From f758b7c3219fd5308d3e47bf94288fca0238e8f3 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Fri, 2 Dec 2022 20:10:27 +0000
Subject: [PATCH 01/33] customized add catalog dialog

---
 lib/SGN/Controller/Catalog.pm           |  3 ++
 mason/order/add_catalog_item_dialog.mas | 58 +++++++++++++++++++++++++
 mason/order/catalog.mas                 |  5 ++-
 3 files changed, 64 insertions(+), 2 deletions(-)

diff --git a/lib/SGN/Controller/Catalog.pm b/lib/SGN/Controller/Catalog.pm
index ea459f12fa..6e00307e81 100644
--- a/lib/SGN/Controller/Catalog.pm
+++ b/lib/SGN/Controller/Catalog.pm
@@ -29,6 +29,9 @@ sub stock_catalog :Path('/catalog/view') :Args(0) {
     my $additional_order_info = $c->config->{additional_order_info};
     $c->stash->{additional_order_info} = $additional_order_info;
 
+    my $ordering_site = $c->config->{ordering_site};
+    $c->stash->{ordering_site} = $ordering_site;
+
     $c->stash->{template} = '/order/catalog.mas';
 
 }
diff --git a/mason/order/add_catalog_item_dialog.mas b/mason/order/add_catalog_item_dialog.mas
index 4c2d662b96..3f1f8f975f 100644
--- a/mason/order/add_catalog_item_dialog.mas
+++ b/mason/order/add_catalog_item_dialog.mas
@@ -1,5 +1,6 @@
 <%args>
 $timestamp => localtime()
+$ordering_site => undef
 </%args>
 
 <div class="modal fade" id="add_catalog_item_dialog" name="add_catalog_item_dialog" tabindex="-1" role="dialog" aria-labelledby="addCatalogItemDialog">
@@ -18,6 +19,62 @@ $timestamp => localtime()
                                 <input class="form-control" id="item_name" placeholder="Item name must be in the database">
                             </div>
                         </div>
+% if ($ordering_site eq 'BAT') {
+                        <div class="form-group">
+                            <label class="col-sm-3 control-label">Item Type: </label>
+                            <div class="col-sm-9">
+                                <select class="form-control" id="item_type">
+                                    <option value="">Select an item type</option>
+                                    <option value="single item">single item</option>
+                                    <option value="set of items">batch</option>
+                                </select>
+                            </div>
+                        </div>
+                        <div class="form-group">
+                            <label class="col-sm-3 control-label">Category: </label>
+                            <div class="col-sm-9">
+                                <select class="form-control" id="item_category">
+                                    <option value="">Select a category</option>
+                                    <option value="seed">seed</option>
+                                    <option value="plant">plant</option>
+                                    <option value="construct">construct</option>
+                                </select>
+                            </div>
+                        </div>
+                        <div class="form-group">
+                            <label class="col-sm-3 control-label">Species: </label>
+                            <div class="col-sm-9">
+                                <select class="form-control" id="item_species">
+                                    <option value="">Select a species</option>
+                                    <option value="Nicotiana benthamiana">Nicotiana benthamiana</option>
+                                    <option value="Nicotiana tabacum">Nicotiana tabacum</option>
+                                </select>
+                            </div>
+                        </div>
+                        <div class="form-group">
+                            <label class="col-sm-3 control-label">Variety: </label>
+                            <div class="col-sm-9">
+                                <select class="form-control" id="item_variety">
+                                    <option value="">Select a variety</option>
+                                    <option value="40754">40754</option>
+                                    <option value="K236">K236</option>
+                                    <option value="mix">Mix</option>
+                                </select>
+                            </div>
+                        </div>
+                        <div class="form-group">
+                            <label class="col-sm-3 control-label">Project: </label>
+                            <div class="col-sm-9" >
+                                <div id="item_breeding_program_div"></div>
+                            </div>
+                        </div>
+                        <div class="form-group">
+                            <label class="col-sm-3 control-label">Contact Person Username: </label>
+                            <div class="col-sm-9" >
+                                <input class="form-control" id="contact_person_name" placeholder="Please provide contact person username">
+                            </div>
+                        </div>
+%} else {
                         <div class="form-group">
                             <label class="col-sm-3 control-label">Item Type: </label>
                             <div class="col-sm-9">
@@ -78,6 +135,7 @@ $timestamp => localtime()
                                 <input class="form-control" id="contact_person_name" placeholder="Please provide contact person username">
                             </div>
                         </div>
+%}
                     </form>
                 </div>
             </div>
diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index 5bb89b2233..cc7847971c 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -3,6 +3,7 @@
 $check_vendor_role
 $ordering_service_name => undef
 $additional_order_info => undef
+$ordering_site => undef
 
 </%args>
 
@@ -129,8 +130,8 @@ $additional_order_info => undef
     </div>
 </div>
 
-<& /order/upload_catalog_items_dialog.mas &>
-<& /order/add_catalog_item_dialog.mas &>
+<& /order/upload_catalog_items_dialog.mas, ordering_site => $ordering_site&>
+<& /order/add_catalog_item_dialog.mas, ordering_site => $ordering_site &>
 
 <script>
 

From b6446da12ab6f345fc3d02cbdba0806d03ddc9b9 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Fri, 2 Dec 2022 22:11:56 +0000
Subject: [PATCH 02/33] store catalog

---
 lib/SGN/Controller/AJAX/Catalog.pm      | 56 +++++++++++++++++--------
 mason/order/add_catalog_item_dialog.mas | 32 +++++++++-----
 2 files changed, 60 insertions(+), 28 deletions(-)

diff --git a/lib/SGN/Controller/AJAX/Catalog.pm b/lib/SGN/Controller/AJAX/Catalog.pm
index 3fbc971754..2c8c991850 100644
--- a/lib/SGN/Controller/AJAX/Catalog.pm
+++ b/lib/SGN/Controller/AJAX/Catalog.pm
@@ -23,6 +23,7 @@ sub add_catalog_item_POST : Args(0) {
     my $c = shift;
     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
     my $dbh = $c->dbc->dbh;
+    my $ordering_site = $c->config->{ordering_site};
 
     my $item_name = $c->req->param('item_name');
     my $item_type = $c->req->param('item_type');
@@ -33,6 +34,10 @@ sub add_catalog_item_POST : Args(0) {
     my $item_availability = $c->req->param('item_availability');
     my $contact_person = $c->req->param('contact_person');
     my $item_prop_id = $c->req->param('item_prop_id');
+
+    my $item_species = $c->req->param('item_species');
+    my $item_variety = $c->req->param('item_variety');
+
     my $item_stock_id;
     if (!$c->user()) {
         print STDERR "User not logged in... not adding a catalog item.\n";
@@ -60,27 +65,44 @@ sub add_catalog_item_POST : Args(0) {
         return;
     }
 
-    my $stock_catalog = CXGN::Stock::Catalog->new({
-        bcs_schema => $schema,
-        parent_id => $item_stock_id,
-        prop_id => $item_prop_id
-    });
 
-    $stock_catalog->item_type($item_type);
-    $stock_catalog->category($item_category);
-    $stock_catalog->description($item_description);
-    $stock_catalog->material_source($item_material_source);
-    $stock_catalog->breeding_program($item_breeding_program_id);
-    $stock_catalog->availability($item_availability);
-    $stock_catalog->contact_person_id($sp_person_id);
+    if ($ordering_site eq 'BAT') {
+        my %catalog_info_hash;
+        my $stock_catalog_json_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'stock_catalog_json', 'stock_property');
+        $catalog_info_hash{'ordering_site'} = $ordering_site;
+        $catalog_info_hash{'item_type'} = $item_type;
+        $catalog_info_hash{'category'} = $item_category;
+        $catalog_info_hash{'breeding_program'} = $item_breeding_program_id;
+        $catalog_info_hash{'species'} = $item_species;
+        $catalog_info_hash{'variety'} = $item_variety;
+        $catalog_info_hash{'contact_person_id'} = $sp_person_id;
 
-    $stock_catalog->store();
+        my $catalog_json_string = encode_json \%catalog_info_hash;
+        print STDERR "CATALOG JSON STRING =".Dumper($catalog_json_string)."\n";
+        $item_rs->create_stockprops({$stock_catalog_json_cvterm->name() => $catalog_json_string});
 
-    if (!$stock_catalog->store()){
-        $c->stash->{rest} = {error_string => "Error saving catalog item",};
-        return;
+    } else {
+        my $stock_catalog = CXGN::Stock::Catalog->new({
+            bcs_schema => $schema,
+            parent_id => $item_stock_id,
+            prop_id => $item_prop_id
+        });
+
+        $stock_catalog->item_type($item_type);
+        $stock_catalog->category($item_category);
+        $stock_catalog->description($item_description);
+        $stock_catalog->material_source($item_material_source);
+        $stock_catalog->breeding_program($item_breeding_program_id);
+        $stock_catalog->availability($item_availability);
+        $stock_catalog->contact_person_id($sp_person_id);
+
+        $stock_catalog->store();
+
+        if (!$stock_catalog->store()){
+            $c->stash->{rest} = {error_string => "Error saving catalog item",};
+            return;
+        }
     }
-
     $c->stash->{rest} = {success => "1",};
 
 }
diff --git a/mason/order/add_catalog_item_dialog.mas b/mason/order/add_catalog_item_dialog.mas
index 3f1f8f975f..8625baad7a 100644
--- a/mason/order/add_catalog_item_dialog.mas
+++ b/mason/order/add_catalog_item_dialog.mas
@@ -56,9 +56,9 @@ $ordering_site => undef
                             <div class="col-sm-9">
                                 <select class="form-control" id="item_variety">
                                     <option value="">Select a variety</option>
-                                    <option value="40754">40754</option>
+                                    <option value="C319">C319</option>
                                     <option value="K236">K236</option>
-                                    <option value="mix">Mix</option>
+                                    <option value="Mix">Mix</option>
                                 </select>
                             </div>
                         </div>
@@ -173,6 +173,8 @@ $ordering_site => undef
 <script>
 jQuery(document).ready(function(){
 
+    var ordering_site = "<% $ordering_site %>";
+
     jQuery("#add_catalog_item_button").click( function() {
 
         jQuery("#item_name").autocomplete({
@@ -193,14 +195,20 @@ jQuery(document).ready(function(){
         var availability = jQuery('#item_availability').val();
         var contact_person = jQuery('#contact_person_name').val();
 
-        if (name == '') { alert("Please provide a name") };
-        if (type == '') { alert("Please select a type") };
-        if (category == '') { alert("Please select a category") };
-        if (description == '') { alert("Please provide a description") };
-        if (material_source == '') { alert("Please select a material source") };
-        if (breeding_program == '') { alert("Please select a breeding program") };
-        if (availability == '') { alert("Please indicate availability") };
-        if (contact_person == '') { alert("Please indicate contact person") };
+        var item_species = jQuery('#item_species').val();
+        var item_variety = jQuery('#item_variety').val();
+
+        if (ordering_site != 'BAT') {
+            if (name == '') { alert("Please provide a name") };
+            if (type == '') { alert("Please select a type") };
+            if (category == '') { alert("Please select a category") };
+            if (description == '') { alert("Please provide a description") };
+            if (material_source == '') { alert("Please select a material source") };
+            if (breeding_program == '') { alert("Please select a breeding program") };
+            if (availability == '') { alert("Please indicate availability") };
+            if (contact_person == '') { alert("Please indicate contact person") };
+        }
+
 
         jQuery.ajax({
             url: '/ajax/catalog/add_item',
@@ -214,7 +222,9 @@ jQuery(document).ready(function(){
                 'item_material_source': material_source,
                 'item_breeding_program': breeding_program,
                 'item_availability': availability,
-                'contact_person': contact_person
+                'contact_person': contact_person,
+                'item_species': item_species,
+                'item_variety': item_variety
             },
             beforeSend: function(response){
                 jQuery('#working_modal').modal('show');

From 1f9d8eddfc412d8433e6c177fc754acb1e77a5a0 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sun, 4 Dec 2022 23:33:42 +0000
Subject: [PATCH 03/33] retrieve catalog items

---
 lib/SGN/Controller/AJAX/Catalog.pm | 89 +++++++++++++++++++++---------
 mason/order/catalog.mas            | 53 ++++++++++++------
 2 files changed, 100 insertions(+), 42 deletions(-)

diff --git a/lib/SGN/Controller/AJAX/Catalog.pm b/lib/SGN/Controller/AJAX/Catalog.pm
index 2c8c991850..ea7268f17a 100644
--- a/lib/SGN/Controller/AJAX/Catalog.pm
+++ b/lib/SGN/Controller/AJAX/Catalog.pm
@@ -238,33 +238,72 @@ sub get_catalog :Path('/ajax/catalog/items') :Args(0) {
     my $self = shift;
     my $c = shift;
     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
+    my $ordering_site = $c->config->{ordering_site};
+    my @catalog_items;
+
+    if ($ordering_site eq 'BAT') {
+        my $stock_catalog_json_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'stock_catalog_json', 'stock_property');
+
+        my $catalog_rs = $schema->resultset("Stock::Stockprop")->search({type_id => $stock_catalog_json_cvterm->cvterm_id() }, { order_by => {-asc => 'stock_id'} });
+        my @catalog_list;
+        while (my $r = $catalog_rs->next()){
+            my @each_row = ();
+            my $catalog_stock_id = $r->stock_id();
+            my $item_detail_json = $r->value();
+            my $detail_hash = decode_json $item_detail_json;
+            my $site_key = $detail_hash->{'ordering_site'};
+            if ($site_key eq 'BAT') {
+                my $item_type = $detail_hash->{'item_type'};
+                my $item_category = $detail_hash->{'category'};
+                my $species = $detail_hash->{'species'};
+                my $variety = $detail_hash->{'variety'};
+                my $program_id = $detail_hash->{'breeding_program'};
+
+                my $stock_rs = $schema->resultset("Stock::Stock")->find({stock_id => $catalog_stock_id });
+                my $item_name = $stock_rs->uniquename();
+
+                my $program_rs = $schema->resultset('Project::Project')->find({project_id => $program_id});
+                my $program_name = $program_rs->name();
+
+                push @catalog_items, {
+                    item_id => $catalog_stock_id,
+                    item_name => $item_name,
+                    item_type => $item_type,
+                    category => $item_category,
+                    species => $species,
+                    variety => $variety,
+                    program => $program_name,
+                };
+            }
+        }
+    } else {
 
-    my $catalog_obj = CXGN::Stock::Catalog->new({ bcs_schema => $schema});
-    my $catalog_ref = $catalog_obj->get_catalog_items();
+        my $catalog_obj = CXGN::Stock::Catalog->new({ bcs_schema => $schema});
+        my $catalog_ref = $catalog_obj->get_catalog_items();
 #    print STDERR "ITEM RESULTS =".Dumper($catalog_ref)."\n";
-    my @catalog_items;
-    my @catalog_list = @$catalog_ref;
-    foreach my $catalog_item (@catalog_list) {
-        my @item_details = ();
-        @item_details = @$catalog_item;
-        my $item_id = shift @item_details;
-        my $stock_rs = $schema->resultset("Stock::Stock")->find({stock_id => $item_id });
-        my $item_name = $stock_rs->uniquename();
-
-        my $program_id = $item_details[4];
-        my $program_rs = $schema->resultset('Project::Project')->find({project_id => $program_id});
-        my $program_name = $program_rs->name();
-
-        push @catalog_items, {
-            item_id => $item_id,
-            item_name => $item_name,
-            item_type => $item_details[0],
-            category => $item_details[1],
-            description => $item_details[2],
-            material_source => $item_details[3],
-            breeding_program => $program_name,
-            availability => $item_details[5],
-        };
+        my @catalog_list = @$catalog_ref;
+        foreach my $catalog_item (@catalog_list) {
+            my @item_details = ();
+            @item_details = @$catalog_item;
+            my $item_id = shift @item_details;
+            my $stock_rs = $schema->resultset("Stock::Stock")->find({stock_id => $item_id });
+            my $item_name = $stock_rs->uniquename();
+
+            my $program_id = $item_details[4];
+            my $program_rs = $schema->resultset('Project::Project')->find({project_id => $program_id});
+            my $program_name = $program_rs->name();
+
+            push @catalog_items, {
+                item_id => $item_id,
+                item_name => $item_name,
+                item_type => $item_details[0],
+                category => $item_details[1],
+                description => $item_details[2],
+                material_source => $item_details[3],
+                breeding_program => $program_name,
+                availability => $item_details[5],
+            };
+        }
     }
 
     $c->stash->{rest} = {data => \@catalog_items};
diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index cc7847971c..4664da7791 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -139,23 +139,42 @@ jQuery(document).ready( function() {
 
     var ordering_service_name = "<% $ordering_service_name %>";
     var additional_order_info = "<% $additional_order_info %>";
-
-    jQuery('#catalog_items_table').DataTable( {
-        'autoWidth': false,
-        'order': false,
-        'search':'applied',
-        'ajax': '/ajax/catalog/items',
-        columns: [
-            { title: "Name", "data": null, "render": function ( data, type, row ) { return "<a href='/catalog/item_details/"+row.item_id+"'>"+row.item_name+"</a>"; } },
-            { title: "Type", "data": "item_type" },
-            { title: "Category", "data": "category" },
-            { title: "Description", "data": "description" },
-            { title: "Material Source", "data": "material_source" },
-            { title: "Breeding Program", "data": "breeding_program" },
-            { title: "Availability", "data": "availability" },
-            { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\")'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
-        ],
-    });
+    var ordering_site = "<% $ordering_site %>";
+
+    if (ordering_site == 'BAT') {
+        jQuery('#catalog_items_table').DataTable( {
+            'autoWidth': false,
+            'order': false,
+            'search':'applied',
+            'ajax': '/ajax/catalog/items',
+            columns: [
+                { title: "Name", "data": null, "render": function ( data, type, row ) { return "<a href='/catalog/item_details/"+row.item_id+"'>"+row.item_name+"</a>"; } },
+                { title: "Type", "data": "item_type" },
+                { title: "Category", "data": "category" },
+                { title: "Species", "data": "species" },
+                { title: "Variety", "data": "variety" },
+                { title: "Project", "data": "program" },
+                { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\")'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
+            ],
+        });
+    } else {
+        jQuery('#catalog_items_table').DataTable( {
+            'autoWidth': false,
+            'order': false,
+            'search':'applied',
+            'ajax': '/ajax/catalog/items',
+            columns: [
+                { title: "Name", "data": null, "render": function ( data, type, row ) { return "<a href='/catalog/item_details/"+row.item_id+"'>"+row.item_name+"</a>"; } },
+                { title: "Type", "data": "item_type" },
+                { title: "Category", "data": "category" },
+                { title: "Description", "data": "description" },
+                { title: "Material Source", "data": "material_source" },
+                { title: "Breeding Program", "data": "breeding_program" },
+                { title: "Availability", "data": "availability" },
+                { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\")'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
+            ],
+        });
+    }
 
     var lo = new CXGN.List();
     var list_id;

From 71250a2f6094904a7a61c1d0bd27b3442cfdeae3 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Mon, 5 Dec 2022 22:44:41 +0000
Subject: [PATCH 04/33] additional info dialog

---
 mason/order/catalog.mas | 38 ++++++++++++++++++++++++++------------
 1 file changed, 26 insertions(+), 12 deletions(-)

diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index 4664da7791..9fbce91461 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -154,7 +154,7 @@ jQuery(document).ready( function() {
                 { title: "Species", "data": "species" },
                 { title: "Variety", "data": "variety" },
                 { title: "Project", "data": "program" },
-                { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\")'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
+                { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_site+"\")'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
             ],
         });
     } else {
@@ -283,22 +283,36 @@ jQuery(document).ready( function() {
 
 });
 
-function addToCart(item_name, additional_order_info, ordering_service_name){
+function addToCart(item_name, additional_order_info, ordering_service_name, ordering_site ){
     var additional_info = additional_order_info.split(",");
     var html = '';
-    html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="cart_item_name" name="cart_item_name" value="'+item_name+'" disabled></div></div>';
-    html = html + '<div class="form-group"><label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div></div>';
-    if (ordering_service_name == 'ONA') {
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Additional Info: </label><div class="col-sm-9" ><select class="form-control" id="item_additional_info" name="item_additional_info"><option disabled value="" selected hidden>Please select a required clone stage</option>';
-        if (additional_info) {
-            for (var i=0; i<additional_info.length; i++) {
-                html = html + '<option value='+additional_info[i]+'>'+additional_info[i]+'</option>';
+
+    if (ordering_site == 'BAT') {
+        html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="cart_item_name" name="cart_item_name" value="'+item_name+'" disabled></div></div>';
+        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div></div>';
+        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Facility: </label><div class="col-sm-9" ><input class="form-control" id="item_facility" name="item_facility" placeholder="Please Select"</div></div>';
+        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Scientist(s): </label><div class="col-sm-9" ><input class="form-control" id="item_scientist" name="item_scientist" placeholder=""</div></div>';
+        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Due/Requested by Date: </label><div class="col-sm-9" ><input class="form-control" id="due_date" name="due_date" placeholder=""</div></div>';
+        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Experiment Name: </label><div class="col-sm-9" ><input class="form-control" id="experiment_name" name="experiment_name" placeholder=""</div></div>';
+        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Experiment Type: </label><div class="col-sm-9" ><input class="form-control" id="experiment_type" name="experiment_type" placeholder="Please Select"</div></div>';
+        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Risk Assessment: </label><div class="col-sm-9" ><input class="form-control" id="risk_assessment" name="risk_assessment" placeholder=""</div></div>';
+        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Containment Zone: </label><div class="col-sm-9" ><input class="form-control" id="containment_zone" name="containment_zone" placeholder=""</div></div>';
+        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Additional Comments: </label><div class="col-sm-9" ><input class="form-control" id="item_comments" name="item_comments" placeholder="eg: Clothing & Special Handling"</div></div></form>';
+
+    } else {
+        html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="cart_item_name" name="cart_item_name" value="'+item_name+'" disabled></div></div>';
+        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div></div>';
+        if (ordering_service_name == 'ONA') {
+            html = html + '<div class="form-group"><label class="col-sm-3 control-label">Additional Info: </label><div class="col-sm-9" ><select class="form-control" id="item_additional_info" name="item_additional_info"><option disabled value="" selected hidden>Please select a required clone stage</option>';
+            if (additional_info) {
+                for (var i=0; i<additional_info.length; i++) {
+                    html = html + '<option value='+additional_info[i]+'>'+additional_info[i]+'</option>';
+                }
             }
+            html = html + '</select></div></div>';
         }
-        html = html + '</select></div></div>';
+        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Comments: </label><div class="col-sm-9" ><input class="form-control" id="item_comments" name="item_comments" placeholder="Optional"</div></div></form>';
     }
-    html = html + '<div class="form-group"><label class="col-sm-3 control-label">Comments: </label><div class="col-sm-9" ><input class="form-control" id="item_comments" name="item_comments" placeholder="Optional"</div></div></form>';
-
     jQuery('#add_item_detail_div').html(html);
     jQuery('#add_item_detail_dialog').modal('show');
 

From 64ce28eb5948abba7ddfd7d013cbd88e7d650d20 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Tue, 6 Dec 2022 21:34:44 +0000
Subject: [PATCH 05/33] modified dialog

---
 mason/order/catalog.mas | 28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index 9fbce91461..067eedcfea 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -122,10 +122,17 @@ $ordering_site => undef
                     </div>
                 </div>
             </div>
+% if ($ordering_site eq 'BAT') {
+            <div class="modal-footer">
+                <button id="close_submit_item_detail_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+                <button id="submit_single_step_button" type="button" class="btn btn-primary" >Submit</button>
+            </div>
+%} else {
             <div class="modal-footer">
                 <button id="close_add_item_detail_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
                 <button id="add_item_button" type="button" class="btn btn-primary" >Add Item</button>
             </div>
+%}
         </div>
     </div>
 </div>
@@ -288,17 +295,16 @@ function addToCart(item_name, additional_order_info, ordering_service_name, orde
     var html = '';
 
     if (ordering_site == 'BAT') {
-        html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="cart_item_name" name="cart_item_name" value="'+item_name+'" disabled></div></div>';
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div></div>';
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Facility: </label><div class="col-sm-9" ><input class="form-control" id="item_facility" name="item_facility" placeholder="Please Select"</div></div>';
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Scientist(s): </label><div class="col-sm-9" ><input class="form-control" id="item_scientist" name="item_scientist" placeholder=""</div></div>';
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Due/Requested by Date: </label><div class="col-sm-9" ><input class="form-control" id="due_date" name="due_date" placeholder=""</div></div>';
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Experiment Name: </label><div class="col-sm-9" ><input class="form-control" id="experiment_name" name="experiment_name" placeholder=""</div></div>';
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Experiment Type: </label><div class="col-sm-9" ><input class="form-control" id="experiment_type" name="experiment_type" placeholder="Please Select"</div></div>';
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Risk Assessment: </label><div class="col-sm-9" ><input class="form-control" id="risk_assessment" name="risk_assessment" placeholder=""</div></div>';
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Containment Zone: </label><div class="col-sm-9" ><input class="form-control" id="containment_zone" name="containment_zone" placeholder=""</div></div>';
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Additional Comments: </label><div class="col-sm-9" ><input class="form-control" id="item_comments" name="item_comments" placeholder="eg: Clothing & Special Handling"</div></div></form>';
-
+        html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="item_name" name="item_name" value="'+item_name+'" disabled></div><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Facility: </label><div class="col-sm-9" ><input class="form-control" id="item_facility" name="item_facility" placeholder="Please Select"></div><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Scientist(s): </label><div class="col-sm-9" ><input class="form-control" id="item_scientist" name="item_scientist" placeholder=""></div><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Due/Requested by Date: </label><div class="col-sm-9" ><input class="form-control" id="item_due_date" name="item_due_date" placeholder=""></div><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Experiment Name: </label><div class="col-sm-9" ><input class="form-control" id="experiment_name" name="experiment_name" placeholder=""></div><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Experiment Type: </label><div class="col-sm-9" ><input class="form-control" id="experiment_type" name="experiment_type" placeholder="Please Select"></div><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Risk Assessment: </label><div class="col-sm-9" ><input class="form-control" id="risk_assessment" name="risk_assessment" placeholder=""></div><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Containment Zone: </label><div class="col-sm-9" ><input class="form-control" id="containment_zone" name="containment_zone" placeholder=""></div><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Additional Comments: </label><div class="col-sm-9" ><input class="form-control" id="additional_comments" name="additional_comments" placeholder="eg: Clothing & Special Handling"></div></div></div></form>';
     } else {
         html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="cart_item_name" name="cart_item_name" value="'+item_name+'" disabled></div></div>';
         html = html + '<div class="form-group"><label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div></div>';

From ac922bf81f7cc7c34b162f956bef5bb1ee721777 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Wed, 7 Dec 2022 21:52:28 +0000
Subject: [PATCH 06/33] remove your cart for single item request

---
 mason/order/catalog.mas | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index 067eedcfea..d0700253e0 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -35,6 +35,7 @@ $ordering_site => undef
                 </div>
             </div>
         </div>
+% if ($ordering_site ne 'BAT') {
         <div class="panel panel-default">
             <div class="panel-body">
                 <button id="your_cart_button" type="button" class="btn btn-primary btn-sm">
@@ -42,6 +43,7 @@ $ordering_site => undef
                 </button>
             </div>
         </div>
+%}
         <td>
             <a href="/order/stocks/view"><p>Go to Manage Order Page</p></a>
         </td>
@@ -161,7 +163,7 @@ jQuery(document).ready( function() {
                 { title: "Species", "data": "species" },
                 { title: "Variety", "data": "variety" },
                 { title: "Project", "data": "program" },
-                { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_site+"\")'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
+                { title: " ", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_site+"\")'>Request</a>"; } },
             ],
         });
     } else {
@@ -295,15 +297,15 @@ function addToCart(item_name, additional_order_info, ordering_service_name, orde
     var html = '';
 
     if (ordering_site == 'BAT') {
-        html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="item_name" name="item_name" value="'+item_name+'" disabled></div><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Facility: </label><div class="col-sm-9" ><input class="form-control" id="item_facility" name="item_facility" placeholder="Please Select"></div><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Scientist(s): </label><div class="col-sm-9" ><input class="form-control" id="item_scientist" name="item_scientist" placeholder=""></div><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Due/Requested by Date: </label><div class="col-sm-9" ><input class="form-control" id="item_due_date" name="item_due_date" placeholder=""></div><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Experiment Name: </label><div class="col-sm-9" ><input class="form-control" id="experiment_name" name="experiment_name" placeholder=""></div><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Experiment Type: </label><div class="col-sm-9" ><input class="form-control" id="experiment_type" name="experiment_type" placeholder="Please Select"></div><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Risk Assessment: </label><div class="col-sm-9" ><input class="form-control" id="risk_assessment" name="risk_assessment" placeholder=""></div><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Containment Zone: </label><div class="col-sm-9" ><input class="form-control" id="containment_zone" name="containment_zone" placeholder=""></div><br><br>';
+        html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="item_name" name="item_name" value="'+item_name+'" disabled></div><br><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div><br><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Facility: </label><div class="col-sm-9" ><input class="form-control" id="item_facility" name="item_facility" placeholder="Please Select"></div><br><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Scientist(s): </label><div class="col-sm-9" ><input class="form-control" id="item_scientist" name="item_scientist" placeholder=""></div><br><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Due/Requested by Date: </label><div class="col-sm-9" ><input class="form-control" id="item_due_date" name="item_due_date" placeholder=""></div><br><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Experiment Name: </label><div class="col-sm-9" ><input class="form-control" id="experiment_name" name="experiment_name" placeholder=""></div><br><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Experiment Type: </label><div class="col-sm-9" ><input class="form-control" id="experiment_type" name="experiment_type" placeholder="Please Select"></div><br><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Risk Assessment: </label><div class="col-sm-9" ><input class="form-control" id="risk_assessment" name="risk_assessment" placeholder=""></div><br><br><br>';
+        html = html + '<label class="col-sm-3 control-label">Containment Zone: </label><div class="col-sm-9" ><input class="form-control" id="containment_zone" name="containment_zone" placeholder=""></div><br><br><br>';
         html = html + '<label class="col-sm-3 control-label">Additional Comments: </label><div class="col-sm-9" ><input class="form-control" id="additional_comments" name="additional_comments" placeholder="eg: Clothing & Special Handling"></div></div></div></form>';
     } else {
         html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="cart_item_name" name="cart_item_name" value="'+item_name+'" disabled></div></div>';

From 41a7377e07ec611e5fe12ef62c49c2db540408eb Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Thu, 8 Dec 2022 23:26:00 +0000
Subject: [PATCH 07/33] save single step submission

---
 lib/SGN/Controller/AJAX/Order.pm | 107 +++++++++++++++++++++++++++++++
 mason/order/catalog.mas          |  53 ++++++++++++++-
 2 files changed, 159 insertions(+), 1 deletion(-)

diff --git a/lib/SGN/Controller/AJAX/Order.pm b/lib/SGN/Controller/AJAX/Order.pm
index 20d1bc23d4..a0d8e9f9d0 100644
--- a/lib/SGN/Controller/AJAX/Order.pm
+++ b/lib/SGN/Controller/AJAX/Order.pm
@@ -547,6 +547,113 @@ sub update_order :Path('/ajax/order/update') :Args(0) {
 
     $c->stash->{rest} = {success => "1",};
 
+}
+
+
+sub single_step_submission : Path('/ajax/order/single_step_submission') : ActionClass('REST'){ }
+
+sub single_step_submission_POST : Args(0) {
+    my $self = shift;
+    my $c = shift;
+    my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
+    my $people_schema = $c->dbic_schema('CXGN::People::Schema');
+    my $dbh = $c->dbc->dbh();
+    my $time = DateTime->now();
+    my $timestamp = $time->ymd()."_".$time->hms();
+    my $request_date = $time->ymd();
+    my $item_name = $c->req->param('item_name');
+    my $quantity = $c->req->param('quantity');
+    my $facility = $c->req->param('facility');
+    my $scientist = $c->req->param('scientist');
+    my $due_date = $c->req->param('due_date');
+    my $experiment_name = $c->req->param('experiment_name');
+    my $experiment_type = $c->req->param('experiment_type');
+    my $risk_assessment = $c->req->param('risk_assessment');
+    my $containment_zone = $c->req->param('containment_zone');
+    my $additional_comments = $c->req->param('additional_comments');
+    my %request_details;
+    my @item_list;
+    $request_details{$item_name}{'quantity'} = $quantity;
+    $request_details{$item_name}{'facility'} = $facility;
+    $request_details{$item_name}{'scientist'} = $scientist;
+    $request_details{$item_name}{'due_date'} = $due_date;
+    $request_details{$item_name}{'experiment_name'} = $experiment_name;
+    $request_details{$item_name}{'experiment_type'} = $experiment_type;
+    $request_details{$item_name}{'risk_assessment'} = $risk_assessment;
+    $request_details{$item_name}{'containment_zone'} = $containment_zone;
+    $request_details{$item_name}{'additional_comments'} = $additional_comments;
+
+    if (!$c->user()) {
+        print STDERR "User not logged in... not adding a catalog item.\n";
+        $c->stash->{rest} = {error_string => "You must be logged in to add a catalog item." };
+        return;
+    }
+    my $user_id = $c->user()->get_object()->get_sp_person_id();
+    my $user_name = $c->user()->get_object()->get_username();
+    my $user_role = $c->user->get_object->get_user_type();
+
+    my $catalog_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'stock_catalog_json', 'stock_property')->cvterm_id();
+    my $item_rs = $schema->resultset("Stock::Stock")->find( { uniquename => $item_name });
+    my $item_id = $item_rs->stock_id();
+    my $item_info_rs = $schema->resultset("Stock::Stockprop")->find({stock_id => $item_id, type_id => $catalog_cvterm_id});
+    my $item_info_string = $item_info_rs->value();
+    my $item_info_hash = decode_json $item_info_string;
+    my $contact_person_id = $item_info_hash->{'contact_person_id'};
+    my $item_type = $item_info_hash->{'item_type'};
+    $request_details{$item_name}{'item_type'} = $item_type;
+    push @item_list, \%request_details;
+    print STDERR "REQUEST DETAILS =".Dumper(\%request_details)."\n";
+    my @history = ();
+    my $history_info = {};
+
+    my $new_order = CXGN::Stock::Order->new( { people_schema => $people_schema, dbh => $dbh});
+    $new_order->order_from_id($user_id);
+    $new_order->order_to_id($contact_person_id);
+    $new_order->order_status("submitted");
+    $new_order->create_date($timestamp);
+    my $order_id = $new_order->store();
+#        print STDERR "ORDER ID =".($order_id)."\n";
+    if (!$order_id){
+        $c->stash->{rest} = {error_string => "Error saving your order",};
+        return;
+    }
+
+    $history_info ->{'submitted'} = $timestamp;
+    push @history, $history_info;
+
+
+    my $order_prop = CXGN::Stock::OrderBatch->new({ bcs_schema => $schema, people_schema => $people_schema});
+    $order_prop->clone_list(\@item_list);
+    $order_prop->parent_id($order_id);
+    $order_prop->history(\@history);
+    my $order_prop_id = $order_prop->store_sp_orderprop();
+#        print STDERR "ORDER PROP ID =".($order_prop_id)."\n";
+
+    if (!$order_prop_id){
+        $c->stash->{rest} = {error_string => "Error saving your order",};
+        return;
+    }
+
+    my $contact_person = CXGN::People::Person -> new($dbh, $contact_person_id);
+    my $contact_email = $contact_person->get_contact_email();
+
+    my $host = $c->config->{main_production_site_url};
+    my $project_name = $c->config->{project_name};
+    my $subject="Ordering Notification from $project_name";
+    my $body=<<END_HEREDOC;
+
+You have an order submitted to $project_name ($host/order/stocks/view).
+Please do *NOT* reply to this message.
+
+Thank you,
+$project_name Team
+
+END_HEREDOC
+
+    CXGN::Contact::send_email($subject,$body,$contact_email);
+
+    $c->stash->{rest}->{success} .= 'Your request has been submitted successfully and the vendor has been notified.';
+
 
 }
 
diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index d0700253e0..ad2fd59870 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -127,7 +127,7 @@ $ordering_site => undef
 % if ($ordering_site eq 'BAT') {
             <div class="modal-footer">
                 <button id="close_submit_item_detail_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
-                <button id="submit_single_step_button" type="button" class="btn btn-primary" >Submit</button>
+                <button id="single_step_submission_button" type="button" class="btn btn-primary" >Submit</button>
             </div>
 %} else {
             <div class="modal-footer">
@@ -290,6 +290,57 @@ jQuery(document).ready( function() {
         location.reload();
     });
 
+    jQuery('#single_step_submission_button').click(function(){
+        var item_name = jQuery('#item_name').val();
+        var quantity = jQuery('#item_quantity').val();
+        var facility = jQuery('#item_facility').val();
+        var scientist = jQuery('#item_scientist').val();
+        var due_date = jQuery('#item_due_date').val();
+        var experiment_name = jQuery('#experiment_name').val();
+        var experiment_type = jQuery('#experiment_type').val();
+        var risk_assessment = jQuery('#risk_assessment').val();
+        var containment_zone = jQuery('#containment_zone').val();
+        var additional_comments = jQuery('#additonal_comments').val();
+
+        jQuery.ajax({
+            url: '/ajax/order/single_step_submission',
+            dataType: "json",
+            type: 'POST',
+            data : {
+                'item_name' : item_name,
+                'quantity': quantity,
+                'facility': facility,
+                'scientist': scientist,
+                'due_date': due_date,
+                'experiment_name': experiment_name,
+                'experiment_type':experiment_type,
+                'risk_assessment': risk_assessment,
+                'containment_zone': containment_zone,
+                'additional_comments': additional_comments
+            },
+            beforeSend: function(response){
+                jQuery('#working_modal').modal('show');
+            },
+            success: function(response) {
+                jQuery('#working_modal').modal('hide');
+                if (response.success) {
+                    jQuery('#ordering_response_div').html(response.success);
+
+                    jQuery('#order_response_dialog').modal('show');
+                    jQuery('#add_item_detail_dialog').modal('hide');
+                }
+                if (response.error_string) {
+                    alert(response.error_string);
+                }
+            },
+            error: function(response){
+                jQuery('#working_modal').modal('hide');
+                alert('An error occurred saving your request');
+            }
+        });
+    });
+
+
 });
 
 function addToCart(item_name, additional_order_info, ordering_service_name, ordering_site ){

From a083e78546f00253e062ef516fc7802be04a6032 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sat, 10 Dec 2022 00:55:59 +0000
Subject: [PATCH 08/33] retrieve order using keys

---
 lib/CXGN/Stock/Order.pm          | 54 +++++++++++++++++++-------------
 lib/SGN/Controller/AJAX/Order.pm | 50 +++++++++++++++++++++++++++--
 mason/order/stocks.mas           |  2 +-
 3 files changed, 81 insertions(+), 25 deletions(-)

diff --git a/lib/CXGN/Stock/Order.pm b/lib/CXGN/Stock/Order.pm
index e6ce2bf8f8..1b3630b090 100644
--- a/lib/CXGN/Stock/Order.pm
+++ b/lib/CXGN/Stock/Order.pm
@@ -92,34 +92,44 @@ sub get_orders_from_person_id {
         my $order_to_name=$person->get_first_name()." ".$person->get_last_name();
 
         my $orderprop_rs = $people_schema->resultset('SpOrderprop')->search( { sp_order_id => $order_id } );
+        my $all_items = ();
         while (my $item_result = $orderprop_rs->next()){
             my @list;
             my $item_json = $item_result->value();
             my $item_hash = JSON::Any->jsonToObj($item_json);
-            my $all_items = $item_hash->{'clone_list'};
-            foreach my $each_item (@$all_items) {
-                my $item_name = (keys %$each_item)[0];
-                my $quantity = $each_item->{$item_name}->{'quantity'};
-                my $comments = $each_item->{$item_name}->{'comments'};
-                my $additional_info = $each_item->{$item_name}->{'additional_info'};
-
-                my $each_item_details;
-                if ($additional_info && $comments) {
-                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info. "," . " " . "comments:" . $comments;
-                } elsif ($additional_info && (!$comments)){
-                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info;
-                } elsif ((!$additional_info) && $comments) {
-                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . "," . " "."comments:" . $comments;
-                } else {
-                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity;
-                }
-                push @list, $each_item_details;
-            }
-            my @sort_list = sort @list;
-            $item_list = join("<br>", @sort_list);
+            $all_items = $item_hash->{'clone_list'};
+#            foreach my $each_item (@$all_items) {
+#                my $item_name = (keys %$each_item)[0];
+#                my $quantity = $each_item->{$item_name}->{'quantity'};
+#                my $comments = $each_item->{$item_name}->{'comments'};
+#                my $additional_info = $each_item->{$item_name}->{'additional_info'};
+
+#                my $each_item_details;
+#                if ($additional_info && $comments) {
+#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info. "," . " " . "comments:" . $comments;
+#                } elsif ($additional_info && (!$comments)){
+#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info;
+#                } elsif ((!$additional_info) && $comments) {
+#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . "," . " "."comments:" . $comments;
+#                } else {
+#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity;
+#                }
+#                push @list, $each_item_details;
+#            }
+#            my @sort_list = sort @list;
+#            $item_list = join("<br>", @sort_list);
         }
 
-        push @orders, [$order_id, $create_date, $item_list, $order_status, $completion_date, $order_to_name, $comments ];
+#        push @orders, [$order_id, $create_date, $item_list, $order_status, $completion_date, $order_to_name, $comments ];
+        push @orders, {
+            order_id => $order_id,
+            create_date => $create_date,
+            clone_list => $all_items,
+            order_status => $order_status,
+            completion_date => $completion_date,
+            order_to_name => $order_to_name,
+            comments => $comments
+        }
     }
 
     return \@orders;
diff --git a/lib/SGN/Controller/AJAX/Order.pm b/lib/SGN/Controller/AJAX/Order.pm
index a0d8e9f9d0..20114e3594 100644
--- a/lib/SGN/Controller/AJAX/Order.pm
+++ b/lib/SGN/Controller/AJAX/Order.pm
@@ -367,6 +367,10 @@ sub get_user_current_orders :Path('/ajax/order/current') Args(0) {
     my $people_schema = $c->dbic_schema('CXGN::People::Schema');
     my $dbh = $c->dbc->dbh;
     my $user_id;
+    my $ordering_site = $c->config->{ordering_site};
+    my $order_properties = $c->config->{order_properties};
+    my @properties = split ',',$order_properties;
+
 
     if (!$c->user){
         $c->stash->{rest} = {error=>'You must be logged in to view your current orders!'};
@@ -379,13 +383,55 @@ sub get_user_current_orders :Path('/ajax/order/current') Args(0) {
 
     my $orders = CXGN::Stock::Order->new({ dbh => $dbh, people_schema => $people_schema, order_from_id => $user_id});
     my $all_orders_ref = $orders->get_orders_from_person_id();
+
     my @current_orders;
     my @all_orders = @$all_orders_ref;
     foreach my $order (@all_orders) {
-        if (($order->[3]) ne 'completed') {
-            push @current_orders, [qq{<a href="/order/details/view/$order->[0]">$order->[0]</a>}, $order->[1], $order->[2], $order->[3], $order->[5], $order->[6]]
+        if (($order->{'order_status'}) ne 'completed') {
+            my $clone_list = $order->{'clone_list'};
+            my $item_name;
+            my $all_details_string;
+            foreach my $each_item (@$clone_list) {
+                my @request_details = ();
+                $item_name = (keys %$each_item)[0];
+                push @request_details, "Item Name". ":"."".$item_name;
+                foreach my $field (@properties) {
+                    my $each_detail = $each_item->{$item_name}->{$field};
+                    my $detail_string = $field. ":"."".$each_detail;
+                    push @request_details, $detail_string;
+                }
+                $all_details_string = join("<br>", @request_details);
+            }
+            push @current_orders, [qq{<a href="/order/details/view/$order->{'order_id'}">$order->{'order_id'}</a>}, $order->{'create_date'}, $all_details_string, $order->{'order_status'}, $order->{'order_to_name'}, $order->{'comments'}]
         }
+
+        #                my $quantity = $each_item->{$item_name}->{'quantity'};
+        #                my $comments = $each_item->{$item_name}->{'comments'};
+        #                my $additional_info = $each_item->{$item_name}->{'additional_info'};
+
+        #                my $each_item_details;
+        #                if ($additional_info && $comments) {
+        #                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info. "," . " " . "comments:" . $comments;
+        #                } elsif ($additional_info && (!$comments)){
+        #                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info;
+        #                } elsif ((!$additional_info) && $comments) {
+        #                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . "," . " "."comments:" . $comments;
+        #                } else {
+        #                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity;
+        #                }
+        #                push @list, $each_item_details;
+        #            }
+        #            my @sort_list = sort @list;
+        #            $item_list = join("<br>", @sort_list);
+
+#            push @current_orders, [qq{<a href="/order/details/view/$order->[0]">$order->[0]</a>}, $order->[1], $order->[2], $order->[3], $order->[5], $order->[6]]
     }
+#    foreach my $order (@all_orders) {
+#        if (($order->[3]) ne 'completed') {
+#            push @current_orders, [qq{<a href="/order/details/view/$order->[0]">$order->[0]</a>}, $order->[1], $order->[2], $order->[3], $order->[5], $order->[6]]
+#        }
+#    }
+
     $c->stash->{rest} = {data => \@current_orders};
 }
 
diff --git a/mason/order/stocks.mas b/mason/order/stocks.mas
index 88f0aa2a94..4c90446377 100644
--- a/mason/order/stocks.mas
+++ b/mason/order/stocks.mas
@@ -53,7 +53,7 @@ $check_vendor_role
                                 <tr>
                                     <th>Order Number</th>
                                     <th>Submitted Date</th>
-                                    <th>Items</th>
+                                    <th>Order Details</th>
                                     <th>Status</th>
                                     <th>Send Order to</th>
                                     <th>Comments from Vendor</th>

From f90e2d6d8d89917891e44846a13d970ea1560639 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sun, 11 Dec 2022 22:23:51 +0000
Subject: [PATCH 09/33] modified order details format

---
 lib/CXGN/Stock/Order.pm          | 45 ++++++++--------
 lib/SGN/Controller/AJAX/Order.pm | 89 +++++++++++++++++++++++++++-----
 mason/order/stocks.mas           |  6 +--
 3 files changed, 101 insertions(+), 39 deletions(-)

diff --git a/lib/CXGN/Stock/Order.pm b/lib/CXGN/Stock/Order.pm
index 1b3630b090..ba43715105 100644
--- a/lib/CXGN/Stock/Order.pm
+++ b/lib/CXGN/Stock/Order.pm
@@ -157,38 +157,39 @@ sub get_orders_to_person_id {
         my $order_from_name=$person->get_first_name()." ".$person->get_last_name();
 
         my $orderprop_rs = $people_schema->resultset('SpOrderprop')->search( { sp_order_id => $order_id } );
+        my $all_items = ();
         while (my $item_result = $orderprop_rs->next()){
             my @list;
             my $item_json = $item_result->value();
             my $item_hash = JSON::Any->jsonToObj($item_json);
-            my $all_items = $item_hash->{'clone_list'};
-            foreach my $each_item (@$all_items) {
-                my $item_name = (keys %$each_item)[0];
-                my $quantity = $each_item->{$item_name}->{'quantity'};
-                my $comments = $each_item->{$item_name}->{'comments'};
-                my $additional_info = $each_item->{$item_name}->{'additional_info'};
-
-                my $each_item_details;
-                if ($additional_info && $comments) {
-                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info. "," . " " . "comments:" . $comments;
-                } elsif ($additional_info && (!$comments)){
-                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info;
-                } elsif ((!$additional_info) && $comments) {
-                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . "," . " "."comments:" . $comments;
-                } else {
-                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity;
-                }
-                push @list, $each_item_details;
-            }
-            my @sort_list = sort @list;
-            $item_list = join("<br>", @sort_list);
+            $all_items = $item_hash->{'clone_list'};
+#            foreach my $each_item (@$all_items) {
+#                my $item_name = (keys %$each_item)[0];
+#                my $quantity = $each_item->{$item_name}->{'quantity'};
+#                my $comments = $each_item->{$item_name}->{'comments'};
+#                my $additional_info = $each_item->{$item_name}->{'additional_info'};
+#
+#                my $each_item_details;
+#                if ($additional_info && $comments) {
+#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info. "," . " " . "comments:" . $comments;
+#                } elsif ($additional_info && (!$comments)){
+#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info;
+#                } elsif ((!$additional_info) && $comments) {
+#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . "," . " "."comments:" . $comments;
+#                } else {
+#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity;
+#                }
+#                push @list, $each_item_details;
+#            }
+#            my @sort_list = sort @list;
+#            $item_list = join("<br>", @sort_list);
         }
 
         push @orders, {
             order_id => $order_id,
             order_from_name => $order_from_name,
             create_date => $create_date,
-            item_list => $item_list,
+            clone_list => $all_items,
             order_status => $order_status,
             completion_date => $completion_date,
             contact_person_comments => $comments
diff --git a/lib/SGN/Controller/AJAX/Order.pm b/lib/SGN/Controller/AJAX/Order.pm
index 20114e3594..5fde98ce5f 100644
--- a/lib/SGN/Controller/AJAX/Order.pm
+++ b/lib/SGN/Controller/AJAX/Order.pm
@@ -366,11 +366,10 @@ sub get_user_current_orders :Path('/ajax/order/current') Args(0) {
     my $schema = $c->dbic_schema("Bio::Chado::Schema");
     my $people_schema = $c->dbic_schema('CXGN::People::Schema');
     my $dbh = $c->dbc->dbh;
-    my $user_id;
     my $ordering_site = $c->config->{ordering_site};
     my $order_properties = $c->config->{order_properties};
     my @properties = split ',',$order_properties;
-
+    my $user_id;
 
     if (!$c->user){
         $c->stash->{rest} = {error=>'You must be logged in to view your current orders!'};
@@ -394,7 +393,7 @@ sub get_user_current_orders :Path('/ajax/order/current') Args(0) {
             foreach my $each_item (@$clone_list) {
                 my @request_details = ();
                 $item_name = (keys %$each_item)[0];
-                push @request_details, "Item Name". ":"."".$item_name;
+                push @request_details, "<b>"."Item Name"."<b>". ":"."".$item_name;
                 foreach my $field (@properties) {
                     my $each_detail = $each_item->{$item_name}->{$field};
                     my $detail_string = $field. ":"."".$each_detail;
@@ -441,6 +440,9 @@ sub get_user_completed_orders :Path('/ajax/order/completed') Args(0) {
     my $schema = $c->dbic_schema("Bio::Chado::Schema");
     my $people_schema = $c->dbic_schema('CXGN::People::Schema');
     my $dbh = $c->dbc->dbh;
+    my $ordering_site = $c->config->{ordering_site};
+    my $order_properties = $c->config->{order_properties};
+    my @properties = split ',',$order_properties;
     my $user_id;
 
     if (!$c->user){
@@ -456,12 +458,34 @@ sub get_user_completed_orders :Path('/ajax/order/completed') Args(0) {
     my $all_orders_ref = $orders->get_orders_from_person_id();
     my @completed_orders;
     my @all_orders = @$all_orders_ref;
+
     foreach my $order (@all_orders) {
-        if (($order->[3]) eq 'completed') {
-            push @completed_orders, [qq{<a href="/order/details/view/$order->[0]">$order->[0]</a>}, $order->[1], $order->[2], $order->[3], $order->[4], $order->[5], $order->[6]]
+        if (($order->{'order_status'}) eq 'completed') {
+            my $clone_list = $order->{'clone_list'};
+            my $item_name;
+            my $all_details_string;
+            foreach my $each_item (@$clone_list) {
+                my @request_details = ();
+                $item_name = (keys %$each_item)[0];
+                push @request_details, "<b>"."Item Name"."<b>". ":"."".$item_name;
+                foreach my $field (@properties) {
+                    my $each_detail = $each_item->{$item_name}->{$field};
+                    my $detail_string = $field. ":"."".$each_detail;
+                    push @request_details, $detail_string;
+                }
+                $all_details_string = join("<br>", @request_details);
+            }
+            push @completed_orders, [qq{<a href="/order/details/view/$order->{'order_id'}">$order->{'order_id'}</a>}, $order->{'create_date'}, $all_details_string, $order->{'order_status'}, $order->{'completion_date'}, $order->{'order_to_name'}, $order->{'comments'}]
         }
     }
 
+
+#    foreach my $order (@all_orders) {
+#        if (($order->[3]) eq 'completed') {
+#            push @completed_orders, [qq{<a href="/order/details/view/$order->[0]">$order->[0]</a>}, $order->[1], $order->[2], $order->[3], $order->[4], $order->[5], $order->[6]]
+#        }
+#    }
+
     $c->stash->{rest} = {data => \@completed_orders};
 
 }
@@ -473,6 +497,9 @@ sub get_vendor_current_orders :Path('/ajax/order/vendor_current_orders') Args(0)
     my $schema = $c->dbic_schema("Bio::Chado::Schema");
     my $people_schema = $c->dbic_schema('CXGN::People::Schema');
     my $dbh = $c->dbc->dbh;
+    my $ordering_site = $c->config->{ordering_site};
+    my $order_properties = $c->config->{order_properties};
+    my @properties = split ',',$order_properties;
     my $user_id;
 
     if (!$c->user){
@@ -491,6 +518,21 @@ sub get_vendor_current_orders :Path('/ajax/order/vendor_current_orders') Args(0)
     my @all_vendor_orders = @$vendor_orders_ref;
         foreach my $vendor_order (@all_vendor_orders) {
             if (($vendor_order->{'order_status'}) ne 'completed') {
+                my $clone_list = $vendor_order->{'clone_list'};
+                my $item_name;
+                my $all_details_string;
+                foreach my $each_item (@$clone_list) {
+                    my @request_details = ();
+                    $item_name = (keys %$each_item)[0];
+                    push @request_details, "<b>"."Item Name"."<b>". ":"."".$item_name;
+                    foreach my $field (@properties) {
+                        my $each_detail = $each_item->{$item_name}->{$field};
+                        my $detail_string = $field. ":"."".$each_detail;
+                        push @request_details, $detail_string;
+                    }
+                    $all_details_string = join("<br>", @request_details);
+                }
+                $vendor_order->{'order_details'} = $all_details_string;
                 push @vendor_current_orders, $vendor_order
             }
         }
@@ -506,6 +548,9 @@ sub get_vendor_completed_orders :Path('/ajax/order/vendor_completed_orders') Arg
     my $schema = $c->dbic_schema("Bio::Chado::Schema");
     my $people_schema = $c->dbic_schema('CXGN::People::Schema');
     my $dbh = $c->dbc->dbh;
+    my $ordering_site = $c->config->{ordering_site};
+    my $order_properties = $c->config->{order_properties};
+    my @properties = split ',',$order_properties;
     my $user_id;
 
     if (!$c->user){
@@ -524,6 +569,22 @@ sub get_vendor_completed_orders :Path('/ajax/order/vendor_completed_orders') Arg
     my @all_vendor_orders = @$vendor_orders_ref;
     foreach my $vendor_order (@all_vendor_orders) {
         if (($vendor_order->{'order_status'}) eq 'completed') {
+            my $clone_list = $vendor_order->{'clone_list'};
+            my $item_name;
+            my $all_details_string;
+            foreach my $each_item (@$clone_list) {
+                my @request_details = ();
+                $item_name = (keys %$each_item)[0];
+                push @request_details, "<b>"."Item Name"."<b>". ":"."".$item_name;
+                foreach my $field (@properties) {
+                    my $each_detail = $each_item->{$item_name}->{$field};
+                    my $detail_string = $field. ":"."".$each_detail;
+                    push @request_details, $detail_string;
+                }
+                $all_details_string = join("<br>", @request_details);
+            }
+            $vendor_order->{'order_details'} = $all_details_string;
+
             push @vendor_completed_orders, $vendor_order
         }
     }
@@ -619,15 +680,15 @@ sub single_step_submission_POST : Args(0) {
     my $additional_comments = $c->req->param('additional_comments');
     my %request_details;
     my @item_list;
-    $request_details{$item_name}{'quantity'} = $quantity;
-    $request_details{$item_name}{'facility'} = $facility;
-    $request_details{$item_name}{'scientist'} = $scientist;
-    $request_details{$item_name}{'due_date'} = $due_date;
-    $request_details{$item_name}{'experiment_name'} = $experiment_name;
-    $request_details{$item_name}{'experiment_type'} = $experiment_type;
-    $request_details{$item_name}{'risk_assessment'} = $risk_assessment;
-    $request_details{$item_name}{'containment_zone'} = $containment_zone;
-    $request_details{$item_name}{'additional_comments'} = $additional_comments;
+    $request_details{$item_name}{'Quantity'} = $quantity;
+    $request_details{$item_name}{'Facility'} = $facility;
+    $request_details{$item_name}{'Scientist'} = $scientist;
+    $request_details{$item_name}{'Required by Date'} = $due_date;
+    $request_details{$item_name}{'Experiment Name'} = $experiment_name;
+    $request_details{$item_name}{'Experiment Type'} = $experiment_type;
+    $request_details{$item_name}{'Risk Assessment'} = $risk_assessment;
+    $request_details{$item_name}{'Containment Zone'} = $containment_zone;
+    $request_details{$item_name}{'Additional Comments'} = $additional_comments;
 
     if (!$c->user()) {
         print STDERR "User not logged in... not adding a catalog item.\n";
diff --git a/mason/order/stocks.mas b/mason/order/stocks.mas
index 4c90446377..1a87d05a5f 100644
--- a/mason/order/stocks.mas
+++ b/mason/order/stocks.mas
@@ -76,7 +76,7 @@ $check_vendor_role
                                 <tr>
                                     <th>Order Number</th>
                                     <th>Submitted Date</th>
-                                    <th>Items</th>
+                                    <th>Order Details</th>
                                     <th>Status</th>
                                     <th>Completed Date</th>
                                     <th>Processed by</th>
@@ -156,7 +156,7 @@ $(window).ready( function() {
             { title: "Order Number", "data": null, "render": function ( data, type, row ) { return "<a href='/order/details/view/"+row.order_id+"'>"+row.order_id+"</a>"; } },
             { title: "Ordered by", "data": "order_from_name" },
             { title: "Submitted Date", "data": "create_date" },
-            { title: "Items", "data": "item_list" },
+            { title: "Order Details", "data": "order_details" },
             { title: "Status", "data": "order_status" },
             { title: "Comments", "data": "contact_person_comments" },
             { title: "Update", "data": "null", "render": function ( data, type, row ) { return "<a onclick='updateOrder(\""+row.order_id+"\", \""+row.order_from_name+"\")' >Update</a>"; } },
@@ -170,7 +170,7 @@ $(window).ready( function() {
             { title: "Order Number", "data": null, "render": function ( data, type, row ) { return "<a href='/order/details/view/"+row.order_id+"'>"+row.order_id+"</a>"; } },
             { title: "Ordered by", "data": "order_from_name" },
             { title: "Submitted Date", "data": "create_date" },
-            { title: "Items", "data": "item_list" },
+            { title: "Order Details", "data": "order_details" },
             { title: "Status", "data": "order_status" },
             { title: "Completion Date", "data": "completion_date" },
             { title: "Comments", "data": "contact_person_comments" },

From a00109103bf8d473105e1a133e7987f0797a60f5 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Mon, 12 Dec 2022 23:54:22 +0000
Subject: [PATCH 10/33]  dynamic dialog for order details input

---
 lib/SGN/Controller/AJAX/Order.pm |  4 +++
 lib/SGN/Controller/Catalog.pm    |  4 +++
 mason/order/catalog.mas          | 58 ++++++++++++++++----------------
 3 files changed, 37 insertions(+), 29 deletions(-)

diff --git a/lib/SGN/Controller/AJAX/Order.pm b/lib/SGN/Controller/AJAX/Order.pm
index 5fde98ce5f..02d77ae29f 100644
--- a/lib/SGN/Controller/AJAX/Order.pm
+++ b/lib/SGN/Controller/AJAX/Order.pm
@@ -669,6 +669,10 @@ sub single_step_submission_POST : Args(0) {
     my $timestamp = $time->ymd()."_".$time->hms();
     my $request_date = $time->ymd();
     my $item_name = $c->req->param('item_name');
+    my $order_details = $c->req->param('order_details');
+    print STDERR "ORDER DETAILS =".Dumper($order_details)."\n";
+    return;
+
     my $quantity = $c->req->param('quantity');
     my $facility = $c->req->param('facility');
     my $scientist = $c->req->param('scientist');
diff --git a/lib/SGN/Controller/Catalog.pm b/lib/SGN/Controller/Catalog.pm
index 6e00307e81..e806b41e0f 100644
--- a/lib/SGN/Controller/Catalog.pm
+++ b/lib/SGN/Controller/Catalog.pm
@@ -32,6 +32,10 @@ sub stock_catalog :Path('/catalog/view') :Args(0) {
     my $ordering_site = $c->config->{ordering_site};
     $c->stash->{ordering_site} = $ordering_site;
 
+    my $order_properties = $c->config->{order_properties};
+
+    $c->stash->{order_properties} = $order_properties;
+
     $c->stash->{template} = '/order/catalog.mas';
 
 }
diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index ad2fd59870..f28e461e8d 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -4,6 +4,7 @@ $check_vendor_role
 $ordering_service_name => undef
 $additional_order_info => undef
 $ordering_site => undef
+$order_properties => undef
 
 </%args>
 
@@ -149,6 +150,9 @@ jQuery(document).ready( function() {
     var ordering_service_name = "<% $ordering_service_name %>";
     var additional_order_info = "<% $additional_order_info %>";
     var ordering_site = "<% $ordering_site %>";
+    var order_properties = "<% $order_properties %>";
+    var property_keys = order_properties.split(",");
+
 
     if (ordering_site == 'BAT') {
         jQuery('#catalog_items_table').DataTable( {
@@ -163,7 +167,7 @@ jQuery(document).ready( function() {
                 { title: "Species", "data": "species" },
                 { title: "Variety", "data": "variety" },
                 { title: "Project", "data": "program" },
-                { title: " ", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_site+"\")'>Request</a>"; } },
+                { title: " ", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_site+"\", \""+order_properties+"\")'>Request</a>"; } },
             ],
         });
     } else {
@@ -291,16 +295,12 @@ jQuery(document).ready( function() {
     });
 
     jQuery('#single_step_submission_button').click(function(){
+        var order_details = {};
         var item_name = jQuery('#item_name').val();
-        var quantity = jQuery('#item_quantity').val();
-        var facility = jQuery('#item_facility').val();
-        var scientist = jQuery('#item_scientist').val();
-        var due_date = jQuery('#item_due_date').val();
-        var experiment_name = jQuery('#experiment_name').val();
-        var experiment_type = jQuery('#experiment_type').val();
-        var risk_assessment = jQuery('#risk_assessment').val();
-        var containment_zone = jQuery('#containment_zone').val();
-        var additional_comments = jQuery('#additonal_comments').val();
+        for(var i=0; i<property_keys.length; i++){
+            var each_value = jQuery('#'+ i +'').val();
+            order_details[property_keys[i]] = each_value;
+        }
 
         jQuery.ajax({
             url: '/ajax/order/single_step_submission',
@@ -308,15 +308,7 @@ jQuery(document).ready( function() {
             type: 'POST',
             data : {
                 'item_name' : item_name,
-                'quantity': quantity,
-                'facility': facility,
-                'scientist': scientist,
-                'due_date': due_date,
-                'experiment_name': experiment_name,
-                'experiment_type':experiment_type,
-                'risk_assessment': risk_assessment,
-                'containment_zone': containment_zone,
-                'additional_comments': additional_comments
+                'order_details': JSON.stringify(order_details),
             },
             beforeSend: function(response){
                 jQuery('#working_modal').modal('show');
@@ -343,21 +335,29 @@ jQuery(document).ready( function() {
 
 });
 
-function addToCart(item_name, additional_order_info, ordering_service_name, ordering_site ){
+function addToCart(item_name, additional_order_info, ordering_service_name, ordering_site, order_properties ){
     var additional_info = additional_order_info.split(",");
+    var properties = order_properties.split(",");
     var html = '';
 
     if (ordering_site == 'BAT') {
         html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="item_name" name="item_name" value="'+item_name+'" disabled></div><br><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div><br><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Facility: </label><div class="col-sm-9" ><input class="form-control" id="item_facility" name="item_facility" placeholder="Please Select"></div><br><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Scientist(s): </label><div class="col-sm-9" ><input class="form-control" id="item_scientist" name="item_scientist" placeholder=""></div><br><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Due/Requested by Date: </label><div class="col-sm-9" ><input class="form-control" id="item_due_date" name="item_due_date" placeholder=""></div><br><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Experiment Name: </label><div class="col-sm-9" ><input class="form-control" id="experiment_name" name="experiment_name" placeholder=""></div><br><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Experiment Type: </label><div class="col-sm-9" ><input class="form-control" id="experiment_type" name="experiment_type" placeholder="Please Select"></div><br><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Risk Assessment: </label><div class="col-sm-9" ><input class="form-control" id="risk_assessment" name="risk_assessment" placeholder=""></div><br><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Containment Zone: </label><div class="col-sm-9" ><input class="form-control" id="containment_zone" name="containment_zone" placeholder=""></div><br><br><br>';
-        html = html + '<label class="col-sm-3 control-label">Additional Comments: </label><div class="col-sm-9" ><input class="form-control" id="additional_comments" name="additional_comments" placeholder="eg: Clothing & Special Handling"></div></div></div></form>';
+//        html = html + '<label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div><br><br><br>';
+//        html = html + '<label class="col-sm-3 control-label">Facility: </label><div class="col-sm-9" ><input class="form-control" id="item_facility" name="item_facility" placeholder="Please Select"></div><br><br><br>';
+//        html = html + '<label class="col-sm-3 control-label">Scientist(s): </label><div class="col-sm-9" ><input class="form-control" id="item_scientist" name="item_scientist" placeholder=""></div><br><br><br>';
+//        html = html + '<label class="col-sm-3 control-label">Due/Requested by Date: </label><div class="col-sm-9" ><input class="form-control" id="item_due_date" name="item_due_date" placeholder=""></div><br><br><br>';
+//        html = html + '<label class="col-sm-3 control-label">Experiment Name: </label><div class="col-sm-9" ><input class="form-control" id="experiment_name" name="experiment_name" placeholder=""></div><br><br><br>';
+//        html = html + '<label class="col-sm-3 control-label">Experiment Type: </label><div class="col-sm-9" ><input class="form-control" id="experiment_type" name="experiment_type" placeholder="Please Select"></div><br><br><br>';
+//        html = html + '<label class="col-sm-3 control-label">Risk Assessment: </label><div class="col-sm-9" ><input class="form-control" id="risk_assessment" name="risk_assessment" placeholder=""></div><br><br><br>';
+//        html = html + '<label class="col-sm-3 control-label">Containment Zone: </label><div class="col-sm-9" ><input class="form-control" id="containment_zone" name="containment_zone" placeholder=""></div><br><br><br>';
+//        html = html + '<label class="col-sm-3 control-label">Additional Comments: </label><div class="col-sm-9" ><input class="form-control" id="additional_comments" name="additional_comments" placeholder="eg: Clothing & Special Handling"></div>';
+
+        for(var i=0; i<properties.length; i++){
+            html = html + '<label class="col-sm-3 control-label">'+ properties[i] +'</label><div class="col-sm-9" ><input class="form-control" id= '+ i +' name= '+ i +' placeholder=""></div><br><br><br>';
+
+        }
+
+        html = html + '</div></div></form>';
     } else {
         html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="cart_item_name" name="cart_item_name" value="'+item_name+'" disabled></div></div>';
         html = html + '<div class="form-group"><label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div></div>';

From b7ed36a16c6ed2d7016a3298403d496958d2b917 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Tue, 13 Dec 2022 19:41:14 +0000
Subject: [PATCH 11/33] modified single step submission function

---
 lib/SGN/Controller/AJAX/Order.pm | 34 ++++++--------------------------
 1 file changed, 6 insertions(+), 28 deletions(-)

diff --git a/lib/SGN/Controller/AJAX/Order.pm b/lib/SGN/Controller/AJAX/Order.pm
index 02d77ae29f..8a2c86a6eb 100644
--- a/lib/SGN/Controller/AJAX/Order.pm
+++ b/lib/SGN/Controller/AJAX/Order.pm
@@ -669,31 +669,10 @@ sub single_step_submission_POST : Args(0) {
     my $timestamp = $time->ymd()."_".$time->hms();
     my $request_date = $time->ymd();
     my $item_name = $c->req->param('item_name');
-    my $order_details = $c->req->param('order_details');
-    print STDERR "ORDER DETAILS =".Dumper($order_details)."\n";
-    return;
-
-    my $quantity = $c->req->param('quantity');
-    my $facility = $c->req->param('facility');
-    my $scientist = $c->req->param('scientist');
-    my $due_date = $c->req->param('due_date');
-    my $experiment_name = $c->req->param('experiment_name');
-    my $experiment_type = $c->req->param('experiment_type');
-    my $risk_assessment = $c->req->param('risk_assessment');
-    my $containment_zone = $c->req->param('containment_zone');
-    my $additional_comments = $c->req->param('additional_comments');
-    my %request_details;
-    my @item_list;
-    $request_details{$item_name}{'Quantity'} = $quantity;
-    $request_details{$item_name}{'Facility'} = $facility;
-    $request_details{$item_name}{'Scientist'} = $scientist;
-    $request_details{$item_name}{'Required by Date'} = $due_date;
-    $request_details{$item_name}{'Experiment Name'} = $experiment_name;
-    $request_details{$item_name}{'Experiment Type'} = $experiment_type;
-    $request_details{$item_name}{'Risk Assessment'} = $risk_assessment;
-    $request_details{$item_name}{'Containment Zone'} = $containment_zone;
-    $request_details{$item_name}{'Additional Comments'} = $additional_comments;
+    my $order_details = decode_json ($c->req->param('order_details'));
+    my %details;
 
+    $details{$item_name} = $order_detail
     if (!$c->user()) {
         print STDERR "User not logged in... not adding a catalog item.\n";
         $c->stash->{rest} = {error_string => "You must be logged in to add a catalog item." };
@@ -711,9 +690,9 @@ sub single_step_submission_POST : Args(0) {
     my $item_info_hash = decode_json $item_info_string;
     my $contact_person_id = $item_info_hash->{'contact_person_id'};
     my $item_type = $item_info_hash->{'item_type'};
-    $request_details{$item_name}{'item_type'} = $item_type;
-    push @item_list, \%request_details;
-    print STDERR "REQUEST DETAILS =".Dumper(\%request_details)."\n";
+    $details{$item_name}{'item_type'} = $item_type;
+    push my @item_list, \%details;
+    print STDERR "REQUEST DETAILS =".Dumper(\%details)."\n";
     my @history = ();
     my $history_info = {};
 
@@ -765,7 +744,6 @@ END_HEREDOC
 
     $c->stash->{rest}->{success} .= 'Your request has been submitted successfully and the vendor has been notified.';
 
-
 }
 
 

From 187e4094f0e727ada837ee228a8fb1c8f6672391 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Wed, 14 Dec 2022 02:22:51 +0000
Subject: [PATCH 12/33] modified catalog fields

---
 lib/CXGN/Stock/Catalog.pm               |  31 +++---
 lib/SGN/Controller/AJAX/Catalog.pm      |  24 ++---
 lib/SGN/Controller/AJAX/Order.pm        |   2 +-
 lib/SGN/Controller/Catalog.pm           |   5 +-
 mason/order/add_catalog_item_dialog.mas | 122 ++++++++++--------------
 mason/order/catalog.mas                 |  73 ++++++--------
 6 files changed, 114 insertions(+), 143 deletions(-)

diff --git a/lib/CXGN/Stock/Catalog.pm b/lib/CXGN/Stock/Catalog.pm
index 098c8aa32d..620c7cf04c 100644
--- a/lib/CXGN/Stock/Catalog.pm
+++ b/lib/CXGN/Stock/Catalog.pm
@@ -6,32 +6,39 @@ use Data::Dumper;
 
 extends 'CXGN::JSONProp';
 
-# a general human readable description of the stock
-has 'description' => ( isa => 'Str', is => 'rw' );
-
 # a list of representative images, given as image_ids
 has 'images' => ( isa => 'Maybe[ArrayRef]', is => 'rw' );
 
-# availability status: in_stock, delayed, currently_unavailable ...
-has 'availability' => ( isa => 'Str', is => 'rw' );
-
 # list of hashrefs like { stock_center => { name => ..., count_available => ..., delivery_time => } }
 has 'order_source' => ( isa => 'ArrayRef', is => 'rw');
 
+# item type such as single accession or a set of 10 accessions
+has 'item_type' => ( isa => 'Str', is => 'rw');
+
+# material type such as seed or plant
+has 'material_type' => ( isa => 'Str', is => 'rw');
+
 # center that generates clones or seed
 has 'material_source' => ( isa => 'Str', is => 'rw');
 
-# item type such as single accession or a set of 10 accessions
-has 'item_type' => ( isa => 'Str', is => 'rw');
+has 'category' => ( isa => 'Str', is => 'rw' );
+
+has 'species' => ( isa => 'Str', is => 'rw' );
+
+has 'variety' => ( isa => 'Str', is => 'rw' );
 
-# the breeding program this clones originated from
 has 'breeding_program' => ( isa => 'Int', is => 'rw');
 
-#
-has 'category' => ( isa => 'Str', is => 'rw' );
+has 'additional_info' => ( isa => 'Str', is => 'rw' );
 
 has 'contact_person_id' => ( isa => 'Int', is => 'rw') ;
 
+# a general human readable description of the stock
+#has 'description' => ( isa => 'Str', is => 'rw' );
+
+# availability status: in_stock, delayed, currently_unavailable ...
+#has 'availability' => ( isa => 'Str', is => 'rw' );
+
 
 sub BUILD {
     my $self = shift;
@@ -42,7 +49,7 @@ sub BUILD {
     $self->prop_primary_key('stockprop_id');
     $self->prop_type('stock_catalog_json');
     $self->cv_name('stock_property');
-    $self->allowed_fields( [ qw | item_type category description material_source breeding_program availability contact_person_id images | ] );
+    $self->allowed_fields( [ qw | item_type species variety material_type material_source additional_info breeding_program contact_person_id images | ] );
     $self->parent_table('stock');
     $self->parent_primary_key('stock_id');
 
diff --git a/lib/SGN/Controller/AJAX/Catalog.pm b/lib/SGN/Controller/AJAX/Catalog.pm
index ea7268f17a..6fd2f560fa 100644
--- a/lib/SGN/Controller/AJAX/Catalog.pm
+++ b/lib/SGN/Controller/AJAX/Catalog.pm
@@ -25,18 +25,17 @@ sub add_catalog_item_POST : Args(0) {
     my $dbh = $c->dbc->dbh;
     my $ordering_site = $c->config->{ordering_site};
 
-    my $item_name = $c->req->param('item_name');
-    my $item_type = $c->req->param('item_type');
-    my $item_category = $c->req->param('item_category');
-    my $item_description = $c->req->param('item_description');
-    my $item_material_source = $c->req->param('item_material_source');
-    my $item_breeding_program_id = $c->req->param('item_breeding_program');
-    my $item_availability = $c->req->param('item_availability');
+    my $item_name = $c->req->param('name');
+    my $item_type = $c->req->param('type');
+    my $item_category = $c->req->param('category');
+    my $item_additional_info = $c->req->param('additional_info');
+    my $item_material_source = $c->req->param('material_source');
+    my $item_breeding_program_id = $c->req->param('breeding_program_id');
     my $contact_person = $c->req->param('contact_person');
     my $item_prop_id = $c->req->param('item_prop_id');
 
-    my $item_species = $c->req->param('item_species');
-    my $item_variety = $c->req->param('item_variety');
+    my $item_species = $c->req->param('species');
+    my $item_variety = $c->req->param('variety');
 
     my $item_stock_id;
     if (!$c->user()) {
@@ -90,10 +89,13 @@ sub add_catalog_item_POST : Args(0) {
 
         $stock_catalog->item_type($item_type);
         $stock_catalog->category($item_category);
-        $stock_catalog->description($item_description);
+#        $stock_catalog->description($item_description);
         $stock_catalog->material_source($item_material_source);
         $stock_catalog->breeding_program($item_breeding_program_id);
-        $stock_catalog->availability($item_availability);
+        $stock_catalog->species($item_species);
+        $stock_catalog->variety($item_variety);
+
+#        $stock_catalog->availability($item_availability);
         $stock_catalog->contact_person_id($sp_person_id);
 
         $stock_catalog->store();
diff --git a/lib/SGN/Controller/AJAX/Order.pm b/lib/SGN/Controller/AJAX/Order.pm
index 8a2c86a6eb..32b85d149c 100644
--- a/lib/SGN/Controller/AJAX/Order.pm
+++ b/lib/SGN/Controller/AJAX/Order.pm
@@ -672,7 +672,7 @@ sub single_step_submission_POST : Args(0) {
     my $order_details = decode_json ($c->req->param('order_details'));
     my %details;
 
-    $details{$item_name} = $order_detail
+    $details{$item_name} = $order_details;
     if (!$c->user()) {
         print STDERR "User not logged in... not adding a catalog item.\n";
         $c->stash->{rest} = {error_string => "You must be logged in to add a catalog item." };
diff --git a/lib/SGN/Controller/Catalog.pm b/lib/SGN/Controller/Catalog.pm
index e806b41e0f..71bc05f4a0 100644
--- a/lib/SGN/Controller/Catalog.pm
+++ b/lib/SGN/Controller/Catalog.pm
@@ -29,8 +29,9 @@ sub stock_catalog :Path('/catalog/view') :Args(0) {
     my $additional_order_info = $c->config->{additional_order_info};
     $c->stash->{additional_order_info} = $additional_order_info;
 
-    my $ordering_site = $c->config->{ordering_site};
-    $c->stash->{ordering_site} = $ordering_site;
+    my $ordering_type = $c->config->{ordering_type};
+    print STDERR "ORDERING TYPE =".Dumper($ordering_type)."\n";
+    $c->stash->{ordering_type} = $ordering_type;
 
     my $order_properties = $c->config->{order_properties};
 
diff --git a/mason/order/add_catalog_item_dialog.mas b/mason/order/add_catalog_item_dialog.mas
index 8625baad7a..4721909876 100644
--- a/mason/order/add_catalog_item_dialog.mas
+++ b/mason/order/add_catalog_item_dialog.mas
@@ -1,6 +1,6 @@
 <%args>
 $timestamp => localtime()
-$ordering_site => undef
+$ordering_type => undef
 </%args>
 
 <div class="modal fade" id="add_catalog_item_dialog" name="add_catalog_item_dialog" tabindex="-1" role="dialog" aria-labelledby="addCatalogItemDialog">
@@ -19,25 +19,24 @@ $ordering_site => undef
                                 <input class="form-control" id="item_name" placeholder="Item name must be in the database">
                             </div>
                         </div>
-% if ($ordering_site eq 'BAT') {
                         <div class="form-group">
                             <label class="col-sm-3 control-label">Item Type: </label>
                             <div class="col-sm-9">
                                 <select class="form-control" id="item_type">
                                     <option value="">Select an item type</option>
-                                    <option value="single item">single item</option>
-                                    <option value="set of items">batch</option>
+                                    <option value="single item">Single item</option>
+                                    <option value="set of items">Set of items</option>
                                 </select>
                             </div>
                         </div>
                         <div class="form-group">
-                            <label class="col-sm-3 control-label">Category: </label>
+                            <label class="col-sm-3 control-label">Material Type: </label>
                             <div class="col-sm-9">
-                                <select class="form-control" id="item_category">
-                                    <option value="">Select a category</option>
-                                    <option value="seed">seed</option>
-                                    <option value="plant">plant</option>
-                                    <option value="construct">construct</option>
+                                <select class="form-control" id="item_material_type">
+                                    <option value="">Select a material type</option>
+                                    <option value="Seed">Seed</option>
+                                    <option value="Plant">Plant</option>
+                                    <option value="Construct">Construct</option>
                                 </select>
                             </div>
                         </div>
@@ -63,45 +62,41 @@ $ordering_site => undef
                             </div>
                         </div>
                         <div class="form-group">
-                            <label class="col-sm-3 control-label">Project: </label>
-                            <div class="col-sm-9" >
-                                <div id="item_breeding_program_div"></div>
+                            <label class="col-sm-3 control-label">Category: </label>
+                            <div class="col-sm-9">
+                                <select class="form-control" id="item_category">
+                                    <option value="">Select a category</option>
+                                    <option value="Released Variety">Released Variety</option>
+                                    <option value="Pathogen Assay ">Pathogen Assay</option>
+                                    <option value="Control">Control</option>
+                                    <option value="Transgenic Line">Transgenic Line</option>
                             </div>
                         </div>
                         <div class="form-group">
-                            <label class="col-sm-3 control-label">Contact Person Username: </label>
+                            <label class="col-sm-3 control-label">Additional Info: </label>
                             <div class="col-sm-9" >
-                                <input class="form-control" id="contact_person_name" placeholder="Please provide contact person username">
+                                <input class="form-control" id="item_additional_info" placeholder="">
                             </div>
                         </div>
-%} else {
                         <div class="form-group">
-                            <label class="col-sm-3 control-label">Item Type: </label>
-                            <div class="col-sm-9">
-                                <select class="form-control" id="item_type">
-                                    <option value="">Select an item type</option>
-                                    <option value="single item">single item</option>
-                                    <option value="set of items">set of items</option>
-                                </select>
+                            <label class="col-sm-3 control-label">Material Source: </label>
+                            <div class="col-sm-9" >
+                                <input class="form-control" id="item_material_source" placeholder="">
                             </div>
                         </div>
                         <div class="form-group">
-                            <label class="col-sm-3 control-label">Category: </label>
-                            <div class="col-sm-9">
-                                <select class="form-control" id="item_category">
-                                    <option value="">Select a category</option>
-                                    <option value="released variety">released variety</option>
-                                    <option value="pathogen assay ">pathogen assay</option>
-                                    <option value="control">control</option>
-                                </select>
+                            <label class="col-sm-3 control-label">Program: </label>
+                            <div class="col-sm-9" >
+                                <div id="item_breeding_program_div"></div>
                             </div>
                         </div>
                         <div class="form-group">
-                            <label class="col-sm-3 control-label">Description: </label>
+                            <label class="col-sm-3 control-label">Contact Person Username: </label>
                             <div class="col-sm-9" >
-                                <input class="form-control" id="item_description" placeholder="">
+                                <input class="form-control" id="contact_person_name" placeholder="Please provide contact person username">
                             </div>
                         </div>
+<!--
                         <div class="form-group">
                             <label class="col-sm-3 control-label">Material Source: </label>
                             <div class="col-sm-9">
@@ -112,12 +107,7 @@ $ordering_site => undef
                                 </select>
                             </div>
                         </div>
-                        <div class="form-group">
-                            <label class="col-sm-3 control-label">Breeding Program: </label>
-                            <div class="col-sm-9" >
-                                <div id="item_breeding_program_div"></div>
-                            </div>
-                        </div>
+
                         <div class="form-group">
                             <label class="col-sm-3 control-label">Availability: </label>
                             <div class="col-sm-9">
@@ -129,13 +119,7 @@ $ordering_site => undef
                                 </select>
                             </div>
                         </div>
-                        <div class="form-group">
-                            <label class="col-sm-3 control-label">Contact Person Username: </label>
-                            <div class="col-sm-9" >
-                                <input class="form-control" id="contact_person_name" placeholder="Please provide contact person username">
-                            </div>
-                        </div>
-%}
+-->
                     </form>
                 </div>
             </div>
@@ -173,8 +157,6 @@ $ordering_site => undef
 <script>
 jQuery(document).ready(function(){
 
-    var ordering_site = "<% $ordering_site %>";
-
     jQuery("#add_catalog_item_button").click( function() {
 
         jQuery("#item_name").autocomplete({
@@ -188,43 +170,37 @@ jQuery(document).ready(function(){
     jQuery('#submit_catalog_item').click( function() {
         var name = jQuery('#item_name').val();
         var type = jQuery('#item_type').val();
+        var material_type = jQuery('#item_material_type').val();
+        var species = jQuery('#item_species').val();
+        var variety = jQuery('#item_variety').val();
         var category = jQuery('#item_category').val();
-        var description = jQuery('#item_description').val();
+        var additional_info = jQuery('#item_additional_info').val();
         var material_source = jQuery('#item_material_source').val();
         var breeding_program = jQuery('#item_breeding_program_id').val();
-        var availability = jQuery('#item_availability').val();
         var contact_person = jQuery('#contact_person_name').val();
 
-        var item_species = jQuery('#item_species').val();
-        var item_variety = jQuery('#item_variety').val();
-
-        if (ordering_site != 'BAT') {
-            if (name == '') { alert("Please provide a name") };
-            if (type == '') { alert("Please select a type") };
-            if (category == '') { alert("Please select a category") };
-            if (description == '') { alert("Please provide a description") };
-            if (material_source == '') { alert("Please select a material source") };
-            if (breeding_program == '') { alert("Please select a breeding program") };
-            if (availability == '') { alert("Please indicate availability") };
-            if (contact_person == '') { alert("Please indicate contact person") };
-        }
-
+        if (name == '') { alert("Please provide a name") };
+        if (type == '') { alert("Please select a type") };
+        if (material_type == '') { alert("Please select a material type") };
+        if (material_source == '') { alert("Please select a material source") };
+        if (breeding_program == '') { alert("Please select a program") };
+        if (contact_person == '') { alert("Please indicate contact person") };
 
         jQuery.ajax({
             url: '/ajax/catalog/add_item',
             dataType: "json",
             type: 'POST',
             data : {
-                'item_name' : name,
-                'item_type': type,
-                'item_category': category,
-                'item_description': description,
-                'item_material_source': material_source,
-                'item_breeding_program': breeding_program,
-                'item_availability': availability,
+                'name' : name,
+                'type': type,
+                'material_type': material_type,
+                'category': category,
+                'additional_info': additional_info,
+                'material_source': material_source,
+                'breeding_program_id': breeding_program,
                 'contact_person': contact_person,
-                'item_species': item_species,
-                'item_variety': item_variety
+                'species': species,
+                'variety': variety
             },
             beforeSend: function(response){
                 jQuery('#working_modal').modal('show');
diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index f28e461e8d..597d5827c9 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -3,7 +3,7 @@
 $check_vendor_role
 $ordering_service_name => undef
 $additional_order_info => undef
-$ordering_site => undef
+$ordering_type => undef
 $order_properties => undef
 
 </%args>
@@ -36,7 +36,7 @@ $order_properties => undef
                 </div>
             </div>
         </div>
-% if ($ordering_site ne 'BAT') {
+% if ($ordering_type ne 'single_step') {
         <div class="panel panel-default">
             <div class="panel-body">
                 <button id="your_cart_button" type="button" class="btn btn-primary btn-sm">
@@ -125,7 +125,7 @@ $order_properties => undef
                     </div>
                 </div>
             </div>
-% if ($ordering_site eq 'BAT') {
+% if ($ordering_type eq 'single_step') {
             <div class="modal-footer">
                 <button id="close_submit_item_detail_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
                 <button id="single_step_submission_button" type="button" class="btn btn-primary" >Submit</button>
@@ -140,8 +140,8 @@ $order_properties => undef
     </div>
 </div>
 
-<& /order/upload_catalog_items_dialog.mas, ordering_site => $ordering_site&>
-<& /order/add_catalog_item_dialog.mas, ordering_site => $ordering_site &>
+<& /order/upload_catalog_items_dialog.mas, ordering_type => $ordering_type&>
+<& /order/add_catalog_item_dialog.mas, ordering_type => $ordering_type &>
 
 <script>
 
@@ -149,45 +149,30 @@ jQuery(document).ready( function() {
 
     var ordering_service_name = "<% $ordering_service_name %>";
     var additional_order_info = "<% $additional_order_info %>";
-    var ordering_site = "<% $ordering_site %>";
+    var ordering_type = "<% $ordering_type %>";
     var order_properties = "<% $order_properties %>";
     var property_keys = order_properties.split(",");
-
-
-    if (ordering_site == 'BAT') {
-        jQuery('#catalog_items_table').DataTable( {
-            'autoWidth': false,
-            'order': false,
-            'search':'applied',
-            'ajax': '/ajax/catalog/items',
-            columns: [
-                { title: "Name", "data": null, "render": function ( data, type, row ) { return "<a href='/catalog/item_details/"+row.item_id+"'>"+row.item_name+"</a>"; } },
-                { title: "Type", "data": "item_type" },
-                { title: "Category", "data": "category" },
-                { title: "Species", "data": "species" },
-                { title: "Variety", "data": "variety" },
-                { title: "Project", "data": "program" },
-                { title: " ", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_site+"\", \""+order_properties+"\")'>Request</a>"; } },
-            ],
-        });
-    } else {
-        jQuery('#catalog_items_table').DataTable( {
-            'autoWidth': false,
-            'order': false,
-            'search':'applied',
-            'ajax': '/ajax/catalog/items',
-            columns: [
-                { title: "Name", "data": null, "render": function ( data, type, row ) { return "<a href='/catalog/item_details/"+row.item_id+"'>"+row.item_name+"</a>"; } },
-                { title: "Type", "data": "item_type" },
-                { title: "Category", "data": "category" },
-                { title: "Description", "data": "description" },
-                { title: "Material Source", "data": "material_source" },
-                { title: "Breeding Program", "data": "breeding_program" },
-                { title: "Availability", "data": "availability" },
-                { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\")'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
-            ],
-        });
-    }
+    alert(ordering_type);
+
+    jQuery('#catalog_items_table').DataTable( {
+        'autoWidth': false,
+        'order': false,
+        'search':'applied',
+        'ajax': '/ajax/catalog/items',
+        columns: [
+            { title: "Name", "data": null, "render": function ( data, type, row ) { return "<a href='/catalog/item_details/"+row.item_id+"'>"+row.item_name+"</a>"; } },
+            { title: "Type", "data": "item_type" },
+            { title: "Material Type", "data": "material_type" },
+            { title: "Species", "data": "species" },
+            { title: "Variety", "data": "variety" },
+            { title: "Category", "data": "category" },
+            { title: "Additional Info", "data": "additional_info" },
+            { title: "Material Source", "data": "material_source" },
+            { title: "Breeding Program", "data": "breeding_program" },
+//          { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties+"\" )'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
+            { title: " ", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties+"\")'>Request</a>"; } },
+        ],
+    });
 
     var lo = new CXGN.List();
     var list_id;
@@ -335,12 +320,12 @@ jQuery(document).ready( function() {
 
 });
 
-function addToCart(item_name, additional_order_info, ordering_service_name, ordering_site, order_properties ){
+function addToCart(item_name, additional_order_info, ordering_service_name, ordering_type, order_properties ){
     var additional_info = additional_order_info.split(",");
     var properties = order_properties.split(",");
     var html = '';
 
-    if (ordering_site == 'BAT') {
+    if (ordering_type == 'single_step') {
         html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="item_name" name="item_name" value="'+item_name+'" disabled></div><br><br><br>';
 //        html = html + '<label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div><br><br><br>';
 //        html = html + '<label class="col-sm-3 control-label">Facility: </label><div class="col-sm-9" ><input class="form-control" id="item_facility" name="item_facility" placeholder="Please Select"></div><br><br><br>';

From f2b66b61ac1e23de8417fe2322f660759f8bea77 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Wed, 14 Dec 2022 23:07:01 +0000
Subject: [PATCH 13/33] modified add catalog item

---
 lib/CXGN/Stock/Catalog.pm               |   2 +-
 lib/SGN/Controller/AJAX/Catalog.pm      | 149 ++++++++----------------
 mason/order/add_catalog_item_dialog.mas |  28 +----
 mason/order/catalog.mas                 |   5 +-
 4 files changed, 55 insertions(+), 129 deletions(-)

diff --git a/lib/CXGN/Stock/Catalog.pm b/lib/CXGN/Stock/Catalog.pm
index 620c7cf04c..23c89082fa 100644
--- a/lib/CXGN/Stock/Catalog.pm
+++ b/lib/CXGN/Stock/Catalog.pm
@@ -49,7 +49,7 @@ sub BUILD {
     $self->prop_primary_key('stockprop_id');
     $self->prop_type('stock_catalog_json');
     $self->cv_name('stock_property');
-    $self->allowed_fields( [ qw | item_type species variety material_type material_source additional_info breeding_program contact_person_id images | ] );
+    $self->allowed_fields( [ qw | item_type species variety material_type category material_source additional_info breeding_program contact_person_id images | ] );
     $self->parent_table('stock');
     $self->parent_primary_key('stock_id');
 
diff --git a/lib/SGN/Controller/AJAX/Catalog.pm b/lib/SGN/Controller/AJAX/Catalog.pm
index 6fd2f560fa..6b6fa2b7ed 100644
--- a/lib/SGN/Controller/AJAX/Catalog.pm
+++ b/lib/SGN/Controller/AJAX/Catalog.pm
@@ -27,6 +27,7 @@ sub add_catalog_item_POST : Args(0) {
 
     my $item_name = $c->req->param('name');
     my $item_type = $c->req->param('type');
+    my $item_material_type = $c->req->param('material_type');
     my $item_category = $c->req->param('category');
     my $item_additional_info = $c->req->param('additional_info');
     my $item_material_source = $c->req->param('material_source');
@@ -64,47 +65,32 @@ sub add_catalog_item_POST : Args(0) {
         return;
     }
 
+    my $stock_catalog = CXGN::Stock::Catalog->new({
+        bcs_schema => $schema,
+        parent_id => $item_stock_id,
+        prop_id => $item_prop_id
+    });
 
-    if ($ordering_site eq 'BAT') {
-        my %catalog_info_hash;
-        my $stock_catalog_json_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'stock_catalog_json', 'stock_property');
-        $catalog_info_hash{'ordering_site'} = $ordering_site;
-        $catalog_info_hash{'item_type'} = $item_type;
-        $catalog_info_hash{'category'} = $item_category;
-        $catalog_info_hash{'breeding_program'} = $item_breeding_program_id;
-        $catalog_info_hash{'species'} = $item_species;
-        $catalog_info_hash{'variety'} = $item_variety;
-        $catalog_info_hash{'contact_person_id'} = $sp_person_id;
+    $stock_catalog->item_type($item_type);
+    $stock_catalog->material_type($item_material_type);
+    $stock_catalog->material_source($item_material_source);
+    $stock_catalog->category($item_category);
+    $stock_catalog->species($item_species);
+    $stock_catalog->variety($item_variety);
+    $stock_catalog->breeding_program($item_breeding_program_id);
+    $stock_catalog->additional_info($item_additional_info);
+    $stock_catalog->contact_person_id($sp_person_id);
 
-        my $catalog_json_string = encode_json \%catalog_info_hash;
-        print STDERR "CATALOG JSON STRING =".Dumper($catalog_json_string)."\n";
-        $item_rs->create_stockprops({$stock_catalog_json_cvterm->name() => $catalog_json_string});
+#    $stock_catalog->description($item_description);
+#    $stock_catalog->availability($item_availability);
 
-    } else {
-        my $stock_catalog = CXGN::Stock::Catalog->new({
-            bcs_schema => $schema,
-            parent_id => $item_stock_id,
-            prop_id => $item_prop_id
-        });
-
-        $stock_catalog->item_type($item_type);
-        $stock_catalog->category($item_category);
-#        $stock_catalog->description($item_description);
-        $stock_catalog->material_source($item_material_source);
-        $stock_catalog->breeding_program($item_breeding_program_id);
-        $stock_catalog->species($item_species);
-        $stock_catalog->variety($item_variety);
-
-#        $stock_catalog->availability($item_availability);
-        $stock_catalog->contact_person_id($sp_person_id);
-
-        $stock_catalog->store();
-
-        if (!$stock_catalog->store()){
-            $c->stash->{rest} = {error_string => "Error saving catalog item",};
-            return;
-        }
+    $stock_catalog->store();
+
+    if (!$stock_catalog->store()){
+        $c->stash->{rest} = {error_string => "Error saving catalog item",};
+        return;
     }
+
     $c->stash->{rest} = {success => "1",};
 
 }
@@ -240,72 +226,35 @@ sub get_catalog :Path('/ajax/catalog/items') :Args(0) {
     my $self = shift;
     my $c = shift;
     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
-    my $ordering_site = $c->config->{ordering_site};
     my @catalog_items;
 
-    if ($ordering_site eq 'BAT') {
-        my $stock_catalog_json_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'stock_catalog_json', 'stock_property');
-
-        my $catalog_rs = $schema->resultset("Stock::Stockprop")->search({type_id => $stock_catalog_json_cvterm->cvterm_id() }, { order_by => {-asc => 'stock_id'} });
-        my @catalog_list;
-        while (my $r = $catalog_rs->next()){
-            my @each_row = ();
-            my $catalog_stock_id = $r->stock_id();
-            my $item_detail_json = $r->value();
-            my $detail_hash = decode_json $item_detail_json;
-            my $site_key = $detail_hash->{'ordering_site'};
-            if ($site_key eq 'BAT') {
-                my $item_type = $detail_hash->{'item_type'};
-                my $item_category = $detail_hash->{'category'};
-                my $species = $detail_hash->{'species'};
-                my $variety = $detail_hash->{'variety'};
-                my $program_id = $detail_hash->{'breeding_program'};
-
-                my $stock_rs = $schema->resultset("Stock::Stock")->find({stock_id => $catalog_stock_id });
-                my $item_name = $stock_rs->uniquename();
-
-                my $program_rs = $schema->resultset('Project::Project')->find({project_id => $program_id});
-                my $program_name = $program_rs->name();
-
-                push @catalog_items, {
-                    item_id => $catalog_stock_id,
-                    item_name => $item_name,
-                    item_type => $item_type,
-                    category => $item_category,
-                    species => $species,
-                    variety => $variety,
-                    program => $program_name,
-                };
-            }
-        }
-    } else {
-
-        my $catalog_obj = CXGN::Stock::Catalog->new({ bcs_schema => $schema});
-        my $catalog_ref = $catalog_obj->get_catalog_items();
+    my $catalog_obj = CXGN::Stock::Catalog->new({ bcs_schema => $schema});
+    my $catalog_ref = $catalog_obj->get_catalog_items();
 #    print STDERR "ITEM RESULTS =".Dumper($catalog_ref)."\n";
-        my @catalog_list = @$catalog_ref;
-        foreach my $catalog_item (@catalog_list) {
-            my @item_details = ();
-            @item_details = @$catalog_item;
-            my $item_id = shift @item_details;
-            my $stock_rs = $schema->resultset("Stock::Stock")->find({stock_id => $item_id });
-            my $item_name = $stock_rs->uniquename();
-
-            my $program_id = $item_details[4];
-            my $program_rs = $schema->resultset('Project::Project')->find({project_id => $program_id});
-            my $program_name = $program_rs->name();
-
-            push @catalog_items, {
-                item_id => $item_id,
-                item_name => $item_name,
-                item_type => $item_details[0],
-                category => $item_details[1],
-                description => $item_details[2],
-                material_source => $item_details[3],
-                breeding_program => $program_name,
-                availability => $item_details[5],
-            };
-        }
+    my @catalog_list = @$catalog_ref;
+    foreach my $catalog_item (@catalog_list) {
+        my @item_details = ();
+        @item_details = @$catalog_item;
+        my $item_id = shift @item_details;
+        my $stock_rs = $schema->resultset("Stock::Stock")->find({stock_id => $item_id });
+        my $item_name = $stock_rs->uniquename();
+
+        my $program_id = $item_details[7];
+        my $program_rs = $schema->resultset('Project::Project')->find({project_id => $program_id});
+        my $program_name = $program_rs->name();
+
+        push @catalog_items, {
+            item_id => $item_id,
+            item_name => $item_name,
+            item_type => $item_details[0],
+            species => $item_details[1],
+            variety => $item_details[2],
+            material_type => $item_details[3],
+            category => $item_details[4],
+            material_source => $item_details[5],
+            additional_info => $item_details[6],
+            breeding_program => $program_name,
+        };
     }
 
     $c->stash->{rest} = {data => \@catalog_items};
diff --git a/mason/order/add_catalog_item_dialog.mas b/mason/order/add_catalog_item_dialog.mas
index 4721909876..cfae5fb776 100644
--- a/mason/order/add_catalog_item_dialog.mas
+++ b/mason/order/add_catalog_item_dialog.mas
@@ -70,6 +70,7 @@ $ordering_type => undef
                                     <option value="Pathogen Assay ">Pathogen Assay</option>
                                     <option value="Control">Control</option>
                                     <option value="Transgenic Line">Transgenic Line</option>
+                                </select>
                             </div>
                         </div>
                         <div class="form-group">
@@ -96,30 +97,6 @@ $ordering_type => undef
                                 <input class="form-control" id="contact_person_name" placeholder="Please provide contact person username">
                             </div>
                         </div>
-<!--
-                        <div class="form-group">
-                            <label class="col-sm-3 control-label">Material Source: </label>
-                            <div class="col-sm-9">
-                                <select class="form-control" id="item_material_source">
-                                    <option value="">Select a material source</option>
-                                    <option value="OrderingSystemTest">OrderingSystemTest</option>
-                                    <option value="Sendusu">Sendusu</option>
-                                </select>
-                            </div>
-                        </div>
-
-                        <div class="form-group">
-                            <label class="col-sm-3 control-label">Availability: </label>
-                            <div class="col-sm-9">
-                                <select class="form-control" id="item_availability">
-                                    <option value="">Select availability</option>
-                                    <option value="in stock">in stock</option>
-                                    <option value="out of stock">out of stock</option>
-                                    <option value="available in 3 months">available in 3 months</option>
-                                </select>
-                            </div>
-                        </div>
--->
                     </form>
                 </div>
             </div>
@@ -182,7 +159,8 @@ jQuery(document).ready(function(){
         if (name == '') { alert("Please provide a name") };
         if (type == '') { alert("Please select a type") };
         if (material_type == '') { alert("Please select a material type") };
-        if (material_source == '') { alert("Please select a material source") };
+        if (species == '') { alert("Please select a species") };
+        if (category == '') { alert("Please select a category") };
         if (breeding_program == '') { alert("Please select a program") };
         if (contact_person == '') { alert("Please indicate contact person") };
 
diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index 597d5827c9..dfa6b56834 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -152,7 +152,6 @@ jQuery(document).ready( function() {
     var ordering_type = "<% $ordering_type %>";
     var order_properties = "<% $order_properties %>";
     var property_keys = order_properties.split(",");
-    alert(ordering_type);
 
     jQuery('#catalog_items_table').DataTable( {
         'autoWidth': false,
@@ -168,9 +167,9 @@ jQuery(document).ready( function() {
             { title: "Category", "data": "category" },
             { title: "Additional Info", "data": "additional_info" },
             { title: "Material Source", "data": "material_source" },
-            { title: "Breeding Program", "data": "breeding_program" },
-//          { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties+"\" )'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
+            { title: "Program", "data": "breeding_program" },
             { title: " ", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties+"\")'>Request</a>"; } },
+//            { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties+"\" )'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
         ],
     });
 

From 9e0c59528a37a520bf63611288d7d625fca672e3 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Thu, 15 Dec 2022 22:15:57 +0000
Subject: [PATCH 14/33] catalog item details page

---
 lib/SGN/Controller/Catalog.pm               | 24 +++++----
 mason/order/catalog_item_details.mas        | 16 +++---
 mason/order/edit_catalog_details_dialog.mas | 55 +++++----------------
 3 files changed, 36 insertions(+), 59 deletions(-)

diff --git a/lib/SGN/Controller/Catalog.pm b/lib/SGN/Controller/Catalog.pm
index 71bc05f4a0..0db624f2b7 100644
--- a/lib/SGN/Controller/Catalog.pm
+++ b/lib/SGN/Controller/Catalog.pm
@@ -82,14 +82,17 @@ sub catalog_item_details : Path('/catalog/item_details') Args(1) {
     my $item_obj = CXGN::Stock::Catalog->new({ bcs_schema => $schema, parent_id => $item_id});
     my $details_ref = $item_obj->get_item_details();
     my @item_details = @$details_ref;
+    print STDERR "ITEM DETAILS =".Dumper(\@item_details)."\n";
     my $item_type = $item_details[0];
-    my $category = $item_details[1];
-    my $description = $item_details[2];
-    my $material_source = $item_details[3];
-    my $program_id = $item_details[4];
-    my $availability = $item_details[5];
-    my $contact_person_id = $item_details[6];
-    my $images = $item_details[7];
+    my $species = $item_details[1];
+    my $variety = $item_details[2];
+    my $material_type = $item_details[3];
+    my $category = $item_details[4];
+    my $material_source = $item_details[5];
+    my $additional_info = $item_details[6];
+    my $program_id = $item_details[7];
+    my $contact_person_id = $item_details[8];
+    my $images = $item_details[9];
     my $image_id = $images->[0];
     my $image_obj = SGN::Image->new($dbh, $image_id);
     my $medium_image  = $image_obj->get_image_url("medium");
@@ -103,14 +106,15 @@ sub catalog_item_details : Path('/catalog/item_details') Args(1) {
 #    print STDERR "CONTACT PERSON NAME=".Dumper($contact_person_username)."\n";
     $c->stash->{item_id} = $item_id;
     $c->stash->{item_name} = $item_name;
-    $c->stash->{species} = $species;
     $c->stash->{item_type} = $item_type;
+    $c->stash->{species} = $species;
+    $c->stash->{variety} = $variety;
+    $c->stash->{material_type} = $material_type;
     $c->stash->{category} = $category;
-    $c->stash->{description} = $description;
     $c->stash->{material_source} = $material_source;
+    $c->stash->{additional_info} = $additional_info;
     $c->stash->{program_id} = $program_id;
     $c->stash->{breeding_program} = $program_name;
-    $c->stash->{availability} = $availability;
     $c->stash->{contact_person_username} = $contact_person_username;
     $c->stash->{item_prop_id} = $item_prop_id;
     $c->stash->{image} = qq|<a href="$medium_image" class="stock_image_group" rel="gallery-figures"><img src="$medium_image"/></a> |,
diff --git a/mason/order/catalog_item_details.mas b/mason/order/catalog_item_details.mas
index c121804ccc..715288c4e0 100644
--- a/mason/order/catalog_item_details.mas
+++ b/mason/order/catalog_item_details.mas
@@ -2,17 +2,18 @@
 $item_id
 $item_name
 $species
+$variety
 $item_type
 $category
-$description
 $material_source
+$material_type
+$additional_info
 $breeding_program
 $program_id
-$availability
 $contact_person_username
 $item_prop_id
 $check_vendor_role
-$image
+$image => undef
 $selected_image_id => undef
 $main_page
 </%args>
@@ -29,13 +30,14 @@ $main_page
             <div class="row">
                 <div class="col-sm-6">
                     <table class="table table-bordered table-hover">
-                        <tr><td><b>Species</b></td><td><% $species %> </td></tr>
                         <tr><td><b>Item Type</b></td><td><% $item_type %> </td></tr>
+                        <tr><td><b>Species</b></td><td><% $species %> </td></tr>
+                        <tr><td><b>Variety</b></td><td><% $variety %> </td></tr>
+                        <tr><td><b>Material Type</b></td><td><% $material_type %> </td></tr>
                         <tr><td><b>Category</b></td><td><% $category %></td></tr>
-                        <tr><td><b>Description</b></td><td><% $description %></td></tr>
+                        <tr><td><b>Additional Info</b></td><td><% $additional_info %></td></tr>
                         <tr><td><b>Material Source</b><td><% $material_source %></td></tr>
                         <tr><td><b>Breeding Program</b></td><td><% $breeding_program %></td></tr>
-                        <tr><td><b>Availability</b></td><td><% $availability %></td></tr>
                         <tr><td><b>Contact Person Username</b></td><td><% $contact_person_username %></td></tr>
                         <tr><td><b>Main Detail Page</b></td><td><% $main_page %></td></tr>
                     </table>
@@ -143,7 +145,7 @@ $main_page
     </div>
 </div>
 
-<& /order/edit_catalog_details_dialog.mas, item_name => $item_name, item_id => $item_id, species => $species, item_type => $item_type, category => $category, description => $description, material_source => $material_source, breeding_program => $breeding_program, program_id => $program_id, availability => $availability, contact_person_username => $contact_person_username, item_prop_id => $item_prop_id  &>
+<& /order/edit_catalog_details_dialog.mas, item_name => $item_name, item_id => $item_id, species => $species, variety => $variety, item_type => $item_type, category => $category, material_type => $material_type, material_source => $material_source, breeding_program => $breeding_program, program_id => $program_id, additional_info => $additional_info, contact_person_username => $contact_person_username, item_prop_id => $item_prop_id  &>
 
 
 <script>
diff --git a/mason/order/edit_catalog_details_dialog.mas b/mason/order/edit_catalog_details_dialog.mas
index 744d1d1a0e..103f7ee102 100644
--- a/mason/order/edit_catalog_details_dialog.mas
+++ b/mason/order/edit_catalog_details_dialog.mas
@@ -2,13 +2,14 @@
 $item_id
 $item_name
 $species
+$variety
+$material_type
 $item_type
 $category
-$description
+$additional_info
 $material_source
 $breeding_program
 $program_id
-$availability
 $contact_person_username
 $item_prop_id
 </%args>
@@ -31,14 +32,6 @@ $item_prop_id
                                 </div>
                             </div>
                         </div>
-                        <div class="form-group">
-                            <label class="col-sm-3 control-label" for="edit_item_species">Species: </label>
-                            <div class="col-sm-8">
-                                <div class="input-group">
-                                    <input class="form-control col-sm-8" id="edit_item_species" type="text" value="<%$species%>" disabled/>
-                                </div>
-                            </div>
-                        </div>
                         <div class="form-group">
                             <label class="col-sm-3 control-label" for="edit_item_type">Item Type: </label>
                             <div class="col-sm-8">
@@ -55,29 +48,27 @@ $item_prop_id
                             <div class="col-sm-8">
                                 <div class="input-group">
                                     <select class="form-control" id="edit_item_category" value="<%$category%>">
-                                        <option value="released variety">released variety</option>
-                                        <option value="pathogen assay ">pathogen assay</option>
-                                        <option value="control">control</option>
+                                        <option value="Released Variety">Released Variety</option>
+                                        <option value="Pathogen Assay ">Pathogen Assay</option>
+                                        <option value="Control">Control</option>
+                                        <option value="Transgenic Line">Transgenic Line</option>
                                     </select>
                                 </div>
                             </div>
                         </div>
                         <div class="form-group">
-                            <label class="col-sm-3 control-label" for="edit_item_description">Description: </label>
+                            <label class="col-sm-3 control-label" for="edit_item_material_source">Material Source: </label>
                             <div class="col-sm-8">
                                 <div class="input-group">
-                                    <textarea class="form-control" id="edit_item_description" rows="3" maxlength="250"><% $description %></textarea>
+                                    <textarea class="form-control" id="edit_item_material_source" <input class="form-control" placeholder="">
                                 </div>
                             </div>
                         </div>
                         <div class="form-group">
-                            <label class="col-sm-3 control-label" for="edit_item_material_source">Material Source: </label>
+                            <label class="col-sm-3 control-label" for="edit_item_additional_info">Additional Info: </label>
                             <div class="col-sm-8">
                                 <div class="input-group">
-                                    <select class="form-control" id="edit_item_material_source" value="<%$material_source%>">
-                                        <option value="OrderingSystemTest">OrderingSystemTest</option>
-                                        <option value="Sendusu">Sendusu</option>
-                                    </select>
+                                    <textarea class="form-control" id="edit_item_additional_info" <input class="form-control" placeholder="">
                                 </div>
                             </div>
                         </div>
@@ -89,18 +80,6 @@ $item_prop_id
                                 </div>
                             </div>
                         </div>
-                        <div class="form-group">
-                            <label class="col-sm-3 control-label" for="edit_item_availability">Availability: </label>
-                            <div class="col-sm-8">
-                                <div class="input-group">
-                                    <select class="form-control" id="edit_item_availability" value="<%$availability%>">
-                                        <option value="in stock">in stock</option>
-                                        <option value="out of stock">out of stock</option>
-                                        <option value="available in 3 months">available in 3 months</option>
-                                    </select>
-                                </div>
-                            </div>
-                        </div>
                         <div class="form-group">
                             <label class="col-sm-3 control-label" for="edit_contact_person">Contact Person Username: </label>
                             <div class="col-sm-8">
@@ -163,22 +142,15 @@ jQuery(document).ready( function() {
         var default_category = document.getElementById("edit_item_category").getAttribute("value");
         jQuery('#edit_item_category option[value="'+default_category+'"]').prop("selected", true);
 
-        var default_source = document.getElementById("edit_item_material_source").getAttribute("value");
-        jQuery('#edit_item_material_source option[value="'+default_source+'"]').prop("selected", true);
-
-        var default_availability = document.getElementById("edit_item_availability").getAttribute("value");
-        jQuery('#edit_item_availability option[value="'+default_availability+'"]').prop("selected", true);
-
     });
 
     jQuery('#save_item_details').click( function() {
         var name = jQuery('#edit_item_name').val();
         var type = jQuery('#edit_item_type').val();
         var category = jQuery('#edit_item_category').val();
-        var description = jQuery('#edit_item_description').val();
+        var additional_info = jQuery('#edit_item_additional_info').val();
         var material_source = jQuery('#edit_item_material_source').val();
         var breeding_program = jQuery('#edit_item_breeding_program').val();
-        var availability = jQuery('#edit_item_availability').val();
         var contact_person = jQuery('#edit_contact_person').val();
         jQuery.ajax({
             url: '/ajax/catalog/add_item',
@@ -188,10 +160,9 @@ jQuery(document).ready( function() {
                 'item_name': name,
                 'item_type': type,
                 'item_category': category,
-                'item_description': description,
+                'item_additional_info': additional_info,
                 'item_material_source': material_source,
                 'item_breeding_program': breeding_program,
-                'item_availability': availability,
                 'contact_person': contact_person,
                 'item_prop_id': item_prop_id
             },

From 1fe943b8fb1817d8165316a6dd6ba971a075fa1f Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Fri, 16 Dec 2022 16:47:28 +0000
Subject: [PATCH 15/33] fixed edit catalog item

---
 mason/order/edit_catalog_details_dialog.mas | 58 +++++++++++++++++----
 1 file changed, 48 insertions(+), 10 deletions(-)

diff --git a/mason/order/edit_catalog_details_dialog.mas b/mason/order/edit_catalog_details_dialog.mas
index 103f7ee102..ee9d0f8f37 100644
--- a/mason/order/edit_catalog_details_dialog.mas
+++ b/mason/order/edit_catalog_details_dialog.mas
@@ -43,6 +43,34 @@ $item_prop_id
                                 </div>
                             </div>
                         </div>
+                        <div class="form-group">
+                            <label class="col-sm-3 control-label" for="edit_item_species">Species: </label>
+                            <div class="col-sm-8">
+                                <div class="input-group">
+                                    <input class="form-control col-sm-8" id="edit_item_species" type="text" value="<%$species%>" disabled/>
+                                </div>
+                            </div>
+                        </div>
+                        <div class="form-group">
+                            <label class="col-sm-3 control-label" for="edit_item_variety">Variety: </label>
+                            <div class="col-sm-8">
+                                <div class="input-group">
+                                    <input class="form-control col-sm-8" id="edit_item_variety" type="text" value="<%$variety%>" disabled/>
+                                </div>
+                            </div>
+                        </div>
+                        <div class="form-group">
+                            <label class="col-sm-3 control-label" for="edit_material_type">Material Type: </label>
+                            <div class="col-sm-8">
+                                <div class="input-group">
+                                    <select class="form-control" id="edit_material_type" value="<%$material_type%>">
+                                        <option value="Plant">Plant</option>
+                                        <option value="Seed">Seed</option>
+                                        <option value="Construct">Construct</option>
+                                    </select>
+                                </div>
+                            </div>
+                        </div>
                         <div class="form-group">
                             <label class="col-sm-3 control-label" for="edit_item_category">Item Category: </label>
                             <div class="col-sm-8">
@@ -60,7 +88,7 @@ $item_prop_id
                             <label class="col-sm-3 control-label" for="edit_item_material_source">Material Source: </label>
                             <div class="col-sm-8">
                                 <div class="input-group">
-                                    <textarea class="form-control" id="edit_item_material_source" <input class="form-control" placeholder="">
+                                    <input class="form-control col-sm-8" id="edit_item_material_source" type="text" value="<%$material_source%>" />
                                 </div>
                             </div>
                         </div>
@@ -68,7 +96,7 @@ $item_prop_id
                             <label class="col-sm-3 control-label" for="edit_item_additional_info">Additional Info: </label>
                             <div class="col-sm-8">
                                 <div class="input-group">
-                                    <textarea class="form-control" id="edit_item_additional_info" <input class="form-control" placeholder="">
+                                    <input class="form-control col-sm-8" id="edit_item_additional_info" type="text" value="<%$additional_info%>" />
                                 </div>
                             </div>
                         </div>
@@ -142,11 +170,18 @@ jQuery(document).ready( function() {
         var default_category = document.getElementById("edit_item_category").getAttribute("value");
         jQuery('#edit_item_category option[value="'+default_category+'"]').prop("selected", true);
 
+        var default_material_type = document.getElementById("edit_material_type").getAttribute("value");
+        jQuery('#edit_material_type option[value="'+default_material_type+'"]').prop("selected", true);
+
+
     });
 
     jQuery('#save_item_details').click( function() {
-        var name = jQuery('#edit_item_name').val();
-        var type = jQuery('#edit_item_type').val();
+        var item_name = jQuery('#edit_item_name').val();
+        var item_type = jQuery('#edit_item_type').val();
+        var species = jQuery('#edit_item_species').val();
+        var variety = jQuery('#edit_item_variety').val();
+        var material_type = jQuery('#edit_material_type').val();
         var category = jQuery('#edit_item_category').val();
         var additional_info = jQuery('#edit_item_additional_info').val();
         var material_source = jQuery('#edit_item_material_source').val();
@@ -157,12 +192,15 @@ jQuery(document).ready( function() {
             dataType: "json",
             type: 'POST',
             data : {
-                'item_name': name,
-                'item_type': type,
-                'item_category': category,
-                'item_additional_info': additional_info,
-                'item_material_source': material_source,
-                'item_breeding_program': breeding_program,
+                'name': item_name,
+                'type': item_type,
+                'species': species,
+                'variety': variety,
+                'material_type': material_type,
+                'category': category,
+                'additional_info': additional_info,
+                'material_source': material_source,
+                'breeding_program_id': breeding_program,
                 'contact_person': contact_person,
                 'item_prop_id': item_prop_id
             },

From 6409fcd6e7f380ddb51d42c8b207514c2bcaafbd Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Fri, 16 Dec 2022 21:57:07 +0000
Subject: [PATCH 16/33] modified order details page

---
 lib/CXGN/Stock/Order.pm     | 47 ++++++++++++++++++++-----------------
 lib/SGN/Controller/Order.pm | 23 +++++++++++++++---
 2 files changed, 45 insertions(+), 25 deletions(-)

diff --git a/lib/CXGN/Stock/Order.pm b/lib/CXGN/Stock/Order.pm
index ba43715105..bb3884f869 100644
--- a/lib/CXGN/Stock/Order.pm
+++ b/lib/CXGN/Stock/Order.pm
@@ -226,29 +226,32 @@ sub get_order_details {
     my $item_json = $orderprop_rs->value();
     my $item_hash = JSON::Any->jsonToObj($item_json);
     my $all_items = $item_hash->{'clone_list'};
-    my @list;
-    foreach my $each_item (@$all_items) {
-        my $item_name = (keys %$each_item)[0];
-        my $quantity = $each_item->{$item_name}->{'quantity'};
-        my $comments = $each_item->{$item_name}->{'comments'};
-        my $additional_info = $each_item->{$item_name}->{'additional_info'};
-
-        my $each_item_details;
-        if ($additional_info && $comments) {
-            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info. "," . " " . "comments:" . $comments;
-        } elsif ($additional_info && (!$comments)){
-            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info;
-        } elsif ((!$additional_info) && $comments) {
-            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . "," . " "."comments:" . $comments;
-        } else {
-            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity;
-        }
-        push @list, $each_item_details;
-    }
-    my @sort_list = sort @list;
-    my $item_list = join("<br>", @sort_list);
 
-    push @order_details, $order_id, $order_from_name, $create_date, $item_list, $order_to_name, $order_status, $comments;
+
+
+#    my @list;
+#    foreach my $each_item (@$all_items) {
+#        my $item_name = (keys %$each_item)[0];
+#        my $quantity = $each_item->{$item_name}->{'quantity'};
+#        my $comments = $each_item->{$item_name}->{'comments'};
+#        my $additional_info = $each_item->{$item_name}->{'additional_info'};
+
+#        my $each_item_details;
+#        if ($additional_info && $comments) {
+#            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info. "," . " " . "comments:" . $comments;
+#        } elsif ($additional_info && (!$comments)){
+#            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info;
+#        } elsif ((!$additional_info) && $comments) {
+#            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . "," . " "."comments:" . $comments;
+#        } else {
+#            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity;
+#        }
+#        push @list, $each_item_details;
+#    }
+#    my @sort_list = sort @list;
+#    my $item_list = join("<br>", @sort_list);
+
+    push @order_details, $order_id, $order_from_name, $create_date, $all_items, $order_to_name, $order_status, $comments;
 #    print STDERR "DETAILS =".Dumper(\@order_details)."\n";
 
     return \@order_details;
diff --git a/lib/SGN/Controller/Order.pm b/lib/SGN/Controller/Order.pm
index 0088665ad5..56185aa419 100644
--- a/lib/SGN/Controller/Order.pm
+++ b/lib/SGN/Controller/Order.pm
@@ -34,6 +34,8 @@ sub order_details :Path('/order/details/view') : Args(1) {
     my $c = shift;
     my $people_schema = $c->dbic_schema('CXGN::People::Schema');
     my $dbh = $c->dbc->dbh;
+    my $order_properties = $c->config->{order_properties};
+    my @properties = split ',',$order_properties;
 
     if (! $c->user()) {
 	$c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
@@ -46,13 +48,28 @@ sub order_details :Path('/order/details/view') : Args(1) {
     }
 
     my $order_number = shift;
-    my $order_rs = CXGN::Stock::Order->new({ dbh => $dbh, people_schema => $people_schema, sp_order_id => $order_number});
-    my $order_result = $order_rs->get_order_details();
+    my $order_obj = CXGN::Stock::Order->new({ dbh => $dbh, people_schema => $people_schema, sp_order_id => $order_number});
+    my $order_result = $order_obj->get_order_details();
+
+    my $all_items = $order_result->[3];
+    my $item_name;
+    my $all_details_string;
+    foreach my $each_item (@$all_items) {
+        my @item_details = ();
+        $item_name = (keys %$each_item)[0];
+        push @item_details, "<b>"."Item Name"."<b>". ":"."".$item_name;
+        foreach my $field (@properties) {
+            my $each_detail = $each_item->{$item_name}->{$field};
+            my $detail_string = $field. ":"."".$each_detail;
+            push @item_details, $detail_string;
+        }
+        $all_details_string = join("<br>", @item_details);
+    }
 
     $c->stash->{order_id} = $order_result->[0];
     $c->stash->{order_from} = $order_result->[1];
     $c->stash->{create_date} = $order_result->[2];
-    $c->stash->{item_list} = $order_result->[3];
+    $c->stash->{item_list} = $all_details_string;
     $c->stash->{order_to} = $order_result->[4];
     $c->stash->{order_status} = $order_result->[5];
     $c->stash->{comments} = $order_result->[6];

From a3e28e8a6ff3f6a2710510d4e91f180c68344a24 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Fri, 16 Dec 2022 23:47:18 +0000
Subject: [PATCH 17/33] modified catalog upload

---
 .../Stock/ParseUpload/Plugin/CatalogXLS.pm    | 215 +++++++++++-------
 lib/SGN/Controller/AJAX/Catalog.pm            |   7 +-
 2 files changed, 144 insertions(+), 78 deletions(-)

diff --git a/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm b/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
index 30b12028ae..0b92ff1a60 100644
--- a/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
+++ b/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
@@ -40,16 +40,16 @@ sub _validate_with_plugin {
     $supported_types{'single item'} = 1;
     $supported_types{'set of items'} = 1;
 
-    $supported_categories{'released variety'} = 1;
-    $supported_categories{'pathogen assay'} = 1;
-    $supported_categories{'control'} = 1;
+#    $supported_categories{'released variety'} = 1;
+#    $supported_categories{'pathogen assay'} = 1;
+#    $supported_categories{'control'} = 1;
 
-    $supported_material_sources{'OrderingSystemTest'} = 1;
-    $supported_material_sources{'Sendusu'} = 1;
+#    $supported_material_sources{'OrderingSystemTest'} = 1;
+#    $supported_material_sources{'Sendusu'} = 1;
 
-    $supported_availability{'in stock'} = 1;
-    $supported_availability{'out of stock'} = 1;
-    $supported_availability{'available in 3 months'} = 1;
+#    $supported_availability{'in stock'} = 1;
+#    $supported_availability{'out of stock'} = 1;
+#    $supported_availability{'available in 3 months'} = 1;
 
     #try to open the excel file and report any errors
     $excel_obj = $parser->parse($filename);
@@ -78,63 +78,82 @@ sub _validate_with_plugin {
     }
 
     #get column headers
-    my $name_header;
-    my $type_header;
+    my $item_name_header;
+    my $item_type_header;
+    my $material_type_header;
+    my $species_header;
+    my $variety_header;
     my $category_header;
-    my $description_header;
+#    my $description_header;
+    my $additional_info_header;
     my $material_source_header;
     my $breeding_program_header;
-    my $availability_header;
+#    my $availability_header;
     my $contact_person_header;
 
     if ($worksheet->get_cell(0,0)) {
-        $name_header  = $worksheet->get_cell(0,0)->value();
+        $item_name_header  = $worksheet->get_cell(0,0)->value();
     }
     if ($worksheet->get_cell(0,1)) {
-        $type_header  = $worksheet->get_cell(0,1)->value();
+        $item_type_header  = $worksheet->get_cell(0,1)->value();
     }
     if ($worksheet->get_cell(0,2)) {
-        $category_header  = $worksheet->get_cell(0,2)->value();
+        $material_type_header  = $worksheet->get_cell(0,2)->value();
     }
     if ($worksheet->get_cell(0,3)) {
-        $description_header  = $worksheet->get_cell(0,3)->value();
+        $species_header  = $worksheet->get_cell(0,3)->value();
     }
     if ($worksheet->get_cell(0,4)) {
-        $material_source_header  = $worksheet->get_cell(0,4)->value();
+        $variety_header  = $worksheet->get_cell(0,4)->value();
     }
     if ($worksheet->get_cell(0,5)) {
-        $breeding_program_header  = $worksheet->get_cell(0,5)->value();
+        $category_header  = $worksheet->get_cell(0,5)->value();
     }
     if ($worksheet->get_cell(0,6)) {
-        $availability_header  = $worksheet->get_cell(0,6)->value();
+        $additional_info_header  = $worksheet->get_cell(0,6)->value();
     }
     if ($worksheet->get_cell(0,7)) {
-        $contact_person_header  = $worksheet->get_cell(0,7)->value();
+        $material_source_header  = $worksheet->get_cell(0,7)->value();
+    }
+    if ($worksheet->get_cell(0,8)) {
+        $breeding_program_header  = $worksheet->get_cell(0,8)->value();
+    }
+    if ($worksheet->get_cell(0,9)) {
+        $contact_person_header  = $worksheet->get_cell(0,9)->value();
     }
 
-    if (!$name_header || $name_header ne 'item_name' ) {
+    if (!$item_name_header || $item_name_header ne 'item_name' ) {
         push @error_messages, "Cell A1: item_name is missing from the header";
     }
-    if (!$type_header || $type_header ne 'type') {
-        push @error_messages, "Cell B1: type is missing from the header";
+    if (!$item_type_header || $item_type_header ne 'item_type') {
+        push @error_messages, "Cell B1: item_type is missing from the header";
+    }
+    if (!$material_type_header || $material_type_header ne 'material_type') {
+        push @error_messages, "Cell C1: material_type is missing from the header";
+    }
+    if (!$species_header || $species_header ne 'species') {
+        push @error_messages, "Cell D1: species is missing from the header";
+    }
+    if (!$variety_header || $variety_header ne 'variety') {
+        push @error_messages, "Cell E1: variety is missing from the header";
     }
     if (!$category_header || $category_header ne 'category') {
-        push @error_messages, "Cell C1: category is missing from the header";
+        push @error_messages, "Cell F1: category is missing from the header";
     }
-    if (!$description_header || $description_header ne 'description') {
-        push @error_messages, "Cell D1: description is missing from the header";
+    if (!$additional_info_header || $additional_info_header ne 'additional_info') {
+        push @error_messages, "Cell G1: additional_info is missing from the header";
     }
     if (!$material_source_header || $material_source_header ne 'material_source') {
-        push @error_messages, "Cell E1: material_source is missing from the header";
+        push @error_messages, "Cell H1: material_source is missing from the header";
     }
     if (!$breeding_program_header || $breeding_program_header ne 'breeding_program') {
-        push @error_messages, "Cell F1: breeding_program is missing from the header";
-    }
-    if (!$availability_header || $availability_header ne 'availability') {
-        push @error_messages, "Cell G1: availability is missing from the header";
+        push @error_messages, "Cell I1: breeding_program is missing from the header";
     }
+#    if (!$availability_header || $availability_header ne 'availability') {
+#        push @error_messages, "Cell G1: availability is missing from the header";
+#    }
     if (!$contact_person_header || $contact_person_header ne 'contact_person_username') {
-        push @error_messages, "Cell H1: contact_person_username is missing from the header";
+        push @error_messages, "Cell J1: contact_person_username is missing from the header";
     }
 
     my %seen_stock_names;
@@ -144,40 +163,56 @@ sub _validate_with_plugin {
         my $row_name = $row+1;
         my $item_name;
         my $item_type;
+        my $material_type;
+        my $species;
+        my $variety;
         my $category;
-        my $description;
+        my $additional_info;
         my $material_source;
         my $breeding_program;
-        my $availability;
+#        my $availability;
         my $contact_person_username;
 
         if ($worksheet->get_cell($row,0)) {
             $item_name = $worksheet->get_cell($row,0)->value();
+            $item_name =~ s/^\s+|\s+$//g;
         }
         if ($worksheet->get_cell($row,1)) {
             $item_type =  $worksheet->get_cell($row,1)->value();
             $item_type =~ s/^\s+|\s+$//g;
         }
         if ($worksheet->get_cell($row,2)) {
-            $category = $worksheet->get_cell($row,2)->value();
-            $category =~ s/^\s+|\s+$//g;
+            $material_type =  $worksheet->get_cell($row,2)->value();
+            $material_type =~ s/^\s+|\s+$//g;
         }
         if ($worksheet->get_cell($row,3)) {
-            $description =  $worksheet->get_cell($row,3)->value();
+            $species =  $worksheet->get_cell($row,3)->value();
+            $species =~ s/^\s+|\s+$//g;
         }
         if ($worksheet->get_cell($row,4)) {
-            $material_source =  $worksheet->get_cell($row,4)->value();
-            $material_source =~ s/^\s+|\s+$//g;
+            $variety =  $worksheet->get_cell($row,4)->value();
+            $variety =~ s/^\s+|\s+$//g;
         }
         if ($worksheet->get_cell($row,5)) {
-            $breeding_program =  $worksheet->get_cell($row,5)->value();
+            $category = $worksheet->get_cell($row,5)->value();
+            $category =~ s/^\s+|\s+$//g;
         }
         if ($worksheet->get_cell($row,6)) {
-            $availability =  $worksheet->get_cell($row,6)->value();
-            $availability =~ s/^\s+|\s+$//g;
+            $additional_info =  $worksheet->get_cell($row,6)->value();
         }
         if ($worksheet->get_cell($row,7)) {
-            $contact_person_username =  $worksheet->get_cell($row,7)->value();
+            $material_source =  $worksheet->get_cell($row,7)->value();
+            $material_source =~ s/^\s+|\s+$//g;
+        }
+        if ($worksheet->get_cell($row,8)) {
+            $breeding_program =  $worksheet->get_cell($row,8)->value();
+        }
+#        if ($worksheet->get_cell($row,6)) {
+#            $availability =  $worksheet->get_cell($row,6)->value();
+#            $availability =~ s/^\s+|\s+$//g;
+#        }
+        if ($worksheet->get_cell($row,9)) {
+            $contact_person_username =  $worksheet->get_cell($row,9)->value();
         }
 
 
@@ -186,35 +221,45 @@ sub _validate_with_plugin {
         }
 
         if (!$item_type || $item_type eq '') {
-            push @error_messages, "Cell B$row_name: type missing";
+            push @error_messages, "Cell B$row_name: item_type missing";
         } elsif (!$supported_types{$item_type}) {
-            push @error_messages, "Cell B$row_name: type is not supported: $item_type";
+            push @error_messages, "Cell B$row_name: item_type is not supported: $item_type";
         }
 
-        if (!$category || $category eq '') {
-            push @error_messages, "Cell C$row_name: category missing";
-        } elsif (!$supported_categories{$category}) {
-            push @error_messages, "Cell C$row_name: category is not supported: $category";
+        if (!$material_type || $material_type eq '') {
+            push @error_messages, "Cell C$row_name: material_type missing";
         }
-        if (!$description || $description eq '') {
-            push @error_messages, "Cell D$row_name: description missing";
+
+        if (!$species || $species eq '') {
+            push @error_messages, "Cell C$row_name: species missing";
         }
 
-        if (!$material_source || $material_source eq '') {
-            push @error_messages, "Cell E$row_name: material_source missing";
-        } elsif (!$supported_material_sources{$material_source}) {
-            push @error_messages, "Cell E$row_name: material source is not supported: $material_source";
+        if (!$category || $category eq '') {
+            push @error_messages, "Cell C$row_name: category missing";
         }
 
+#        } elsif (!$supported_categories{$category}) {
+#            push @error_messages, "Cell C$row_name: category is not supported: $category";
+#        }
+#        if (!$description || $description eq '') {
+#            push @error_messages, "Cell D$row_name: description missing";
+#        }
+
+#        if (!$material_source || $material_source eq '') {
+#            push @error_messages, "Cell E$row_name: material_source missing";
+#        } elsif (!$supported_material_sources{$material_source}) {
+#            push @error_messages, "Cell E$row_name: material source is not supported: $material_source";
+#        }
+
         if (!$breeding_program || $breeding_program eq '') {
             push @error_messages, "Cell F$row_name: breeding_program missing";
         }
 
-        if (!$availability || $availability eq '') {
-            push @error_messages, "Cell G$row_name: availability missing";
-        } elsif (!$supported_availability{$availability}) {
-            push @error_messages, "Cell G$row_name: availability is not supported: $availability";
-        }
+#        if (!$availability || $availability eq '') {
+#            push @error_messages, "Cell G$row_name: availability missing";
+#        } elsif (!$supported_availability{$availability}) {
+#            push @error_messages, "Cell G$row_name: availability is not supported: $availability";
+#        }
 
         if (!$contact_person_username || $contact_person_username eq '') {
             push @error_messages, "Cell H$row_name: contact person username missing";
@@ -237,16 +282,18 @@ sub _validate_with_plugin {
 
     }
 
-    my @stocks_missing;
+#    my @stocks_missing;
     my @catalog_items = keys %seen_stock_names;
     my $catalog_item_validator = CXGN::List::Validate->new();
-    my @accessions_missing = @{$catalog_item_validator->validate($schema,'uniquenames',\@catalog_items)->{'missing'}};
-    if (scalar(@accessions_missing) > 0) {
-        @stocks_missing = @{$catalog_item_validator->validate($schema,'populations',\@accessions_missing)->{'missing'}};
-    }
+#    my @accessions_missing = @{$catalog_item_validator->validate($schema,'uniquenames',\@catalog_items)->{'missing'}};
+#    if (scalar(@accessions_missing) > 0) {
+#        @stocks_missing = @{$catalog_item_validator->validate($schema,'populations',\@accessions_missing)->{'missing'}};
+#    }
+
+    my @stocks_missing = @{$catalog_item_validator->validate($schema,'stocks',\@catalog_items)->{'missing'}};
 
     if (scalar(@stocks_missing) > 0){
-        push @error_messages, "The following catalog items are not in the database as accession or population: ".join(',',@stocks_missing);
+        push @error_messages, "The following catalog items are not in the database: ".join(',',@stocks_missing);
     }
 
     my @breeding_programs = keys %seen_program_names;
@@ -302,11 +349,15 @@ sub _parse_with_plugin {
         my $row_name = $row+1;
         my $item_name;
         my $item_type;
+        my $material_type;
+        my $species;
+        my $variety;
         my $category;
-        my $description;
+#        my $description;
+        my $additional_info;
         my $material_source;
         my $breeding_program;
-        my $availability;
+#        my $availability;
         my $contact_person_username;
 
         if ($worksheet->get_cell($row,0)) {
@@ -316,22 +367,31 @@ sub _parse_with_plugin {
             $item_type =  $worksheet->get_cell($row,1)->value();
         }
         if ($worksheet->get_cell($row,2)) {
-            $category = $worksheet->get_cell($row,2)->value();
+            $material_type =  $worksheet->get_cell($row,2)->value();
         }
         if ($worksheet->get_cell($row,3)) {
-            $description =  $worksheet->get_cell($row,3)->value();
+            $species =  $worksheet->get_cell($row,3)->value();
         }
         if ($worksheet->get_cell($row,4)) {
-            $material_source =  $worksheet->get_cell($row,4)->value();
+            $variety =  $worksheet->get_cell($row,4)->value();
         }
         if ($worksheet->get_cell($row,5)) {
-            $breeding_program =  $worksheet->get_cell($row,5)->value();
+            $category = $worksheet->get_cell($row,5)->value();
         }
         if ($worksheet->get_cell($row,6)) {
-            $availability =  $worksheet->get_cell($row,6)->value();
+            $additional_info =  $worksheet->get_cell($row,6)->value();
         }
         if ($worksheet->get_cell($row,7)) {
-            $contact_person_username =  $worksheet->get_cell($row,7)->value();
+            $material_source =  $worksheet->get_cell($row,7)->value();
+        }
+        if ($worksheet->get_cell($row,8)) {
+            $breeding_program =  $worksheet->get_cell($row,8)->value();
+        }
+#        if ($worksheet->get_cell($row,6)) {
+#            $availability =  $worksheet->get_cell($row,6)->value();
+#        }
+        if ($worksheet->get_cell($row,9)) {
+            $contact_person_username =  $worksheet->get_cell($row,9)->value();
         }
 
         my $contact_person_id = CXGN::People::Person->get_person_by_username($dbh, $contact_person_username);
@@ -341,11 +401,14 @@ sub _parse_with_plugin {
 
         $parsed_result{$item_name} = {
             'item_type' => $item_type,
+            'material_type' => $material_type,
+            'species' => $species,
+            'variety' => $variety,
             'category' => $category,
-            'description' => $description,
+            'additional_info' => $description,
             'material_source' => $material_source,
             'breeding_program' => $breeding_program_id,
-            'availability' => $availability,
+#            'availability' => $availability,
             'contact_person_id' => $contact_person_id,
         }
     }
diff --git a/lib/SGN/Controller/AJAX/Catalog.pm b/lib/SGN/Controller/AJAX/Catalog.pm
index 6b6fa2b7ed..21b436bda0 100644
--- a/lib/SGN/Controller/AJAX/Catalog.pm
+++ b/lib/SGN/Controller/AJAX/Catalog.pm
@@ -199,11 +199,14 @@ sub upload_catalog_items_POST : Args(0) {
             my $stock_catalog = CXGN::Stock::Catalog->new({
                 bcs_schema => $schema,
                 item_type => $catalog_info_hash{item_type},
+                material_type => $catalog_info_hash{material_type},
+                species => $catalog_info_hash{species},
+                variety => $catalog_info_hash{variety},
                 category => $catalog_info_hash{category},
-                description => $catalog_info_hash{description},
+                additional_info => $catalog_info_hash{additional_info},
                 material_source => $catalog_info_hash{material_source},
                 breeding_program => $catalog_info_hash{breeding_program},
-                availability => $catalog_info_hash{availability},
+#                availability => $catalog_info_hash{availability},
                 contact_person_id => $catalog_info_hash{contact_person_id},
                 parent_id => $stock_id
             });

From cd9b137170dc416f083048e4a6ad26da5933d018 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sat, 17 Dec 2022 20:28:46 +0000
Subject: [PATCH 18/33] catalog table

---
 .../Stock/ParseUpload/Plugin/CatalogXLS.pm    |  2 +-
 mason/order/catalog.mas                       | 58 +++++++++++++------
 2 files changed, 40 insertions(+), 20 deletions(-)

diff --git a/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm b/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
index 0b92ff1a60..ca775b9bf8 100644
--- a/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
+++ b/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
@@ -405,7 +405,7 @@ sub _parse_with_plugin {
             'species' => $species,
             'variety' => $variety,
             'category' => $category,
-            'additional_info' => $description,
+            'additional_info' => $additional_info,
             'material_source' => $material_source,
             'breeding_program' => $breeding_program_id,
 #            'availability' => $availability,
diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index dfa6b56834..fd2890ce5b 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -153,25 +153,45 @@ jQuery(document).ready( function() {
     var order_properties = "<% $order_properties %>";
     var property_keys = order_properties.split(",");
 
-    jQuery('#catalog_items_table').DataTable( {
-        'autoWidth': false,
-        'order': false,
-        'search':'applied',
-        'ajax': '/ajax/catalog/items',
-        columns: [
-            { title: "Name", "data": null, "render": function ( data, type, row ) { return "<a href='/catalog/item_details/"+row.item_id+"'>"+row.item_name+"</a>"; } },
-            { title: "Type", "data": "item_type" },
-            { title: "Material Type", "data": "material_type" },
-            { title: "Species", "data": "species" },
-            { title: "Variety", "data": "variety" },
-            { title: "Category", "data": "category" },
-            { title: "Additional Info", "data": "additional_info" },
-            { title: "Material Source", "data": "material_source" },
-            { title: "Program", "data": "breeding_program" },
-            { title: " ", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties+"\")'>Request</a>"; } },
-//            { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties+"\" )'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
-        ],
-    });
+    if (ordering_type == 'single_step') {
+        jQuery('#catalog_items_table').DataTable( {
+            'autoWidth': false,
+            'order': false,
+            'search':'applied',
+            'ajax': '/ajax/catalog/items',
+            columns: [
+                { title: "Name", "data": null, "render": function ( data, type, row ) { return "<a href='/catalog/item_details/"+row.item_id+"'>"+row.item_name+"</a>"; } },
+                { title: "Type", "data": "item_type" },
+                { title: "Material Type", "data": "material_type" },
+                { title: "Species", "data": "species" },
+                { title: "Variety", "data": "variety" },
+                { title: "Category", "data": "category" },
+                { title: "Additional Info", "data": "additional_info" },
+                { title: "Material Source", "data": "material_source" },
+                { title: "Program", "data": "breeding_program" },
+                { title: " ", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties+"\")'>Request</a>"; } },
+            ],
+        });
+    } else {
+            jQuery('#catalog_items_table').DataTable( {
+            'autoWidth': false,
+            'order': false,
+            'search':'applied',
+            'ajax': '/ajax/catalog/items',
+            columns: [
+                { title: "Name", "data": null, "render": function ( data, type, row ) { return "<a href='/catalog/item_details/"+row.item_id+"'>"+row.item_name+"</a>"; } },
+                { title: "Type", "data": "item_type" },
+                { title: "Material Type", "data": "material_type" },
+                { title: "Species", "data": "species" },
+                { title: "Variety", "data": "variety" },
+                { title: "Category", "data": "category" },
+                { title: "Additional Info", "data": "additional_info" },
+                { title: "Material Source", "data": "material_source" },
+                { title: "Program", "data": "breeding_program" },
+                { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties+"\" )'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
+            ],
+        });
+    }
 
     var lo = new CXGN.List();
     var list_id;

From ff012e6abd9f26c6304d495832bacffc180295ca Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sat, 17 Dec 2022 22:15:18 +0000
Subject: [PATCH 19/33] retrieve species and variety directly from database

---
 lib/CXGN/Stock/Catalog.pm                     |  4 +-
 .../Stock/ParseUpload/Plugin/CatalogXLS.pm    | 92 ++++++-------------
 lib/SGN/Controller/AJAX/Catalog.pm            | 35 +++++--
 mason/order/add_catalog_item_dialog.mas       | 48 +++-------
 4 files changed, 68 insertions(+), 111 deletions(-)

diff --git a/lib/CXGN/Stock/Catalog.pm b/lib/CXGN/Stock/Catalog.pm
index 23c89082fa..bcf20f1d77 100644
--- a/lib/CXGN/Stock/Catalog.pm
+++ b/lib/CXGN/Stock/Catalog.pm
@@ -25,11 +25,11 @@ has 'category' => ( isa => 'Str', is => 'rw' );
 
 has 'species' => ( isa => 'Str', is => 'rw' );
 
-has 'variety' => ( isa => 'Str', is => 'rw' );
+has 'variety' => ( isa => 'Str', is => 'rw', required => 0);
 
 has 'breeding_program' => ( isa => 'Int', is => 'rw');
 
-has 'additional_info' => ( isa => 'Str', is => 'rw' );
+has 'additional_info' => ( isa => 'Str', is => 'rw', required => 0 );
 
 has 'contact_person_id' => ( isa => 'Int', is => 'rw') ;
 
diff --git a/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm b/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
index ca775b9bf8..a64d798418 100644
--- a/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
+++ b/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
@@ -81,10 +81,7 @@ sub _validate_with_plugin {
     my $item_name_header;
     my $item_type_header;
     my $material_type_header;
-    my $species_header;
-    my $variety_header;
     my $category_header;
-#    my $description_header;
     my $additional_info_header;
     my $material_source_header;
     my $breeding_program_header;
@@ -101,25 +98,19 @@ sub _validate_with_plugin {
         $material_type_header  = $worksheet->get_cell(0,2)->value();
     }
     if ($worksheet->get_cell(0,3)) {
-        $species_header  = $worksheet->get_cell(0,3)->value();
+        $category_header  = $worksheet->get_cell(0,3)->value();
     }
     if ($worksheet->get_cell(0,4)) {
-        $variety_header  = $worksheet->get_cell(0,4)->value();
+        $additional_info_header  = $worksheet->get_cell(0,4)->value();
     }
     if ($worksheet->get_cell(0,5)) {
-        $category_header  = $worksheet->get_cell(0,5)->value();
+        $material_source_header  = $worksheet->get_cell(0,5)->value();
     }
     if ($worksheet->get_cell(0,6)) {
-        $additional_info_header  = $worksheet->get_cell(0,6)->value();
+        $breeding_program_header  = $worksheet->get_cell(0,6)->value();
     }
     if ($worksheet->get_cell(0,7)) {
-        $material_source_header  = $worksheet->get_cell(0,7)->value();
-    }
-    if ($worksheet->get_cell(0,8)) {
-        $breeding_program_header  = $worksheet->get_cell(0,8)->value();
-    }
-    if ($worksheet->get_cell(0,9)) {
-        $contact_person_header  = $worksheet->get_cell(0,9)->value();
+        $contact_person_header  = $worksheet->get_cell(0,7)->value();
     }
 
     if (!$item_name_header || $item_name_header ne 'item_name' ) {
@@ -131,29 +122,23 @@ sub _validate_with_plugin {
     if (!$material_type_header || $material_type_header ne 'material_type') {
         push @error_messages, "Cell C1: material_type is missing from the header";
     }
-    if (!$species_header || $species_header ne 'species') {
-        push @error_messages, "Cell D1: species is missing from the header";
-    }
-    if (!$variety_header || $variety_header ne 'variety') {
-        push @error_messages, "Cell E1: variety is missing from the header";
-    }
     if (!$category_header || $category_header ne 'category') {
-        push @error_messages, "Cell F1: category is missing from the header";
+        push @error_messages, "Cell D1: category is missing from the header";
     }
     if (!$additional_info_header || $additional_info_header ne 'additional_info') {
-        push @error_messages, "Cell G1: additional_info is missing from the header";
+        push @error_messages, "Cell E1: additional_info is missing from the header";
     }
     if (!$material_source_header || $material_source_header ne 'material_source') {
-        push @error_messages, "Cell H1: material_source is missing from the header";
+        push @error_messages, "Cell F1: material_source is missing from the header";
     }
     if (!$breeding_program_header || $breeding_program_header ne 'breeding_program') {
-        push @error_messages, "Cell I1: breeding_program is missing from the header";
+        push @error_messages, "Cell G1: breeding_program is missing from the header";
     }
 #    if (!$availability_header || $availability_header ne 'availability') {
 #        push @error_messages, "Cell G1: availability is missing from the header";
 #    }
     if (!$contact_person_header || $contact_person_header ne 'contact_person_username') {
-        push @error_messages, "Cell J1: contact_person_username is missing from the header";
+        push @error_messages, "Cell H1: contact_person_username is missing from the header";
     }
 
     my %seen_stock_names;
@@ -164,8 +149,6 @@ sub _validate_with_plugin {
         my $item_name;
         my $item_type;
         my $material_type;
-        my $species;
-        my $variety;
         my $category;
         my $additional_info;
         my $material_source;
@@ -186,33 +169,25 @@ sub _validate_with_plugin {
             $material_type =~ s/^\s+|\s+$//g;
         }
         if ($worksheet->get_cell($row,3)) {
-            $species =  $worksheet->get_cell($row,3)->value();
-            $species =~ s/^\s+|\s+$//g;
+            $category = $worksheet->get_cell($row,3)->value();
+            $category =~ s/^\s+|\s+$//g;
         }
         if ($worksheet->get_cell($row,4)) {
-            $variety =  $worksheet->get_cell($row,4)->value();
-            $variety =~ s/^\s+|\s+$//g;
+            $additional_info =  $worksheet->get_cell($row,4)->value();
         }
         if ($worksheet->get_cell($row,5)) {
-            $category = $worksheet->get_cell($row,5)->value();
-            $category =~ s/^\s+|\s+$//g;
-        }
-        if ($worksheet->get_cell($row,6)) {
-            $additional_info =  $worksheet->get_cell($row,6)->value();
-        }
-        if ($worksheet->get_cell($row,7)) {
-            $material_source =  $worksheet->get_cell($row,7)->value();
+            $material_source =  $worksheet->get_cell($row,5)->value();
             $material_source =~ s/^\s+|\s+$//g;
         }
-        if ($worksheet->get_cell($row,8)) {
-            $breeding_program =  $worksheet->get_cell($row,8)->value();
+        if ($worksheet->get_cell($row,6)) {
+            $breeding_program =  $worksheet->get_cell($row,6)->value();
         }
 #        if ($worksheet->get_cell($row,6)) {
 #            $availability =  $worksheet->get_cell($row,6)->value();
 #            $availability =~ s/^\s+|\s+$//g;
 #        }
-        if ($worksheet->get_cell($row,9)) {
-            $contact_person_username =  $worksheet->get_cell($row,9)->value();
+        if ($worksheet->get_cell($row,7)) {
+            $contact_person_username =  $worksheet->get_cell($row,7)->value();
         }
 
 
@@ -230,12 +205,8 @@ sub _validate_with_plugin {
             push @error_messages, "Cell C$row_name: material_type missing";
         }
 
-        if (!$species || $species eq '') {
-            push @error_messages, "Cell C$row_name: species missing";
-        }
-
         if (!$category || $category eq '') {
-            push @error_messages, "Cell C$row_name: category missing";
+            push @error_messages, "Cell D$row_name: category missing";
         }
 
 #        } elsif (!$supported_categories{$category}) {
@@ -252,7 +223,7 @@ sub _validate_with_plugin {
 #        }
 
         if (!$breeding_program || $breeding_program eq '') {
-            push @error_messages, "Cell F$row_name: breeding_program missing";
+            push @error_messages, "Cell G$row_name: breeding_program missing";
         }
 
 #        if (!$availability || $availability eq '') {
@@ -350,10 +321,7 @@ sub _parse_with_plugin {
         my $item_name;
         my $item_type;
         my $material_type;
-        my $species;
-        my $variety;
         my $category;
-#        my $description;
         my $additional_info;
         my $material_source;
         my $breeding_program;
@@ -370,28 +338,22 @@ sub _parse_with_plugin {
             $material_type =  $worksheet->get_cell($row,2)->value();
         }
         if ($worksheet->get_cell($row,3)) {
-            $species =  $worksheet->get_cell($row,3)->value();
+            $category = $worksheet->get_cell($row,3)->value();
         }
         if ($worksheet->get_cell($row,4)) {
-            $variety =  $worksheet->get_cell($row,4)->value();
+            $additional_info =  $worksheet->get_cell($row,4)->value();
         }
         if ($worksheet->get_cell($row,5)) {
-            $category = $worksheet->get_cell($row,5)->value();
+            $material_source =  $worksheet->get_cell($row,5)->value();
         }
         if ($worksheet->get_cell($row,6)) {
-            $additional_info =  $worksheet->get_cell($row,6)->value();
-        }
-        if ($worksheet->get_cell($row,7)) {
-            $material_source =  $worksheet->get_cell($row,7)->value();
-        }
-        if ($worksheet->get_cell($row,8)) {
-            $breeding_program =  $worksheet->get_cell($row,8)->value();
+            $breeding_program =  $worksheet->get_cell($row,6)->value();
         }
 #        if ($worksheet->get_cell($row,6)) {
 #            $availability =  $worksheet->get_cell($row,6)->value();
 #        }
-        if ($worksheet->get_cell($row,9)) {
-            $contact_person_username =  $worksheet->get_cell($row,9)->value();
+        if ($worksheet->get_cell($row,7)) {
+            $contact_person_username =  $worksheet->get_cell($row,7)->value();
         }
 
         my $contact_person_id = CXGN::People::Person->get_person_by_username($dbh, $contact_person_username);
@@ -402,8 +364,6 @@ sub _parse_with_plugin {
         $parsed_result{$item_name} = {
             'item_type' => $item_type,
             'material_type' => $material_type,
-            'species' => $species,
-            'variety' => $variety,
             'category' => $category,
             'additional_info' => $additional_info,
             'material_source' => $material_source,
diff --git a/lib/SGN/Controller/AJAX/Catalog.pm b/lib/SGN/Controller/AJAX/Catalog.pm
index 21b436bda0..978b5aaf42 100644
--- a/lib/SGN/Controller/AJAX/Catalog.pm
+++ b/lib/SGN/Controller/AJAX/Catalog.pm
@@ -35,9 +35,6 @@ sub add_catalog_item_POST : Args(0) {
     my $contact_person = $c->req->param('contact_person');
     my $item_prop_id = $c->req->param('item_prop_id');
 
-    my $item_species = $c->req->param('species');
-    my $item_variety = $c->req->param('variety');
-
     my $item_stock_id;
     if (!$c->user()) {
         print STDERR "User not logged in... not adding a catalog item.\n";
@@ -45,12 +42,26 @@ sub add_catalog_item_POST : Args(0) {
         return;
     }
 
+    my $item_stock_id;
+    my $item_species;
+    my $item_variety;
     my $item_rs = $schema->resultset("Stock::Stock")->find({uniquename => $item_name});
+    my $variety_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'variety', 'stock_property')->cvterm_id();
+
     if (!$item_rs) {
         $c->stash->{rest} = {error_string => "Item name is not in the database!",};
         return;
     } else {
         $item_stock_id = $item_rs->stock_id();
+        my $organism_id = $item_rs->organism_id();
+        my $organism = $schema->resultset("Organism::Organism")->find({organism_id => $organism_id});
+        $item_species = $organism->species();
+        my $item_stockprop = $schema->resultset("Stock::Stockprop")->find({stock_id => $item_stock_id, type_id => $variety_type_id});
+        if ($item_stockprop) {
+            $item_variety = $item_stockprop->value();
+        } else {
+            $item_variety = 'NA';
+        }
     }
 
     my $sp_person_id = CXGN::People::Person->get_person_by_username($dbh, $contact_person);
@@ -189,19 +200,31 @@ sub upload_catalog_items_POST : Args(0) {
     }
 
     if ($parsed_data) {
+        my $variety_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'variety', 'stock_property')->cvterm_id();
         my %catalog_info = %{$parsed_data};
         foreach my $item_name (keys %catalog_info) {
+            my $item_species;
+            my $item_variety;
             my $stock_rs = $schema->resultset("Stock::Stock")->find({uniquename => $item_name});
             my $stock_id = $stock_rs->stock_id();
-            print STDERR "STOCK ID =".Dumper($stock_id)."\n";
+            my $organism_id = $stock_rs->organism_id();
+            my $organism = $schema->resultset("Organism::Organism")->find({organism_id => $organism_id});
+            $item_species = $organism->species();
+            my $item_stockprop = $schema->resultset("Stock::Stockprop")->find({stock_id => $stock_id, type_id => $variety_type_id});
+            if ($item_stockprop) {
+                $item_variety = $item_stockprop->value();
+            } else {
+                $item_variety = 'NA';
+            }
+
             my %catalog_info_hash = %{$catalog_info{$item_name}};
 
             my $stock_catalog = CXGN::Stock::Catalog->new({
                 bcs_schema => $schema,
                 item_type => $catalog_info_hash{item_type},
                 material_type => $catalog_info_hash{material_type},
-                species => $catalog_info_hash{species},
-                variety => $catalog_info_hash{variety},
+                species => $item_species,
+                variety => $item_variety,
                 category => $catalog_info_hash{category},
                 additional_info => $catalog_info_hash{additional_info},
                 material_source => $catalog_info_hash{material_source},
diff --git a/mason/order/add_catalog_item_dialog.mas b/mason/order/add_catalog_item_dialog.mas
index cfae5fb776..092f6592d0 100644
--- a/mason/order/add_catalog_item_dialog.mas
+++ b/mason/order/add_catalog_item_dialog.mas
@@ -24,8 +24,8 @@ $ordering_type => undef
                             <div class="col-sm-9">
                                 <select class="form-control" id="item_type">
                                     <option value="">Select an item type</option>
-                                    <option value="single item">Single item</option>
-                                    <option value="set of items">Set of items</option>
+                                    <option value="single item">single item</option>
+                                    <option value="set of items">set of items</option>
                                 </select>
                             </div>
                         </div>
@@ -34,30 +34,9 @@ $ordering_type => undef
                             <div class="col-sm-9">
                                 <select class="form-control" id="item_material_type">
                                     <option value="">Select a material type</option>
-                                    <option value="Seed">Seed</option>
-                                    <option value="Plant">Plant</option>
-                                    <option value="Construct">Construct</option>
-                                </select>
-                            </div>
-                        </div>
-                        <div class="form-group">
-                            <label class="col-sm-3 control-label">Species: </label>
-                            <div class="col-sm-9">
-                                <select class="form-control" id="item_species">
-                                    <option value="">Select a species</option>
-                                    <option value="Nicotiana benthamiana">Nicotiana benthamiana</option>
-                                    <option value="Nicotiana tabacum">Nicotiana tabacum</option>
-                                </select>
-                            </div>
-                        </div>
-                        <div class="form-group">
-                            <label class="col-sm-3 control-label">Variety: </label>
-                            <div class="col-sm-9">
-                                <select class="form-control" id="item_variety">
-                                    <option value="">Select a variety</option>
-                                    <option value="C319">C319</option>
-                                    <option value="K236">K236</option>
-                                    <option value="Mix">Mix</option>
+                                    <option value="seed">seed</option>
+                                    <option value="plant">plant</option>
+                                    <option value="construct">construct</option>
                                 </select>
                             </div>
                         </div>
@@ -66,17 +45,17 @@ $ordering_type => undef
                             <div class="col-sm-9">
                                 <select class="form-control" id="item_category">
                                     <option value="">Select a category</option>
-                                    <option value="Released Variety">Released Variety</option>
-                                    <option value="Pathogen Assay ">Pathogen Assay</option>
-                                    <option value="Control">Control</option>
-                                    <option value="Transgenic Line">Transgenic Line</option>
+                                    <option value="released variety">released variety</option>
+                                    <option value="pathogen assay ">pathogen assay</option>
+                                    <option value="control">control</option>
+                                    <option value="transgenic line">transgenic line</option>
                                 </select>
                             </div>
                         </div>
                         <div class="form-group">
                             <label class="col-sm-3 control-label">Additional Info: </label>
                             <div class="col-sm-9" >
-                                <input class="form-control" id="item_additional_info" placeholder="">
+                                <input class="form-control" id="item_additional_info" placeholder="optional">
                             </div>
                         </div>
                         <div class="form-group">
@@ -86,7 +65,7 @@ $ordering_type => undef
                             </div>
                         </div>
                         <div class="form-group">
-                            <label class="col-sm-3 control-label">Program: </label>
+                            <label class="col-sm-3 control-label">Breeding Program: </label>
                             <div class="col-sm-9" >
                                 <div id="item_breeding_program_div"></div>
                             </div>
@@ -148,8 +127,6 @@ jQuery(document).ready(function(){
         var name = jQuery('#item_name').val();
         var type = jQuery('#item_type').val();
         var material_type = jQuery('#item_material_type').val();
-        var species = jQuery('#item_species').val();
-        var variety = jQuery('#item_variety').val();
         var category = jQuery('#item_category').val();
         var additional_info = jQuery('#item_additional_info').val();
         var material_source = jQuery('#item_material_source').val();
@@ -159,7 +136,6 @@ jQuery(document).ready(function(){
         if (name == '') { alert("Please provide a name") };
         if (type == '') { alert("Please select a type") };
         if (material_type == '') { alert("Please select a material type") };
-        if (species == '') { alert("Please select a species") };
         if (category == '') { alert("Please select a category") };
         if (breeding_program == '') { alert("Please select a program") };
         if (contact_person == '') { alert("Please indicate contact person") };
@@ -177,8 +153,6 @@ jQuery(document).ready(function(){
                 'material_source': material_source,
                 'breeding_program_id': breeding_program,
                 'contact_person': contact_person,
-                'species': species,
-                'variety': variety
             },
             beforeSend: function(response){
                 jQuery('#working_modal').modal('show');

From d08ea86eb88f9efaad4a27623c97e460cbe53958 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sun, 18 Dec 2022 01:15:23 +0000
Subject: [PATCH 20/33] clean up

---
 mason/order/catalog.mas | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index fd2890ce5b..b4613764b1 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -346,21 +346,9 @@ function addToCart(item_name, additional_order_info, ordering_service_name, orde
 
     if (ordering_type == 'single_step') {
         html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="item_name" name="item_name" value="'+item_name+'" disabled></div><br><br><br>';
-//        html = html + '<label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div><br><br><br>';
-//        html = html + '<label class="col-sm-3 control-label">Facility: </label><div class="col-sm-9" ><input class="form-control" id="item_facility" name="item_facility" placeholder="Please Select"></div><br><br><br>';
-//        html = html + '<label class="col-sm-3 control-label">Scientist(s): </label><div class="col-sm-9" ><input class="form-control" id="item_scientist" name="item_scientist" placeholder=""></div><br><br><br>';
-//        html = html + '<label class="col-sm-3 control-label">Due/Requested by Date: </label><div class="col-sm-9" ><input class="form-control" id="item_due_date" name="item_due_date" placeholder=""></div><br><br><br>';
-//        html = html + '<label class="col-sm-3 control-label">Experiment Name: </label><div class="col-sm-9" ><input class="form-control" id="experiment_name" name="experiment_name" placeholder=""></div><br><br><br>';
-//        html = html + '<label class="col-sm-3 control-label">Experiment Type: </label><div class="col-sm-9" ><input class="form-control" id="experiment_type" name="experiment_type" placeholder="Please Select"></div><br><br><br>';
-//        html = html + '<label class="col-sm-3 control-label">Risk Assessment: </label><div class="col-sm-9" ><input class="form-control" id="risk_assessment" name="risk_assessment" placeholder=""></div><br><br><br>';
-//        html = html + '<label class="col-sm-3 control-label">Containment Zone: </label><div class="col-sm-9" ><input class="form-control" id="containment_zone" name="containment_zone" placeholder=""></div><br><br><br>';
-//        html = html + '<label class="col-sm-3 control-label">Additional Comments: </label><div class="col-sm-9" ><input class="form-control" id="additional_comments" name="additional_comments" placeholder="eg: Clothing & Special Handling"></div>';
-
         for(var i=0; i<properties.length; i++){
             html = html + '<label class="col-sm-3 control-label">'+ properties[i] +'</label><div class="col-sm-9" ><input class="form-control" id= '+ i +' name= '+ i +' placeholder=""></div><br><br><br>';
-
         }
-
         html = html + '</div></div></form>';
     } else {
         html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="cart_item_name" name="cart_item_name" value="'+item_name+'" disabled></div></div>';

From 112597abd17c2c2694b2d053b5bac71a4bf5b724 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sun, 18 Dec 2022 02:37:17 +0000
Subject: [PATCH 21/33] modified two steps ordering

---
 lib/SGN/Controller/AJAX/Order.pm | 98 ++++++++++++++++++--------------
 mason/order/catalog.mas          | 83 +++++++++++++++------------
 2 files changed, 101 insertions(+), 80 deletions(-)

diff --git a/lib/SGN/Controller/AJAX/Order.pm b/lib/SGN/Controller/AJAX/Order.pm
index 32b85d149c..036a5750c7 100644
--- a/lib/SGN/Controller/AJAX/Order.pm
+++ b/lib/SGN/Controller/AJAX/Order.pm
@@ -46,6 +46,9 @@ sub submit_order_POST : Args(0) {
     my $time = DateTime->now();
     my $timestamp = $time->ymd()."_".$time->hms();
     my $request_date = $time->ymd();
+    my $order_properties = $c->config->{order_properties};
+    my @properties = split ',',$order_properties;
+
 #    print STDERR "LIST ID =".Dumper($list_id)."\n";
 
     if (!$c->user()) {
@@ -66,9 +69,17 @@ sub submit_order_POST : Args(0) {
     my @all_items = @$items;
     foreach my $ordered_item (@all_items) {
         my @ona_info = ();
-        my @ordered_item_split = split /,/, $ordered_item;
-        my $number_of_fields = @ordered_item_split;
-        my $item_name = $ordered_item_split[0];
+        my $order_details_ref = decode_json ($ordered_item);
+        my %order_details = %{$order_details_ref};
+        my $item_name = $order_details{'Item Name'};
+        my %each_item_details;
+        foreach my $field (@properties) {
+            $each_item_details{$field} = $order_details{$field};
+        }
+
+#        my @ordered_item_split = split /,/, $ordered_item;
+#        my $number_of_fields = @ordered_item_split;
+#        my $item_name = $ordered_item_split[0];
         my $item_rs = $schema->resultset("Stock::Stock")->find( { uniquename => $item_name });
         my $item_id = $item_rs->stock_id();
         my $item_info_rs = $schema->resultset("Stock::Stockprop")->find({stock_id => $item_id, type_id => $catalog_cvterm_id});
@@ -79,46 +90,47 @@ sub submit_order_POST : Args(0) {
         my $item_source = $item_info_hash->{'material_source'};
         $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'item_type'} = $item_type;
         $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'material_source'} = $item_source;
+        $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name} = \%each_item_details;
+
+#        my $quantity_string = $ordered_item_split[1];
+#        my @quantity_info = split /:/, $quantity_string;
+#        my $quantity = $quantity_info[1];
+#        $quantity =~ s/^\s+|\s+$//g;
+#        $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'quantity'} = $quantity;
+
+#        my $ona_additional_info;
+#        if ($number_of_fields == 3) {
+#            my $optional_field = $ordered_item_split[2];
+#            my @optional_field_array = split /:/, $optional_field;
+#            my $optional_title = $optional_field_array[0];
+#            $optional_title =~ s/^\s+|\s+$//g;
+#            print STDERR "OPTIONAL TITLE =".Dumper($optional_title)."\n";
+#            my $optional_info = $optional_field_array[1];
+#            $optional_info =~ s/^\s+|\s+$//g;
+#            print STDERR "OPTIONAL INFO =".Dumper($optional_info)."\n";
+#            if ($optional_title eq 'Comments') {
+#                $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'comments'} = $optional_info;
+#            } elsif ($optional_title eq 'Additional Info') {
+#                $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'additional_info'} = $optional_info;
+#                $ona_additional_info = $optional_info;
+#                print STDERR "ONA ADDITIONAL INFO =".Dumper($ona_additional_info)."\n";
+#            }
+#        } elsif ($number_of_fields == 4) {
+#            my $additional_info_field = $ordered_item_split[2];
+#            my @additional_info_array = split /:/, $additional_info_field;
+#            my $additional_info = $additional_info_array[1];
+#            $additional_info =~ s/^\s+|\s+$//g;
+#            $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'additional_info'} = $additional_info;
+#            $ona_additional_info = $additional_info;
+#            my $comments_field = $ordered_item_split[3];
+#            my @comments_array = split /:/, $comments_field;
+#            my $comments = $comments_array[1];
+#            $comments =~ s/^\s+|\s+$//g;
+#            $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'comments'} = $comments;
+#        }
 
-        my $quantity_string = $ordered_item_split[1];
-        my @quantity_info = split /:/, $quantity_string;
-        my $quantity = $quantity_info[1];
-        $quantity =~ s/^\s+|\s+$//g;
-        $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'quantity'} = $quantity;
-
-        my $ona_additional_info;
-        if ($number_of_fields == 3) {
-            my $optional_field = $ordered_item_split[2];
-            my @optional_field_array = split /:/, $optional_field;
-            my $optional_title = $optional_field_array[0];
-            $optional_title =~ s/^\s+|\s+$//g;
-            print STDERR "OPTIONAL TITLE =".Dumper($optional_title)."\n";
-            my $optional_info = $optional_field_array[1];
-            $optional_info =~ s/^\s+|\s+$//g;
-            print STDERR "OPTIONAL INFO =".Dumper($optional_info)."\n";
-            if ($optional_title eq 'Comments') {
-                $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'comments'} = $optional_info;
-            } elsif ($optional_title eq 'Additional Info') {
-                $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'additional_info'} = $optional_info;
-                $ona_additional_info = $optional_info;
-                print STDERR "ONA ADDITIONAL INFO =".Dumper($ona_additional_info)."\n";
-            }
-        } elsif ($number_of_fields == 4) {
-            my $additional_info_field = $ordered_item_split[2];
-            my @additional_info_array = split /:/, $additional_info_field;
-            my $additional_info = $additional_info_array[1];
-            $additional_info =~ s/^\s+|\s+$//g;
-            $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'additional_info'} = $additional_info;
-            $ona_additional_info = $additional_info;
-            my $comments_field = $ordered_item_split[3];
-            my @comments_array = split /:/, $comments_field;
-            my $comments = $comments_array[1];
-            $comments =~ s/^\s+|\s+$//g;
-            $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'comments'} = $comments;
-        }
-
-        @ona_info = ($item_source, $item_name, $quantity, $ona_additional_info, $request_date);
-        $group_by_contact_id{$contact_person_id}{'ona'}{$item_name} = \@ona_info;
+#        @ona_info = ($item_source, $item_name, $quantity, $ona_additional_info, $request_date);
+#        $group_by_contact_id{$contact_person_id}{'ona'}{$item_name} = \@ona_info;
     }
 
     my $ordering_service_name = $c->config->{ordering_service_name};
@@ -147,7 +159,7 @@ sub submit_order_POST : Args(0) {
 
         $history_info ->{'submitted'} = $timestamp;
         push @history, $history_info;
-
+        print STDERR "ITEM LIST =".Dumper(\@item_list)."\n";
         my $order_prop = CXGN::Stock::OrderBatch->new({ bcs_schema => $schema, people_schema => $people_schema});
         $order_prop->clone_list(\@item_list);
         $order_prop->parent_id($order_id);
diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index b4613764b1..4a063bbb70 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -210,30 +210,39 @@ jQuery(document).ready( function() {
     });
 
     jQuery('#add_item_button').click(function(){
-        var item_name = jQuery('#cart_item_name').val();
-        var item_quantity = jQuery('#item_quantity').val();
-        if (!item_quantity) {
-            item_quantity = '1';
-        }
-        if (ordering_service_name == 'ONA') {
-            var item_additional_info = jQuery('#item_additional_info').val();
-            if (!item_additional_info) {
-                alert("Please select additional info");
-                return;
-            }
-        }
-        var item_comments = jQuery('#item_comments').val();
-
-        if (!item_comments && !item_additional_info) {
-            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity;
-        } else if ((!item_comments) && (item_additional_info)) {
-            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity + ',' + ' ' + 'Additional Info:' + ' ' + item_additional_info;
-        } else if ((item_comments) && (!item_additional_info)) {
-            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity + ',' + ' ' + 'Comments:' + ' ' + item_comments;
-        } else if (item_comments && item_additional_info) {
-            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity + ',' + ' ' + 'Additional Info:' + ' ' + item_additional_info + ',' + ' ' + 'Comments:' + ' ' + item_comments;
+        var order_details = {};
+        var item_name = jQuery('#item_name').val();
+        order_details['Item Name'] = item_name;
+        for(var i=0; i<property_keys.length; i++){
+            var each_value = jQuery('#'+ i +'').val();
+            order_details[property_keys[i]] = each_value;
         }
 
+        var item_string = JSON.stringify(order_details);
+
+//        var item_quantity = jQuery('#item_quantity').val();
+//        if (!item_quantity) {
+//            item_quantity = '1';
+//        }
+//        if (ordering_service_name == 'ONA') {
+//            var item_additional_info = jQuery('#item_additional_info').val();
+//            if (!item_additional_info) {
+//                alert("Please select additional info");
+//                return;
+//            }
+//        }
+//        var item_comments = jQuery('#item_comments').val();
+
+//        if (!item_comments && !item_additional_info) {
+//            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity;
+//        } else if ((!item_comments) && (item_additional_info)) {
+//            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity + ',' + ' ' + 'Additional Info:' + ' ' + item_additional_info;
+//        } else if ((item_comments) && (!item_additional_info)) {
+//            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity + ',' + ' ' + 'Comments:' + ' ' + item_comments;
+//        } else if (item_comments && item_additional_info) {
+//            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity + ',' + ' ' + 'Additional Info:' + ' ' + item_additional_info + ',' + ' ' + 'Comments:' + ' ' + item_comments;
+//        }
+
         var lo = new CXGN.List();
 
         var myCart = lo.availableLists('catalog_items')
@@ -344,26 +353,26 @@ function addToCart(item_name, additional_order_info, ordering_service_name, orde
     var properties = order_properties.split(",");
     var html = '';
 
-    if (ordering_type == 'single_step') {
+//    if (ordering_type == 'single_step') {
         html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="item_name" name="item_name" value="'+item_name+'" disabled></div><br><br><br>';
         for(var i=0; i<properties.length; i++){
             html = html + '<label class="col-sm-3 control-label">'+ properties[i] +'</label><div class="col-sm-9" ><input class="form-control" id= '+ i +' name= '+ i +' placeholder=""></div><br><br><br>';
         }
         html = html + '</div></div></form>';
-    } else {
-        html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="cart_item_name" name="cart_item_name" value="'+item_name+'" disabled></div></div>';
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div></div>';
-        if (ordering_service_name == 'ONA') {
-            html = html + '<div class="form-group"><label class="col-sm-3 control-label">Additional Info: </label><div class="col-sm-9" ><select class="form-control" id="item_additional_info" name="item_additional_info"><option disabled value="" selected hidden>Please select a required clone stage</option>';
-            if (additional_info) {
-                for (var i=0; i<additional_info.length; i++) {
-                    html = html + '<option value='+additional_info[i]+'>'+additional_info[i]+'</option>';
-                }
-            }
-            html = html + '</select></div></div>';
-        }
-        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Comments: </label><div class="col-sm-9" ><input class="form-control" id="item_comments" name="item_comments" placeholder="Optional"</div></div></form>';
-    }
+//    } else {
+//        html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="cart_item_name" name="cart_item_name" value="'+item_name+'" disabled></div></div>';
+//        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div></div>';
+//        if (ordering_service_name == 'ONA') {
+//            html = html + '<div class="form-group"><label class="col-sm-3 control-label">Additional Info: </label><div class="col-sm-9" ><select class="form-control" id="item_additional_info" name="item_additional_info"><option disabled value="" selected hidden>Please select a required clone stage</option>';
+//            if (additional_info) {
+//                for (var i=0; i<additional_info.length; i++) {
+//                    html = html + '<option value='+additional_info[i]+'>'+additional_info[i]+'</option>';
+//                }
+//            }
+//            html = html + '</select></div></div>';
+//        }
+//        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Comments: </label><div class="col-sm-9" ><input class="form-control" id="item_comments" name="item_comments" placeholder="Optional"</div></div></form>';
+//    }
     jQuery('#add_item_detail_div').html(html);
     jQuery('#add_item_detail_dialog').modal('show');
 

From 3ee59d75ad2a4d430fc3d8b1ddba83b131a7a4d1 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sun, 18 Dec 2022 16:28:56 +0000
Subject: [PATCH 22/33] modified item details display

---
 lib/SGN/Controller/AJAX/Order.pm | 66 ++++++++++++++++++++++----------
 1 file changed, 45 insertions(+), 21 deletions(-)

diff --git a/lib/SGN/Controller/AJAX/Order.pm b/lib/SGN/Controller/AJAX/Order.pm
index 036a5750c7..13f1d7d7db 100644
--- a/lib/SGN/Controller/AJAX/Order.pm
+++ b/lib/SGN/Controller/AJAX/Order.pm
@@ -91,6 +91,7 @@ sub submit_order_POST : Args(0) {
         $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'item_type'} = $item_type;
         $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'material_source'} = $item_source;
         $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name} = \%each_item_details;
+    }
 
 #        my $quantity_string = $ordered_item_split[1];
 #        my @quantity_info = split /:/, $quantity_string;
@@ -131,7 +132,7 @@ sub submit_order_POST : Args(0) {
 
 #        @ona_info = ($item_source, $item_name, $quantity, $ona_additional_info, $request_date);
 #        $group_by_contact_id{$contact_person_id}{'ona'}{$item_name} = \@ona_info;
-    }
+#    }
 
     my $ordering_service_name = $c->config->{ordering_service_name};
     my $ordering_service_url = $c->config->{ordering_service_url};
@@ -401,7 +402,9 @@ sub get_user_current_orders :Path('/ajax/order/current') Args(0) {
         if (($order->{'order_status'}) ne 'completed') {
             my $clone_list = $order->{'clone_list'};
             my $item_name;
+            my @all_item_details = ();
             my $all_details_string;
+            my $empty_string = '';
             foreach my $each_item (@$clone_list) {
                 my @request_details = ();
                 $item_name = (keys %$each_item)[0];
@@ -411,8 +414,11 @@ sub get_user_current_orders :Path('/ajax/order/current') Args(0) {
                     my $detail_string = $field. ":"."".$each_detail;
                     push @request_details, $detail_string;
                 }
-                $all_details_string = join("<br>", @request_details);
+                push @request_details, $empty_string;
+                my $details_string = join("<br>", @request_details);
+                push @all_item_details, $details_string;
             }
+            $all_details_string = join("<br>", @all_item_details);
             push @current_orders, [qq{<a href="/order/details/view/$order->{'order_id'}">$order->{'order_id'}</a>}, $order->{'create_date'}, $all_details_string, $order->{'order_status'}, $order->{'order_to_name'}, $order->{'comments'}]
         }
 
@@ -475,6 +481,8 @@ sub get_user_completed_orders :Path('/ajax/order/completed') Args(0) {
         if (($order->{'order_status'}) eq 'completed') {
             my $clone_list = $order->{'clone_list'};
             my $item_name;
+            my @all_item_details = ();
+            my $empty_string = '';
             my $all_details_string;
             foreach my $each_item (@$clone_list) {
                 my @request_details = ();
@@ -485,8 +493,12 @@ sub get_user_completed_orders :Path('/ajax/order/completed') Args(0) {
                     my $detail_string = $field. ":"."".$each_detail;
                     push @request_details, $detail_string;
                 }
-                $all_details_string = join("<br>", @request_details);
+                push @request_details, $empty_string;
+                my $details_string = join("<br>", @request_details);
+                push @all_item_details, $details_string;
             }
+            $all_details_string = join("<br>", @all_item_details);
+
             push @completed_orders, [qq{<a href="/order/details/view/$order->{'order_id'}">$order->{'order_id'}</a>}, $order->{'create_date'}, $all_details_string, $order->{'order_status'}, $order->{'completion_date'}, $order->{'order_to_name'}, $order->{'comments'}]
         }
     }
@@ -528,26 +540,33 @@ sub get_vendor_current_orders :Path('/ajax/order/vendor_current_orders') Args(0)
 
     my @vendor_current_orders;
     my @all_vendor_orders = @$vendor_orders_ref;
-        foreach my $vendor_order (@all_vendor_orders) {
-            if (($vendor_order->{'order_status'}) ne 'completed') {
-                my $clone_list = $vendor_order->{'clone_list'};
-                my $item_name;
-                my $all_details_string;
-                foreach my $each_item (@$clone_list) {
-                    my @request_details = ();
-                    $item_name = (keys %$each_item)[0];
-                    push @request_details, "<b>"."Item Name"."<b>". ":"."".$item_name;
-                    foreach my $field (@properties) {
-                        my $each_detail = $each_item->{$item_name}->{$field};
-                        my $detail_string = $field. ":"."".$each_detail;
-                        push @request_details, $detail_string;
-                    }
-                    $all_details_string = join("<br>", @request_details);
+    foreach my $vendor_order (@all_vendor_orders) {
+        if (($vendor_order->{'order_status'}) ne 'completed') {
+            my $clone_list = $vendor_order->{'clone_list'};
+            my $item_name;
+            my @all_item_details = ();
+            my $all_details_string;
+            my $empty_string = '';
+            foreach my $each_item (@$clone_list) {
+                my @request_details = ();
+                $item_name = (keys %$each_item)[0];
+                push @request_details, "<b>"."Item Name"."<b>". ":"."".$item_name;
+                foreach my $field (@properties) {
+                    my $each_detail = $each_item->{$item_name}->{$field};
+                    my $detail_string = $field. ":"."".$each_detail;
+                    push @request_details, $detail_string;
                 }
-                $vendor_order->{'order_details'} = $all_details_string;
-                push @vendor_current_orders, $vendor_order
+                push @request_details, $empty_string;
+                my $details_string = join("<br>", @request_details);
+
+                push @all_item_details, $details_string;
             }
+            $all_details_string = join("<br>", @all_item_details);
+
+            $vendor_order->{'order_details'} = $all_details_string;
+            push @vendor_current_orders, $vendor_order
         }
+    }
 
     $c->stash->{rest} = {data => \@vendor_current_orders};
 
@@ -583,6 +602,8 @@ sub get_vendor_completed_orders :Path('/ajax/order/vendor_completed_orders') Arg
         if (($vendor_order->{'order_status'}) eq 'completed') {
             my $clone_list = $vendor_order->{'clone_list'};
             my $item_name;
+            my @all_item_details = ();
+            my $empty_string = '';
             my $all_details_string;
             foreach my $each_item (@$clone_list) {
                 my @request_details = ();
@@ -593,8 +614,11 @@ sub get_vendor_completed_orders :Path('/ajax/order/vendor_completed_orders') Arg
                     my $detail_string = $field. ":"."".$each_detail;
                     push @request_details, $detail_string;
                 }
-                $all_details_string = join("<br>", @request_details);
+                push @request_details, $empty_string;
+                my $details_string = join("<br>", @request_details);
+                push @all_item_details, $details_string;
             }
+            $all_details_string = join("<br>", @all_item_details);
             $vendor_order->{'order_details'} = $all_details_string;
 
             push @vendor_completed_orders, $vendor_order

From 2bcc1e751b26ede51493d89f7a277ec5e395eab9 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sun, 18 Dec 2022 18:34:19 +0000
Subject: [PATCH 23/33] clean up

---
 lib/CXGN/Stock/Catalog.pm          |  3 +-
 lib/CXGN/Stock/Order.pm            | 69 +------------------------
 lib/SGN/Controller/AJAX/Catalog.pm |  9 ----
 lib/SGN/Controller/AJAX/Order.pm   | 81 +-----------------------------
 lib/SGN/Controller/Catalog.pm      |  1 -
 5 files changed, 3 insertions(+), 160 deletions(-)

diff --git a/lib/CXGN/Stock/Catalog.pm b/lib/CXGN/Stock/Catalog.pm
index bcf20f1d77..6affea6310 100644
--- a/lib/CXGN/Stock/Catalog.pm
+++ b/lib/CXGN/Stock/Catalog.pm
@@ -19,7 +19,7 @@ has 'item_type' => ( isa => 'Str', is => 'rw');
 has 'material_type' => ( isa => 'Str', is => 'rw');
 
 # center that generates clones or seed
-has 'material_source' => ( isa => 'Str', is => 'rw');
+has 'material_source' => ( isa => 'Str', is => 'rw')
 
 has 'category' => ( isa => 'Str', is => 'rw' );
 
@@ -99,7 +99,6 @@ sub get_item_details {
     foreach my $field (@fields){
         push @item_details, $detail_hash->{$field};
     }
-#    print STDERR "ITEM DETAILS =".Dumper(\@item_details)."\n";
 
     return \@item_details;
 }
diff --git a/lib/CXGN/Stock/Order.pm b/lib/CXGN/Stock/Order.pm
index bb3884f869..53fe594560 100644
--- a/lib/CXGN/Stock/Order.pm
+++ b/lib/CXGN/Stock/Order.pm
@@ -98,29 +98,8 @@ sub get_orders_from_person_id {
             my $item_json = $item_result->value();
             my $item_hash = JSON::Any->jsonToObj($item_json);
             $all_items = $item_hash->{'clone_list'};
-#            foreach my $each_item (@$all_items) {
-#                my $item_name = (keys %$each_item)[0];
-#                my $quantity = $each_item->{$item_name}->{'quantity'};
-#                my $comments = $each_item->{$item_name}->{'comments'};
-#                my $additional_info = $each_item->{$item_name}->{'additional_info'};
-
-#                my $each_item_details;
-#                if ($additional_info && $comments) {
-#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info. "," . " " . "comments:" . $comments;
-#                } elsif ($additional_info && (!$comments)){
-#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info;
-#                } elsif ((!$additional_info) && $comments) {
-#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . "," . " "."comments:" . $comments;
-#                } else {
-#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity;
-#                }
-#                push @list, $each_item_details;
-#            }
-#            my @sort_list = sort @list;
-#            $item_list = join("<br>", @sort_list);
         }
 
-#        push @orders, [$order_id, $create_date, $item_list, $order_status, $completion_date, $order_to_name, $comments ];
         push @orders, {
             order_id => $order_id,
             create_date => $create_date,
@@ -148,7 +127,6 @@ sub get_orders_to_person_id {
         my $item_list;
         my $order_id = $result->sp_order_id();
         my $order_from_id = $result->order_from_id();
-#        my $order_to_id = $result->order_to_id();
         my $order_status = $result->order_status();
         my $create_date = $result->create_date();
         my $completion_date = $result->completion_date();
@@ -163,26 +141,6 @@ sub get_orders_to_person_id {
             my $item_json = $item_result->value();
             my $item_hash = JSON::Any->jsonToObj($item_json);
             $all_items = $item_hash->{'clone_list'};
-#            foreach my $each_item (@$all_items) {
-#                my $item_name = (keys %$each_item)[0];
-#                my $quantity = $each_item->{$item_name}->{'quantity'};
-#                my $comments = $each_item->{$item_name}->{'comments'};
-#                my $additional_info = $each_item->{$item_name}->{'additional_info'};
-#
-#                my $each_item_details;
-#                if ($additional_info && $comments) {
-#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info. "," . " " . "comments:" . $comments;
-#                } elsif ($additional_info && (!$comments)){
-#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info;
-#                } elsif ((!$additional_info) && $comments) {
-#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . "," . " "."comments:" . $comments;
-#                } else {
-#                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity;
-#                }
-#                push @list, $each_item_details;
-#            }
-#            my @sort_list = sort @list;
-#            $item_list = join("<br>", @sort_list);
         }
 
         push @orders, {
@@ -195,7 +153,7 @@ sub get_orders_to_person_id {
             contact_person_comments => $comments
         }
     }
-#    print STDERR "ORDERS =".Dumper(\@orders)."\n";
+
     return \@orders;
 }
 
@@ -227,32 +185,7 @@ sub get_order_details {
     my $item_hash = JSON::Any->jsonToObj($item_json);
     my $all_items = $item_hash->{'clone_list'};
 
-
-
-#    my @list;
-#    foreach my $each_item (@$all_items) {
-#        my $item_name = (keys %$each_item)[0];
-#        my $quantity = $each_item->{$item_name}->{'quantity'};
-#        my $comments = $each_item->{$item_name}->{'comments'};
-#        my $additional_info = $each_item->{$item_name}->{'additional_info'};
-
-#        my $each_item_details;
-#        if ($additional_info && $comments) {
-#            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info. "," . " " . "comments:" . $comments;
-#        } elsif ($additional_info && (!$comments)){
-#            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info;
-#        } elsif ((!$additional_info) && $comments) {
-#            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . "," . " "."comments:" . $comments;
-#        } else {
-#            $each_item_details = $item_name . "," . " " . "quantity:" . $quantity;
-#        }
-#        push @list, $each_item_details;
-#    }
-#    my @sort_list = sort @list;
-#    my $item_list = join("<br>", @sort_list);
-
     push @order_details, $order_id, $order_from_name, $create_date, $all_items, $order_to_name, $order_status, $comments;
-#    print STDERR "DETAILS =".Dumper(\@order_details)."\n";
 
     return \@order_details;
 
diff --git a/lib/SGN/Controller/AJAX/Catalog.pm b/lib/SGN/Controller/AJAX/Catalog.pm
index 978b5aaf42..af4182d617 100644
--- a/lib/SGN/Controller/AJAX/Catalog.pm
+++ b/lib/SGN/Controller/AJAX/Catalog.pm
@@ -92,9 +92,6 @@ sub add_catalog_item_POST : Args(0) {
     $stock_catalog->additional_info($item_additional_info);
     $stock_catalog->contact_person_id($sp_person_id);
 
-#    $stock_catalog->description($item_description);
-#    $stock_catalog->availability($item_availability);
-
     $stock_catalog->store();
 
     if (!$stock_catalog->store()){
@@ -317,18 +314,12 @@ sub item_image_list :Path('/ajax/catalog/image_list') :Args(1) {
         my $image_page  = "/image/view/$image_obj_id";
         my $small_image = $image_obj->get_image_url("thumbnail");
 
-#        print STDERR "IMAGE OBJECT ID =".Dumper($image_obj_id)."\n";
-#        print STDERR "IMAGE OBJECT NAME =".Dumper($image_obj_name)."\n";
-#        print STDERR "IMAGE OBJECT DESCRIPTION =".Dumper($image_obj_description)."\n";
-#        print STDERR "IMAGE MEDIUM =".Dumper($medium_image)."\n";
-#        print STDERR "IMAGE PAGE =".Dumper($image_page)."\n";
         push @image_list, {
                 image_id => $image_obj_id,
                 image_name => $image_obj_name,
                 small_image => qq|<a href="$medium_image"  title="<a href=$image_page>Go to image page ($image_obj_name)</a>" class="stock_image_group" rel="gallery-figures"><img src="$small_image"/></a> |,
                 image_description => $image_obj_description,
             };
-#            print STDERR "IMAGE LIST =".Dumper(\@image_list)."\n";
     }
 
     $c->stash->{rest} = {data => \@image_list};
diff --git a/lib/SGN/Controller/AJAX/Order.pm b/lib/SGN/Controller/AJAX/Order.pm
index 13f1d7d7db..3125dabaa0 100644
--- a/lib/SGN/Controller/AJAX/Order.pm
+++ b/lib/SGN/Controller/AJAX/Order.pm
@@ -49,8 +49,6 @@ sub submit_order_POST : Args(0) {
     my $order_properties = $c->config->{order_properties};
     my @properties = split ',',$order_properties;
 
-#    print STDERR "LIST ID =".Dumper($list_id)."\n";
-
     if (!$c->user()) {
         print STDERR "User not logged in... not adding a catalog item.\n";
         $c->stash->{rest} = {error_string => "You must be logged in to add a catalog item." };
@@ -77,9 +75,6 @@ sub submit_order_POST : Args(0) {
             $each_item_details{$field} = $order_details{$field};
         }
 
-#        my @ordered_item_split = split /,/, $ordered_item;
-#        my $number_of_fields = @ordered_item_split;
-#        my $item_name = $ordered_item_split[0];
         my $item_rs = $schema->resultset("Stock::Stock")->find( { uniquename => $item_name });
         my $item_id = $item_rs->stock_id();
         my $item_info_rs = $schema->resultset("Stock::Stockprop")->find({stock_id => $item_id, type_id => $catalog_cvterm_id});
@@ -93,46 +88,8 @@ sub submit_order_POST : Args(0) {
         $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name} = \%each_item_details;
     }
 
-#        my $quantity_string = $ordered_item_split[1];
-#        my @quantity_info = split /:/, $quantity_string;
-#        my $quantity = $quantity_info[1];
-#        $quantity =~ s/^\s+|\s+$//g;
-#        $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'quantity'} = $quantity;
-
-#        my $ona_additional_info;
-#        if ($number_of_fields == 3) {
-#            my $optional_field = $ordered_item_split[2];
-#            my @optional_field_array = split /:/, $optional_field;
-#            my $optional_title = $optional_field_array[0];
-#            $optional_title =~ s/^\s+|\s+$//g;
-#            print STDERR "OPTIONAL TITLE =".Dumper($optional_title)."\n";
-#            my $optional_info = $optional_field_array[1];
-#            $optional_info =~ s/^\s+|\s+$//g;
-#            print STDERR "OPTIONAL INFO =".Dumper($optional_info)."\n";
-#            if ($optional_title eq 'Comments') {
-#                $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'comments'} = $optional_info;
-#            } elsif ($optional_title eq 'Additional Info') {
-#                $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'additional_info'} = $optional_info;
-#                $ona_additional_info = $optional_info;
-#                print STDERR "ONA ADDITIONAL INFO =".Dumper($ona_additional_info)."\n";
-#            }
-#        } elsif ($number_of_fields == 4) {
-#            my $additional_info_field = $ordered_item_split[2];
-#            my @additional_info_array = split /:/, $additional_info_field;
-#            my $additional_info = $additional_info_array[1];
-#            $additional_info =~ s/^\s+|\s+$//g;
-#            $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'additional_info'} = $additional_info;
-#            $ona_additional_info = $additional_info;
-#            my $comments_field = $ordered_item_split[3];
-#            my @comments_array = split /:/, $comments_field;
-#            my $comments = $comments_array[1];
-#            $comments =~ s/^\s+|\s+$//g;
-#            $group_by_contact_id{$contact_person_id}{'item_list'}{$item_name}{'comments'} = $comments;
-#        }
-
 #        @ona_info = ($item_source, $item_name, $quantity, $ona_additional_info, $request_date);
 #        $group_by_contact_id{$contact_person_id}{'ona'}{$item_name} = \@ona_info;
-#    }
 
     my $ordering_service_name = $c->config->{ordering_service_name};
     my $ordering_service_url = $c->config->{ordering_service_url};
@@ -152,7 +109,6 @@ sub submit_order_POST : Args(0) {
         $new_order->order_status("submitted");
         $new_order->create_date($timestamp);
         my $order_id = $new_order->store();
-#        print STDERR "ORDER ID =".($order_id)."\n";
         if (!$order_id){
             $c->stash->{rest} = {error_string => "Error saving your order",};
             return;
@@ -160,7 +116,7 @@ sub submit_order_POST : Args(0) {
 
         $history_info ->{'submitted'} = $timestamp;
         push @history, $history_info;
-        print STDERR "ITEM LIST =".Dumper(\@item_list)."\n";
+
         my $order_prop = CXGN::Stock::OrderBatch->new({ bcs_schema => $schema, people_schema => $people_schema});
         $order_prop->clone_list(\@item_list);
         $order_prop->parent_id($order_id);
@@ -221,7 +177,6 @@ sub submit_order_POST : Args(0) {
                     my $message_hash_d = decode_json $message_d;
                     foreach my $t (@$message_hash_d) {
                         if ($t->{'data_value'} eq $order_file_name) {
-#                        print STDERR "DELETE INFO =".Dumper($t)."\n";
                             getstore($t->{media_url}, $previous_order_temp_file_path);
                             $order_ona_id = $t->{id};
                         }
@@ -422,33 +377,6 @@ sub get_user_current_orders :Path('/ajax/order/current') Args(0) {
             push @current_orders, [qq{<a href="/order/details/view/$order->{'order_id'}">$order->{'order_id'}</a>}, $order->{'create_date'}, $all_details_string, $order->{'order_status'}, $order->{'order_to_name'}, $order->{'comments'}]
         }
 
-        #                my $quantity = $each_item->{$item_name}->{'quantity'};
-        #                my $comments = $each_item->{$item_name}->{'comments'};
-        #                my $additional_info = $each_item->{$item_name}->{'additional_info'};
-
-        #                my $each_item_details;
-        #                if ($additional_info && $comments) {
-        #                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info. "," . " " . "comments:" . $comments;
-        #                } elsif ($additional_info && (!$comments)){
-        #                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . ",". " "."additional info:". $additional_info;
-        #                } elsif ((!$additional_info) && $comments) {
-        #                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity . "," . " "."comments:" . $comments;
-        #                } else {
-        #                    $each_item_details = $item_name . "," . " " . "quantity:" . $quantity;
-        #                }
-        #                push @list, $each_item_details;
-        #            }
-        #            my @sort_list = sort @list;
-        #            $item_list = join("<br>", @sort_list);
-
-#            push @current_orders, [qq{<a href="/order/details/view/$order->[0]">$order->[0]</a>}, $order->[1], $order->[2], $order->[3], $order->[5], $order->[6]]
-    }
-#    foreach my $order (@all_orders) {
-#        if (($order->[3]) ne 'completed') {
-#            push @current_orders, [qq{<a href="/order/details/view/$order->[0]">$order->[0]</a>}, $order->[1], $order->[2], $order->[3], $order->[5], $order->[6]]
-#        }
-#    }
-
     $c->stash->{rest} = {data => \@current_orders};
 }
 
@@ -503,13 +431,6 @@ sub get_user_completed_orders :Path('/ajax/order/completed') Args(0) {
         }
     }
 
-
-#    foreach my $order (@all_orders) {
-#        if (($order->[3]) eq 'completed') {
-#            push @completed_orders, [qq{<a href="/order/details/view/$order->[0]">$order->[0]</a>}, $order->[1], $order->[2], $order->[3], $order->[4], $order->[5], $order->[6]]
-#        }
-#    }
-
     $c->stash->{rest} = {data => \@completed_orders};
 
 }
diff --git a/lib/SGN/Controller/Catalog.pm b/lib/SGN/Controller/Catalog.pm
index 0db624f2b7..daf78ddb74 100644
--- a/lib/SGN/Controller/Catalog.pm
+++ b/lib/SGN/Controller/Catalog.pm
@@ -70,7 +70,6 @@ sub catalog_item_details : Path('/catalog/item_details') Args(1) {
         return;
     } else {
         $item_prop_id = $stock_catalog_info->stockprop_id();
-#        print STDERR "STOCKPROP ID =".Dumper($item_prop_id)."\n";
     }
 
     my $stock_catalog_item = $schema->resultset("Stock::Stock")->find({stock_id => $item_id});

From fc9e100e9bc94f170faa132a0d0343bc2924e92b Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sun, 18 Dec 2022 20:29:58 +0000
Subject: [PATCH 24/33] fixed syntax

---
 lib/CXGN/Stock/Catalog.pm        | 2 +-
 lib/SGN/Controller/AJAX/Order.pm | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/CXGN/Stock/Catalog.pm b/lib/CXGN/Stock/Catalog.pm
index 6affea6310..2d2cacba48 100644
--- a/lib/CXGN/Stock/Catalog.pm
+++ b/lib/CXGN/Stock/Catalog.pm
@@ -19,7 +19,7 @@ has 'item_type' => ( isa => 'Str', is => 'rw');
 has 'material_type' => ( isa => 'Str', is => 'rw');
 
 # center that generates clones or seed
-has 'material_source' => ( isa => 'Str', is => 'rw')
+has 'material_source' => ( isa => 'Str', is => 'rw');
 
 has 'category' => ( isa => 'Str', is => 'rw' );
 
diff --git a/lib/SGN/Controller/AJAX/Order.pm b/lib/SGN/Controller/AJAX/Order.pm
index 3125dabaa0..893351a23e 100644
--- a/lib/SGN/Controller/AJAX/Order.pm
+++ b/lib/SGN/Controller/AJAX/Order.pm
@@ -376,6 +376,7 @@ sub get_user_current_orders :Path('/ajax/order/current') Args(0) {
             $all_details_string = join("<br>", @all_item_details);
             push @current_orders, [qq{<a href="/order/details/view/$order->{'order_id'}">$order->{'order_id'}</a>}, $order->{'create_date'}, $all_details_string, $order->{'order_status'}, $order->{'order_to_name'}, $order->{'comments'}]
         }
+    }
 
     $c->stash->{rest} = {data => \@current_orders};
 }

From 9a6a9649fa8bc0017d0826d66517e7a3993d0675 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sun, 18 Dec 2022 21:39:57 +0000
Subject: [PATCH 25/33] clean up

---
 mason/order/catalog.mas | 26 ++++++--------------------
 1 file changed, 6 insertions(+), 20 deletions(-)

diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index 4a063bbb70..1ccb5d64b2 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -353,26 +353,12 @@ function addToCart(item_name, additional_order_info, ordering_service_name, orde
     var properties = order_properties.split(",");
     var html = '';
 
-//    if (ordering_type == 'single_step') {
-        html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="item_name" name="item_name" value="'+item_name+'" disabled></div><br><br><br>';
-        for(var i=0; i<properties.length; i++){
-            html = html + '<label class="col-sm-3 control-label">'+ properties[i] +'</label><div class="col-sm-9" ><input class="form-control" id= '+ i +' name= '+ i +' placeholder=""></div><br><br><br>';
-        }
-        html = html + '</div></div></form>';
-//    } else {
-//        html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="cart_item_name" name="cart_item_name" value="'+item_name+'" disabled></div></div>';
-//        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Quantity: </label><div class="col-sm-9" ><input class="form-control" id="item_quantity" name="item_quantity" placeholder=""></div></div>';
-//        if (ordering_service_name == 'ONA') {
-//            html = html + '<div class="form-group"><label class="col-sm-3 control-label">Additional Info: </label><div class="col-sm-9" ><select class="form-control" id="item_additional_info" name="item_additional_info"><option disabled value="" selected hidden>Please select a required clone stage</option>';
-//            if (additional_info) {
-//                for (var i=0; i<additional_info.length; i++) {
-//                    html = html + '<option value='+additional_info[i]+'>'+additional_info[i]+'</option>';
-//                }
-//            }
-//            html = html + '</select></div></div>';
-//        }
-//        html = html + '<div class="form-group"><label class="col-sm-3 control-label">Comments: </label><div class="col-sm-9" ><input class="form-control" id="item_comments" name="item_comments" placeholder="Optional"</div></div></form>';
-//    }
+    html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="item_name" name="item_name" value="'+item_name+'" disabled></div><br><br><br>';
+    for(var i=0; i<properties.length; i++){
+        html = html + '<label class="col-sm-3 control-label">'+ properties[i] +'</label><div class="col-sm-9" ><input class="form-control" id= '+ i +' name= '+ i +' placeholder=""></div><br><br><br>';
+    }
+    html = html + '</div></div></form>';
+
     jQuery('#add_item_detail_div').html(html);
     jQuery('#add_item_detail_dialog').modal('show');
 

From 7c40c9665eb33be586c228a6698db8355a735c6f Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sun, 18 Dec 2022 21:41:55 +0000
Subject: [PATCH 26/33] removed old format

---
 mason/order/catalog.mas | 23 -----------------------
 1 file changed, 23 deletions(-)

diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index 1ccb5d64b2..e79f3ba964 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -220,29 +220,6 @@ jQuery(document).ready( function() {
 
         var item_string = JSON.stringify(order_details);
 
-//        var item_quantity = jQuery('#item_quantity').val();
-//        if (!item_quantity) {
-//            item_quantity = '1';
-//        }
-//        if (ordering_service_name == 'ONA') {
-//            var item_additional_info = jQuery('#item_additional_info').val();
-//            if (!item_additional_info) {
-//                alert("Please select additional info");
-//                return;
-//            }
-//        }
-//        var item_comments = jQuery('#item_comments').val();
-
-//        if (!item_comments && !item_additional_info) {
-//            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity;
-//        } else if ((!item_comments) && (item_additional_info)) {
-//            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity + ',' + ' ' + 'Additional Info:' + ' ' + item_additional_info;
-//        } else if ((item_comments) && (!item_additional_info)) {
-//            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity + ',' + ' ' + 'Comments:' + ' ' + item_comments;
-//        } else if (item_comments && item_additional_info) {
-//            var item_string = item_name + ',' + ' ' + 'Quantity:' + ' ' + item_quantity + ',' + ' ' + 'Additional Info:' + ' ' + item_additional_info + ',' + ' ' + 'Comments:' + ' ' + item_comments;
-//        }
-
         var lo = new CXGN.List();
 
         var myCart = lo.availableLists('catalog_items')

From 16cef4e293be5aaacdb3779d1b66297c6d4f051e Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sun, 18 Dec 2022 22:13:33 +0000
Subject: [PATCH 27/33] fixed spreadsheet format info

---
 mason/order/upload_catalog_items_dialog.mas | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/mason/order/upload_catalog_items_dialog.mas b/mason/order/upload_catalog_items_dialog.mas
index 8b43020719..0a76a04679 100644
--- a/mason/order/upload_catalog_items_dialog.mas
+++ b/mason/order/upload_catalog_items_dialog.mas
@@ -98,12 +98,12 @@
                         <tbody>
                             <tr>
                                 <td>item_name</td>
-                                <td>type</td>
+                                <td>item_type</td>
+                                <td>material_type</td>
                                 <td>category</td>
-                                <td>description</td>
+                                <td>additional_info</td>
                                 <td>material_source</td>
                                 <td>breeding_program</td>
-                                <td>availability</td>
                                 <td>contact_person_username</td>
                             </tr>
                         </tbody>
@@ -111,12 +111,12 @@
                     <b>Required columns:</b>
                     <ul>
                         <li><b>item_name:</b>Item name must be in the database.</li>
-                        <li><b>type:</b>Must be one of the following (single item, set of items). This field can be customized, please contact us.</li>
-                        <li><b>category:</b>Must be one of the following (released variety, pathogen assay, control). This field can be customized, please contact us.</li>
-                        <li><b>description:</b>Please describe the key features of each item.</li>
-                        <li><b>material_source:</b>Must be one of the following (OrderingSystemTest, Sendusu). This field can be customized, please contact admin.</li>
+                        <li><b>item_type:</b>Must be one of the following (single item, set of items). This field can be customized, please contact us.</li>
+                        <li><b>material_type:</b>e.g. plant, seed, construct.</li>
+                        <li><b>category:</b> e.g. released variety, pathogen assay, control, transgenic line </li>
+                        <li><b>additional_info:</b> optional </li>
+                        <li><b>material_source:</b></li>
                         <li><b>breeding_program:</b>Breeding program must be in the database.</li>
-                        <li><b>availability:</b>Must be one of the following (in stock, out of stock, available in 3 months). This field can be customized, please contact us.</li>
                         <li><b>contact_person_username:</b>Please indicate contact person of each item. Contact person username must be in the database</li>
                     </ul>
                 </div>

From 6eaac3715137b7b73944f023106699f4f2a77bbe Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Mon, 19 Dec 2022 15:49:24 +0000
Subject: [PATCH 28/33] customize dropdown options based on each field

---
 lib/SGN/Controller/Catalog.pm |  3 ++-
 mason/order/catalog.mas       | 22 +++++++++++++++++-----
 2 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/lib/SGN/Controller/Catalog.pm b/lib/SGN/Controller/Catalog.pm
index daf78ddb74..84c037e6e1 100644
--- a/lib/SGN/Controller/Catalog.pm
+++ b/lib/SGN/Controller/Catalog.pm
@@ -30,12 +30,13 @@ sub stock_catalog :Path('/catalog/view') :Args(0) {
     $c->stash->{additional_order_info} = $additional_order_info;
 
     my $ordering_type = $c->config->{ordering_type};
-    print STDERR "ORDERING TYPE =".Dumper($ordering_type)."\n";
     $c->stash->{ordering_type} = $ordering_type;
 
     my $order_properties = $c->config->{order_properties};
+    my $order_properties_dialog = $c->config->{order_properties_dialog};
 
     $c->stash->{order_properties} = $order_properties;
+    $c->stash->{order_properties_dialog} = $order_properties_dialog;
 
     $c->stash->{template} = '/order/catalog.mas';
 
diff --git a/mason/order/catalog.mas b/mason/order/catalog.mas
index e79f3ba964..e3459513e5 100644
--- a/mason/order/catalog.mas
+++ b/mason/order/catalog.mas
@@ -5,6 +5,7 @@ $ordering_service_name => undef
 $additional_order_info => undef
 $ordering_type => undef
 $order_properties => undef
+$order_properties_dialog => undef
 
 </%args>
 
@@ -152,6 +153,8 @@ jQuery(document).ready( function() {
     var ordering_type = "<% $ordering_type %>";
     var order_properties = "<% $order_properties %>";
     var property_keys = order_properties.split(",");
+    var order_properties_dialog = "<% $order_properties_dialog %>";
+    var property_dialog_keys = order_properties_dialog.split(",");
 
     if (ordering_type == 'single_step') {
         jQuery('#catalog_items_table').DataTable( {
@@ -169,7 +172,7 @@ jQuery(document).ready( function() {
                 { title: "Additional Info", "data": "additional_info" },
                 { title: "Material Source", "data": "material_source" },
                 { title: "Program", "data": "breeding_program" },
-                { title: " ", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties+"\")'>Request</a>"; } },
+                { title: " ", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties_dialog+"\")'>Request</a>"; } },
             ],
         });
     } else {
@@ -188,7 +191,7 @@ jQuery(document).ready( function() {
                 { title: "Additional Info", "data": "additional_info" },
                 { title: "Material Source", "data": "material_source" },
                 { title: "Program", "data": "breeding_program" },
-                { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties+"\" )'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
+                { title: "Add to Cart", "data": "null", "render": function ( data, type, row ) { return "<a onclick='addToCart(\""+row.item_name+"\", \""+additional_order_info+"\", \""+ordering_service_name+"\", \""+ordering_type+"\", \""+order_properties_dialog+"\" )'><span class='glyphicon glyphicon-shopping-cart'></span></a>"; } },
             ],
         });
     }
@@ -325,14 +328,23 @@ jQuery(document).ready( function() {
 
 });
 
-function addToCart(item_name, additional_order_info, ordering_service_name, ordering_type, order_properties ){
+function addToCart(item_name, additional_order_info, ordering_service_name, ordering_type, order_properties_dialog ){
     var additional_info = additional_order_info.split(",");
-    var properties = order_properties.split(",");
+    var properties = order_properties_dialog.split(",");
     var html = '';
 
     html = html + '<form class="form-horizontal"><div class="form-group"><label class="col-sm-3 control-label">Item Name: </label><div class="col-sm-9" ><input class="form-control" id="item_name" name="item_name" value="'+item_name+'" disabled></div><br><br><br>';
     for(var i=0; i<properties.length; i++){
-        html = html + '<label class="col-sm-3 control-label">'+ properties[i] +'</label><div class="col-sm-9" ><input class="form-control" id= '+ i +' name= '+ i +' placeholder=""></div><br><br><br>';
+        var each_property_info = properties[i].split(":");
+        if (each_property_info.length == 1) {
+            html = html + '<label class="col-sm-3 control-label">'+ properties[i] +'</label><div class="col-sm-9" ><input class="form-control" id= '+ i +' name= '+ i +' placeholder=""></div><br><br><br>';
+        } else {
+            html = html + '<label class="col-sm-3 control-label">'+ each_property_info[0] +'</label><div class="col-sm-9" ><select class="form-control" id= '+ i +' name= '+ i +'> ';
+            for (var j=1; j<each_property_info.length; j++) {
+                html = html + "<option value='"+each_property_info[j]+"'>" + each_property_info[j] + "</option>";
+            }
+            html = html + "</select></div><br><br><br>";
+        }
     }
     html = html + '</div></div></form>';
 

From a53e96629e0ee61c75fff9728db1fd714ef24e6f Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Mon, 19 Dec 2022 22:00:49 +0000
Subject: [PATCH 29/33] add order_properties in sgn conf file

---
 lib/SGN/Controller/AJAX/Order.pm |  2 +-
 sgn.conf                         | 15 +++++++++++++++
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/lib/SGN/Controller/AJAX/Order.pm b/lib/SGN/Controller/AJAX/Order.pm
index 893351a23e..e46e7a19d8 100644
--- a/lib/SGN/Controller/AJAX/Order.pm
+++ b/lib/SGN/Controller/AJAX/Order.pm
@@ -101,7 +101,7 @@ sub submit_order_POST : Args(0) {
         my $history_info = {};
         my $item_ref = $group_by_contact_id{$contact_id}{'item_list'};
         my %item_hashes = %{$item_ref};
-        my @item_list = map { { $_ => $item_hashes{$_} } } keys %item_hashes;
+        my @item_list = map { { $_ => $item_hashes{$_} } } sort keys %item_hashes;
 
         my $new_order = CXGN::Stock::Order->new( { people_schema => $people_schema, dbh => $dbh});
         $new_order->order_from_id($user_id);
diff --git a/sgn.conf b/sgn.conf
index ec02d91dfc..0aea72d2b4 100644
--- a/sgn.conf
+++ b/sgn.conf
@@ -286,6 +286,21 @@ design_types Completely Randomized,Complete Block,Resolvable Row-Column,Doubly-R
 trial_activities Started Phenotyping, Phenotyping Completed, Data Cleaning Completed, Data Analysis Completed
 ##
 
+### properties for ordering system (required 2 sets of order properties: order_properties and order_properties_dialog)
+### customized dropdown menu can be included in the order_properties_dialog. Dropdown menu can be linked with each property by using ":"
+### for example Facility and Experiment Type properties have customized dropdown menu:
+#order_properties Quantity,Facility,Scientist,Required by Date,Experiment Name,Experiment Type
+#order_properties_dialog Quantity,Facility:green house:growth chamber,Scientist,Required by Date,Experiment Name,Experiment Type:seed production:experimentation
+
+###for setting up a single step submission use the following:
+#ordering_type single_step
+##two steps (adding to your cart first) is by default
+
+order_properties Quantity,Comments
+order_properties_dialog Quantity,Comments
+
+##
+
 <feature SGN::Feature::FeaturePages>
     enabled      1
 </feature>

From acaaaecdef48bfa0ce03ff0d7e0d4fc52d7b9906 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Mon, 19 Dec 2022 22:34:42 +0000
Subject: [PATCH 30/33] fixed error messages

---
 mason/order/add_catalog_item_dialog.mas | 30 ++++++++++++++++++++-----
 1 file changed, 24 insertions(+), 6 deletions(-)

diff --git a/mason/order/add_catalog_item_dialog.mas b/mason/order/add_catalog_item_dialog.mas
index 092f6592d0..1882180b16 100644
--- a/mason/order/add_catalog_item_dialog.mas
+++ b/mason/order/add_catalog_item_dialog.mas
@@ -133,12 +133,30 @@ jQuery(document).ready(function(){
         var breeding_program = jQuery('#item_breeding_program_id').val();
         var contact_person = jQuery('#contact_person_name').val();
 
-        if (name == '') { alert("Please provide a name") };
-        if (type == '') { alert("Please select a type") };
-        if (material_type == '') { alert("Please select a material type") };
-        if (category == '') { alert("Please select a category") };
-        if (breeding_program == '') { alert("Please select a program") };
-        if (contact_person == '') { alert("Please indicate contact person") };
+        if (name == '') {
+            alert("Please provide a name");
+            return;
+        }
+        if (type == '') {
+            alert("Please select an item type");
+            return;
+        }
+        if (material_type == '') {
+            alert("Please select a material type");
+            return;
+        }
+        if (category == '') {
+            alert("Please select a category");
+            return;
+        }
+        if (breeding_program == '') {
+            alert("Please select a program");
+            return;
+        }
+        if (contact_person == '') {
+            alert("Please provide contact username");
+            return;
+        }
 
         jQuery.ajax({
             url: '/ajax/catalog/add_item',

From a348db9f082f92c55c4b6d2eed0810f4cb3cae3e Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Tue, 20 Dec 2022 15:47:30 +0000
Subject: [PATCH 31/33] fixed tests for catalog

---
 sgn_test.conf                            |  32 ++++++++++++-----------
 t/data/stock/catalog_items.xls           | Bin 7168 -> 7168 bytes
 t/data/stock/catalog_items.xlsx          | Bin 8940 -> 7212 bytes
 t/unit_fixture/CXGN/Stock/CatalogOrder.t |  27 ++++++++++++++-----
 4 files changed, 38 insertions(+), 21 deletions(-)

diff --git a/sgn_test.conf b/sgn_test.conf
index 16013c6b9c..e062968756 100644
--- a/sgn_test.conf
+++ b/sgn_test.conf
@@ -124,21 +124,23 @@ solyc_conversion_files /home/production/solcyc_conversion_files/tomato_unigenes_
   search_path gem
 </DatabaseConnection>
 
-
-#ODK Services
-odk_crossing_data_service_name ONA
-odk_crossing_data_service_url https://ona.io
-odk_crossing_data_service_username seedtracker
-odk_crossing_data_service_password Seedtracking101
-odk_crossing_data_form_name BTractTest
-odk_crossing_data_test_form_name NULL
-odk_crossing_data_separate_wishlist_by_location 1
-odk_phenotyping_data_service_name NULL
-odk_phenotyping_data_service_url https://bio.smap.com.au
-odk_phenotyping_data_service_username SMAPUSER
-odk_phenotyping_data_service_password SMAPPASS
-crontab_file NULL
-crontab_log_filepath NULL
+order_properties Quantity,Comments
+order_properties_dialog Quantity,Comments
+
+##ODK Services
+##odk_crossing_data_service_name NULL
+##odk_crossing_data_service_url https://ona.io
+##odk_crossing_data_service_username seedtracker
+##odk_crossing_data_service_password Seedtracking101
+##odk_crossing_data_form_name BTractTest
+##odk_crossing_data_test_form_name NULL
+##odk_crossing_data_separate_wishlist_by_location 1
+##odk_phenotyping_data_service_name NULL
+##odk_phenotyping_data_service_url https://bio.smap.com.au
+##odk_phenotyping_data_service_username SMAPUSER
+##odk_phenotyping_data_service_password SMAPPASS
+##crontab_file NULL
+##crontab_log_filepath NULL
 
 
 noaa_ncdc_access_token DLPxdOEIwKyoiMSuQMRYrtMaiIUpNAwk
diff --git a/t/data/stock/catalog_items.xls b/t/data/stock/catalog_items.xls
index dfa7bfb88fcfa4efd39ee421b580aaac8e88bfd3..5a34a2310f26f8c07f828d1eb6cc4d6a47301e42 100644
GIT binary patch
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diff --git a/t/unit_fixture/CXGN/Stock/CatalogOrder.t b/t/unit_fixture/CXGN/Stock/CatalogOrder.t
index 3fb4d14140..039ba97c70 100644
--- a/t/unit_fixture/CXGN/Stock/CatalogOrder.t
+++ b/t/unit_fixture/CXGN/Stock/CatalogOrder.t
@@ -43,18 +43,33 @@ for my $extension ("xls", "xlsx") {
 
     my $program_id = $schema->resultset('Project::Project')->find({ name => 'test' })->project_id();
 
-    my $item_id = $schema->resultset("Stock::Stock")->find({ name => 'UG120001' })->stock_id();
+    my $item_rs = $schema->resultset("Stock::Stock")->find({ name => 'UG120001' });
+    my $item_id = $item_rs->stock_id();
     my $stock_catalog = CXGN::Stock::Catalog->new({
         bcs_schema => $schema,
         parent_id  => $item_id,
     });
 
+    my $variety_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'variety', 'stock_property')->cvterm_id();
+    my $organism_id = $item_rs->organism_id();
+    my $organism = $schema->resultset("Organism::Organism")->find({organism_id => $organism_id});
+    my $item_species = $organism->species();
+    my $item_variety;
+    my $item_stockprop = $schema->resultset("Stock::Stockprop")->find({stock_id => $item_id, type_id => $variety_type_id});
+    if ($item_stockprop) {
+        $item_variety = $item_stockprop->value();
+    } else {
+        $item_variety = 'NA';
+    }
+
     $stock_catalog->item_type('single item');
+    $stock_catalog->material_type('plant');
+    $stock_catalog->material_source('BTI');
     $stock_catalog->category('released variety');
-    $stock_catalog->description('test item');
-    $stock_catalog->material_source('Sendusu');
+    $stock_catalog->species($item_species);
+    $stock_catalog->variety($item_variety);
     $stock_catalog->breeding_program($program_id);
-    $stock_catalog->availability('in stock');
+    $stock_catalog->additional_info('test adding info');
     $stock_catalog->contact_person_id($johndoe_id);
 
     ok($stock_catalog->store(), "check adding catalog");
@@ -107,10 +122,10 @@ for my $extension ("xls", "xlsx") {
             bcs_schema        => $schema,
             item_type         => $catalog_info_hash{item_type},
             category          => $catalog_info_hash{category},
-            description       => $catalog_info_hash{description},
+            material_type       => $catalog_info_hash{material_type},
             material_source   => $catalog_info_hash{material_source},
             breeding_program  => $catalog_info_hash{breeding_program},
-            availability      => $catalog_info_hash{availability},
+            additional_info      => $catalog_info_hash{additional_info},
             contact_person_id => $catalog_info_hash{contact_person_id},
             parent_id         => $stock_id
         });

From 70be199dcf5fce26ed23ac769e10ad7b6b3991c1 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Tue, 20 Dec 2022 20:37:29 +0000
Subject: [PATCH 32/33] fixed tests for ordering

---
 t/unit_fixture/CXGN/Stock/CatalogOrder.t | 78 ++++++++++--------------
 1 file changed, 32 insertions(+), 46 deletions(-)

diff --git a/t/unit_fixture/CXGN/Stock/CatalogOrder.t b/t/unit_fixture/CXGN/Stock/CatalogOrder.t
index 039ba97c70..ec1cb2069e 100644
--- a/t/unit_fixture/CXGN/Stock/CatalogOrder.t
+++ b/t/unit_fixture/CXGN/Stock/CatalogOrder.t
@@ -15,7 +15,7 @@ use CXGN::Stock::OrderBatch;
 use CXGN::UploadFile;
 use CXGN::Stock::ParseUpload;
 use CXGN::List;
-
+use Test::WWW::Mechanize;
 use DateTime;
 
 use Data::Dumper;
@@ -27,8 +27,16 @@ my $schema = $f->bcs_schema();
 my $people_schema = $f->people_schema;
 my $dbh = $f->dbh();
 
+my $mech = Test::WWW::Mechanize->new;
+
 for my $extension ("xls", "xlsx") {
 
+    $mech->post_ok('http://localhost:3010/brapi/v1/token', [ "username" => "janedoe", "password" => "secretpw", "grant_type" => "password" ]);
+    my $response = decode_json $mech->content;
+    is($response->{'metadata'}->{'status'}->[2]->{'message'}, 'Login Successfull');
+    my $sgn_session_id = $response->{access_token};
+    print STDERR $sgn_session_id . "\n";
+
     #add vendor role for johndoe
     my $johndoe_id = CXGN::People::Person->get_person_by_username($dbh, 'johndoe');
     my $role_rs = $people_schema->resultset("SpRole")->find({ name => 'vendor' });
@@ -144,47 +152,14 @@ for my $extension ("xls", "xlsx") {
     my $your_cart_id = CXGN::List::create_list($dbh, 'your_cart', 'test shopping cart', $janedoe_id);
     my $list = CXGN::List->new({ dbh => $dbh, list_id => $your_cart_id });
     my $your_cart_type = $list->type('catalog_items');
-    my $item1 = $list->add_element("UG120001,Quantity: 2");
-    my $item2 = $list->add_element("UG120002,Quantity: 3");
+    my $item1 = $list->add_element('{"Item Name":"UG120001","Quantity":"2","Comments":""}');
+    my $item2 = $list->add_element('{"Item Name":"UG120002","Quantity":"3","Comments":""}');
 
     #test storing an order from janedoe, to johndoe
-    my $new_order = CXGN::Stock::Order->new({ people_schema => $people_schema, dbh => $dbh });
-    $new_order->order_from_id($janedoe_id);
-    $new_order->order_to_id($johndoe_id);
-    $new_order->order_status("submitted");
-    $new_order->create_date($timestamp);
-    ok(my $order_id = $new_order->store(), "check storing order");
-
-    #test storing orderprop
-    my $your_cart = CXGN::List->new({ dbh => $dbh, list_id => $your_cart_id });
-    my $items = $list->elements();
-    is_deeply($items, [ 'UG120001,Quantity: 2', 'UG120002,Quantity: 3' ], 'check items');
-
-    my @all_items = @$items;
-    my @clone_list;
-    foreach my $ordered_item (@all_items) {
-        my %item_hash;
-        my @ordered_item_split = split /,/, $ordered_item;
-        my $item_name = $ordered_item_split[0];
-
-        my $quantity_string = $ordered_item_split[1];
-        my @quantity_info = split /:/, $quantity_string;
-        my $quantity = $quantity_info[1];
-        $quantity =~ s/^\s+|\s+$//g;
-        $item_hash{$item_name}{'quantity'} = $quantity;
-        push @clone_list, \%item_hash;
-    }
-
-    my @history;
-    my $history_info = {};
-    $history_info->{'submitted'} = $timestamp;
-    push @history, $history_info;
 
-    my $order_prop = CXGN::Stock::OrderBatch->new({ bcs_schema => $schema, people_schema => $people_schema });
-    $order_prop->clone_list(\@clone_list);
-    $order_prop->parent_id($order_id);
-    $order_prop->history(\@history);
-    ok(my $order_prop_id = $order_prop->store_sp_orderprop(), "check storing orderprop");
+    $mech->post_ok('http://localhost:3010/ajax/order/submit', ['list_id' => $your_cart_id,]);
+    $response = decode_json $mech->content;
+    is($response->{'success'}, 'Your order has been submitted successfully and the vendor has been notified.');
 
     #delete your cart
     CXGN::List::delete_list($dbh, $your_cart_id);
@@ -192,24 +167,35 @@ for my $extension ("xls", "xlsx") {
     #test retrieving order from janedoe
     my $buyer_order_obj = CXGN::Stock::Order->new({ dbh => $dbh, people_schema => $people_schema, order_from_id => $janedoe_id });
     my $buyer_orders = $buyer_order_obj->get_orders_from_person_id();
-    is($buyer_orders->[0][0], '1');
-    is($buyer_orders->[0][2], 'UG120001, quantity:2<br>UG120002, quantity:3');
-    is($buyer_orders->[0][3], 'submitted');
-    is($buyer_orders->[0][4], undef);
-    is($buyer_orders->[0][5], 'John Doe');
-    is($buyer_orders->[0][6], undef);
+    my $first_order_info = $buyer_orders->[0];
+    is($first_order_info->{'order_id'}, '1');
+    is($first_order_info->{'order_status'}, 'submitted');
+    is($first_order_info->{'order_to_name'}, 'John Doe');
+
+    my $items = $first_order_info->{'clone_list'};
+    my $buyer_num_items = @$items;
+    is($buyer_num_items, '2');
 
     #test retrieving order to johndoe
     my $vendor_order_obj = CXGN::Stock::Order->new({ dbh => $dbh, people_schema => $people_schema, order_to_id => $johndoe_id });
     my $vendor_orders = $vendor_order_obj->get_orders_to_person_id();
+
     my $order = $vendor_orders->[0];
     is($order->{'order_id'}, '1');
-    is($order->{'item_list'}, 'UG120001, quantity:2<br>UG120002, quantity:3');
     is($order->{'order_status'}, 'submitted');
     is($order->{'order_from_name'}, 'Jane Doe');
     is($order->{'completion_date'}, undef);
     is($order->{'contact_person_comments'}, undef);
 
+    my $clone_list = $order->{'clone_list'};
+    my $vendor_num_items = @$clone_list;
+    is($vendor_num_items, '2');
+
+    #test_single_step_submission
+    $mech->post_ok('http://localhost:3010/ajax/order/single_step_submission', ['item_name' => 'UG120001', 'order_details' => '{"Quantity":"2","Comments":""}']);
+    $response = decode_json $mech->content;
+    is($response->{'success'}, 'Your request has been submitted successfully and the vendor has been notified.');
+
     #test deleting catalog
     my $catalog_rs = $schema->resultset("Stock::Stockprop")->search({ type_id => $catalog_type_id });
 

From b74a8be817a5a3602f423d8b5c58239c08946f51 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Tue, 20 Dec 2022 21:15:50 +0000
Subject: [PATCH 33/33] fixed plugin for catalog upload

---
 .../Stock/ParseUpload/Plugin/CatalogXLS.pm    | 24 ++++++++++---------
 mason/order/edit_catalog_details_dialog.mas   | 14 +++++------
 mason/order/upload_catalog_items_dialog.mas   | 10 ++++----
 3 files changed, 26 insertions(+), 22 deletions(-)

diff --git a/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm b/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
index a64d798418..8830a5f16f 100644
--- a/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
+++ b/lib/CXGN/Stock/ParseUpload/Plugin/CatalogXLS.pm
@@ -35,14 +35,19 @@ sub _validate_with_plugin {
     my %supported_types;
     my %supported_categories;
     my %supported_material_sources;
-    my %supported_availability;
+    my %supported_material_types;
 
     $supported_types{'single item'} = 1;
     $supported_types{'set of items'} = 1;
 
-#    $supported_categories{'released variety'} = 1;
-#    $supported_categories{'pathogen assay'} = 1;
-#    $supported_categories{'control'} = 1;
+    $supported_categories{'released variety'} = 1;
+    $supported_categories{'pathogen assay'} = 1;
+    $supported_categories{'control'} = 1;
+    $supported_categories{'transgenic line'} = 1;
+
+    $supported_material_types{'seed'} = 1;
+    $supported_material_types{'plant'} = 1;
+    $supported_material_types{'construct'} = 1;
 
 #    $supported_material_sources{'OrderingSystemTest'} = 1;
 #    $supported_material_sources{'Sendusu'} = 1;
@@ -203,19 +208,16 @@ sub _validate_with_plugin {
 
         if (!$material_type || $material_type eq '') {
             push @error_messages, "Cell C$row_name: material_type missing";
+        } elsif (!$supported_material_types{$material_type}) {
+            push @error_messages, "Cell C$row_name: material type is not supported: $material_type";
         }
 
         if (!$category || $category eq '') {
             push @error_messages, "Cell D$row_name: category missing";
+        } elsif (!$supported_categories{$category}) {
+            push @error_messages, "Cell C$row_name: category is not supported: $category";
         }
 
-#        } elsif (!$supported_categories{$category}) {
-#            push @error_messages, "Cell C$row_name: category is not supported: $category";
-#        }
-#        if (!$description || $description eq '') {
-#            push @error_messages, "Cell D$row_name: description missing";
-#        }
-
 #        if (!$material_source || $material_source eq '') {
 #            push @error_messages, "Cell E$row_name: material_source missing";
 #        } elsif (!$supported_material_sources{$material_source}) {
diff --git a/mason/order/edit_catalog_details_dialog.mas b/mason/order/edit_catalog_details_dialog.mas
index ee9d0f8f37..040068b5ec 100644
--- a/mason/order/edit_catalog_details_dialog.mas
+++ b/mason/order/edit_catalog_details_dialog.mas
@@ -64,9 +64,9 @@ $item_prop_id
                             <div class="col-sm-8">
                                 <div class="input-group">
                                     <select class="form-control" id="edit_material_type" value="<%$material_type%>">
-                                        <option value="Plant">Plant</option>
-                                        <option value="Seed">Seed</option>
-                                        <option value="Construct">Construct</option>
+                                        <option value="plant">plant</option>
+                                        <option value="seed">seed</option>
+                                        <option value="construct">construct</option>
                                     </select>
                                 </div>
                             </div>
@@ -76,10 +76,10 @@ $item_prop_id
                             <div class="col-sm-8">
                                 <div class="input-group">
                                     <select class="form-control" id="edit_item_category" value="<%$category%>">
-                                        <option value="Released Variety">Released Variety</option>
-                                        <option value="Pathogen Assay ">Pathogen Assay</option>
-                                        <option value="Control">Control</option>
-                                        <option value="Transgenic Line">Transgenic Line</option>
+                                        <option value="released variety">released variety</option>
+                                        <option value="pathogen assay ">pathogen assay</option>
+                                        <option value="control">control</option>
+                                        <option value="transgenic line">transgenic line</option>
                                     </select>
                                 </div>
                             </div>
diff --git a/mason/order/upload_catalog_items_dialog.mas b/mason/order/upload_catalog_items_dialog.mas
index 0a76a04679..8b8e9ca81e 100644
--- a/mason/order/upload_catalog_items_dialog.mas
+++ b/mason/order/upload_catalog_items_dialog.mas
@@ -94,6 +94,8 @@
                     <br>
                     <b>Header:</b>
                     <br>
+                    The first row (header) must contain the following:
+                    <br>
                     <table class="table table-bordered table-hover">
                         <tbody>
                             <tr>
@@ -112,10 +114,10 @@
                     <ul>
                         <li><b>item_name:</b>Item name must be in the database.</li>
                         <li><b>item_type:</b>Must be one of the following (single item, set of items). This field can be customized, please contact us.</li>
-                        <li><b>material_type:</b>e.g. plant, seed, construct.</li>
-                        <li><b>category:</b> e.g. released variety, pathogen assay, control, transgenic line </li>
-                        <li><b>additional_info:</b> optional </li>
-                        <li><b>material_source:</b></li>
+                        <li><b>material_type:</b>Must be one of the following (plant, seed, construct). This field can be customized, please contact us.</li>
+                        <li><b>category:</b>Must be one of the following (released variety, pathogen assay, control, transgenic line). This field can be customized, please contact us. </li>
+                        <li><b>additional_info:</b> (optional) </li>
+                        <li><b>material_source:</b> (optional)</li>
                         <li><b>breeding_program:</b>Breeding program must be in the database.</li>
                         <li><b>contact_person_username:</b>Please indicate contact person of each item. Contact person username must be in the database</li>
                     </ul>