src/hg/utils/scanSettings.pl 1.2
1.2 2009/11/19 22:04:02 hiram
Add some arguments to make it at least a little bit useful
Index: src/hg/utils/scanSettings.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/scanSettings.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/utils/scanSettings.pl 19 Nov 2009 21:05:53 -0000 1.1
+++ src/hg/utils/scanSettings.pl 19 Nov 2009 22:04:02 -0000 1.2
@@ -1,171 +1,210 @@
#!/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
+usage: scanSettings.pl [options] hg18.settings.txt
+options:
+ -type=trackType - show only tracks of 'trackType'
+ where trackType is the first word of type line
+ -noParents - do not show parent composite container tracks
+ -show=comma,separated,list - of settings to display
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 $noParents = 0; # 1 indicates do not show parents
+my $trackType = ""; # first word of track type line
+my %showList; # key is setting name to show
+my $listOnly = 0; # 1 means to check the showList
+
my %tableList; # key is table name, value is hash of settings
-my $file = shift;
+my $file = "noFileSpecified";
+while (my $arg = shift) {
+ if ($arg =~ m/-noParents/) {
+ $noParents = 1;
+ printf STDERR "# not showing composite parents\n";
+ } elsif ($arg =~ m/-type/) {
+ (my $dummy, $trackType) = split('=', $arg);
+ printf STDERR "# showing only track type '$trackType'\n";
+ } elsif ($arg =~ m/-show/) {
+ (my $dummy, my $list) = split('=', $arg);
+ my @show = split(',', $list);
+ for (my $i = 0; $i < scalar(@show); ++$i) {
+ $showList{$show[$i]} = 1;
+ }
+ $listOnly = 1 if (scalar(@show) > 0);
+ } else {
+ $file = $arg;
+ }
+}
if ($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 STDERR "no track type for '$table'\n" if (length($type) < 1);
+ next if (length($type) < 1);
+ my @typeWords = split('\s+', $type);
+ next if ($noParents == 1 && exists($hashRef->{'compositeTrack'}));
+ next if ( (length($trackType) > 0) && ($typeWords[0] ne $trackType) );
# printf "%s: type='%s'", $table, $hashRef->{'type'};
printf "%s:", $table;
foreach my $setting (sort keys %$hashRef) {
- if ( 1 == 1 || $setting !~ m/type/) {
+ if ($listOnly) {
+ printf " %s='%s'", $setting, $hashRef->{$setting}
+ if exists($showList{$setting});
+ } else {
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) {
+ if ($listOnly) {
+ printf " %s='%s'", $viewName, $viewHash->{$viewName}
+ if exists($showList{$viewName});
+ } else {
printf " %s='%s'", $viewName, $viewHash->{$viewName};
}
}
}
}
printf "\n";
- }
}