src/hg/utils/automation/makePushQSql.pl 1.26

Index: src/hg/utils/automation/makePushQSql.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/makePushQSql.pl,v
retrieving revision 1.25
retrieving revision 1.26
diff -b -B -U 4 -r1.25 -r1.26
--- src/hg/utils/automation/makePushQSql.pl	8 Jun 2009 18:37:16 -0000	1.25
+++ src/hg/utils/automation/makePushQSql.pl	30 Jul 2009 22:34:07 -0000	1.26
@@ -155,9 +155,9 @@
   foreach my $f (@gbdbFiles, @goldenPathFiles, $gatewayPhoto) {
     if (&HgAutomate::machineHasFile($dbHost, $f)) {
       push @files, $f;
     } else {
-      &HgAutomate::verbose(1, "$dbHost does not have $f\n")
+      &HgAutomate::verbose(1, "WARNING: $dbHost does not have $f\n")
 	unless ($f =~ /${db}To$SameSpecies/ ||
 		($f =~ m@/chromosomes/@ && !&dbIsChromBased()));
     }
   }
@@ -170,9 +170,9 @@
       $entry{'tables'} .= "$t ";
       delete $allTables->{$t};
       &HgAutomate::verbose(3, "Deleted $t\n");
     } else {
-      &HgAutomate::verbose(1, "$db does not have $t\n");
+      &HgAutomate::verbose(1, "WARNING: $db does not have $t\n");
     }
   }
   return (\%entry);
 } # getInfrastructureEntry
@@ -192,14 +192,14 @@
     refFlat refLink refSeqAli refSeqStatus refSeqSummary
     xenoRefFlat xenoRefSeqAli
     );
   my @genbankRequiredTables = qw(
-    author cds cell description development estOrientInfo gbCdnaInfo
+    author cds cell description development gbCdnaInfo
     gbExtFile gbLoaded gbSeq gbStatus geneName imageClone keyword
     library mrnaClone mrnaOrientInfo organism productName sex source tissue
     );
   my @genbankHelpfulTables = qw(
-    gbMiscDiff gbWarn
+    estOrientInfo gbMiscDiff gbWarn
     );
   my @genbankTablesInDb = ();
   foreach my $t (@genbankTrackTables) {
     if (defined $allTables->{$t}) {
@@ -213,17 +213,17 @@
       if (defined $allTables->{$t}) {
 	push @genbankTablesInDb, $t;
 	delete $allTables->{$t};
       } else {
-	die "\n$db does not have required genbank table $t\n\n";
+	die "\nERROR: $db does not have required genbank table $t\n\n";
       }
     }
     foreach my $t (@genbankHelpfulTables) {
       if (defined $allTables->{$t}) {
 	push @genbankTablesInDb, $t;
 	delete $allTables->{$t};
       } else {
-	&HgAutomate::verbose(1, "$db does not have $t\n");
+	&HgAutomate::verbose(1, "WARNING: $db does not have $t\n");
       }
     }
   }
   my %entry = ();
@@ -356,9 +356,9 @@
 	       "$HgAutomate::gbdb/$db/liftOver/$over") {
 	      if (&HgAutomate::machineHasFile($dbHost, $downloads)) {
 		$entry{'files'} .= $downloads . '\r\n';
 	      } else {
-		&HgAutomate::verbose(0, "$dbHost does not have " .
+		&HgAutomate::verbose(0, "WARNING: $dbHost does not have " .
 				     "chain/net download $downloads !\n");
 	      }
 	    }
 	    my $oDb = $ODb;  $oDb =~ s/^(\w)/\l$1/;
@@ -372,9 +372,9 @@
 	  my $gif = "$HgAutomate::images/phylo/${db}_$1.gif";
 	  if (&HgAutomate::machineHasFile($dbHost, $gif)) {
 	    $entry{'files'} .= $gif . '\r\n';
 	  } else {
-	    &HgAutomate::verbose(0, "$dbHost does not have phyloGif-" .
+	    &HgAutomate::verbose(0, "WARNING: $dbHost does not have phyloGif-" .
 				    "generated $gif for $table.\n");
 	  }
 	}
       }
@@ -397,11 +397,11 @@
 	  my $downloads = "$HgAutomate::goldenPath/$db/vs$ODb/*";
 	  if (&HgAutomate::machineHasFile($dbHost, $downloads)) {
 	    $entry{'files'} = $downloads;
 	  } else {
-	    &HgAutomate::verbose(1, "$dbHost does not have $downloads\n");
+	    &HgAutomate::verbose(1, "WARNING: $dbHost does not have $downloads\n");
 	  }
-	  &HgAutomate::verbose(1, "Found net table $table that was not " .
+	  &HgAutomate::verbose(1, "WARNING: Found net table $table that was not " .
 		       "already lumped in with chain entry $chainTrack...?\n");
 	} else {
 	  # This net has already been included in the corresponding Chain
 	  # track entry, and removed from the hash, so skip to the next table.
@@ -552,9 +552,9 @@
        "$HgAutomate::gbdb/$oDb/liftOver/$over") {
 	  if (&HgAutomate::machineHasFile($dbHost, $downloads)) {
 	    $entry{'files'} .= $downloads . '\r\n';
 	  } else {
-	    &HgAutomate::verbose(0, "$dbHost:$oDb does not have " .
+	    &HgAutomate::verbose(0, "WARNING: $dbHost:$oDb does not have " .
 			     "chain/net download $downloads !\n");
 	  }
       }
     &printEntry(\%entry, $id, $oDb, "$oO Chain and Net");
@@ -601,10 +601,10 @@
   my ($stragglers) = @_;
   my @names = sort (keys %{$stragglers});
   if (scalar(@names) > 0) {
     &HgAutomate::verbose(0, "
-Could not tell (from trackDb, all.joiner and hardcoded lists of supporting
-and genbank tables) which tracks to assign these tables to:\n");
+WARNING: Could not tell (from trackDb, all.joiner and hardcoded lists of
+supporting and genbank tables) which tracks to assign these tables to:\n");
     foreach my $t (@names) {
       &HgAutomate::verbose(0, "  $t\n");
     }
     &HgAutomate::verbose(0, "\n");