Merge branch 'solgenomics/sgn:master' into develop

.github/workflows/test.yml

@@ -89,7 +89,7 @@ jobs:
     if: false #disabled for now, as testing script is broken
     runs-on: ubuntu-latest
     container:
-      image: breedbase/breedbase:v0.82
+      image: breedbase/breedbase:latest
       env:
         HOME: /root
         MODE: 'TESTING'

db/00174/AddListCreateDate.pm

@@ -57,7 +57,7 @@ sub patch {
         $self->dbh->do(<<EOSQL);
 
  --do your SQL here
-alter table sgn_people.list add column create_date timestamp NULL DEFAULT now();
+ALTER TABLE sgn_people.list ADD COLUMN IF NOT EXISTS create_date timestamp NULL DEFAULT now();
 EOSQL
 
         return 1;

db/00178/AddPhenotypeStderr.pm

@@ -0,0 +1,86 @@
+#!/usr/bin/env perl
+
+
+=head1 NAME
+
+ AddPhenotypeStderr.pm
+
+=head1 SYNOPSIS
+
+mx-run AddPhenotypeStderr.pm [options] -H hostname -D dbname -u username [-F]
+
+this is a subclass of L<CXGN::Metadata::Dbpatch>
+see the perldoc of parent class for more details.
+
+=head1 DESCRIPTION
+This patch adds phenotype_property cvterm for storing a phenotype standard error.
+This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
+
+=head1 AUTHOR
+
+Naama Menda<nm249@cornell.edu>
+
+=head1 COPYRIGHT & LICENSE
+
+Copyright 2010 Boyce Thompson Institute for Plant Research
+
+This program is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+
+package AddPhenotypeStderr;
+
+use Moose;
+use Bio::Chado::Schema;
+use Try::Tiny;
+extends 'CXGN::Metadata::Dbpatch';
+
+
+has '+description' => ( default => <<'' );
+This patch adds phenotype_property cvterm for storing phenotype standard error.
+
+has '+prereq' => (
+	default => sub {
+        [],
+    },
+
+  );
+
+sub patch {
+    my $self=shift;
+
+    print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
+
+    print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
+
+    print STDOUT "\nExecuting the SQL commands.\n";
+    my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
+
+
+    print STDERR "INSERTING CV TERMS...\n";
+
+    my $terms = {
+        'phenotype_property' => [
+            'phenotype_stderr',
+        ]
+    };
+
+	foreach my $t (keys %$terms){
+		foreach (@{$terms->{$t}}){
+			$schema->resultset("Cv::Cvterm")->create_with({
+				name => $_,
+				cv => $t
+			});
+		}
+	}
+
+
+print "You're done!\n";
+}
+
+
+####
+1; #
+####

docs/03_managing_breeding_data/03_12.md

@@ -2,24 +2,30 @@
 title: "3.12 Using the Label Designer"
 layout: doc_page
 ---
+
+<!-- TOC-START -->
+* TOC
+{:toc}
+<!-- TOC-END -->
+
 Breedbase provides an interactive design tool for creating custom labels. To access the Label Desginer, click on “Label Designer” in the “Manage” menu. The following sections explain your many options as you advance through each step of the design workflow.
 
-1: Select a Datasource
+### 3.12.1 Select a Datasource
 
-The first step is to select a data source. Select a field, genotyping, or crossing trial to populate your labels with the trial design information. Or select a list to populate your label with the list contents.
-For data sources with multiple levels of information you will also be asked to pick a level (plot, plant, etc.) before proceeding.
+The first step is to select a data source. Since the label designer can generate labels for different data types, you can optionally filter the source selection by the data type you're interested in.  Then, select a field, genotyping, or crossing trial to populate your labels with the trial design information. Or select a list to populate your label with the list contents.
+For data sources with multiple levels of information you will also be asked to pick a level (plot, plant, etc.) before proceeding. To generate plot-level labels for more than one trial at once, select a list of trials as the source and plot as the level.
 
 ![]({{"assets/gifs/gif1.gif" | relative_url }})
 
-2: Set Page and Label Size
+### 3.12.2 Set Page and Label Size
 
 Now choose whether to create a new design or load a saved design. If you choose new, you will be prompted to select a page size and label size.
 If you do not see your page or label size as an option, then select Custom and enter your desired dimensions in pixels, or 1/72nds of an inch.
 If you choose saved, you will be prompted to select a saved design then will be taken directly to the design step with the saved design elements preloaded.
 
 ![]({{"assets/gifs/gif2.gif" | relative_url }})
 
-3: Design Your Label
+### 3.12.3 Design Your Label
 
 Below is a draw area where you can begin adding elements to your label. First select a type, then field, size, and font, then click 'Add'
 You can add text to an exisiting field or create a completely custom field by clicking 'Create Custom Field'
@@ -31,10 +37,10 @@ When you are satisfied with your design, click next!
 
 ![]({{"assets/gifs/gif3.gif" | relative_url }})
 
-4: Set Page and Label Size
+### 3.12.4 Set Page and Label Size and Sorting Options
 
 Last step! Here you can tweak your formatting and page layout, save your design, or download your labels.
-The additional settings dialog will allow you to fine tune the print margins and margins between labels. The units are pixels or 1/72nds of an inch. It's not recommended to change these until you've already done a test print.
+The additional settings dialog will allow you to fine tune the print margins and margins between labels. The units are pixels or 1/72nds of an inch. It's not recommended to change these until you've already done a test print.  Here you can also set sorting options to adjust the order of the individual labels.  You can sort by 1-3 different properties (the available properties will depend on the data type of the labels).  For example, if you're printing plot-level labels for multiple trials, you can sort first by trial name and then by plot number.
 You can also set the # of copies per label, filter by rep, or download just the first page for test purposes.
 To save you're design just type a unique name and hit save. This will save your design to your list manager where you can set it to public to share it with others.
 Finally if you are ready just hit download to generate and download your labels!

js/source/legacy/CXGN/BreedersToolbox/AddTrial.js

@@ -53,6 +53,7 @@ jQuery(document).ready(function ($) {
         var breeding_program = $("#select_breeding_program").val();
         var location = $("#add_project_location").val().toString().trim(); // remove whitespace
         var trial_year = $("#add_project_year").val();
+        var planting_date = $("#add_project_planting_date").val();
         var description = $("#add_project_description").val();
         var design_type = $("#select_design_method").val();
         var stock_type = $("#select_stock_type").val();
@@ -74,6 +75,9 @@ jQuery(document).ready(function ($) {
         else if (trial_year === '') {
             alert("Please select a trial year");
         }
+        else if (planting_date === '') {
+            alert("Please select a trial planting date");
+        }
         else if (plot_width < 0 ){
             alert("Please check the plot width");
         }
@@ -487,6 +491,11 @@ jQuery(document).ready(function ($) {
     function generate_experimental_design() {
         var name = $('#new_trial_name').val();
         var year = $('#add_project_year').val();
+        var planting_date = $('#add_project_planting_date').val();
+        // date formatting here from js to breedbase format
+        if (planting_date) {
+            planting_date = new Date(planting_date).toLocaleDateString("en-CA");
+        }
         var desc = $('#add_project_description').val();
         var locations = jQuery('#add_project_location').val();
         var trial_location =  JSON.stringify(locations);
@@ -496,7 +505,7 @@ jQuery(document).ready(function ($) {
         var row_number_per_block=$('#row_number_per_block').val();
         var col_number_per_block=$('#col_number_per_block').val();
         var col_number=$('#col_number').val();
-	var plot_numbering_scheme = jQuery('input[name="plot_numbering_scheme"]:checked').val();
+	    var plot_numbering_scheme = jQuery('input[name="plot_numbering_scheme"]:checked').val();
 
         var stock_list_id;
         var control_stock_list_id;
@@ -649,6 +658,7 @@ jQuery(document).ready(function ($) {
                 'project_name': name,
                 'project_description': desc,
                 'year': year,
+                'planting date' : planting_date,
                 'trial_location': trial_location,
                 'trial_stock_type': trial_stock_type,
                 'stock_list': stock_list,
@@ -915,6 +925,7 @@ jQuery(document).ready(function ($) {
         jQuery("#container_field_map_view").css("display", "none");
         var name = $('#new_trial_name').val();
         var year = $('#add_project_year').val();
+        var planting_date = $('#add_project_planting_date').val();
         var desc = $('textarea#add_project_description').val();
         if (name == '') {
             alert('Trial name required');
@@ -924,7 +935,10 @@ jQuery(document).ready(function ($) {
             alert('Year and description are required.');
             return;
         }
-
+        if(planting_date === '' || desc === '') {
+            alert('Planting date and description are required.');
+            return;
+        }
         if (stock_list_verified == 1 && seedlot_list_verified == 1){
             generate_experimental_design();
         } else if (cross_list_verified == 1 && stock_list_verified == 0 && family_name_list_verified == 0){
@@ -2014,6 +2028,11 @@ jQuery(document).ready(function ($) {
         var list = new CXGN.List();
         var name = jQuery('#new_trial_name').val();
         var year = jQuery('#add_project_year').val();
+        var planting_date = jQuery('#add_project_planting_date').val();
+        // date formatting here from js to breedbase format
+        if (planting_date) {
+            planting_date = new Date(planting_date).toLocaleDateString("en-CA");
+        }
         var desc = jQuery('#add_project_description').val();
         var locations = jQuery('#add_project_location').val();
         var trial_location =  JSON.stringify(locations);
@@ -2081,7 +2100,7 @@ jQuery(document).ready(function ($) {
            use_same_layout = "";
         }
 
-	var plot_numbering_scheme = jQuery('input[name="plot_numbering_scheme"]:checked').val();
+	    var plot_numbering_scheme = jQuery('input[name="plot_numbering_scheme"]:checked').val();
 
         jQuery.ajax({
            type: 'POST',
@@ -2096,6 +2115,7 @@ jQuery(document).ready(function ($) {
                 'project_description': desc,
                 //'trial_name': trial_name,
                 'year': year,
+                'planting_date' : planting_date,
                 'trial_type': trial_type,
                 'trial_location': trial_location,
                 'trial_stock_type': trial_stock_type,
@@ -2300,6 +2320,7 @@ jQuery(document).ready(function ($) {
 
     jQuery('#new_trial_add_treatments_submit').click(function(){
         var new_treatment_year = jQuery('#new_treatment_year').val();
+        var new_treament_planting_date = jQuery('#new_treatment_planting_date').val();
         var new_treatment_description = jQuery('#new_treatment_description').val();
         var new_treatment_date = jQuery('#new_treatment_date').val();
         var new_treatment_type = jQuery('#new_treatment_type').val();
@@ -2333,6 +2354,7 @@ jQuery(document).ready(function ($) {
                     trial[trial_treatment]["new_treatment_type"] = new_treatment_type;
                     trial[trial_treatment]["new_treatment_date"] = new_treatment_date;
                     trial[trial_treatment]["new_treatment_year"] = new_treatment_year;
+                    trial[trial_treatment]["new_treatment_planting_date"] = new_treatment_planting_date;
                     trial[trial_treatment]["new_treatment_description"] = new_treatment_description;
 
                     trial_treatments[trial_index] = trial;