# 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;
=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
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 => [],
debug => 0,
help => 0,
man => 0,
- directory => '',
+ results => '',
);
GetOptions(\%options,'keywords=s@','databases=s@',
- 'restart_at|restart-at=s',
+ 'restart_at|restart-at=s','results=s',
'debug|d+','help|h|?','man|m');
pod2usage() if $options{help};
pod2usage({verbose=>2}) if $options{man};
+my $base_dir = basename($0);
+
my $ERRORS='';
$ERRORS.="restart-at must be one of get, parse or combine\n" if
@{$options{databases}} and
grep {$_ !~ /^(?:ncbi|genecards|harvester)$/i} @{$options{databases}};
-if (not length $options{directory}) {
- $ERRORS.="directory not specified";
+if (not length $options{results}) {
+ $ERRORS.="results directory not specified";
}
-elsif (not -d $options{directory} or not -w $options{directory}) {
- $ERRORS.="directory $options{directory} does not exist or is not writeable";
+elsif (not -d $options{results} or not -w $options{results}) {
+ $ERRORS.="results directory $options{results} does not exist or is not writeable";
}
pod2usage($ERRORS) if length $ERRORS;
my %state;
-if (-e "$options{directory}/do_it_all_state") {
+$options{keywords} = [map {abs_path($_)} @{$options{keywords}}];
+
+chdir $options{results} or die "Unable to chdir to $options{results}";
+
+if (-e "do_it_all_state") {
ADVISE("Using existing state information");
- my $state_fh = IO::File->new("$options{directory}/do_it_all_state",'r') or die
+ my $state_fh = IO::File->new("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 $!";
+ my $state_file = <$state_fh>;
%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 => {},
+ done_keywords => {
+ get => {},
+ parse => {},
+ combine => {},
+ },
);
}
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};
}
}
# 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 $combine_needed = 0;
+my %actions = (combine => 0,
+ get => {},
+ parse => {},
+ );
+
+if (not @{$state{keywords}}) {
+ ADVISE("There are no keywords specified");
+}
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 $state{done_keywords}{get}{$database}{$keyword}) {
+ push @{$actions{get}{$database}}, $keyword;
+ delete $state{done_keywords}{parse}{$database}{$keyword} if
+ exists $state{done_keywords}{parse}{$database}{$keyword};
+ delete $state{done_keywords}{combine}{$database}{$keyword} if
+ exists $state{done_keywords}{combine}{$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 $state{done_keywords}{parse}{$database}{$keyword}) {
+ push @{$actions{parse}{$database}},$keyword;
+ delete $state{done_keywords}{combine}{$database}{$keyword} if
+ exists $state{done_keywords}{combine}{$database}{$keyword};
}
- if (not exists $state{combined_keywords}{$database}{$keyword}) {
- $combine_needed = 1;
+ if (not exists $state{done_keywords}{combine}{$database}{$keyword}) {
+ $actions{combine} = 1;
}
}
}
-# handle getting needed results
-for my $action (@get_needed) {
-
+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}->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 (@{$failed_keywords}) {
+ ADVISE("These keywords failed during '$state' of '$database':",@{$failed_keywords});
+ $ERRORS=1;
+ }
+ @{$state{done_keywords}{$state}{$database}}{@{$actioned_keywords}} = (1) x @{$actioned_keywords};
+ delete @{$state{done_keywords}{$state}{$database}}{@{$failed_keywords}};
+ }
+ save_state(\%state);
+ if ($ERRORS) {
+ WARN("Stoping, as there are errors");
+ exit 1;
+ }
+}
+
+if ($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?]');
}
-# handle parsing needed results
-for my $action (@parse_needed) {
+
+sub handle_action{
+ my ($state,$database,$queue) = @_;
+ my $keyword;
+ my $actioned_keywords = ();
+ 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;
+ }
+ return ($actioned_keywords,$failed_keywords);
}
-# handle combining results
+sub save_state{
+ my ($state) = @_;
+ my $state_fh = IO::File->new("do_it_all_state",'w') or die
+ "Unable to open state file for writing: $!";
+ print {$state_fh} freeze($state) or die "Unable to freeze state file";
+ 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{
projects / function2gene.git / blobdiff