Changeset 225

Timestamp:

06/22/09 16:20:18 (5 months ago)

Author:

cholt

Message:

fix more mpi_iprscan

Files:

• MPI/mpi_iprscan (modified) (2 diffs)
• lib/Process/IPRchunk.pm (modified) (3 diffs)
• lib/Widget/iprscan.pm (modified) (1 diff)

MPI/mpi_iprscan

@@ -173 +173 @@
-           "cli" => \$cli, #just used to strip off the option
-           );
+
+$main::quiet = 1; #suppress status messages
-
-if(! @appl){
@@ -750 +752 @@
-                push (@chunks, $o_chnk);
-            }
-            #get chunk results from other nodes
-            while(my $res = shift @returned_chunks){
-                $res = ${thaw($res)};
-                $tier->update_chunk($res);
-            }
-
-            #run the tier as far as possible
-            $tier->run;
-            
-            #get all chunks available
-            my $chnk = $tier->next_chunk;
-            while(my $o_chnk = $tier->next_chunk){
-                $o_chnk = freeze(\$o_chnk);
-                push (@chunks, $o_chnk);
-            }
-            
-            #run chunks one at a time

lib/Process/IPRchunk.pm

@@ -82 +82 @@
-      $VARS->{seq_id} = Fasta::getSeqID(\$VARS->{fasta});
-      $VARS->{safe_id} = Fasta::seqID2SafeID($VARS->{seq_id});
-
-      $VARS->{DS_CTL}->add_entry($VARS->{seq_id}, 'STARTED');
-      $VARS->{c_flag} = $VARS->{DS_CTL}->continue_flag($VARS->{seq_id});
-
-      my $failed .= "$outname.failed/".$VARS->{safe_id}.".fasta";
+
-      if(! $VARS->{c_flag}){
-          warn "WARNING: ".$VARS->{seq_id} ."failed 2 time and will not be tried again\n",
@@ -96 +95 @@
-          print $OUT $VARS->{fasta};
-          close($OUT);
+          $VARS->{DS_CTL}->add_entry($VARS->{seq_id}, 'DIED_PERMANENT');
-      }
-      else{
-          unlink($failed) if(-e $failed); #remove old failed
-      }
+
+      $VARS->{DS_CTL}->add_entry($VARS->{seq_id}, 'STARTED');
-   }
-   catch Error::Simple with {
@@ -305 +307 @@
-
-            my $w = new Widget::iprscan();
-
+ unless($main::quiet)
-            $w->run($command);
-

lib/Widget/iprscan.pm

@@ -36 +36 @@
-           my $pid = open3(\*CHLD_IN, \*CHLD_OUT, \*CHLD_ERR, $command);
-           local $/ = \1;
+           my $err;
-           while (my $line = <CHLD_ERR>){
-              print STDERR $line unless($main::quiet);
+              $err .= $line;
-           }
-           waitpid $pid, 0;
+           
+           my $fail;
+           if($err !~ /^SUBMITTED iprscan-\d+-\d+\n*$/){
+               $fail = 1;
+           }
+
+           die "ERROR: Iprscan failed\n" if ($? != 0 || $fail);
-        }
-        else {