From f008038c37ebdd7bc0535da8645f11b59a4d5bde Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 11 Nov 2008 07:03:12 +0000
Subject: [PATCH] finished remove_ucsc_tracks

git-svn-id: http://biopieces.googlecode.com/svn/trunk@307 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/Biopieces.pm | 20 ++++++++++----------
 code_perl/Maasha/UCSC.pm      |  7 +++++--
 2 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index f4bb834..fc7cd05 100644
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -5109,7 +5109,15 @@ sub script_remove_ucsc_tracks
 
     map { push @new_tracks, $_ if not exists $track_hash{ $_->{ 'track' } } } @tracks;
 
-    Maasha::Common::error( qq(track not found in config file: "$options->{ 'config_file' }") ) if scalar @tracks == scalar @new_tracks;
+    print STDERR qq(WARNING: track not found in config file: "$options->{ 'config_file' }"\n) if scalar @tracks == scalar @new_tracks;
+
+    rename "$options->{ 'config_file' }", "$options->{ 'config_file' }~";
+
+    $fh_out = Maasha::Common::write_open( $options->{ 'config_file' } );
+
+    map { Maasha::UCSC::ucsc_config_put_entry( $_, $fh_out ) } @new_tracks;
+
+    close $fh_out;
 
     # ---- locate track in database ----
 
@@ -5125,18 +5133,10 @@ sub script_remove_ucsc_tracks
         }
         else
         {
-            Maasha::Common::error qq(table "$track" not found in database "$options->{ 'database' }");
+            print STDERR qq(WARNING: table "$track" not found in database "$options->{ 'database' }\n");
         }
     }
 
-    rename "$options->{ 'config_file' }", "$options->{ 'config_file' }~";
-
-    $fh_out = Maasha::Common::write_open( $options->{ 'config_file' } );
-
-    map { Maasha::UCSC::ucsc_config_put_entry( $_, $fh_out ) } @new_tracks;
-
-    close $fh_out;
-
     Maasha::SQL::disconnect( $dbh );
 }
 
diff --git a/code_perl/Maasha/UCSC.pm b/code_perl/Maasha/UCSC.pm
index adb8c93..7ae2e37 100644
--- a/code_perl/Maasha/UCSC.pm
+++ b/code_perl/Maasha/UCSC.pm
@@ -919,7 +919,10 @@ sub ucsc_config_get_entry
 
     while ( $line = <$fh> )
     {
-        if ( $line =~ /^# date: (.+)/ ) {
+        if ( $line =~ /Track added by 'upload_to_ucsc' (\S+) (\S+)/) {
+             $record{ 'date' } = $1;
+             $record{ 'time' } = $2;
+        } elsif ( $line =~ /^# date: (.+)/ ) {
             $record{ 'date' } = $1;
         } elsif ( $line =~ /^# time: (.+)/ ) {
             $record{ 'time' } = $1;
@@ -964,7 +967,7 @@ sub ucsc_config_put_entry
 
     print $fh_out "\n# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n\n";
 
-    map { print $fh_out "# $record->{ $_ }\n" if exists $record->{ $_ } } qw( date time database );
+    map { print $fh_out "# $_: $record->{ $_ }\n" if exists $record->{ $_ } } qw( date time database );
     map { print $fh_out "$_ $record->{ $_ }\n" if exists $record->{ $_ } } qw( track
                                                                                name
                                                                                description
-- 
2.39.5