redunant changes

htgt · Nov 10, 2015 · c6e95b1 · c6e95b1
1 parent 194b572
commit c6e95b1
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Showing 4 changed files with 5 additions and 7 deletions.
diff --git a/.nfs0000000000f931ef00001f62 b/.nfs0000000000f931ef00001f62
diff --git a/bin/lims2_setup.sh b/bin/lims2_setup.sh
@@ -5,7 +5,7 @@ export LIMS2_DEBUG_DEFINITION="perl -d"
 
 #TODO: check that we are in the correct directory
 export LIMS2_MIGRATION_ROOT=`pwd`;
-export LIMS2_SHARED=~/git-checkout
+export LIMS2_SHARED=$GIT_CHECKOUT_ROOT
 
 function lims2 {
 case $1 in

diff --git a/lib/LIMS2/Model/Util/ImportSequencing.pm b/lib/LIMS2/Model/Util/ImportSequencing.pm
@@ -23,8 +23,7 @@ use Data::Dumper;
 Log::Log4perl->easy_init( { level => $INFO } );
 
 my $STRING_TO_REMOVE = qr/_premix-w\.-temp/;
-my $PROJECT_NAME_RX = qr/^(.*)_\d+[a-z]{1}\d{2}\./;
-
+my $PROJECT_NAME_RX = qr/^(.*)_\d+[A-Z]?[a-z]{1}\d{2}\./;
 sub extract_eurofins_data{
 	my ($archive, $move) = @_;
 
@@ -135,11 +134,10 @@ sub fix_scf_file{
 
     my $new_file = file($new_name);
     $file->move_to( $new_file ) or die "Could not move $file to $new_file";
-
     my ($project_name) = ( $new_file->basename =~ /$PROJECT_NAME_RX/g );
 
     DEBUG "New SCF file name: $new_file\n";
-    DEBUG "Project name: $project_name\n\n";
+    DEBUG "Project name: " . ($project_name // "Undefined") . "\n\n";
     return ($project_name, $new_file);
 }
 
@@ -166,7 +164,7 @@ sub fix_seq_file{
 
     my ($project_name) = ( $new_file->basename =~ /$PROJECT_NAME_RX/g );
     DEBUG "New seq file name: $new_file\n";
-    DEBUG "Project name: $project_name\n\n";
+    DEBUG "Project name: " . ($project_name // "Undefined") . "\n\n";
     return ($project_name, $new_file);
 }
 

diff --git a/script/extract_eurofins_data.pl b/script/extract_eurofins_data.pl
@@ -79,4 +79,4 @@ =head1 DESCRIPTION
 
 =head1 AUTHOR
 
-Anna Farne
+Anna Farne