diff --git a/misc-scripts/analysis_description/load_analysis_descriptions.pl b/misc-scripts/analysis_description/load_analysis_descriptions.pl
index 56085ba63e0316b19b8e4b2156c8149cdfe7d81e..b0eb7a5f81aae2e0f63a7e2854a04b394e2e088e 100644
--- a/misc-scripts/analysis_description/load_analysis_descriptions.pl
+++ b/misc-scripts/analysis_description/load_analysis_descriptions.pl
@@ -48,7 +48,10 @@
if you want to update all databases for a type
perl load_analysis_descriptions.pl -dbhost my_host -dbuser user -dbpass *****
- -pattern '%core_55_%' -file analysis.descriptions
+ -pattern '%_55_%' -file analysis.descriptions > & load_analysis_descriptions.log
+
+to identify logic_names mising from the definition file:
+grep 'MSG' load_analysis_descriptions.log
=cut
@@ -56,6 +59,7 @@ use strict;
use Data::Dumper;
use Getopt::Long;
use DBI;
+
use Bio::EnsEMBL::Utils::Exception qw(warning throw);
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Gene;
@@ -74,25 +78,26 @@ my $noupdate;
my $help = 0;
my $pattern;
+
&GetOptions (
- 'host|dbhost=s' => \$dbhost,
- 'dbname=s' => \$dbname,
- 'user|dbuser=s' => \$dbuser,
- 'pass|dbpass=s' => \$dbpass,
- 'port|dbport=s' => \$dbport,
- 'file|descriptions=s' => \@files,
- 'noupdate' => \$noupdate,
- 'pattern=s' => \$pattern,
- 'h|help!' => \$help
- );
+ 'host|dbhost=s' => \$dbhost,
+ 'dbname=s' => \$dbname,
+ 'user|dbuser=s' => \$dbuser,
+ 'pass|dbpass=s' => \$dbpass,
+ 'port|dbport=s' => \$dbport,
+ 'file|descriptions=s' => \@files,
+ 'noupdate' => \$noupdate,
+ 'pattern=s' => \$pattern,
+ 'h|help!' => \$help
+);
if (!$dbhost){
- print ("Need to pass a dbhost\n");
- $help =1;
+ print ("Need to pass a dbhost\n");
+ $help =1;
}
if (!$dbname and !$pattern){
- print("Need to enter either a database name in -dbname or a pattern in -pattern\n");
- $help = 1;
+ print("Need to enter either a database name in -dbname or a pattern in -pattern\n");
+ $help = 1;
}
unless(@files){
@@ -110,7 +115,7 @@ if($help){
#connect to database
$dsn = "DBI:mysql:host=" . $dbhost . ";port=" . $dbport;
-eval{
+eval{
$dbh = DBI->connect($dsn, $dbuser, $dbpass,
{'RaiseError' => 1,
'PrintError' => 0});
@@ -124,92 +129,100 @@ $sth = $dbh->prepare($sql);
$sth->execute;
while (my ($dbname) = $sth->fetchrow_array){
- print "Looking at ... $dbname\n";
- my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
- -host => $dbhost,
- -user => $dbuser,
- -dbname => $dbname,
- -pass => $dbpass,
- -port => $dbport
- );
-
-# Pre-fetch all analyses in the database
- my $aa = $db->get_AnalysisAdaptor();
- my $analyses = $aa->fetch_all();
- my (%hash,%reference);
- foreach my $analysis(@$analyses){
- $hash{lc($analysis->logic_name())} = $analysis;
- }
-
-# Parse the description files
- foreach my $file( @files ){
- open(FH, $file) or throw("Failed to open $file $@");
+ next unless $dbname =~ /core|cdna|otherfeatures/;
+ next if $dbname =~ /coreexpression/;
+ print "\n\nLooking at ... $dbname\n";
+ my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+ -host => $dbhost,
+ -user => $dbuser,
+ -dbname => $dbname,
+ -pass => $dbpass,
+ -port => $dbport
+ );
+
+ # Pre-fetch all analyses in the database
+ my $aa = $db->get_AnalysisAdaptor();
+ my $analyses = $aa->fetch_all();
+ my (%hash,%reference);
+ foreach my $analysis(@$analyses){
+ $hash{lc($analysis->logic_name())} = $analysis;
+ }
+
+# Parse the description files and check formatting
+ foreach my $file( @files ){
+ open(FH, $file) or throw("Failed to open $file $@");
- LINE: while(my $row = <FH>){
-
- chomp($row);
-
- next if ($row =~ /^\#/); # skip comments
- next if ($row =~ /^$/); # and blank lines
- next if ($row =~ /^\s+$/); # and whitespace-only lines
-
- my ($nr, $logic_name, $description, $display_label, $displayable, $web_data) = split(/\t/, $row);
- #print join("\t", $logic_name, $description, $display_label, $displayable, $web_data), "\n";
-
- $reference{lc($logic_name)} = {
- nr => $nr,
- description => $description || '',
- display_label => $display_label || '',
- displayable => $displayable || '',
- web_data => $web_data || '',
- };
+ LINE: while(my $row = <FH>){
+ chomp($row);
+ next if ($row =~ /^\#/); # skip comments
+ next if ($row =~ /^$/); # and blank lines
+ next if ($row =~ /^\s+$/); # and whitespace-only lines
+
+ my ($nr, $logic_name, $description, $display_label, $displayable, $web_data) = split(/\t/, $row);
+# print join("\t", $logic_name, $description, $display_label, $displayable, $web_data), "\n";
+
+ unless ($logic_name && defined($displayable)) {
+ throw("Please check description file entry for logic_name $logic_name (" . join("\n", $logic_name, $description, $display_label, $displayable, $web_data) . ")");
+ exit;
+ }
+ unless (defined $displayable){
+ throw("In the analysis_description file, logic name '$logic_name' should contain, at least, 5 columns: Number, logic_name, description, display_label and displayable. Fix it !!");
+ }
+ unless ($displayable =~ m/^[01]$/) {
+ throw("Displayable flag for analysis '$logic_name' has to be either 0 or 1, but not '$displayable'!");
+ }
+
+ $reference{lc($logic_name)} = {
+ nr => $nr,
+ description => $description || '',
+ display_label => $display_label || '',
+ displayable => $displayable || '',
+ web_data => $web_data || '',
+ };
- $description =~ s/^\s+//;
- $description =~ s/\s+$//;
+ $description =~ s/^\s+//;
+ $description =~ s/\s+$//;
- next if not $description;
+ next if not $description;
- if (exists $hash{lc($logic_name)}) {
+ if (exists $hash{lc($logic_name)}) {
- my $analysis = $hash{lc($logic_name)};
+ my $analysis = $hash{lc($logic_name)};
- $analysis->description($description);
- $analysis->displayable($displayable);
- $analysis->display_label($display_label);
- $web_data ? $analysis->web_data($aa->get_dumped_data($web_data)) : $analysis->{_web_data} = undef;
+ $analysis->description($description);
+ $analysis->displayable($displayable);
+ $analysis->display_label($display_label);
+ $web_data ? $analysis->web_data($aa->get_dumped_data($web_data)) : $analysis->{_web_data} = undef;
# print Dumper $analysis->web_data();
- unless ( $noupdate ) {
- $aa->update($analysis) ;
- }
+ unless ( $noupdate ) {
+ $aa->update($analysis) ;
+ }
- delete $hash{lc($logic_name)};
- }
+ delete $hash{lc($logic_name)};
}
- close(FH) or throw("Failed to close $file $@");
}
+ close(FH) or throw("Failed to close $file $@");
+ }
- if ( scalar(keys %hash)==0) {
- unless ($noupdate) {
- print STDERR "\nAll analysis descriptions have been updated, every analysis has a description now\n";
- } else {
- print STDERR "\nEvery analysis has a description in the file, all analysis descriptions can be updated.\n".
- "To write analysis descriptions to the analysis_description table in your DB,\n".
- "please run this script including the -update option on the commandline\n";
- }
- }
- else {
- foreach my $ln (keys %hash) {
- warning ("Analysis '$ln' doesn't exist in reference file(s) '"
- . join( "','", @files )
- . "'! It needs to be added first")
- unless (exists $reference{$ln});
- warning "[$dbname] No description was found for logic_name '$ln':\n".
- "\tref:\t display_label='".$reference{$ln}{display_label}."'; displayable=".$reference{$ln}{displayable}."; nr=".$reference{$ln}{nr}."\n".
- "\tdb: \t display_label='".$hash{$ln}->display_label."'; displayable=".$hash{$ln}->displayable."; dbID=".$hash{$ln}->dbID."\n";
-
- }
+ if ( scalar(keys %hash)==0) {
+ unless ($noupdate) {
+ print STDERR "\nAll analysis descriptions have been updated, every analysis has a description now\n";
+ } else {
+ print STDERR "\nEvery analysis has a description in the file, all analysis descriptions can be updated.\n".
+ "To write analysis descriptions to the analysis_description table in your DB,\n".
+ "please run this script excluding the -noupdate option on the commandline\n";
}
+ }
+ else {
+ foreach my $ln (keys %hash) {
+ unless (exists $reference{$ln}) {
+ warning ("[$dbname]: Analysis '$ln' doesn't exist in reference file(s) '"
+ . join( "','", @files )
+ . "'! It needs to be added first");
+ }
+ }
+ }
}
sub usage{