src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl 1.30
1.30 2010/03/24 00:59:42 tdreszer
Expanded to a near complet sort order list, added noMetaTbl option to compare old and new metadata methods, expanded fileMask to include bigWig, bigBed and BAM.
Index: src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl,v
retrieving revision 1.29
retrieving revision 1.30
diff -b -B -U 4 -r1.29 -r1.30
--- src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl 20 Mar 2010 00:15:36 -0000 1.29
+++ src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl 24 Mar 2010 00:59:42 -0000 1.30
@@ -30,8 +30,9 @@
$opt_preamble
$opt_db
$opt_verbose
$opt_checksum
+ $opt_noMetaTbl
/;
our $checksumFile = "md5sum.txt";
our $textFile = "files.txt"; # plain text file list with metadata
@@ -44,8 +45,9 @@
options:
-help Displays this usage info
-checksum Generate checksum file
+ -noMetaTbl Don't use metaTbl. Instead, use the old trackDb/fileDb.ra methods
-preamble=file File containing introductory information (written in HTML) that will be included in this file (default preamble.html)
-db=hg18 Use a database other than the default hg18 (For aquiring releaseDate and metadata from trackDb)
-fileType=mask mask for file types included (default '*.gz')
-verbose=num Set verbose level to num (default 1).
@@ -281,12 +283,13 @@
"preamble=s",
"db=s",
"verbose=i",
"checksum",
+ "noMetaTbl",
);
usage() if (!$ok);
$opt_verbose = 1 if (!defined $opt_verbose);
-my $fileMask = "*.gz";
+my $fileMask = "*.gz *.bb *.bw *.bam";
$fileMask = $opt_fileType if(defined $opt_fileType);
my $preamble = "preamble.html";
$preamble = $opt_preamble if(defined $opt_preamble);
@@ -298,9 +301,10 @@
my $downloadsDir = cwd();
$downloadsDir = $ARGV[1] if (scalar(@ARGV) > 1);
# Now find some files
-my @fileList = `ls -hogL --time-style=long-iso $downloadsDir/$fileMask 2> /dev/null`;
+#my @fileList = `ls -hogL --time-style=long-iso $downloadsDir/$fileMask 2> /dev/null`;
+my @fileList = `cd $downloadsDir;ls -hogL --time-style=long-iso $fileMask 2> /dev/null`;
# -rw-rw-r-- 1 101M 2008-10-27 14:34 /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalK562Pol2.wig.gz
if(length(@fileList) == 0) {
die ("ERROR; No files were found in \'$downloadsDir\' that match \'$fileMask\'.\n");
}
@@ -359,9 +363,15 @@
my $submitDate = "";
my %metaData;
### TODO: Developer: set sort order here; sortables must have same number of strings and '~' is lowest val printable
- my @sortFields = ("cell","dataType","rnaExtract","localization","fragSize","mapAlgorithm","ripAntibody","ripTgtProtein","treatment","antibody","protocol","input","lab","type","view","level","annotation","rank","replicate","subId");
+ #my @sortFields = ("cell","dataType","rnaExtract","localization","fragSize","mapAlgorithm","ripAntibody","ripTgtProtein","treatment","antibody","protocol","input","lab","type","view","level","annotation","rank","replicate","subId");
+ # Complete sort order, (I hope)
+ my @sortFields = ("species","assembly","dataType","cell","rnaExtract","localization","phase","treatment","antibody","protocol","ripAntibody",
+ "ripTgtProtein","restrictionEnzyme","promoter","input","control","replicate","submitteDataVersion","subId","dataVersion",
+ "dateSubmitted","dateResubmitted","dateReloaded","dateUnrestricted","project","grant","lab","labVersion","softwareVersion",
+ "mapAlgorithm","fragSize","fragLength","medianFragmentLength","fragmentLengthRange","chromStart","view","type","composite",
+ "tableName","parentTable","fileName","accession");
my @sortables = map( "~", (1..scalar(@sortFields))); # just has to have a tilde for each field
my $typePrefix = "";
my $results = $db->quickQuery("select type from $database.trackDb where tableName = '$tableName'");
@@ -373,8 +383,9 @@
$metaData{type} = $dataType;
}
# Use the metaTbl for metadata
+ if (!defined $opt_noMetaTbl) {
my $queryResults = $db->execute("select var,val from $database.metaTbl where objName = '$tableName'");
if($queryResults) {
my @pairVars;
push @pairVars, "metadata";
@@ -387,8 +398,11 @@
#push @pairVars, $onePair;
}
$results = join(' ',@pairVars );
}
+ } else {
+ $results = "";
+ }
if(!$results) {
$results = $db->quickQuery("select settings from $database.trackDb where tableName = '$tableName'");
}