From 80238bc63d407a908edc474a5c2ec363dcb666c2 Mon Sep 17 00:00:00 2001
From: Naama Menda <nm249@cornell.edu>
Date: Sun, 6 Nov 2011 01:26:59 -0400
Subject: [PATCH] adding phenotype props to solcap phenotypes

---
 bin/loading_scripts/solcap/load_solcap_TA_phenotypes.pl | 8 ++++++++
 bin/loading_scripts/solcap/load_solcap_data_entry.pl    | 7 +++++++
 2 files changed, 15 insertions(+)

diff --git a/bin/loading_scripts/solcap/load_solcap_TA_phenotypes.pl b/bin/loading_scripts/solcap/load_solcap_TA_phenotypes.pl
index 3ede8fe..528211c 100644
--- a/bin/loading_scripts/solcap/load_solcap_TA_phenotypes.pl
+++ b/bin/loading_scripts/solcap/load_solcap_TA_phenotypes.pl
@@ -58,6 +58,10 @@ getopts('H:i:tD:l:y:');
 my $dbhost = $opt_H;
 my $dbname = $opt_D;
 my $file = $opt_i;
+my $method;
+$method = 'Fruit color' if $file =~ m/color/;
+$method = 'Fruit longitudinal section' if $file =~ m/long/;
+$method = 'Fruit cross section' if $file =~ m/lat/;
 
 my $dbh = CXGN::DB::InsertDBH->new( { dbhost=>$dbhost,
 				      dbname=>$dbname,
@@ -228,6 +232,10 @@ my $coderef = sub {
                   cvterm_id => $unit_cvterm->cvterm_id() } ) ;
               print "*Loaded phenotype_cvterm with unit '" . $unit_cvterm->name() . "'\n";
           }
+          #store the appropriate method phenotypeprop
+          $phenotype->create_phenotypeprops(
+              { method => $method } , { autocreate => 1 } ) if $method;
+          ####
 	  #check if the phenotype is already associated with an experiment
 	  # which means this loading script has been run before .
 	  if ( $phenotype->find_related("nd_experiment_phenotypes", {} ) ) {
diff --git a/bin/loading_scripts/solcap/load_solcap_data_entry.pl b/bin/loading_scripts/solcap/load_solcap_data_entry.pl
index 7aad160..68282fa 100644
--- a/bin/loading_scripts/solcap/load_solcap_data_entry.pl
+++ b/bin/loading_scripts/solcap/load_solcap_data_entry.pl
@@ -282,6 +282,13 @@ my $coderef = sub {
 		    value => $value ,
                     uniquename => "Stock: " . $stock->stock_id . ", Replicate: $rep, plot: $plot," . ", Term: " . $sp_term->name() . ", parent:  $term",
               });
+          #add phenotype prop for quality terms (yield, brix, ph, acids)
+          if ($label =~ m/SP:0000198|SP:0000165|SP:0000170|SP:0000345/) {
+              my $method = 'quality';
+              ##not sure if this should be phenotypeprop 
+              $phenotype->create_phenotypeprops(
+                  { method => $method } , { autocreate => 1 } ) ;
+          }
           #for qualitative traits, store the value also in phenotyep_cvterm
           if ($child_term) {
               $phenotype->find_or_create_related(
-- 
2.11.4.GIT