+     my $state_file = <$state_fh> or die "Unabel to read state file $!";
+     %state = %{thaw($state_file)} or die "Unable to thaw state file";
+}
+else {
+     ADVISE("Starting new run");
+     %state = (keywords => [],
+              databases => [map {lc($_)} @{$options{databases}}],
+              gotten_keywords => {},
+              parsed_keywords => {},
+              combined_keywords => {},
+             );
+}
+
+my @new_keywords;
+if (@{$options{keywords}}) {
+     # uniqify keywords
+     my %old_keywords;
+     @old_keywords{@{$state{keywords}}} = (1) x @{$state{keywords}};
+     for my $keyword_file (@{$options{keywords}}) {
+         my $keyword_fh = IO::File->new($keyword_file,'r') or die
+              "Unable to open $keyword_file for reading: $!";
+         local $/;
+         while (<$keyword_fh>) {
+              next if /^\s*[#;]/;
+              chomp;
+              if (not $old_keywords{$_}) {
+                   DEBUG("Adding new keyword '$_'");
+                   push @new_keywords, $_;
+              }
+              else {
+                   DEBUG("Not adding duplicate keyword '$_'");
+              }
+         }
+     }
+}
+
+if (exists $options{restart_at} and length $options{restart_at}) {
+     if (lc($options{restart_at}) eq 'get') {
+         delete $state{gotten_keywords};
+         delete $state{parsed_keywords};
+         delete $state{combined_keywords};
+     }
+     elsif (lc($options{restart_at}) eq 'parse') {
+         delete $state{parsed_keywords};
+         delete $state{combined_keywords};
+     }
+     elsif (lc($options{restart_at}) eq 'combine') {
+         delete $state{combined_keywords};
+     }
+}
+
+# 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.
+
+my @get_needed = ();
+my @parse_needed = ();
+my $combine_needed = 0;
+
+for my $keyword (@{$state{keywords}}) {
+     for my $database (@{$state{databases}}) {
+         if (not exists $state{gotten_keywords}{$database}{$keyword}) {
+              push @get_needed,[$database,$keyword];
+              delete $state{parsed_keywords}{$database}{$keyword} if
+                   exists $state{gotten_keywords}{$database}{$keyword};
+              delete $state{combined_keywords}{$database}{$keyword} if
+                   exists $state{gotten_keywords}{$database}{$keyword};
+         }
+         if (not exists $state{parsed_keywords}{$database}{$keyword}) {
+              push @parse_needed,[$database,$keyword];
+              delete $state{combined_keywords}{$database}{$keyword} if
+                   exists $state{gotten_keywords}{$database}{$keyword};
+         }
+         if (not exists $state{combined_keywords}{$database}{$keyword}) {
+             $combine_needed = 1;
+         }
+     }
+}
+
+# handle getting needed results
+for my $action (@get_needed) {
+     
+}
+# handle parsing needed results
+for my $action (@parse_needed) {
+}
+
+# handle combining results
+
+
+
+sub ADVISE{
+     print STDOUT map {($_,qq(\n))} @_;
+}
+
+sub DEBUG{
+     print STDERR map {($_,qq(\n))} @_;
+}
+
+
+sub WARN {
+     print STDERR map {($_,qq(\n))} @_;
+}
+
+__END__