From 9a4a369e55fb3de30893e66d40d5f7bfb4f230c3 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Fri, 15 Nov 2024 14:21:05 -0500
Subject: [PATCH] fixed dialog info and cleaned up

---
 .../ParseUpload/Plugin/TransformationIdentifiersGeneric.pm  | 1 -
 lib/CXGN/Transformation/Transformation.pm                   | 2 +-
 mason/transformation/add_transformation_project_dialog.mas  | 2 +-
 mason/transformation/manage_transformation.mas              | 6 +++---
 4 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/lib/CXGN/Stock/ParseUpload/Plugin/TransformationIdentifiersGeneric.pm b/lib/CXGN/Stock/ParseUpload/Plugin/TransformationIdentifiersGeneric.pm
index 751af15a36..85b8e2faf2 100644
--- a/lib/CXGN/Stock/ParseUpload/Plugin/TransformationIdentifiersGeneric.pm
+++ b/lib/CXGN/Stock/ParseUpload/Plugin/TransformationIdentifiersGeneric.pm
@@ -65,7 +65,6 @@ sub _validate_with_plugin {
     }
 
     my $rs = $schema->resultset("Stock::Stock")->search({
-        'is_obsolete' => { '!=' => 't' },
         'uniquename' => { -in => $seen_transformation_identifiers }
     });
     while (my $r=$rs->next){
diff --git a/lib/CXGN/Transformation/Transformation.pm b/lib/CXGN/Transformation/Transformation.pm
index dc88ded5f4..2d8f31e365 100644
--- a/lib/CXGN/Transformation/Transformation.pm
+++ b/lib/CXGN/Transformation/Transformation.pm
@@ -206,7 +206,7 @@ sub get_transformation_info {
     while (my ($plant_id, $plant_name, $vector_id, $vector_name, $notes, $updated_status) = $h->fetchrow_array()){
         push @transformation_info, [$plant_id, $plant_name, $vector_id, $vector_name, $notes, $updated_status]
     }
-    print STDERR "TRANSFORMATION INFO =".Dumper(\@transformation_info)."\n";
+
     return \@transformation_info;
 
 }
diff --git a/mason/transformation/add_transformation_project_dialog.mas b/mason/transformation/add_transformation_project_dialog.mas
index decdd16dcb..ae5eae9dd2 100644
--- a/mason/transformation/add_transformation_project_dialog.mas
+++ b/mason/transformation/add_transformation_project_dialog.mas
@@ -102,7 +102,7 @@ foreach my $program (@$programs) {
                             <ul>
                                 <li>Please click on 'Refresh' button to view your newly created project on the manage page.</li>
                                 <li>You can use your transformation project page to create transformation IDs.</li>
-                                <li><b>If your transformation project is automatically connected to tracking tool, please set up a prefix for autogenerated names for your transformation project before using tracking tool.</b></li>
+                                <li><b>If your transformation project is automatically linked to the tracking tool, please set up a naming format for the autogenerated names of your transformation project before using the tracking tool.</b></li>
                             </ul>
                             <br/>
                         </&>
diff --git a/mason/transformation/manage_transformation.mas b/mason/transformation/manage_transformation.mas
index fdbe847a2a..a0336b3c5c 100644
--- a/mason/transformation/manage_transformation.mas
+++ b/mason/transformation/manage_transformation.mas
@@ -23,9 +23,9 @@ $user_id
                         <li>Transformation projects allow you to organize and track progress of different transformation experiments.</li>
                         <li>Each transformation project can be automatically linked to a tracking project (please contact us).</li>
                         <li>To streamline transformation experiments, you can set <b>default plant material</b> used for transformation and set <b>autogenerated names</b> for newly generated transformants.</li>
-                        <li>Each breeding program can store multiple sets of prefixes for autogenerated names. All stored prefixes and related metadata are displayed in the Autogenerated Name Metadata section on Manage Breeding Programs page. The link for adding autogenerated name metadata can be found on both Manage Breeding Programs page and Manage Transformations page.</li>
-                        <li><b>Links for setting prefix for autogenerated names and setting default plant material can be found on transformation project details page.</b></li>
-                        <li>Progress of each experiment can be easily tracked and organized. On going transformation experiments are grouped in the same table on tranformation project details page. Once the status of a particular experiment is updated to completed/discarded status, the completed/discarded experiment will be automatically moved to a separate table.</li>
+                        <li>Each breeding program can store multiple sets of naming formats for autogenerated names. All stored naming formats and related metadata are displayed in the Autogenerated Name Metadata section on the 'Manage Breeding Programs' page. The link for adding Autogenerated Name Metadata can be found on both the 'Manage Breeding Programs' page and on the 'Manage Transformations' page.</li>
+                        <li><b>Links for setting a naming format for autogenerated names and for setting default plant material can be found on the 'Transformation Project' detail page.</b></li>
+                        <li>Progress of each experiment can be easily tracked and organized. Ongoing transformation experiments are grouped in the same table on the 'Transformation Project' detail page. Once the status of a particular experiment is updated to completed/discarded status, the completed/discarded experiment will be automatically moved to a separate table.</li>
                     </ul>
                     <b><p>What are transformation identifiers?</p></b>
                     <ul>