X-Git-Url: https://git.donarmstrong.com/?p=function2gene.git;a=blobdiff_plain;f=bin%2Fdo_it_all;h=9a681ecd6047aac77cccf84d37e62894b88abd6e;hp=788319a03226fab077cda0ca67543ac5702340ee;hb=59bb41e2cadc989c299822191d8e8ee7d348779c;hpb=79c0f28d89ba108bcfca68a8b5d4f0e3855455dc

diff --git a/bin/do_it_all b/bin/do_it_all
index 788319a..9a681ec 100755
--- a/bin/do_it_all
+++ b/bin/do_it_all
@@ -5,6 +5,7 @@
 # Copyright 2007 by Don Armstrong <don@donarmstrong.com>.
 
 
+use threads;
 use warnings;
 use strict;
 
@@ -81,7 +82,8 @@ use vars qw($DEBUG);
 use Cwd qw(abs_path);
 use IO::File;
 use Storable qw(thaw freeze);
-use File::Basename qw(basename);
+use File::Basename qw(basename dirname);
+use Thread::Queue;
 
 my %options = (databases       => [],
 	       keywords        => [],
@@ -98,7 +100,7 @@ GetOptions(\%options,'keywords=s@','databases=s@',
 pod2usage() if $options{help};
 pod2usage({verbose=>2}) if $options{man};
 
-my $base_dir = basename($0);
+my $base_dir = dirname(abs_path($0));
 
 my $ERRORS='';
 
@@ -107,7 +109,7 @@ $ERRORS.="restart-at must be one of get, parse or combine\n" if
 
 $ERRORS.="unknown database(s)" if
      @{$options{databases}} and
-     grep {$_ !~ /^(?:ncbi|genecards|harvester)$/i} @{$options{databases}};
+     grep {$_ !~ /^(?:ncbi|genecard|harvester)$/i} @{$options{databases}};
 
 if (not length $options{results}) {
      $ERRORS.="results directory not specified";
@@ -119,7 +121,7 @@ elsif (not -d $options{results} or not -w $options{results}) {
 pod2usage($ERRORS) if length $ERRORS;
 
 if (not @{$options{databases}}) {
-     $options{databases} = [qw(ncbi genecards harvester)]
+     $options{databases} = [qw(ncbi genecard harvester)]
 }
 
 $DEBUG = $options{debug};
@@ -165,9 +167,9 @@ if (@{$options{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*[#;]/;
+	       next unless /\w+/;
 	       chomp;
 	       if (not $old_keywords{$_}) {
 		    DEBUG("Adding new keyword '$_'");
@@ -178,6 +180,7 @@ if (@{$options{keywords}}) {
 	       }
 	  }
      }
+     push @{$state{keywords}},@new_keywords;
 }
 
 if (exists $options{restart_at} and length $options{restart_at}) {
@@ -228,22 +231,26 @@ for my $keyword (@{$state{keywords}}) {
      }
 }
 
-use threads;
-use Thread::Queue;
 
 for my $state (qw(get parse)) {
      my %databases;
      for my $database (keys %{$actions{$state}}) {
 	  next unless @{$actions{$state}{$database}};
-	  $databases{$database}{queue} = Thread::Queue->new;
-	  $databases{$database}{thread} = threads->new(\&handle_action($state,$database,$databases{database}{queue}));
+	  $databases{$database}{queue} = Thread::Queue->new
+	       or die "Unable to create new thread queue";
+	  $databases{$database}{thread} = threads->create(\&handle_action,$state,$database,$databases{$database}{queue})
+	       or die "Unable to create new thread";
 	  $databases{$database}{queue}->enqueue(@{$actions{$state}{$database}});
 	  $databases{$database}{queue}->enqueue(undef);
      }
      my $ERRORS=0;
      for my $database (keys %databases) {
-	  my ($actioned_keywords,$failed_keywords) = $databases{$database}{thread}->join;
-	  if (@{$failed_keywords}) {
+	  my ($actioned_keywords,$failed_keywords) = @{$databases{$database}{thread}->join||[]};
+	  if (not defined $failed_keywords) {
+	       ADVISE("Something bad happened during '$state' of '$database'");
+	       $ERRORS = 1;
+	  }
+	  elsif (@{$failed_keywords}) {
 	       ADVISE("These keywords failed during '$state' of '$database':",@{$failed_keywords});
 	       $ERRORS=1;
 	  }
@@ -286,32 +293,41 @@ else {
 sub handle_action{
      my ($state,$database,$queue) = @_;
      my $keyword;
-     my $actioned_keywords = ();
-     my $failed_keywords = ();
+     my $actioned_keywords = [];
+     my $failed_keywords = [];
+     DEBUG("Beginning to handle actions for state '$state' database '$database'");
      while ($keyword = $queue->dequeue) {
+	  DEBUG("Handling state '$state' database '$database' keyword '$keyword'");
 	  # 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));
+	       eval {
+		    open($command_fh,'|-',
+			 "$base_dir/get_${database}_results",
+			) or die "unable to execute '$base_dir/get_${database}_results'";
+		    print {$command_fh} "$keyword\n" or die "unable to print $keyword to 'get_${database}_results'";
+		    close($command_fh) or die "Unable to close filehandle";
+		    if ($? != 0) {
+			 die "get_${database}_results with keyword $keyword failed with error code ".($?>>8);
+		    }
+	       };
+	       if ($@) {
+		    WARN($@);
+		    push @{$failed_keywords}, $keyword;
 		    next;
 	       }
 	  }
 	  elsif ($state eq 'parse') {
 	       eval {
 		    write_command_to_file("parsed_results_${database}_${keyword}.txt",
-					  "parse_${database}_results",
+					  "$base_dir/parse_${database}_results",
 					  '--keywords',
 					  $keyword,
 					 );
 	       };
 	       if ($@) {
 		    WARN("parse_${database}_results failed with $@");
+		    push @{$failed_keywords}, $keyword;
 		    next;
 	       }
 	  }
@@ -321,7 +337,7 @@ sub handle_action{
 	  ADVISE("$state results from '$database' for '$keyword'");
 	  push @{$actioned_keywords},$keyword;
      }
-     return ($actioned_keywords,$failed_keywords);
+     return [$actioned_keywords,$failed_keywords];
 }
 
 sub save_state{
@@ -333,7 +349,7 @@ sub save_state{
 }
 
 sub write_command_to_file{
-     my ($file,@command);
+     my ($file,@command) = @_;
      my $fh = IO::File->new($file,'w') or
 	  die "Unable to open $file for writing: $!";
      my $command_fh;