src/hg/instinct/createDescriptionHTML/createSingleDescriptionHTML.pl 1.2

Index: src/hg/instinct/createDescriptionHTML/createSingleDescriptionHTML.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/createDescriptionHTML/createSingleDescriptionHTML.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/instinct/createDescriptionHTML/createSingleDescriptionHTML.pl	9 Sep 2009 18:31:27 -0000	1.1
+++ src/hg/instinct/createDescriptionHTML/createSingleDescriptionHTML.pl	23 Oct 2009 20:05:55 -0000	1.2
@@ -1,127 +1,125 @@
 #!/usr/bin/perl -w
 
 ################################
 # cszeto Aug 27th 2009
 # Small script designed to make HTML pages for datasets
 ################################
 
 my $tableName = "";
 my $datasetsFile = "";
 my $whoami = `whoami`;
 chomp($whoami);
 if(!defined($ARGV[0])){
     print "ERROR: Incorrect usage.\n";
     printHelp();
 }else{
     $tableName = $ARGV[0];
     if(defined($ARGV[1])){
         $datasetsFile = $ARGV[1];
     }else{
         $datasetsFile = "/data/home/$whoami/kent/src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra";
     }
 }
 
 #iterate to the entry for the specified tableName in the datasets.ra file.
 open(DATASETS, $datasetsFile) || die "Couldn't open $datasetsFile\n";
 my $flag = 0;
 while(<DATASETS>){
     if($_ !~ m/^#/){
         if($_ =~ m/^name\s$tableName$/){
             $flag++;
             last;
         }
     }
 }
 if($flag == 0){
     die "Couldn't find an entry named $tableName in $datasetsFile\n";
 }
 
 #create a hash of the contents for the dataset, so you can look them up when creating your html entry
 my %elements = ();
 while(<DATASETS>){
     if($_ =~ m/^\W*$/){
         last;
     }else{
         chomp($_);
         my $key = $_;
         $key =~ s/^(\S+)\s.+/$1/g;
         my $val = $_;
         $val =~ s/^\S+\s(.+)/$1/g;
         $elements{$key} = $val; 
     }
 }
 close(DATASETS);
 
 #open the template html file for copying, and print in your own details
 open(TEMPLATE, "/var/www/html/cancerGenomics/data-descriptions/template.htm") || die "Couldn't open template HTML file.\n";
 my $outputFile = "/var/www/html/cancerGenomics/data-descriptions/".$tableName.".html";
 open(OUTFILE, ">$outputFile") || die "Couldn't open $outputFile. for writing\n";
 while(<TEMPLATE>){
     if($_ =~ m/DATA_TITLE/){
         if(defined($elements{'longLabel'})){
             $_ =~ s/DATA_TITLE/$elements{'longLabel'}/g;
         }else{
             die "No longLabel found in datasets.ra file";
         }
     }
     if($_ =~ m/DATA_DESCRIPTION/){
         $_ = "\t\t\t<P>\n";
         if(defined($elements{'article_title'})){
             $_ = $_."\t\t\tArticle Title: ".$elements{'article_title'}."<BR><BR>\n";
         }else{
             $_ = $_."Article Title: Unknown<BR><BR>\n";
         }
         if(defined($elements{'author_list'})){
             $_ = $_."\t\t\tAuthor List: ".$elements{'author_list'}."<BR><BR>\n";
         }else{
             $_ = $_."Author List: Unknown<BR><BR>\n";
         }
         if(defined($elements{'citation'})){
             if(defined($elements{'url'})){
                 $_ = $_."\t\t\tCitation: <A HREF=".$elements{'url'}.">".$elements{'citation'}."</A><BR><BR>\n";
             }else{
                 $_  = $_."Citation: ".$elements{'citation'}."<BR><BR>\n";
             }
         }else{
             if(defined($elements{'url'})){
                 $_ = $_."<A HREF=".$elements{'url'}.">".$elements{'url'}."</A><BR><BR>\n";
             }else{
                 $_ = $_."Citation: Unknown<BR><BR>\n";
             }
         }
         if(defined($elements{'wrangler'})){
             $_ = $_."\t\t\tWrangled by: ".$elements{'wrangler'}."<BR><BR>\n";
         }else{
             $_ = $_."Wrangled by: Unknown<BR><BR>\n";
         }
         if(defined($elements{'wrangling_procedure'})){
             $_ = $_."\t\t\tWrangling Procedure: ".$elements{'wrangling_procedure'}."<BR>\n";
         }else{
             $_ = $_."Wrangling Procedure: Unknown\n";
         }
         $_ = $_."\t\t\t</P>\n";
     } 
     print OUTFILE "$_";
 }
 close(TEMPLATE);
 close(OUTFILE);
 `chmod 755 $outputFile`; #this is needed for the blue bar to appear at the top
 
 print "Success!\n";
 my $relativeOutputFile = "../cancerGenomics/data-descriptions/".$tableName.".html";
 if(!defined($elements{'local_url'})){
     print "Add the following line to your $datasetsFile entry:\n";
     print "local_url $relativeOutputFile\n";
 }else{
-    if($elements{'local_url'} ne $relativeOutputFile){
-        print "Change the local_url field in $tableName entry of $datasetsFile to the following:\n";
+    print "Make sure the local_url field in $tableName entry of $datasetsFile is the following:\n";
         print "local_url $relativeOutputFile\n";
-    }
 }
 
 sub printHelp {
     print "Usage:\n\$perl createDescriptionHTML.pl [tableName] (optional: [datasets.ra file])\n";
     print "If you don't specify a datasets.ra file, it'll look in hgHeatmap2/hgHeatmapData/datasets.ra\n";
     print "This will create a file called [tableName].html in your /var/www/html/cancerGenomics/dataset-descriptions/ directory\n";
     exit(1);
 }