From b44049954d71427ff634384b314536c6a6a5b6d9 Mon Sep 17 00:00:00 2001
From: Naama Menda <nm249@cornell.edu>
Date: Sat, 17 Sep 2011 05:20:10 -0400
Subject: [PATCH] using txn_do for the transaction

---
 .../solcap/load_solcap_TA_phenotypes.pl            | 36 ++++++++++++----------
 .../solcap/load_solcap_data_entry.pl               | 33 ++++++++++----------
 2 files changed, 36 insertions(+), 33 deletions(-)

diff --git a/bin/loading_scripts/solcap/load_solcap_TA_phenotypes.pl b/bin/loading_scripts/solcap/load_solcap_TA_phenotypes.pl
index 2f206a3..4a4d463 100644
--- a/bin/loading_scripts/solcap/load_solcap_TA_phenotypes.pl
+++ b/bin/loading_scripts/solcap/load_solcap_TA_phenotypes.pl
@@ -49,7 +49,7 @@ use Date::Calc qw(
 use File::Basename;
 
 use Carp qw /croak/ ;
-
+use Try::Tiny;
 
 
 our ($opt_H, $opt_D, $opt_i, $opt_t, $opt_l);
@@ -136,15 +136,14 @@ my $spreadsheet=CXGN::Tools::File::Spreadsheet->new($file, 2);
 my @rows = $spreadsheet->row_labels();
 my @columns = $spreadsheet->column_labels();
 
-eval {
+my $coderef = sub {
 
     foreach my $row_label (@rows ) { 
 	#$plot number is the row label. Need to get the matching stock 
 	print "label # = $row_label\n";
 
         my $plot = $spreadsheet->value_at($row_label, "Plot #");
-       
-	##########################################
+       	##########################################
 	# find the child stock based on plot name 
 	my ($stock) = $schema->resultset("Stock::Stockprop")->search( {
 	    value => $location,
@@ -184,9 +183,9 @@ eval {
 
 	  my ($db_name, $sp_accession) = split (/\:/ , $label);
 	  next() if (!$sp_accession);
-          if (!$value || $value =~ /\./) { next; } ;
+          if (!$value || $value =~ /^\.$/) { next; } ;
 
-	  my ($sp_term) = $schema->resultset("General::Db")->find( {
+          my ($sp_term) = $schema->resultset("General::Db")->find( {
 	      name => $db_name } )->find_related("dbxrefs", { 
 		  accession=>$sp_accession , } )->search_related("cvterm");
 
@@ -227,18 +226,21 @@ eval {
 	  #print "Loaded phenotype_cvterm with cvterm '" . $unit_cvterm->name() . " '\n" if $unit_cvterm ;
       }
     }
+    if ($opt_t) {
+        die "TEST RUN! rolling back\n";
+    }
 };
 
-if ($@) { print "An error occured! Rolling backl!\n\n $@ \n\n "; }
-elsif ($opt_t) {
-    print "TEST RUN. Rolling back and reseting database sequences!!\n\n";
+
+try {
+    $schema->txn_do($coderef);
+    print "Transaction succeeded! Commiting phenotyping experiments! \n\n" if !$opt_t;
+} catch {
+    # Transaction failed
     foreach my $value ( keys %seq ) {
-	my $maxval= $seq{$value} || 0;
-	if ($maxval) { $dbh->do("SELECT setval ('$value', $maxval, true)") ;  }
-	else {  $dbh->do("SELECT setval ('$value', 1, false)");  }
+        my $maxval= $seq{$value} || 0;
+        if ($maxval) { $dbh->do("SELECT setval ('$value', $maxval, true)") ;  }
+        else {  $dbh->do("SELECT setval ('$value', 1, false)");  }
     }
-    $dbh->rollback;
-}else {
-    print "Transaction succeeded! Commiting phenotyping experiments! \n\n";
-    $dbh->commit();
-}
+    die "An error occured! Rolling back  and reseting database sequences! " . $_ . "\n";
+};
diff --git a/bin/loading_scripts/solcap/load_solcap_data_entry.pl b/bin/loading_scripts/solcap/load_solcap_data_entry.pl
index e13a7d6..7b4023f 100644
--- a/bin/loading_scripts/solcap/load_solcap_data_entry.pl
+++ b/bin/loading_scripts/solcap/load_solcap_data_entry.pl
@@ -46,6 +46,7 @@ use Date::Calc qw(
 		  check_date
 		  );
 use Carp qw /croak/ ;
+use Try::Tiny;
 
 our ($opt_H, $opt_D, $opt_i, $opt_t);
 
@@ -135,8 +136,7 @@ my $unit_cv = $schema->resultset("Cv::Cv")->find(
 my @rows = $spreadsheet->row_labels();
 my @columns = $spreadsheet->column_labels();
 
-eval {
-
+my $coderef = sub {
     foreach my $uniq_id (@rows ) {
 	my $sct = $spreadsheet->value_at($uniq_id, "Line #");
         my $plot = $spreadsheet->value_at($uniq_id, "Plot Number");
@@ -186,7 +186,7 @@ eval {
       COLUMN: foreach my $label (@columns) {
           my $value =  $spreadsheet->value_at($uniq_id, $label);
           ($value, undef) = split (/\s/, $value) ;
-          $value = undef if $value =~ /\./ ; #for some reason data files came with '.' instead of empty cells.
+          $value = undef if $value =~ /^\.$/ ; #for some reason data files came with '.' instead of empty cells.
           
           #sp terms have a label to determine if these have a scale or a quantitative unit
           my ($term, $type) = split (/\|/ , $label) ;
@@ -289,20 +289,21 @@ eval {
           print "Loaded phenotype_cvterm with cvterm '" . $unit_cvterm->name() . " '\n" if $unit_cvterm ;
       }
     }
+    if ($opt_t) {
+        die "TEST RUN! rolling back\n";
+    }
 };
 
 
-if ($@) { print "An error occured! Rolling backl!\n\n $@ \n\n "; }
-elsif ($opt_t) {
-    print "TEST RUN. Rolling back and reseting database sequences!!\n\n";
-    foreach my $value ( keys %seq ) { 
-	my $maxval= $seq{$value} || 0;
-	if ($maxval) { $dbh->do("SELECT setval ('$value', $maxval, true)") ;  }
-	else {  $dbh->do("SELECT setval ('$value', 1, false)");  }
+try {
+    $schema->txn_do($coderef);
+    if (!$opt_t) { print "Transaction succeeded! Commiting phenotyping experiments! \n\n"; }
+} catch {
+    # Transaction failed
+    foreach my $value ( keys %seq ) {
+        my $maxval= $seq{$value} || 0;
+        if ($maxval) { $dbh->do("SELECT setval ('$value', $maxval, true)") ;  }
+        else {  $dbh->do("SELECT setval ('$value', 1, false)");  }
     }
-    $dbh->rollback;
-
-}else {
-    print "Transaction succeeded! Commiting phenotyping experiments! \n\n";
-    $dbh->commit();
-}
+    die "An error occured! Rolling back  and reseting database sequences!" . $_ . "\n";
+};
-- 
2.11.4.GIT