X-Git-Url: https://git.donarmstrong.com/?p=function2gene.git;a=blobdiff_plain;f=bin%2Fdo_it_all;fp=bin%2Fdo_it_all;h=788319a03226fab077cda0ca67543ac5702340ee;hp=3d3cfa3effb42640cbe917f9ebb41da3fbcad279;hb=79c0f28d89ba108bcfca68a8b5d4f0e3855455dc;hpb=672a430873e686b884bccb1b027321658c541b25

diff --git a/bin/do_it_all b/bin/do_it_all
index 3d3cfa3..788319a 100755
--- a/bin/do_it_all
+++ b/bin/do_it_all
@@ -3,7 +3,6 @@
 # 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;
@@ -16,8 +15,8 @@ use Storable;
 
 =head1 NAME
 
-do_it_all - Call out to each of the search modules to search for each
-of the terms
+  do_it_all - Call out to each of the search modules to search for
+  each of the terms
 
 =head1 SYNOPSIS
 
@@ -82,6 +81,7 @@ use vars qw($DEBUG);
 use Cwd qw(abs_path);
 use IO::File;
 use Storable qw(thaw freeze);
+use File::Basename qw(basename);
 
 my %options = (databases       => [],
 	       keywords        => [],
@@ -98,6 +98,8 @@ GetOptions(\%options,'keywords=s@','databases=s@',
 pod2usage() if $options{help};
 pod2usage({verbose=>2}) if $options{man};
 
+my $base_dir = basename($0);
+
 my $ERRORS='';
 
 $ERRORS.="restart-at must be one of get, parse or combine\n" if
@@ -180,16 +182,16 @@ if (@{$options{keywords}}) {
 
 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};
+	  delete $state{done_keywords}{get};
+	  delete $state{done_keywords}{parse};
+	  delete $state{done_keywords}{combine};
      }
      elsif (lc($options{restart_at}) eq 'parse') {
-	  delete $state{parsed_keywords};
-	  delete $state{combined_keywords};
+	  delete $state{done_keywords}{parse};
+	  delete $state{done_keywords}{combine};
      }
      elsif (lc($options{restart_at}) eq 'combine') {
-	  delete $state{combined_keywords};
+	  delete $state{done_keywords}{combine};
      }
 }
 
@@ -217,7 +219,7 @@ for my $keyword (@{$state{keywords}}) {
 	  }
 	  if (not exists $state{done_keywords}{parse}{$database}{$keyword}) {
 	       push @{$actions{parse}{$database}},$keyword;
-       delete $state{done_keywords}{combine}{$database}{$keyword} if
+	       delete $state{done_keywords}{combine}{$database}{$keyword} if
 		    exists $state{done_keywords}{combine}{$database}{$keyword};
 	  }
 	  if (not exists $state{done_keywords}{combine}{$database}{$keyword}) {
@@ -255,6 +257,32 @@ for my $state (qw(get parse)) {
      }
 }
 
+if ($actions{combine}) {
+     save_state(\%state);
+     # deal with combining results
+     my @parsed_results = map { my $db = $_;
+				map {
+				     "parsed_results_${db}_${_}.txt"
+				} keys %{$state{done_keywords}{parse}{$db}}
+			   } keys %{$state{done_keywords}{parse}};
+
+     write_command_to_file('combined_results.txt',
+			   "$base_dir/combine_results",
+			   @parsed_results,
+			  );
+     for my $result (@parsed_results) {
+	  s/^parsed_results_//;
+	  s/\.txt$//;
+	  my ($db,$keyword) = split /_/, $_, 2;
+	  $state{done_keywords}{combined}{$db}{$keyword} = 1;
+     }
+     save_state(\%state);
+     ADVISE("Finished; results in $options{results}/combined_results");
+}
+else {
+     ADVISE('Nothing to do. [Perhaps you wanted --restart-at?]');
+}
+
 sub handle_action{
      my ($state,$database,$queue) = @_;
      my $keyword;
@@ -262,6 +290,34 @@ sub handle_action{
      my $failed_keywords = ();
      while ($keyword = $queue->dequeue) {
 	  # handle the action, baybee
+	  if ($state eq 'get') {
+	       my $command_fh;
+	       open($command_fh,'|-',
+		    "get_${database}_results",
+		   );
+	       print {$command_fh} "$keyword\n";
+	       close($command_fh);
+	       if ($? != 0) {
+		    WARN("get_${database}_results with keyword $keyword failed with error code ".($?>>8));
+		    next;
+	       }
+	  }
+	  elsif ($state eq 'parse') {
+	       eval {
+		    write_command_to_file("parsed_results_${database}_${keyword}.txt",
+					  "parse_${database}_results",
+					  '--keywords',
+					  $keyword,
+					 );
+	       };
+	       if ($@) {
+		    WARN("parse_${database}_results failed with $@");
+		    next;
+	       }
+	  }
+	  else {
+	       die "I don't know how to handle state $state";
+	  }
 	  ADVISE("$state results from '$database' for '$keyword'");
 	  push @{$actioned_keywords},$keyword;
      }
@@ -276,6 +332,19 @@ sub save_state{
      close $state_fh or die "Unable to close state file: $!";
 }
 
+sub write_command_to_file{
+     my ($file,@command);
+     my $fh = IO::File->new($file,'w') or
+	  die "Unable to open $file for writing: $!";
+     my $command_fh;
+     open($command_fh,'-|',
+	  @command,
+	 ) or die "Unable to execute $command[0] $!";
+     print {$fh} <$command_fh>;
+     close $fh;
+     close $command_fh or die "$command[0] failed with ".($?>>8);
+}
+
 
 sub ADVISE{
      print STDOUT map {($_,qq(\n))} @_;