src/hg/utils/scanSettings.pl 1.1

Index: src/hg/utils/scanSettings.pl
===================================================================
RCS file: src/hg/utils/scanSettings.pl
diff -N src/hg/utils/scanSettings.pl
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/utils/scanSettings.pl	19 Nov 2009 21:05:53 -0000	1.1
@@ -0,0 +1,171 @@
+#!/usr/bin/env perl
+
+# $Id$
+
+use strict;
+use warnings;
+
+my $argc = scalar(@ARGV);
+
+if ($argc < 1) {
+    printf STDERR "scanSettings.pl - scan output of hgTrackDb -settings,
+    implement ClosestToHome API to indicate applicable settings for each table.
+
+usage: scanSettings.pl hg18.settings.txt
+
+  where hg18.settings.txt is from this in trackDb directory:
+  make EXTRA='-strict -settings' DBS=hg18 > hg18.settings.txt 2>&1
+The input file can also be 'stdin', thus:
+  make EXTRA='-strict -settings' DBS=hg18 2>&1 \\
+     | ../../utils/scanSettings.pl stdin\n";
+    exit 255;
+}
+
+my %tableList;	# key is table name, value is hash of settings
+my $file = shift;
+
+if ($file =~ m/stdin/) {
+    open (FH, "</dev/stdin") or die "can not read stdin";
+} else {
+    open (FH, "<$file") or die "can not read $file";
+}
+while (my $line = <FH>) {
+    next if ($line =~ m/^#/);
+    next if ($line =~ m/^Warning: /);
+    next if ($line =~ m/^Loaded /);
+    next if ($line =~ m/^Sorted /);
+    next if ($line =~ m/^hgTrackDb /);
+    next if ($line =~ m/^hgFindSpec /);
+    next if ($line =~ m#^./loadTracks #);
+    chomp $line;
+    my ($tableName, $rest) = split(': ', $line, 2);
+    my @a = split('; ', $rest);
+    die "no type= for $tableName" if ($a[0] !~ m/^type='/);
+    my $fieldCount = scalar(@a);
+    die "no fields for $tableName" if ($fieldCount < 1);
+    $a[0] =~ s/^type='//;
+    $a[0] =~ s/';$//;
+    $a[0] =~ s/'$//;
+    $a[$fieldCount-1] =~ s/;\s*$//;
+    my %settingsHash;
+    die "duplicate table name $tableName ?" if (exists($tableList{$tableName}));
+    $tableList{$tableName} = \%settingsHash;
+    $settingsHash{'type'} = $a[0];
+    my $minLimit = "";
+    my $maxLimit = "";
+    my $viewLimits = "";
+    for (my $i = 1; $i < $fieldCount; ++$i) {
+	my ($name, $setting) = split('\s', $a[$i], 2);
+	$settingsHash{$name} = $setting;
+    }
+#    printf "%s: '%s'\n", $tableName, $a[$fieldCount-1];
+#    printf "%s - %s %s %s %s\n", $tableName, $a[0], $minLimit,
+#	$maxLimit, $viewLimits;
+}
+close (FH);
+
+# scan all composite tracks and pick up all view settings from them
+my %viewSettings;  # key is table.view value are settings for that view
+foreach my $table (keys %tableList) {
+    my $hashRef = $tableList{$table};
+    if (exists($hashRef->{'compositeTrack'})) {
+	next if (exists($hashRef->{'superTrack'}));
+	die "compositeTrack not 'on' ? $hashRef->{'compositeTrack'}"
+		if ($hashRef->{'compositeTrack'} !~ m/^on$/);
+	foreach my $setting (keys %$hashRef) {
+	    if ($setting =~ m/settingsByView/) {
+		my @views = split('\s+', $hashRef->{$setting});
+		for (my $j = 0; $j < scalar(@views); ++$j) {
+		    my ($view, $values) = split(':', $views[$j], 2);
+		    my $viewKey = "$table.$view";
+		    my @viewSettings = split(',', $values);
+		    my %viewHash;
+		    die "duplicate settings view $viewKey"
+			if (exists($viewSettings{$viewKey}));
+		    $viewSettings{$viewKey} = \%viewHash;
+		    for (my $k = 0; $k < scalar(@viewSettings); ++$k) {
+			my ($name, $value) = split('=', $viewSettings[$k], 2);
+#			$viewHash{$name} = $value;
+			$viewHash{$name} = $viewSettings[$k];
+		    }
+		}
+#		printf "%s: %s='%s'\n", $table, $setting, $hashRef->{$setting};
+	    }
+	}
+    }
+}
+
+# scan all sub tracks and add view settings or parent settings
+#	when OK to do that.  This implements the ClosestToHome API
+foreach my $table (keys %tableList) {
+    my $hashRef = $tableList{$table};
+    if (exists($hashRef->{'subTrack'})) {
+	my $parent = $hashRef->{'subTrack'};
+	# first priority are subGroup viewSettings coming in from the parent
+	if (exists($hashRef->{'subGroups'})) {
+	    my @b = split('\s+', $hashRef->{'subGroups'});
+	    for (my $m = 0; $m < scalar(@b); ++$m) {
+		if ($b[$m] =~ m/^view=/) {
+		    my ($dummy, $view) = split('=', $b[$m], 2);
+		    my $viewKey = "$parent.$view";
+		    my $viewHash = $viewSettings{$viewKey};
+		    foreach my $viewKey (keys %$viewHash) {
+			next if (exists($hashRef->{$viewKey}));
+			# OK to inherit this setting
+# printf "inheriting from $parent view $view to $table '$viewHash->{$viewKey}'\n";
+			$hashRef->{$viewKey} = $viewHash->{$viewKey};
+		    }
+		}
+	    }
+	}
+	#	next priority are parent composite settings when inherit OK
+	my $parentSettings = $tableList{$parent};
+	if ( (!exists($hashRef->{'noInherit'}) ||
+		$hashRef->{'noInherit'} !~ m/^on$/) &&
+	    (!exists($parentSettings->{'noInherit'}) ||
+		$parentSettings->{'noInherit'} !~ m/^on$/) ) {
+	    foreach my $parentKey (keys %$parentSettings) {
+		next if ($parentKey =~ m/^track$/);
+		next if ($parentKey =~ m/^compositeTrack$/);
+		next if ($parentKey =~ m/^subGroup[0-9]*$/);
+		next if ($parentKey =~ m/^dimensions$/);
+		next if ($parentKey =~ m/^sortOrder$/);
+		next if ($parentKey =~ m/^dragAndDrop$/);
+		next if ($parentKey =~ m/^noInherit$/);
+		next if ($parentKey =~ m/^visibilityViewDefaults$/);
+		next if ($parentKey =~ m/^settingsByView$/);
+		next if (exists $hashRef->{$parentKey} );
+		next if (!defined $parentSettings->{$parentKey} );
+		# OK to inherit this setting
+		my $parentSetting = $parentSettings->{$parentKey};
+# printf "inheriting from $parent to $table $parentKey='$parentSetting'\n";
+		$hashRef->{$parentKey} = $parentSetting;
+	    }
+	}
+    }
+}
+
+# ready to print out everything
+foreach my $table (keys %tableList) {
+    my $hashRef = $tableList{$table};
+    my $type = $hashRef->{'type'};
+    if ( 1 == 1 || $type =~ m/^wig|^bedGraph/ || exists($hashRef->{'compositeTrack'})) {
+#	printf "%s: type='%s'", $table, $hashRef->{'type'};
+	printf "%s:", $table;
+	foreach my $setting (sort keys %$hashRef) {
+	    if ( 1 == 1 || $setting !~ m/type/) {
+		printf " %s='%s'", $setting, $hashRef->{$setting};
+		if ($setting =~ m/^view$/) {
+		    my $viewKey = "$table.$hashRef->{$setting}";
+		    die "can not find viewKey $viewKey"
+			if (!exists($viewSettings{$viewKey}));
+		    my $viewHash = $viewSettings{$viewKey};
+		    foreach my $viewName (keys %$viewHash) {
+			printf " %s='%s'", $viewName, $viewHash->{$viewName};
+		    }
+		}
+	    }
+	}
+	printf "\n";
+    }
+}