src/hg/encode/encodeValidate/doEncodeValidate.pl 1.196

1.196 2009/10/06 00:53:03 kate
Add support for 'sql' field in DAF. Allows specifying the schema for a non-standard table. The .sql file needs to be copied to /cluster/bin//sqlCreate

Index: src/hg/encode/encodeValidate/doEncodeValidate.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeValidate/doEncodeValidate.pl,v
retrieving revision 1.195
retrieving revision 1.196
diff -b -B -U 4 -r1.195 -r1.196
--- src/hg/encode/encodeValidate/doEncodeValidate.pl	2 Oct 2009 22:39:46 -0000	1.195
+++ src/hg/encode/encodeValidate/doEncodeValidate.pl	6 Oct 2009 00:53:03 -0000	1.196
@@ -1625,8 +1625,9 @@
     $ddfLineNumber++;
     my $diePrefix = "ERROR on DDF lineNumber $ddfLineNumber:";
     my $view = $ddfLine->{view};
     my $type = $daf->{TRACKS}{$view}{type} || die "Missing DAF entry for view '$view'\n";
+    my $sql = $daf->{TRACKS}{$view}{sql};
     my $metadata = "project=wgEncode grant=$daf->{grant} lab=$daf->{lab} dataType=$daf->{dataType}";
     $metadata .= " cell=$ddfLine->{cell}" if $ddfLine->{cell}; # force some order
     $metadata .= " antibody=$ddfLine->{antibody}" if $ddfLine->{antibody};
     for my $key (keys %{$ddfLine}) {
@@ -1848,8 +1849,11 @@
 
     print LOADER_RA "tablename $tableName\n";
     print LOADER_RA "view $view\n";
     print LOADER_RA "type $type\n";
+    if($sql) {
+        print LOADER_RA "sql $sql\n";
+    }
     if($species) {
         print LOADER_RA "assembly $species\n";
     } else {
         print LOADER_RA "assembly $daf->{assembly}\n";