diff --git a/js/source/entries/fieldmap.js b/js/source/entries/fieldmap.js index 70ee521751..45bf1cfbb1 100644 --- a/js/source/entries/fieldmap.js +++ b/js/source/entries/fieldmap.js @@ -148,96 +148,20 @@ export function init() { } } - traverse_map(plot_arr, planting_or_harvesting_order_layout) { - var local_this = this; - let coord_matrix = []; - var row = this.meta_data[planting_or_harvesting_order_layout].includes('row') ? "positionCoordinateY" : "positionCoordinateX"; - var col = this.meta_data[planting_or_harvesting_order_layout].includes('row') ? "positionCoordinateX" : "positionCoordinateY"; - - for (let plot of plot_arr) { - if (!coord_matrix[plot.observationUnitPosition[row]]) { - coord_matrix[plot.observationUnitPosition[row]] = []; - coord_matrix[plot.observationUnitPosition[row]][plot.observationUnitPosition[col]] = plot; - } else { - coord_matrix[plot.observationUnitPosition[row]][plot.observationUnitPosition[col]] = plot; - } - } - - coord_matrix = coord_matrix.filter(plot_arr => Array.isArray(plot_arr)); - if (!document.getElementById("invert_row_checkmark").checked && this.meta_data[planting_or_harvesting_order_layout].includes('row') && planting_or_harvesting_order_layout.includes('planting')) { - if ((this.meta_data.top_border_selection && !this.meta_data.bottom_border_selection) || (!this.meta_data.top_border_selection && this.meta_data.bottom_border_selection)) { - if (this.meta_data.top_border_selection) { - var top_borders = coord_matrix.shift(); - coord_matrix.push(top_borders); - } else if (this.meta_data.bottom_border_selection) { - var bottom_borders = coord_matrix.pop(); - coord_matrix.unshift(bottom_borders); - } - } - } - - - if (this.meta_data[planting_or_harvesting_order_layout].includes('serpentine')) { - for (let i = 0; i < coord_matrix.length; i++) { - if (i % 2 == 1) { - coord_matrix[i].reverse(); - } - } - } - - var final_arr = []; - for (let plot_arr of coord_matrix) { - plot_arr = plot_arr.filter(plot => plot !== undefined); - if (!document.getElementById("invert_row_checkmark").checked && local_this.meta_data[planting_or_harvesting_order_layout].includes('col') && planting_or_harvesting_order_layout.includes('planting')) { - if ((local_this.meta_data.top_border_selection && !local_this.meta_data.bottom_border_selection) || (!local_this.meta_data.top_border_selection && local_this.meta_data.bottom_border_selection)) { - if (local_this.meta_data.top_border_selection) { - var top_border_plot = plot_arr.shift(); - plot_arr.push(top_border_plot); - } else if (local_this.meta_data.bottom_border_selection) { - var bottom_border_plot = plot_arr.pop(); - plot_arr.unshift(bottom_border_plot); - } - } - } - final_arr.push(...plot_arr); - } - - var csv = [ - planting_or_harvesting_order_layout == "planting_order_layout" ? 'planting_order': "harvesting_order", - 'location_name', - 'trial_name', - 'plot_number', - 'plot_name', - 'accession_name', - 'seedlot_name', - ].join(','); - csv += "\n"; - final_arr = final_arr.filter(plot => plot !== undefined); - let order_number = 1; - final_arr.forEach(function(plot) { - csv += [ - order_number++, - "\"" + plot.locationName + "\"", - plot.studyName, - plot.observationUnitPosition.observationLevel ? plot.observationUnitPosition.observationLevel.levelCode : "N/A", - plot.observationUnitName, - plot.germplasmName, - plot.seedLotName ? plot.seedLotName : '' - ].join(','); - csv += "\n"; - }); - - var hiddenElement = document.createElement('a'); - hiddenElement.href = 'data:text/csv;charset=utf-8,' + encodeURI(csv); - hiddenElement.target = '_blank'; - hiddenElement.download = `Trial_${this.trial_id}_${this.meta_data[planting_or_harvesting_order_layout]}_${planting_or_harvesting_order_layout}.csv`; - hiddenElement.click(); - } - - get_plot_order(type, order, include_borders) { - let k = type === 'planting' ? 'planting_order_layout' : 'harvesting_order_layout'; - this.meta_data[k] = order; - this.traverse_map(this.plot_arr.filter(plot => include_borders || plot.type !== "border"), k); + get_plot_order(type, order, start, include_borders, include_gaps, additional_properties) { + let q = new URLSearchParams({ + 'trial_ids': [this.trial_id, ...Object.keys(this.linked_trials).map((e) => this.linked_trials[e].id)].join(','), + 'type': type, + 'order': order, + 'start': start, + 'top_border': !!include_borders && !!this.meta_data.top_border_selection, + 'right_border': !!include_borders && !!this.meta_data.right_border_selection, + 'bottom_border': !!include_borders && !!this.meta_data.bottom_border_selection, + 'left_border': !!include_borders && !!this.meta_data.left_border_selection, + 'gaps': !!include_gaps, + ...additional_properties + }).toString(); + window.open(`/ajax/breeders/trial_plot_order?${q}`, '_blank'); } set_meta_data() { @@ -419,14 +343,14 @@ export function init() { this.meta_data.num_cols = this.meta_data.num_rows; this.meta_data.num_rows = tempNumCols; - d3.select("svg").remove(); + d3v3.select("svg").remove(); this.add_borders(); this.render(); } clickcancel() { - var event = d3.dispatch('click', 'dblclick'); + var event = d3v3.dispatch('click', 'dblclick'); function cc(selection) { var down, tolerance = 5, @@ -436,33 +360,33 @@ export function init() { return Math.sqrt(Math.pow(a[0] - b[0], 2), Math.pow(a[1] - b[1], 2)); } selection.on('mousedown', function() { - down = d3.mouse(document.body); + down = d3v3.mouse(document.body); last = +new Date(); }); selection.on('mouseup', function() { - if (dist(down, d3.mouse(document.body)) > tolerance) { + if (dist(down, d3v3.mouse(document.body)) > tolerance) { return; } else { if (wait) { window.clearTimeout(wait); wait = null; - event.dblclick(d3.event); + event.dblclick(d3v3.event); } else { wait = window.setTimeout((function(e) { return function() { event.click(e); wait = null; }; - })(d3.event), 300); + })(d3v3.event), 300); } } }); }; - return d3.rebind(cc, event, 'on'); + return d3v3.rebind(cc, event, 'on'); } heatmap_plot_click(plot, heatmap_object, trait_name) { - if (d3.event && d3.event.detail > 1) { + if (d3v3.event && d3v3.event.detail > 1) { return; } else if (trait_name in heatmap_object && heatmap_object[trait_name][plot.observationUnitDbId]) { let val, plot_name, pheno_id; @@ -478,7 +402,7 @@ export function init() { } fieldmap_plot_click(plot) { - if (d3.event && d3.event.detail > 1) { + if (d3v3.event && d3v3.event.detail > 1) { return; } else { function btnClick(n){ @@ -559,7 +483,7 @@ export function init() { for (let obs_unit of Object.values(plots_with_selected_trait)) { trait_vals.push(obs_unit.val); } - var colorScale = d3.scale.quantile() + var colorScale = d3v3.scale.quantile() .domain(trait_vals) .range(colors); } @@ -648,7 +572,7 @@ export function init() { var handle_mouseover = function(d) { if (d.observationUnitPosition.observationLevel) { - d3.select(`#fieldmap-plot-${d.observationUnitDbId}`) + d3v3.select(`#fieldmap-plot-${d.observationUnitDbId}`) .style('fill', 'green') .style('cursor', 'pointer') .style("stroke-width", 3) @@ -661,7 +585,7 @@ export function init() { } var handle_mouseout = function(d) { - d3.select(`#fieldmap-plot-${d.observationUnitDbId}`) + d3v3.select(`#fieldmap-plot-${d.observationUnitDbId}`) .style('fill', !isHeatMap ? get_fieldmap_plot_color(d) : get_heatmap_plot_color(d)) .style('cursor', 'default') .style("stroke-width", 2) @@ -734,12 +658,12 @@ export function init() { var num_rows = this.meta_data.num_rows; var isHeatMap = this.heatmap_selected; - var grid = d3.select("#fieldmap_chart") + var grid = d3v3.select("#fieldmap_chart") .append("svg") .attr("width", width * 50 + 20 + "px") .attr("height", height * 50 + 20 + "px") - var tooltip = d3.select("#fieldmap_chart") + var tooltip = d3v3.select("#fieldmap_chart") .append("rect") .attr("id", "tooltip") .attr("class", "tooltip") @@ -764,11 +688,11 @@ export function init() { .call(cc); cc.on("click", (el) => { - var plot = d3.select(el.srcElement).data()[0]; + var plot = d3v3.select(el.srcElement).data()[0]; plot_click(plot, heatmap_object, trait_name) }); cc.on("dblclick", (el) => { - var me = d3.select(el.srcElement); + var me = d3v3.select(el.srcElement); var d = me.data()[0]; if (d.observationUnitDbId) { window.open('/stock/'+d.observationUnitDbId+'/view'); @@ -861,7 +785,7 @@ export function init() { load() { - d3.select("svg").remove(); + d3v3.select("svg").remove(); this.change_dimensions(this.meta_data.num_cols, this.meta_data.num_rows); this.add_borders(); this.render(); diff --git a/js/source/legacy/d3/d3Min.js b/js/source/legacy/d3/d3Min.js index dba599303c..1665bd0ca7 100644 --- a/js/source/legacy/d3/d3Min.js +++ b/js/source/legacy/d3/d3Min.js @@ -1,4 +1,4 @@ -d3=function(){function n(n){return null!=n&&!isNaN(n)}function t(n){return n.length}function e(n){for(var t=1;n*t%1;)t*=10;return t}function 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Download") { - $("#d3-draw-area").prependTo("#save_and_download"); + $("#d3-draw-area").prependTo("#save-labels-display"); } }); @@ -327,7 +323,7 @@ $(document).ready(function($) { var title = $(this).children().text(); //console.log("workflow element with title "+title+" was just clicked\n"); if (title == "More Options, Save, And Download") { - $("#d3-draw-area").prependTo("#save_and_download"); + $("#d3-draw-area").prependTo("#save-labels-display"); } }); @@ -704,7 +700,7 @@ function updateFields(data_type, source_id, data_level){ reps = response.reps; num_units = response.num_units; addPlotFilter(reps); - addSortOrders(add_fields); + addSortOrders(add_fields, data_type, data_level); createAdders(add_fields); initializeCustomModal(add_fields); showLoadOption(); @@ -1299,10 +1295,27 @@ function addPlotFilter(reps) { } -function addSortOrders(add_fields) { +function addSortOrders(add_fields, data_type, data_level) { + + // Set type-specific sorting options + let data_type_fields = []; + // Sort by trial layout for plot-level labels... + if ( ['Field Trials', 'Lists', 'Public Lists'].includes(data_type) && data_level === 'plots' ) { + data_type_fields = ['Trial Layout: Plot Order']; + } + //load options d3.selectAll("#sort_order_1, #sort_order_2, #sort_order_3").selectAll("option").remove(); - d3.selectAll("#sort_order_1, #sort_order_2, #sort_order_3").selectAll("option") + d3.selectAll("#sort_order_1").selectAll("option") + .data(["Select a field", ...data_type_fields, ...Object.keys(add_fields).sort()]) + .enter().append("option") + .text(function(d) { + return d + }) + .attr("value", function(d) { + return d + }); + d3.selectAll("#sort_order_2, #sort_order_3").selectAll("option") .data(["Select a field", ...Object.keys(add_fields).sort()]) .enter().append("option") .text(function(d) { @@ -1315,9 +1328,15 @@ function addSortOrders(add_fields) { const sel = jQuery("#sort_order_1").val(); if ( sel === 'Select a field' ) { jQuery("#sort_order_2_container, #sort_order_3_container").hide(); + jQuery("#sort_order_layout_order_container, #sort_order_layout_start_container").hide(); + } + else if ( sel === 'Trial Layout: Plot Order' ) { + jQuery("#sort_order_2_container, #sort_order_3_container").hide(); + jQuery("#sort_order_layout_order_container, #sort_order_layout_start_container").show(); } else { jQuery("#sort_order_2_container").show(); + jQuery("#sort_order_layout_order_container, #sort_order_layout_start_container").hide(); } }); jQuery("#sort_order_2").off("change").on("change", () => { @@ -1419,6 +1438,8 @@ function retrievePageParams() { sort_order_1: document.getElementById("sort_order_1").value, sort_order_2: document.getElementById("sort_order_2").value, sort_order_3: document.getElementById("sort_order_3").value, + sort_order_layout_order: document.getElementById("sort_order_layout_order").value, + sort_order_layout_start: document.getElementById("sort_order_layout_start").value, copies_per_plot: document.getElementById("copies_per_plot").value, labels_to_download: document.getElementById("label_designer_labels_to_download").value, start_number: document.getElementById("label_designer_start_number").value, diff --git a/lib/CXGN/List.pm b/lib/CXGN/List.pm index afe813c9cb..4af022270d 100644 --- a/lib/CXGN/List.pm +++ b/lib/CXGN/List.pm @@ -222,7 +222,7 @@ sub exists_list { my $name = shift; my $owner = shift; - my $q = "SELECT list_id, cvterm.name FROM sgn_people.list AS list LEFT JOIN cvterm ON (type_id=cvterm_id) WHERE list.name = ? AND list.owner=?"; + my $q = "SELECT list_id, cvterm.name FROM sgn_people.list AS list LEFT JOIN cvterm ON (type_id=cvterm_id) WHERE list.name=? AND (list.owner=? OR list.is_public=TRUE)"; my $h = $dbh->prepare($q); $h->execute($name, $owner); my ($list_id, $list_type) = $h->fetchrow_array(); diff --git a/lib/CXGN/Stock/RelatedStocks.pm b/lib/CXGN/Stock/RelatedStocks.pm index d0235e5c76..1b02404ed8 100644 --- a/lib/CXGN/Stock/RelatedStocks.pm +++ b/lib/CXGN/Stock/RelatedStocks.pm @@ -24,14 +24,14 @@ sub get_trial_related_stock { my $plant_of_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plant_of', 'stock_relationship')->cvterm_id(); my $subplot_of_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'subplot_of', 'stock_relationship')->cvterm_id(); my $plant_of_subplot_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plant_of_subplot', 'stock_relationship')->cvterm_id(); - my $seed_transaction_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'seed transaction', 'stock_relationship')->cvterm_id(); +# my $seed_transaction_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'seed transaction', 'stock_relationship')->cvterm_id(); my $tissue_sample_of_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'tissue_sample_of', 'stock_relationship')->cvterm_id(); my $q = "SELECT stock.stock_id, stock.uniquename, cvterm.name FROM stock_relationship INNER JOIN stock ON (stock_relationship.subject_id = stock.stock_id) INNER JOIN cvterm ON (stock.type_id = cvterm.cvterm_id) WHERE stock_relationship.object_id = ? AND (stock_relationship.type_id = ? - OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ?) + OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? ) UNION ALL @@ -39,11 +39,11 @@ sub get_trial_related_stock { INNER JOIN stock ON (stock_relationship.object_id = stock.stock_id) INNER JOIN cvterm ON (stock.type_id = cvterm.cvterm_id) WHERE stock_relationship.subject_id = ? AND (stock_relationship.type_id = ? - OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ?) "; + OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? ) "; my $h = $schema->storage->dbh()->prepare($q); - $h->execute($stock_id, $plot_of_type_id, $plant_of_type_id, $subplot_of_type_id, $plant_of_subplot_type_id, $seed_transaction_type_id, $tissue_sample_of_type_id, $stock_id, $plot_of_type_id, $plant_of_type_id, $subplot_of_type_id, $plant_of_subplot_type_id, $seed_transaction_type_id, $tissue_sample_of_type_id); + $h->execute($stock_id, $plot_of_type_id, $plant_of_type_id, $subplot_of_type_id, $plant_of_subplot_type_id, $tissue_sample_of_type_id, $stock_id, $plot_of_type_id, $plant_of_type_id, $subplot_of_type_id, $plant_of_subplot_type_id, $tissue_sample_of_type_id); my @trial_related_stock =(); while(my($stock_id, $stock_name, $cvterm_name) = $h->fetchrow_array()){ @@ -175,4 +175,43 @@ sub get_cross_of_progeny { } +sub get_plot_plant_related_seedlots { + my $self = shift; + my $stock_id = $self->stock_id; + my $schema = $self->dbic_schema(); + my $seed_transaction_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'seed transaction', 'stock_relationship')->cvterm_id(); + + my @related_seedlots; + + my $q1 = "SELECT distinct(stock.stock_id), stock.uniquename, cvterm.name FROM stock_relationship + INNER JOIN stock ON (stock_relationship.subject_id = stock.stock_id) + INNER JOIN cvterm ON (stock.type_id = cvterm.cvterm_id) + WHERE stock_relationship.object_id = ? AND stock_relationship.type_id = ? "; + + my $h1 = $schema->storage->dbh()->prepare($q1); + + $h1->execute($stock_id, $seed_transaction_type_id); + + while(my($stock_id, $stock_name, $stock_type) = $h1->fetchrow_array()){ + push @related_seedlots, ['source of', $stock_type, $stock_id, $stock_name] + } + + my $q2 = "SELECT distinct(stock.stock_id), stock.uniquename, cvterm.name FROM stock_relationship + INNER JOIN stock ON (stock_relationship.object_id = stock.stock_id) + INNER JOIN cvterm ON (stock.type_id = cvterm.cvterm_id) + WHERE stock_relationship.subject_id = ? AND stock_relationship.type_id = ? "; + + my $h2 = $schema->storage->dbh()->prepare($q2); + + $h2->execute($stock_id, $seed_transaction_type_id); + + while(my($stock_id, $stock_name, $stock_type) = $h2->fetchrow_array()){ + push @related_seedlots, ['derived from', $stock_type, $stock_id, $stock_name] + } + + return\@related_seedlots; + +} + + 1; diff --git a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotHarvestedXLS.pm b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotHarvestedXLS.pm index 1f80b8a2aa..21584a16f7 100644 --- a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotHarvestedXLS.pm +++ b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotHarvestedXLS.pm @@ -148,6 +148,10 @@ sub _validate_with_plugin { $box_name = $worksheet->get_cell($row,6)->value(); } + if (!defined $seedlot_name && !defined $cross_name) { + last; + } + if (!$seedlot_name || $seedlot_name eq '' ) { push @error_messages, "Cell A$row_name: seedlot_name missing."; } @@ -197,15 +201,16 @@ sub _validate_with_plugin { $errors{'missing_crosses'} = \@crosses_missing; } - # Not checking if seedlot name already exists because the database will just update the seedlot entries - # my @seedlots = keys %seen_seedlot_names; - # my $rs = $schema->resultset("Stock::Stock")->search({ - # 'is_obsolete' => { '!=' => 't' }, - # 'uniquename' => { -in => \@seedlots } - # }); - # while (my $r=$rs->next){ - # push @error_messages, "Cell A".$seen_seedlot_names{$r->uniquename}.": seedlot name already exists in database: ".$r->uniquename; - # } + # Check if Seedlot names already exist as other stock names + my @seedlots = keys %seen_seedlot_names; + my $rs = $schema->resultset("Stock::Stock")->search({ + 'uniquename' => { -in => \@seedlots } + }); + while (my $r=$rs->next) { + if ( $r->type->name ne 'seedlot' ) { + push @error_messages, "Cell A".$seen_seedlot_names{$r->uniquename}.": stock name already exists in database: ".$r->uniquename.". The seedlot name must be unique."; + } + } #store any errors found in the parsed file to parse_errors accessor if (scalar(@error_messages) >= 1) { @@ -262,6 +267,11 @@ sub _parse_with_plugin { $cross_name =~ s/^\s+|\s+$//g; $seen_cross_names{$cross_name}++; } + + if (!defined $seedlot_name && !defined $cross_name) { + last; + } + } my $cross_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'cross', 'stock_type')->cvterm_id(); my $seedlot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'seedlot', 'stock_type')->cvterm_id(); @@ -324,9 +334,8 @@ sub _parse_with_plugin { $box_name =~ s/^\s+|\s+$//g; } - #skip blank lines - if (!$seedlot_name && !$cross_name && !$description) { - next; + if (!defined $seedlot_name && !defined $cross_name) { + last; } diff --git a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotXLS.pm b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotXLS.pm index 543b7c18fe..2042f58166 100644 --- a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotXLS.pm +++ b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotXLS.pm @@ -168,6 +168,11 @@ sub _validate_with_plugin { $source = $worksheet->get_cell($row, 8)->value(); $source =~ s/^\s+|\s+$//g; } + + if (!defined $seedlot_name && !defined $accession_name) { + last; + } + if (!$seedlot_name || $seedlot_name eq '' ) { push @error_messages, "Cell A$row_name: seedlot_name missing."; } @@ -237,15 +242,17 @@ sub _validate_with_plugin { push @error_messages, "The following source seedlots could not be found in the database: ".join(',',@sources_missing); $errors{'missing_sources'} = \@sources_missing; } - # Not checking if seedlot name already exists because the database will just update the seedlot entries - # my @seedlots = keys %seen_seedlot_names; - # my $rs = $schema->resultset("Stock::Stock")->search({ - # 'is_obsolete' => { '!=' => 't' }, - # 'uniquename' => { -in => \@seedlots } - # }); - # while (my $r=$rs->next){ - # push @error_messages, "Cell A".$seen_seedlot_names{$r->uniquename}.": seedlot name already exists in database: ".$r->uniquename; - # } + + # Check if Seedlot names already exist as other stock names + my @seedlots = keys %seen_seedlot_names; + my $rs = $schema->resultset("Stock::Stock")->search({ + 'uniquename' => { -in => \@seedlots } + }); + while (my $r=$rs->next) { + if ( $r->type->name ne 'seedlot' ) { + push @error_messages, "Cell A".$seen_seedlot_names{$r->uniquename}.": stock name already exists in database: ".$r->uniquename.". The seedlot name must be unique."; + } + } #store any errors found in the parsed file to parse_errors accessor if (scalar(@error_messages) >= 1) { @@ -302,7 +309,13 @@ sub _parse_with_plugin { $accession_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end... $seen_accession_names{$accession_name}++; } + + if (!defined $seedlot_name && !defined $accession_name) { + last; + } + } + my $accession_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type')->cvterm_id(); my $seedlot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'seedlot', 'stock_type')->cvterm_id(); my $synonym_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'stock_synonym', 'stock_property')->cvterm_id(); @@ -377,15 +390,14 @@ sub _parse_with_plugin { $source = $worksheet->get_cell($row, 8)->value(); } + if (!defined $seedlot_name && !defined $accession_name) { + last; + } + $seedlot_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end... $accession_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end... $source =~ s/^\s+|\s+$//g; # also trim - #skip blank lines - if (!$seedlot_name && !$accession_name && !$description) { - next; - } - my $accession_stock_id; if ($acc_synonyms_lookup{$accession_name}){ my @accession_names = keys %{$acc_synonyms_lookup{$accession_name}}; diff --git a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToNewSeedlots.pm b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToNewSeedlots.pm index 2f55b65ee9..6e6744fd11 100644 --- a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToNewSeedlots.pm +++ b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToNewSeedlots.pm @@ -164,6 +164,10 @@ sub _validate_with_plugin { $new_seedlot_box_name = $worksheet->get_cell($row,6)->value(); } + if (!defined $from_seedlot_name && !defined $to_new_seedlot_name) { + last; + } + if (!$from_seedlot_name || $from_seedlot_name eq '' ) { push @error_messages, "Cell A$row_name: from_seedlot_name missing."; } else { @@ -335,9 +339,8 @@ sub _parse_with_plugin { $new_seedlot_quality = $worksheet->get_cell($row,8)->value(); } - #skip blank lines - if (!$to_new_seedlot_name && !$from_seedlot_name) { - next; + if (!defined $to_new_seedlot_name && !defined $from_seedlot_name) { + last; } my $from_seedlot_rs = $schema->resultset("Stock::Stock")->find({ diff --git a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToPlots.pm b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToPlots.pm index af6304587b..5e6ec10eb9 100644 --- a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToPlots.pm +++ b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToPlots.pm @@ -137,6 +137,10 @@ sub _validate_with_plugin { $transaction_description = $worksheet->get_cell($row,5)->value(); } + if (!defined $from_seedlot_name && !defined $to_plot_name) { + last; + } + if (!$from_seedlot_name || $from_seedlot_name eq '' ) { push @error_messages, "Cell A$row_name: from_seedlot_name missing."; } else { @@ -280,9 +284,8 @@ sub _parse_with_plugin { $transaction_description = $worksheet->get_cell($row,5)->value(); } - #skip blank lines - if (!$to_plot_name && !$from_seedlot_name) { - next; + if (!defined $from_seedlot_name && !defined $to_plot_name) { + last; } my $from_seedlot_rs = $schema->resultset("Stock::Stock")->find({ diff --git a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToSeedlots.pm b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToSeedlots.pm index 7589c50ed4..a9f8e76c98 100644 --- a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToSeedlots.pm +++ b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToSeedlots.pm @@ -136,6 +136,10 @@ sub _validate_with_plugin { $transaction_description = $worksheet->get_cell($row,5)->value(); } + if (!defined $from_seedlot_name && !defined $to_seedlot_name) { + last; + } + if (!$from_seedlot_name || $from_seedlot_name eq '' ) { push @error_messages, "Cell A$row_name: from_seedlot_name missing."; } else { @@ -270,9 +274,8 @@ sub _parse_with_plugin { $transaction_description = $worksheet->get_cell($row,5)->value(); } - #skip blank lines - if (!$to_seedlot_name && !$from_seedlot_name) { - next; + if (!defined $from_seedlot_name && !defined $to_seedlot_name) { + last; } my $from_seedlot_rs = $schema->resultset("Stock::Stock")->find({ diff --git a/lib/CXGN/Stock/Vector/ParseUpload.pm b/lib/CXGN/Stock/Vector/ParseUpload.pm new file mode 100644 index 0000000000..1c5e9e62c3 --- /dev/null +++ b/lib/CXGN/Stock/Vector/ParseUpload.pm @@ -0,0 +1,91 @@ +package CXGN::Stock::Vector::ParseUpload; + +use Moose; +use Data::Dumper; +use MooseX::FollowPBP; +use Moose::Util::TypeConstraints; + +with 'MooseX::Object::Pluggable'; + + +has 'chado_schema' => ( + is => 'ro', + isa => 'DBIx::Class::Schema', + required => 1, + ); + +has 'filename' => ( + is => 'ro', + isa => 'Str', + required => 1, + ); + +has 'editable_stock_props' => ( + is => 'ro', + isa => 'ArrayRef', + required => 1, +); + +has 'do_fuzzy_search' => ( + is => 'ro', + isa => 'Bool', + default => 1 +); + +has 'autogenerate_uniquename' => ( + is => 'ro', + isa => 'Bool', + default => 0 +); + +has 'parse_errors' => ( + is => 'ro', + isa => 'HashRef', + writer => '_set_parse_errors', + reader => 'get_parse_errors', + predicate => 'has_parse_errors', + ); + +has '_parsed_data' => ( + is => 'ro', + isa => 'HashRef', + writer => '_set_parsed_data', + predicate => '_has_parsed_data', + ); + +sub parse { + my $self = shift; + + if (!$self->_validate_with_plugin()) { + my $errors = $self->get_parse_errors(); + print STDERR "\nCould not validate trial file: ".$self->get_filename()."\nError:".Dumper($errors)."\n"; + return; + } + + print STDERR "Check 3.1: CXGN::Stock::ParseUpload ".localtime(); + + if (!$self->_parse_with_plugin()) { + my $errors = $self->get_parse_errors(); + print STDERR "\nCould not parse trial file: ".$self->get_filename()."\nError:".Dumper($errors)."\n"; + return; + } + + print STDERR "Check 3.2: CXGN::Stock::ParseUpload ".localtime(); + + if (!$self->_has_parsed_data()) { + my $errors = $self->get_parse_errors(); + print STDERR "\nNo parsed data for trial file: ".$self->get_filename()."\nError:".Dumper($errors)."\n"; + return; + } else { + return $self->_parsed_data(); + } + + print STDERR "Check 3.3: CXGN::Stock::ParseUpload ".localtime(); + + my $errors = $self->get_parse_errors(); + print STDERR "\nError parsing trial file: ".$self->get_filename()."\nError:".Dumper($errors)."\n"; + return; +} + + +1; diff --git a/lib/CXGN/Stock/ParseUpload/Plugin/VectorsXLS.pm b/lib/CXGN/Stock/Vector/ParseUpload/Plugin/VectorsXLS.pm similarity index 90% rename from lib/CXGN/Stock/ParseUpload/Plugin/VectorsXLS.pm rename to lib/CXGN/Stock/Vector/ParseUpload/Plugin/VectorsXLS.pm index 4a78db8460..0bc3a88732 100644 --- a/lib/CXGN/Stock/ParseUpload/Plugin/VectorsXLS.pm +++ b/lib/CXGN/Stock/Vector/ParseUpload/Plugin/VectorsXLS.pm @@ -1,4 +1,4 @@ -package CXGN::Stock::ParseUpload::Plugin::VectorsXLS; +package CXGN::Stock::Vector::ParseUpload::Plugin::VectorsXLS; use Moose::Role; use Spreadsheet::ParseExcel; @@ -16,9 +16,10 @@ sub _validate_with_plugin { my $filename = $self->get_filename(); my $schema = $self->get_chado_schema(); my $editable_stockprops = $self->get_editable_stock_props(); + my $autogenerate_uniquename = $self->get_autogenerate_uniquename(); # Match a dot, extension .xls / .xlsx - my $extension = $filename =~ /(\.[^.]+)$/; + my ($extension) = $filename =~ /(\.[^.]+)$/; my $parser; if ($extension eq '.xlsx') { @@ -106,7 +107,9 @@ sub _validate_with_plugin { } if (!$vector_name || $vector_name eq '' ) { - push @error_messages, "Cell A$row_name: vector_name missing."; + if (! $autogenerate_uniquename ){ + push @error_messages, "Cell A$row_name: vector_name missing."; + } } else { $vector_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end... $seen_vector_names{$vector_name}=$row_name; @@ -154,6 +157,7 @@ sub _parse_with_plugin { my $filename = $self->get_filename(); my $schema = $self->get_chado_schema(); my $do_fuzzy_search = $self->get_do_fuzzy_search(); + my $autogenerate_uniquename = $self->get_autogenerate_uniquename(); # Match a dot, extension .xls / .xlsx my ($extension) = $filename =~ /(\.[^.]+)$/; @@ -181,12 +185,33 @@ sub _parse_with_plugin { my %seen_vector_names; my %seen_species_names; + my $vector_max_id; + + if($autogenerate_uniquename > 0){ + my $stock_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'vector_construct', 'stock_type')->cvterm_id(); + + my $stocks = $schema->resultset("Stock::Stock")->search({ type_id => $stock_type_id, }); + + my $id; + $vector_max_id = 0; + while (my $r = $stocks->next()) { + $id = $r->uniquename; + if ($id =~ m/T[0-9]+/){ + $id =~ s/T//; + if($vector_max_id < $id){ + $vector_max_id = $id; + } + } + } + } + for my $row ( 1 .. $row_max ) { my $vector_name; my $species_name; - - if ($worksheet->get_cell($row,0)) { + if($autogenerate_uniquename > 0 ){ + $vector_name = "T" . ($vector_max_id + $row); + } elsif ($worksheet->get_cell($row,0)) { $vector_name = $worksheet->get_cell($row,0)->value(); } if ($worksheet->get_cell($row,1)) { @@ -238,7 +263,9 @@ sub _parse_with_plugin { my $vector_name; my $species_name; - if ($worksheet->get_cell($row,0)) { + if($autogenerate_uniquename > 0 ){ + $vector_name = "T" . ($vector_max_id + $row); + } elsif ($worksheet->get_cell($row,0)) { $vector_name = $worksheet->get_cell($row,0)->value(); } if ($worksheet->get_cell($row,1)) { @@ -336,6 +363,7 @@ sub _parse_with_plugin { } } + %return_data = ( parsed_data => \%parsed_entries, found_vectors => $found_vectors, @@ -345,7 +373,6 @@ sub _parse_with_plugin { fuzzy_organisms => $fuzzy_organisms, absent_organisms => $absent_organisms ); - # print STDERR "\n\nVectorsXLS parsed results :\n".Data::Dumper::Dumper(%return_data)."\n\n"; $self->_set_parsed_data(\%return_data); return 1; diff --git a/lib/CXGN/Trial.pm b/lib/CXGN/Trial.pm index 10b01268df..cdd9db5d9d 100644 --- a/lib/CXGN/Trial.pm +++ b/lib/CXGN/Trial.pm @@ -255,4 +255,341 @@ sub get_all_phenotype_metadata { } + + +=head2 function get_sorted_plots() + + Usage: CXGN::Trial->get_sorted_plots($schema, $trials, $order, $start, $gaps) + Desc: Get an array of plot metadata (plot_id, plot_name, row_number, col_number, etc) + for plots in the trial. Sort the plots by the provided traversal parameters. + Requirements: The Trial(s) MUST have row/col positions for every plot AND there must not + be any overlapping plots (more than one plot with the same row/col position). + Ret: An array of sorted plot metadata + Args: trials = an arrayref of trial ids to include + order = the order to traverse the plots ('by_col_serpentine', 'by_col_zigzag', 'by_row_serpentine', 'by_row_zigzag') + start = the corner of the trial layout to start the traversal ('bottom_left', 'top_left', 'top_right', 'bottom_right') + borders = a hashref with keys top, right, bottom, left. If the value is 1, then include that side as a border + gaps = when set to 1, include missing plots / gaps as items in the order + Side Effects: + Example: + +=cut + +sub get_sorted_plots { + my $class = shift; + my $schema = shift; + my $trials = shift; + my $order = shift || 'by_row_serpentine'; + my $start = shift || 'bottom_left'; + my $borders = shift || { top => 0, right => 0, bottom => 0, left => 0 }; + my $gaps = shift || 0; + + # Parse each trial + my @plot_details; + my ($min_row, $max_row, $min_col, $max_col, %seen_row_cols); + foreach my $trial_id (@$trials) { + + # Get plot details from the stored layout information + my $trial_layout_download = CXGN::Trial::TrialLayoutDownload->new({ + schema => $schema, + trial_id => $trial_id, + data_level => 'plots', + selected_columns => { + "location_name"=>1,"trial_name"=>1,"plot_name"=>1,"plot_id"=>1,"plot_number"=>1, + "row_number"=>1,"col_number"=>1,"accession_name"=>1,"seedlot_name"=>1, + "rep_number"=>1,"block_number"=>1,"is_a_control"=>1 + }, + }); + my $output = $trial_layout_download->get_layout_output()->{output}; + + # Convert plot layout array into hash and add each plot to the plot_details array (of hashes) + # Check for plot row/col requirements + # Set the overall min/max row/col positions + my @outer_array = @{$output}; + my ($inner_array, @keys); + for my $i (0 .. $#outer_array) { + $inner_array = $outer_array[$i]; + if (scalar @keys > 0) { + my %detail_hash; + @detail_hash{@keys} = @{$outer_array[$i]}; + my $row = $detail_hash{'row_number'}; + my $col = $detail_hash{'col_number'}; + my $key = "$row|$col"; + + # Check for undefined row and column positions + if ( !defined($row) || !defined($col) ) { + return { error => "One or more plots do not have a row and/or column defined!" }; + } + + # Check for duplicate positions (plots with the same row / col positions) + if ( exists $seen_row_cols{$key} ) { + return { error => "One or more plots share the same row and column position!" }; + } + + # Set the min/max row/col + $row = int($row); + $col = int($col); + if ( !defined($min_row) || $row < $min_row ) { + $min_row = $row; + } + if ( !defined($max_row) || $row > $max_row ) { + $max_row = $row; + } + if ( !defined($min_col) || $col < $min_col ) { + $min_col = $col; + } + if ( !defined($max_col) || $col > $max_col ) { + $max_col = $col; + } + + push(@plot_details, \%detail_hash); + } + else { + @keys = @{$inner_array}; + } + } + } + + # Set starting position: + # right = col from max to min + # left = col from min to max + # top = row from max to min + # bottom = row from min to max + # Add a row/col on either side for the borders + my ($start_row, $end_row, $delta_row); + my ($start_col, $end_col, $delta_col); + if ( $start =~ /right/ ) { + $start_col = $max_col + 1; + $end_col = $min_col - 1; + $delta_col = -1; + } + else { + $start_col = $min_col - 1; + $end_col = $max_col + 1; + $delta_col = 1; + } + if ( $start =~ /top/ ) { + $start_row = $max_row + 1; + $end_row = $min_row - 1; + $delta_row = -1; + } + else { + $start_row = $min_row - 1; + $end_row = $max_row + 1; + $delta_row = 1; + } + + # Set traversal order: + # by_col = first by column (outer loop) then by row (inner loop) + # by_row = first by row (outer loop) then by col (inner loop) + my ($outerloop_key, $outerloop_start, $outerloop_end, $outerloop_delta); + my ($innerloop_key, $innerloop_start, $innerloop_end, $innerloop_delta); + if ( $order =~ /by_col/ ) { + $outerloop_key = 'col_number'; + $outerloop_start = $start_col; + $outerloop_end = $end_col; + $outerloop_delta = $delta_col; + $innerloop_key = 'row_number'; + $innerloop_start = $start_row; + $innerloop_end = $end_row; + $innerloop_delta = $delta_row; + } + else { + $outerloop_key = 'row_number'; + $outerloop_start = $start_row; + $outerloop_end = $end_row; + $outerloop_delta = $delta_row; + $innerloop_key = 'col_number'; + $innerloop_start = $start_col; + $innerloop_end = $end_col; + $innerloop_delta = $delta_col; + } + + # Start the traversal + my @ordered_plots; + my $o_count = 0; + my $p_order = 1; + + # Start the outerloop... + for ( my $o = $outerloop_start; $outerloop_delta > 0 ? $o <= $outerloop_end : $o >= $outerloop_end; $o=$o+$outerloop_delta ) { + my $starting_p_order = $p_order; + + # Invert the order of every other innerloop when serpentine + my $i_start = $innerloop_start; + my $i_end = $innerloop_end; + my $i_delta = $innerloop_delta; + if ( $order =~ /serpentine/ ) { + if ( $o_count % 2 ) { + $i_start = $innerloop_end; + $i_end = $innerloop_start; + $i_delta = $innerloop_delta*-1; + } + } + + # Start the innerloop... + for ( my $i = $i_start; $i_delta > 0 ? $i <= $i_end : $i >= $i_end; $i=$i+$i_delta ) { + + # + # ADD BORDERS + # + + # Determine border type based on current position + my $obt_start = $outerloop_key eq 'row_number' ? ($outerloop_delta > 0 ? 'bottom' : 'top') : ($outerloop_delta > 0 ? 'left' : 'right'); + my $obt_end = $outerloop_key eq 'row_number' ? ($outerloop_delta > 0 ? 'top' : 'bottom') : ($outerloop_delta > 0 ? 'right' : 'left'); + my $ibt_start = $innerloop_key eq 'col_number' ? ($innerloop_delta > 0 ? 'left' : 'right') : ($innerloop_delta > 0 ? 'bottom' : 'top'); + my $ibt_end = $innerloop_key eq 'col_number' ? ($innerloop_delta > 0 ? 'right' : 'left') : ($innerloop_delta > 0 ? 'top' : 'bottom'); + + # Add corner 1 + if ( $o == $outerloop_start && $i == $innerloop_start ) { + if ( $borders->{$obt_start} && $borders->{$ibt_start} ) { + push(@ordered_plots, { + order => $p_order, + type => 'border', + border => $obt_start . "_" . $ibt_start, + $outerloop_key => $o, + $innerloop_key => $i + }); + $p_order++; + } + } + + # Add corner 2 + elsif ( $o == $outerloop_end && $i == $innerloop_start ) { + if ( $borders->{$obt_end} && $borders->{$ibt_start} ) { + push(@ordered_plots, { + order => $p_order, + type => 'border', + border => $obt_end . "_" . $ibt_start, + $outerloop_key => $o, + $innerloop_key => $i + }); + $p_order++; + } + } + + # Add corner 3 + elsif ( $o == $outerloop_end && $i == $innerloop_end ) { + if ( $borders->{$obt_end} && $borders->{$ibt_end} ) { + push(@ordered_plots, { + order => $p_order, + type => 'border', + border => $obt_end . "_" . $ibt_end, + $outerloop_key => $o, + $innerloop_key => $i + }); + $p_order++; + } + } + + # Add corner 4 + elsif ( $o == $outerloop_start && $i == $innerloop_end ) { + if ( $borders->{$obt_start} && $borders->{$ibt_end} ) { + push(@ordered_plots, { + order => $p_order, + type => 'border', + border => $obt_start . "_" . $ibt_end, + $outerloop_key => $o, + $innerloop_key => $i + }); + $p_order++; + } + } + + # Add outer start border + elsif ( $o == $outerloop_start ) { + if ( $borders->{$obt_start} ) { + push(@ordered_plots, { + order => $p_order, + type => 'border', + border => $obt_start, + $outerloop_key => $o, + $innerloop_key => $i + }); + $p_order++; + } + } + + # Add outer end border + elsif ( $o == $outerloop_end ) { + if ( $borders->{$obt_end} ) { + push(@ordered_plots, { + order => $p_order, + type => 'border', + border => $obt_end, + $outerloop_key => $o, + $innerloop_key => $i + }); + $p_order++; + } + } + + # Add inner start border + elsif ( $i == $innerloop_start ) { + if ( $borders->{$ibt_start} ) { + push(@ordered_plots, { + order => $p_order, + type => 'border', + border => $ibt_start, + $outerloop_key => $o, + $innerloop_key => $i + }); + $p_order++; + } + } + + # Add inner end border + elsif ( $i == $innerloop_end ) { + if ( $borders->{$ibt_end} ) { + push(@ordered_plots, { + order => $p_order, + type => 'border', + border => $ibt_end, + $outerloop_key => $o, + $innerloop_key => $i + }); + $p_order++; + } + } + + + # + # ADD PLOTS + # + else { + + # Find the plot with the matching row / col position + my ($p) = grep { $_->{$outerloop_key} == $o && $_->{$innerloop_key} == $i } @plot_details; + + # Add the plot, if it's found + if ( defined($p) ) { + $p->{order} = $p_order; + $p->{type} = 'plot'; + push(@ordered_plots, $p); + $p_order++; + } + + # Add a gap item when there is no plot, if requested + elsif ( $gaps ) { + push(@ordered_plots, { + order => $p_order, + type => 'gap', + $outerloop_key => $o, + $innerloop_key => $i + }); + $p_order++; + } + + } + + } + + if ( $p_order > $starting_p_order ) { + $o_count++; + } + } + + return { plots => \@ordered_plots }; +} + + 1; diff --git a/lib/CXGN/Trial/ParseUpload/Plugin/MultipleTrialDesignExcelFormat.pm b/lib/CXGN/Trial/ParseUpload/Plugin/MultipleTrialDesignExcelFormat.pm index 0df487e5e1..f70ea9191f 100644 --- a/lib/CXGN/Trial/ParseUpload/Plugin/MultipleTrialDesignExcelFormat.pm +++ b/lib/CXGN/Trial/ParseUpload/Plugin/MultipleTrialDesignExcelFormat.pm @@ -94,6 +94,7 @@ sub _validate_with_plugin { my $breeding_program; my $location; my $year; + my $transplanting_date; my $design_type; my $description; my $trial_type; @@ -148,49 +149,55 @@ sub _validate_with_plugin { } if ($worksheet->get_cell($row,4)) { - $design_type = $worksheet->get_cell($row,4)->value(); + $transplanting_date = $worksheet->get_cell($row,4)->value(); } else { - $design_type = undef; + $transplanting_date = undef; } if ($worksheet->get_cell($row,5)) { - $description = $worksheet->get_cell($row,5)->value(); + $design_type = $worksheet->get_cell($row,5)->value(); } else { - $description = undef; + $design_type = undef; } if ($worksheet->get_cell($row,6)) { - $trial_type = $worksheet->get_cell($row,6)->value(); + $description = $worksheet->get_cell($row,6)->value(); } else { - $trial_type = undef; + $description = undef; } if ($worksheet->get_cell($row,7)) { - $plot_width = $worksheet->get_cell($row,7)->value(); + $trial_type = $worksheet->get_cell($row,7)->value(); } else { - $plot_width = undef; + $trial_type = undef; } if ($worksheet->get_cell($row,8)) { - $plot_length = $worksheet->get_cell($row,8)->value(); + $plot_width = $worksheet->get_cell($row,8)->value(); } else { - $plot_length = undef; + $plot_width = undef; } if ($worksheet->get_cell($row,9)) { - $field_size = $worksheet->get_cell($row,9)->value(); + $plot_length = $worksheet->get_cell($row,9)->value(); } else { - $field_size = undef; + $plot_length = undef; } if ($worksheet->get_cell($row,10)) { - $planting_date = $worksheet->get_cell($row,10)->value(); + $field_size = $worksheet->get_cell($row,10)->value(); } else { - $planting_date = undef; + $field_size = undef; } if ($worksheet->get_cell($row,11)) { - $harvest_date = $worksheet->get_cell($row,11)->value(); + $planting_date = $worksheet->get_cell($row,11)->value(); + } else { + $planting_date = undef; + } + + if ($worksheet->get_cell($row,12)) { + $harvest_date = $worksheet->get_cell($row,12)->value(); } else { $harvest_date = undef; } @@ -212,41 +219,41 @@ sub _validate_with_plugin { next; } - if ($worksheet->get_cell($row,12)) { - $plot_name = $worksheet->get_cell($row,12)->value(); - } if ($worksheet->get_cell($row,13)) { - $accession_name = $worksheet->get_cell($row,13)->value(); + $plot_name = $worksheet->get_cell($row,13)->value(); } if ($worksheet->get_cell($row,14)) { - $plot_number = $worksheet->get_cell($row,14)->value(); + $accession_name = $worksheet->get_cell($row,14)->value(); } if ($worksheet->get_cell($row,15)) { - $block_number = $worksheet->get_cell($row,15)->value(); + $plot_number = $worksheet->get_cell($row,15)->value(); } if ($worksheet->get_cell($row,16)) { - $is_a_control = $worksheet->get_cell($row,16)->value(); + $block_number = $worksheet->get_cell($row,16)->value(); } if ($worksheet->get_cell($row,17)) { - $rep_number = $worksheet->get_cell($row,17)->value(); + $is_a_control = $worksheet->get_cell($row,17)->value(); } if ($worksheet->get_cell($row,18)) { - $range_number = $worksheet->get_cell($row,18)->value(); + $rep_number = $worksheet->get_cell($row,18)->value(); } if ($worksheet->get_cell($row,19)) { - $row_number = $worksheet->get_cell($row,19)->value(); + $range_number = $worksheet->get_cell($row,19)->value(); } if ($worksheet->get_cell($row,20)) { - $col_number = $worksheet->get_cell($row,20)->value(); + $row_number = $worksheet->get_cell($row,20)->value(); } if ($worksheet->get_cell($row,21)) { - $seedlot_name = $worksheet->get_cell($row,21)->value(); + $col_number = $worksheet->get_cell($row,21)->value(); } if ($worksheet->get_cell($row,22)) { - $num_seed_per_plot = $worksheet->get_cell($row,22)->value(); + $seedlot_name = $worksheet->get_cell($row,22)->value(); } if ($worksheet->get_cell($row,23)) { - $weight_gram_seed_per_plot = $worksheet->get_cell($row,23)->value(); + $num_seed_per_plot = $worksheet->get_cell($row,23)->value(); + } + if ($worksheet->get_cell($row,24)) { + $weight_gram_seed_per_plot = $worksheet->get_cell($row,24)->value(); } if ( $row_number && $col_number ) { @@ -313,9 +320,16 @@ sub _validate_with_plugin { push @error_messages, "Cell D$row_name: $year is not a valid year, must be a 4 digit positive integer."; } + ## TRANSPLANTING DATE CHECK + if ($transplanting_date) { + unless ($calendar_funcs->check_value_format($transplanting_date)) { + push @error_messages, "Cell E$row_name: transplanting_date $transplanting_date must be in the format YYYY-MM-DD."; + } + } + ## DESIGN TYPE CHECK if (!$design_type || $design_type eq '' ) { - push @error_messages, "Cell E$row_name: design_type missing."; + push @error_messages, "Cell F$row_name: design_type missing."; } else { $design_type =~ s/^\s+|\s+$//g; #trim whitespace from front and end... @@ -324,7 +338,7 @@ sub _validate_with_plugin { ## DESCRIPTION CHECK if (!$description || $description eq '' ) { - push @error_messages, "Cell F$row_name: description missing."; + push @error_messages, "Cell G$row_name: description missing."; } ## TRIAL TYPE CHECK @@ -335,30 +349,30 @@ sub _validate_with_plugin { ## PLOT WIDTH CHECK if ($plot_width && !($plot_width =~ /^([\d]*)([\.]?)([\d]+)$/)){ - push @error_messages, "Cell H$row_name: plot_width $plot_width must be a positive number."; + push @error_messages, "Cell I$row_name: plot_width $plot_width must be a positive number."; } ## PLOT LENGTH CHECK if ($plot_length && !($plot_length =~ /^([\d]*)([\.]?)([\d]+)$/)){ - push @error_messages, "Cell I$row_name: plot_length $plot_length must be a positive number."; + push @error_messages, "Cell J$row_name: plot_length $plot_length must be a positive number."; } ## FIELD SIZE CHECK if ($field_size && !($field_size =~ /^([\d]*)([\.]?)([\d]+)$/)){ - push @error_messages, "Cell J$row_name: field_size $field_size must be a positive number."; + push @error_messages, "Cell K$row_name: field_size $field_size must be a positive number."; } ## PLANTING DATE CHECK if ($planting_date) { unless ($calendar_funcs->check_value_format($planting_date)) { - push @error_messages, "Cell K$row_name: planting_date $planting_date must be in the format YYYY-MM-DD."; + push @error_messages, "Cell L$row_name: planting_date $planting_date must be in the format YYYY-MM-DD."; } } ## HARVEST DATE CHECK if ($harvest_date) { unless ($calendar_funcs->check_value_format($harvest_date)) { - push @error_messages, "Cell L$row_name: harvest_date $harvest_date must be in the format YYYY-MM-DD."; + push @error_messages, "Cell M$row_name: harvest_date $harvest_date must be in the format YYYY-MM-DD."; } } @@ -367,25 +381,25 @@ sub _validate_with_plugin { ## PLOT NAME CHECK if (!$plot_name || $plot_name eq '' ) { - push @error_messages, "Cell M$row_name: plot name missing."; + push @error_messages, "Cell N$row_name: plot name missing."; } elsif ($plot_name =~ /\s/ ) { - push @error_messages, "Cell M$row_name: plot name $plot_name must not contain spaces."; + push @error_messages, "Cell N$row_name: plot name $plot_name must not contain spaces."; } elsif ($plot_name =~ /\// || $plot_name =~ /\\/) { - push @warning_messages, "Cell M$row_name: plot name $plot_name contains slashes. Note that slashes can cause problems for third-party applications; however, plotnames can be saved with slashes."; + push @warning_messages, "Cell N$row_name: plot name $plot_name contains slashes. Note that slashes can cause problems for third-party applications; however, plotnames can be saved with slashes."; } else { $plot_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end... if ($seen_plot_names{$plot_name}) { - push @error_messages, "Cell M$row_name: duplicate plot name $plot_name seen before at cell M".$seen_plot_names{$plot_name}."."; + push @error_messages, "Cell N$row_name: duplicate plot name $plot_name seen before at cell M".$seen_plot_names{$plot_name}."."; } $seen_plot_names{$plot_name}=$row_name; } ## ACCESSSION NAME CHECK if (!$accession_name || $accession_name eq '') { - push @error_messages, "Cell N$row_name: accession name missing"; + push @error_messages, "Cell O$row_name: accession name missing"; } else { $accession_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end... $seen_accession_names{$accession_name}++; @@ -393,40 +407,40 @@ sub _validate_with_plugin { ## PLOT NUMBER CHECK if (!$plot_number || $plot_number eq '') { - push @error_messages, "Cell O$row_name: plot number missing"; + push @error_messages, "Cell P$row_name: plot number missing"; } if (!($plot_number =~ /^\d+?$/)) { - push @error_messages, "Cell O$row_name: plot number $plot_number is not a positive integer."; + push @error_messages, "Cell P$row_name: plot number $plot_number is not a positive integer."; } $seen_plot_numbers{$plot_number}++; ## BLOCK NUMBER CHECK if (!$block_number || $block_number eq '') { - push @error_messages, "Cell P$row_name: block number missing"; + push @error_messages, "Cell Q$row_name: block number missing"; } if (!($block_number =~ /^\d+?$/)) { - push @error_messages, "Cell P$row_name: block number $block_number is not a positive integer."; + push @error_messages, "Cell Q$row_name: block number $block_number is not a positive integer."; } ## IS A CONTROL CHECK if ($is_a_control) { if (!($is_a_control eq "yes" || $is_a_control eq "no" || $is_a_control eq "1" ||$is_a_control eq "0" || $is_a_control eq '')) { - push @error_messages, "Cell Q$row_name: is_a_control $is_a_control is not either yes, no 1, 0, or blank."; + push @error_messages, "Cell R$row_name: is_a_control $is_a_control is not either yes, no 1, 0, or blank."; } } ## REP, ROW, RANGE AND COLUMN CHECKS if ($rep_number && !($rep_number =~ /^\d+?$/)){ - push @error_messages, "Cell R$row_name: rep_number $rep_number must be a positive integer."; + push @error_messages, "Cell S$row_name: rep_number $rep_number must be a positive integer."; } if ($range_number && !($range_number =~ /^\d+?$/)){ - push @error_messages, "Cell S$row_name: range_number $range_number must be a positive integer."; + push @error_messages, "Cell T$row_name: range_number $range_number must be a positive integer."; } if ($row_number && !($row_number =~ /^\d+?$/)){ - push @error_messages, "Cell T$row_name: row_number $row_number must be a positive integer."; + push @error_messages, "Cell U$row_name: row_number $row_number must be a positive integer."; } if ($col_number && !($col_number =~ /^\d+?$/)){ - push @error_messages, "Cell U$row_name: col_number $col_number must be a positive integer."; + push @error_messages, "Cell V$row_name: col_number $col_number must be a positive integer."; } ## SEEDLOT CHECKS @@ -436,14 +450,14 @@ sub _validate_with_plugin { push @pairs, [$seedlot_name, $accession_name]; } if (defined($num_seed_per_plot) && $num_seed_per_plot ne '' && !($num_seed_per_plot =~ /^\d+?$/)){ - push @error_messages, "Cell W$row_name: num_seed_per_plot $num_seed_per_plot must be a positive integer."; + push @error_messages, "Cell X$row_name: num_seed_per_plot $num_seed_per_plot must be a positive integer."; } if (defined($weight_gram_seed_per_plot) && $weight_gram_seed_per_plot ne '' && !($weight_gram_seed_per_plot =~ /^\d+?$/)){ - push @error_messages, "Cell X$row_name: weight_gram_seed_per_plot $weight_gram_seed_per_plot must be a positive integer."; + push @error_messages, "Cell Y$row_name: weight_gram_seed_per_plot $weight_gram_seed_per_plot must be a positive integer."; } ## TREATMENT CHECKS - my $treatment_col = 24; + my $treatment_col = 25; foreach my $treatment_name (@treatment_names){ if($worksheet->get_cell($row,$treatment_col)){ my $apply_treatment = $worksheet->get_cell($row,$treatment_col)->value(); @@ -765,27 +779,35 @@ sub _parse_with_plugin { $single_design{'breeding_program'} = $worksheet->get_cell($row,1)->value(); $single_design{'location'} = $location; $single_design{'year'} = $worksheet->get_cell($row,3)->value(); - $single_design{'design_type'} = $worksheet->get_cell($row,4)->value(); - $single_design{'description'} = $worksheet->get_cell($row,5)->value(); + # $single_design{'transplanting_date'} = $worksheet->get_cell($row,4)->value(); + $single_design{'design_type'} = $worksheet->get_cell($row,5)->value(); + $single_design{'description'} = $worksheet->get_cell($row,6)->value(); - if ($worksheet->get_cell($row,6)) { # get and save trial type cvterm_id using trial type name - my $trial_type_id = $trial_type_map{$worksheet->get_cell($row,6)->value()}; - $single_design{'trial_type'} = $trial_type_id; + + # for a moment transplanting_date is moves as not required but whole design of that features must be redone + # including use cases + if ($worksheet->get_cell($row,4)) { + $single_design{'transplanting_date'} = $worksheet->get_cell($row,4)->value(); } - if ($worksheet->get_cell($row,7)) { - $single_design{'plot_width'} = $worksheet->get_cell($row,7)->value(); + + if ($worksheet->get_cell($row,7)) { # get and save trial type cvterm_id using trial type name + my $trial_type_id = $trial_type_map{$worksheet->get_cell($row,7)->value()}; + $single_design{'trial_type'} = $trial_type_id; } if ($worksheet->get_cell($row,8)) { - $single_design{'plot_length'} = $worksheet->get_cell($row,8)->value(); + $single_design{'plot_width'} = $worksheet->get_cell($row,8)->value(); } if ($worksheet->get_cell($row,9)) { - $single_design{'field_size'} = $worksheet->get_cell($row,9)->value(); + $single_design{'plot_length'} = $worksheet->get_cell($row,9)->value(); } if ($worksheet->get_cell($row,10)) { - $single_design{'planting_date'} = $worksheet->get_cell($row,10)->value(); + $single_design{'field_size'} = $worksheet->get_cell($row,10)->value(); } if ($worksheet->get_cell($row,11)) { - $single_design{'harvest_date'} = $worksheet->get_cell($row,11)->value(); + $single_design{'planting_date'} = $worksheet->get_cell($row,11)->value(); + } + if ($worksheet->get_cell($row,12)) { + $single_design{'harvest_date'} = $worksheet->get_cell($row,12)->value(); } ## Update trial name $trial_name = $current_trial_name; @@ -807,49 +829,50 @@ sub _parse_with_plugin { next; } - if ($worksheet->get_cell($row,12)) { - $plot_name = $worksheet->get_cell($row,12)->value(); - } - $plot_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end... if ($worksheet->get_cell($row,13)) { - $accession_name = $worksheet->get_cell($row,13)->value(); + $plot_name = $worksheet->get_cell($row,13)->value(); } - $accession_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end... + $plot_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end... if ($worksheet->get_cell($row,14)) { - $plot_number = $worksheet->get_cell($row,14)->value(); + $accession_name = $worksheet->get_cell($row,14)->value(); } + $accession_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end... if ($worksheet->get_cell($row,15)) { - $block_number = $worksheet->get_cell($row,15)->value(); + $plot_number = $worksheet->get_cell($row,15)->value(); } if ($worksheet->get_cell($row,16)) { - $is_a_control = $worksheet->get_cell($row,16)->value(); + $block_number = $worksheet->get_cell($row,16)->value(); } if ($worksheet->get_cell($row,17)) { - $rep_number = $worksheet->get_cell($row,17)->value(); + $is_a_control = $worksheet->get_cell($row,17)->value(); } if ($worksheet->get_cell($row,18)) { - $range_number = $worksheet->get_cell($row,18)->value(); + $rep_number = $worksheet->get_cell($row,18)->value(); } if ($worksheet->get_cell($row,19)) { - $row_number = $worksheet->get_cell($row, 19)->value(); + $range_number = $worksheet->get_cell($row,19)->value(); } if ($worksheet->get_cell($row,20)) { - $col_number = $worksheet->get_cell($row, 20)->value(); + $row_number = $worksheet->get_cell($row, 20)->value(); } if ($worksheet->get_cell($row,21)) { - $seedlot_name = $worksheet->get_cell($row, 21)->value(); + $col_number = $worksheet->get_cell($row, 21)->value(); + } + if ($worksheet->get_cell($row,22)) { + $seedlot_name = $worksheet->get_cell($row, 22)->value(); } + if ($seedlot_name){ $seedlot_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end... } - if ($worksheet->get_cell($row,22)) { - $num_seed_per_plot = $worksheet->get_cell($row, 22)->value(); - } if ($worksheet->get_cell($row,23)) { - $weight_gram_seed_per_plot = $worksheet->get_cell($row, 23)->value(); + $num_seed_per_plot = $worksheet->get_cell($row, 23)->value(); + } + if ($worksheet->get_cell($row,24)) { + $weight_gram_seed_per_plot = $worksheet->get_cell($row, 24)->value(); } - my $treatment_col = 24; + my $treatment_col = 25; foreach my $treatment_name (@treatment_names){ if($worksheet->get_cell($row,$treatment_col)){ if($worksheet->get_cell($row,$treatment_col)->value()){ @@ -922,6 +945,7 @@ sub _parse_header { my $breeding_program_head; my $location_head; my $year_head; + my $transplanting_date_head; my $design_type_head; my $description_head; my $trial_type_head; @@ -956,64 +980,67 @@ sub _parse_header { $year_head= $worksheet->get_cell(0,3)->value(); } if ($worksheet->get_cell(0,4)) { - $design_type_head= $worksheet->get_cell(0,4)->value(); + $transplanting_date_head= $worksheet->get_cell(0,4)->value(); } if ($worksheet->get_cell(0,5)) { - $description_head= $worksheet->get_cell(0,5)->value(); + $design_type_head= $worksheet->get_cell(0,5)->value(); } if ($worksheet->get_cell(0,6)) { - $trial_type_head= $worksheet->get_cell(0,6)->value(); + $description_head= $worksheet->get_cell(0,6)->value(); } if ($worksheet->get_cell(0,7)) { - $plot_width_head= $worksheet->get_cell(0,7)->value(); + $trial_type_head= $worksheet->get_cell(0,7)->value(); } if ($worksheet->get_cell(0,8)) { - $plot_length_head= $worksheet->get_cell(0,8)->value(); + $plot_width_head= $worksheet->get_cell(0,8)->value(); } if ($worksheet->get_cell(0,9)) { - $field_size_head= $worksheet->get_cell(0,9)->value(); + $plot_length_head= $worksheet->get_cell(0,9)->value(); } if ($worksheet->get_cell(0,10)) { - $planting_date_head= $worksheet->get_cell(0,10)->value(); + $field_size_head= $worksheet->get_cell(0,10)->value(); } if ($worksheet->get_cell(0,11)) { - $harvest_date_head= $worksheet->get_cell(0,11)->value(); + $planting_date_head= $worksheet->get_cell(0,11)->value(); } if ($worksheet->get_cell(0,12)) { - $plot_name_head = $worksheet->get_cell(0,12)->value(); + $harvest_date_head= $worksheet->get_cell(0,12)->value(); } if ($worksheet->get_cell(0,13)) { - $accession_name_head = $worksheet->get_cell(0,13)->value(); + $plot_name_head = $worksheet->get_cell(0,13)->value(); } if ($worksheet->get_cell(0,14)) { - $plot_number_head = $worksheet->get_cell(0,14)->value(); + $accession_name_head = $worksheet->get_cell(0,14)->value(); } if ($worksheet->get_cell(0,15)) { - $block_number_head = $worksheet->get_cell(0,15)->value(); + $plot_number_head = $worksheet->get_cell(0,15)->value(); } - if ($worksheet->get_cell(0,16)) { - $is_a_control_head = $worksheet->get_cell(0,16)->value(); + if ($worksheet->get_cell(0,15)) { + $block_number_head = $worksheet->get_cell(0,16)->value(); } if ($worksheet->get_cell(0,17)) { - $rep_number_head = $worksheet->get_cell(0,17)->value(); + $is_a_control_head = $worksheet->get_cell(0,17)->value(); } if ($worksheet->get_cell(0,18)) { - $range_number_head = $worksheet->get_cell(0,18)->value(); + $rep_number_head = $worksheet->get_cell(0,18)->value(); } if ($worksheet->get_cell(0,19)) { - $row_number_head = $worksheet->get_cell(0,19)->value(); + $range_number_head = $worksheet->get_cell(0,19)->value(); } if ($worksheet->get_cell(0,20)) { - $col_number_head = $worksheet->get_cell(0,20)->value(); + $row_number_head = $worksheet->get_cell(0,20)->value(); } if ($worksheet->get_cell(0,21)) { - $seedlot_name_head = $worksheet->get_cell(0,21)->value(); + $col_number_head = $worksheet->get_cell(0,21)->value(); } if ($worksheet->get_cell(0,22)) { - $num_seed_per_plot_head = $worksheet->get_cell(0,22)->value(); + $seedlot_name_head = $worksheet->get_cell(0,22)->value(); } if ($worksheet->get_cell(0,23)) { - $weight_gram_seed_per_plot_head = $worksheet->get_cell(0,23)->value(); + $num_seed_per_plot_head = $worksheet->get_cell(0,23)->value(); + } + if ($worksheet->get_cell(0,24)) { + $weight_gram_seed_per_plot_head = $worksheet->get_cell(0,24)->value(); } my @error_messages; @@ -1030,65 +1057,68 @@ sub _parse_header { if (!$year_head || $year_head ne 'year' ) { push @error_messages, "Cell D1: year is missing from the header"; } + if (!$transplanting_date_head || $transplanting_date_head ne 'transplanting_date' ) { + push @error_messages, "Cell E1: year is missing from the header"; + } if (!$design_type_head || $design_type_head ne 'design_type' ) { - push @error_messages, "Cell E1: design_type is missing from the header"; + push @error_messages, "Cell F1: design_type is missing from the header"; } if (!$description_head || $description_head ne 'description' ) { - push @error_messages, "Cell F1: description is missing from the header"; + push @error_messages, "Cell G1: description is missing from the header"; } if (!$trial_type_head || $trial_type_head ne 'trial_type' ) { - push @error_messages, "Cell G1: trial_type is missing from the header"; + push @error_messages, "Cell H1: trial_type is missing from the header"; } if (!$plot_width_head || $plot_width_head ne 'plot_width' ) { - push @error_messages, "Cell H1: plot_width is missing from the header"; + push @error_messages, "Cell I1: plot_width is missing from the header"; } if (!$plot_length_head || $plot_length_head ne 'plot_length' ) { - push @error_messages, "Cell I1: plot_length is missing from the header"; + push @error_messages, "Cell J1: plot_length is missing from the header"; } if (!$field_size_head || $field_size_head ne 'field_size' ) { - push @error_messages, "Cell J1: field_size is missing from the header"; + push @error_messages, "Cell K1: field_size is missing from the header"; } if (!$planting_date_head || $planting_date_head ne 'planting_date' ) { - push @error_messages, "Cell K1: planting_date is missing from the header"; + push @error_messages, "Cell L1: planting_date is missing from the header"; } if (!$harvest_date_head || $harvest_date_head ne 'harvest_date' ) { - push @error_messages, "Cell L1: harvest_date is missing from the header"; + push @error_messages, "Cell M1: harvest_date is missing from the header"; } if (!$plot_name_head || $plot_name_head ne 'plot_name' ) { - push @error_messages, "Cell M1: plot_name is missing from the header"; + push @error_messages, "Cell N1: plot_name is missing from the header"; } if (!$accession_name_head || $accession_name_head ne 'accession_name') { - push @error_messages, "Cell N1: accession_name is missing from the header"; + push @error_messages, "Cell O1: accession_name is missing from the header"; } if (!$plot_number_head || $plot_number_head ne 'plot_number') { - push @error_messages, "Cell O1: plot_number is missing from the header"; + push @error_messages, "Cell P1: plot_number is missing from the header"; } if (!$block_number_head || $block_number_head ne 'block_number') { - push @error_messages, "Cell P1: block_number is missing from the header"; + push @error_messages, "Cell Q1: block_number is missing from the header"; } if (!$is_a_control_head || $is_a_control_head ne 'is_a_control') { - push @error_messages, "Cell Q1: is_a_control is missing from the header. (Header is required, but values are optional)"; + push @error_messages, "Cell R1: is_a_control is missing from the header. (Header is required, but values are optional)"; } if (!$rep_number_head || $rep_number_head ne 'rep_number') { - push @error_messages, "Cell R1: rep_number is missing from the header. (Header is required, but values are optional)"; + push @error_messages, "Cell S1: rep_number is missing from the header. (Header is required, but values are optional)"; } if (!$range_number_head || $range_number_head ne 'range_number') { - push @error_messages, "Cell S1: range_number is missing from the header. (Header is required, but values are optional)"; + push @error_messages, "Cell T1: range_number is missing from the header. (Header is required, but values are optional)"; } if (!$row_number_head || $row_number_head ne 'row_number') { - push @error_messages, "Cell T1: row_number is missing from the header. (Header is required, but values are optional)"; + push @error_messages, "Cell U1: row_number is missing from the header. (Header is required, but values are optional)"; } if (!$col_number_head || $col_number_head ne 'col_number') { - push @error_messages, "Cell U1: col_number is missing from the header. (Header is required, but values are optional)"; + push @error_messages, "Cell V1: col_number is missing from the header. (Header is required, but values are optional)"; } if (!$seedlot_name_head || $seedlot_name_head ne 'seedlot_name') { - push @error_messages, "Cell V1: seedlot_name is missing from the header. (Header is required, but values are optional)"; + push @error_messages, "Cell W1: seedlot_name is missing from the header. (Header is required, but values are optional)"; } if (!$num_seed_per_plot_head || $num_seed_per_plot_head ne 'num_seed_per_plot') { - push @error_messages, "Cell W1: num_seed_per_plot is missing from the header. (Header is required, but values are optional)"; + push @error_messages, "Cell X1: num_seed_per_plot is missing from the header. (Header is required, but values are optional)"; } if (!$weight_gram_seed_per_plot_head || $weight_gram_seed_per_plot_head ne 'weight_gram_seed_per_plot') { - push @error_messages, "Cell X1: weight_gram_seed_per_plot is missing from the header. (Header is required, but values are optional)"; + push @error_messages, "Cell Y1: weight_gram_seed_per_plot is missing from the header. (Header is required, but values are optional)"; } return \@error_messages; diff --git a/lib/CXGN/Trial/TrialCreate.pm b/lib/CXGN/Trial/TrialCreate.pm index d0a7d7659f..b236906303 100644 --- a/lib/CXGN/Trial/TrialCreate.pm +++ b/lib/CXGN/Trial/TrialCreate.pm @@ -162,6 +162,7 @@ has 'field_size' => (isa => 'Num', is => 'rw', predicate => 'has_field_size', re has 'plot_width' => (isa => 'Num', is => 'rw', predicate => 'has_plot_width', required => 0); has 'plot_length' => (isa => 'Num', is => 'rw', predicate => 'has_plot_length', required => 0); has 'planting_date' => (isa => 'Str', is => 'rw', predicate => 'has_planting_date', required => 0); +has 'transplanting_date' => (isa => 'Str', is => 'rw', predicate => 'has_transplanting_date', required => 0); has 'harvest_date' => (isa => 'Str', is => 'rw', predicate => 'has_harvest_date', required => 0); has 'operator' => (isa => 'Str', is => 'rw', predicate => 'has_operator', required => 1); has 'trial_stock_type' => (isa => 'Str', is => 'rw', predicate => 'has_trial_stock_type', required => 0, default => 'accession'); @@ -398,6 +399,9 @@ sub save_trial { if ($self->get_harvest_date()){ # here is local getter $t->set_harvest_date($self->get_harvest_date); # here is Project.pm unusual setter with writing to db instead of object } + if ($self->get_transplanting_date()){ # here is local getter + $t->set_transplanting_date($self->get_transplanting_date); # here is Project.pm unusual setter with writing to db instead of object + } #link to the project $nd_experiment->find_or_create_related('nd_experiment_projects',{project_id => $project->project_id()}); diff --git a/lib/SGN/Controller/AJAX/LabelDesigner.pm b/lib/SGN/Controller/AJAX/LabelDesigner.pm index 7e9d7f9ad9..eb49907164 100644 --- a/lib/SGN/Controller/AJAX/LabelDesigner.pm +++ b/lib/SGN/Controller/AJAX/LabelDesigner.pm @@ -413,13 +413,60 @@ __PACKAGE__->config( my $sort_order_1 = $design_params->{'sort_order_1'}; my $sort_order_2 = $design_params->{'sort_order_2'}; my $sort_order_3 = $design_params->{'sort_order_3'}; + my @sorted_keys; + + # Sort by Field Layout + if ( $sort_order_1 eq 'Trial Layout: Plot Order') { + my $layout_order = $design_params->{'sort_order_layout_order'}; + my $layout_start = $design_params->{'sort_order_layout_start'}; + + # Set the Trial IDs + # - a single trial = the source id is the trial id + # - a list of trials = the source id is the list id + # get the list contents and convert to database ids + my @trial_ids; + if ( $data_type eq 'Field Trials' ) { + push(@trial_ids, $source_id); + } + elsif ( $data_type eq 'Lists' ) { + my $list = CXGN::List->new({ dbh => $schema->storage->dbh(), list_id => $source_id }); + my $list_elements = $list->retrieve_elements_with_ids($source_id); + my @trial_names = map { $_->[1] } @$list_elements; + my $lt = CXGN::List::Transform->new(); + my $tr = $lt->transform($schema, "projects_2_project_ids", \@trial_names); + @trial_ids = @{$tr->{transform}}; + } - my @sorted_keys = sort { - ncmp($design->{$a}{$sort_order_1}, $design->{$b}{$sort_order_1}) || - ncmp($design->{$a}{$sort_order_2}, $design->{$b}{$sort_order_2}) || - ncmp($design->{$a}{$sort_order_3}, $design->{$b}{$sort_order_3}) || - ncmp($a, $b) - } keys %design; + # Get the sorted plots, individually by trial + # Add a _plot_order key to each plot in the label design + foreach my $trial_id (@trial_ids) { + my $results = CXGN::Trial->get_sorted_plots($schema, [$trial_id], $layout_order, $layout_start); + if ( $results->{plots} ) { + foreach (@{$results->{plots}}) { + $design->{$_->{plot_name}}{_plot_order} = $_->{order}; + } + } + } + + # Sort the label design elements by trial, plot order, plot number + # (if the trial does not have a layout, it will default to sorting by plot number) + @sorted_keys = sort { + ncmp($design->{$a}{trial_name}, $design->{$b}{trial_name}) || + ncmp($design->{$a}{_plot_order}, $design->{$b}{_plot_order}) || + ncmp($design->{$a}{plot_number}, $design->{$b}{plot_numer}) || + ncmp($a, $b) + } keys %design; + } + + # Sort by designated data property(s) + else { + @sorted_keys = sort { + ncmp($design->{$a}{$sort_order_1}, $design->{$b}{$sort_order_1}) || + ncmp($design->{$a}{$sort_order_2}, $design->{$b}{$sort_order_2}) || + ncmp($design->{$a}{$sort_order_3}, $design->{$b}{$sort_order_3}) || + ncmp($a, $b) + } keys %design; + } my $qrcode = Imager::QRCode->new( margin => 0, diff --git a/lib/SGN/Controller/AJAX/Search/Vector.pm b/lib/SGN/Controller/AJAX/Search/Vector.pm index a0543c034b..78941a4aca 100644 --- a/lib/SGN/Controller/AJAX/Search/Vector.pm +++ b/lib/SGN/Controller/AJAX/Search/Vector.pm @@ -52,7 +52,7 @@ sub stock_search :Path('/ajax/search/vectors') Args(0) { people_schema=>$people_schema, phenome_schema=>$phenome_schema, match_type=>$params->{any_name_matchtype}, - match_name=>$params->{any_name}, + match_name=>$params->{any_name}, operator=>$params->{operator}, stockprops_values=>$stockprops_values, stockprop_columns_view=>$stockprop_columns_view, diff --git a/lib/SGN/Controller/AJAX/Stock.pm b/lib/SGN/Controller/AJAX/Stock.pm index ccf0ac27aa..24d8b63c4b 100644 --- a/lib/SGN/Controller/AJAX/Stock.pm +++ b/lib/SGN/Controller/AJAX/Stock.pm @@ -1924,15 +1924,65 @@ sub get_trial_related_stock:Chained('/stock/get_stock') PathPart('datatables/tri my $trial_related_stock = CXGN::Stock::RelatedStocks->new({dbic_schema => $schema, stock_id =>$stock_id}); my $result = $trial_related_stock->get_trial_related_stock(); my @stocks; + my @accessions; + my @crosses; + my @family_names; + my @plots; + my @subplots; + my @plants; + my @tissue_samples; + my @seedlots; + my @others; foreach my $r (@$result){ - my ($stock_id, $stock_name, $cvterm_name) = @$r; - my $url; - if ($cvterm_name eq 'seedlot'){ - $url = qq{$stock_name}; - } else { - $url = qq{$stock_name}; - } - push @stocks, [$url, $cvterm_name, $stock_name]; + my ($stock_id, $stock_name, $cvterm_name) = @$r; + my $url; + + if ($cvterm_name eq 'cross') { + $url = qq{$stock_name}; + } elsif ($cvterm_name eq 'family_name') { + $url = qq{$stock_name}; + } else { + $url = qq{$stock_name}; + } + + if ($cvterm_name eq 'accession') { + push @accessions, [$cvterm_name, $url, $stock_name]; + } elsif ($cvterm_name eq 'cross') { + push @crosses, [$cvterm_name, $url, $stock_name]; + } elsif ($cvterm_name eq 'family_name') { + push @family_names, [$cvterm_name, $url, $stock_name]; + } elsif ($cvterm_name eq 'plot') { + push @plots, [$cvterm_name, $url, $stock_name]; + } elsif ($cvterm_name eq 'subplot') { + push @subplots, [$cvterm_name, $url, $stock_name]; + } elsif ($cvterm_name eq 'plant') { + push @plants, [$cvterm_name, $url, $stock_name]; + } + } + + if (scalar(@accessions) > 0) { + push @stocks, @accessions; + } + if (scalar(@crosses) > 0) { + push @stocks, @crosses; + } + if (scalar(@family_names) > 0) { + push @stocks, @family_names; + } + if (scalar(@plots) > 0) { + push @stocks, @plots; + } + if (scalar(@subplots) > 0) { + push @stocks, @subplots; + } + if (scalar(@plants) > 0) { + push @stocks, @plants; + } + if (scalar(@seedlots) > 0) { + push @stocks, @seedlots; + } + if (scalar(@others) > 0) { + push @stocks, @others; } $c->stash->{rest}={data=>\@stocks}; @@ -2019,13 +2069,32 @@ sub get_stock_for_tissue:Chained('/stock/get_stock') PathPart('datatables/stock_ my ($stock_id, $stock_name, $cvterm_name) = @$r; - push @stocks, [qq{$stock_name}, $cvterm_name, $stock_name]; + push @stocks, [$cvterm_name, qq{$stock_name}, $stock_name]; } $c->stash->{rest}={data=>\@stocks}; } + +sub get_plot_plant_related_seedlots:Chained('/stock/get_stock') PathPart('datatables/plot_plant_related_seedlots') Args(0){ + my $self = shift; + my $c = shift; + my $stock_id = $c->stash->{stock_row}->stock_id(); + + my $schema = $c->dbic_schema("Bio::Chado::Schema", 'sgn_chado'); + my $progenies = CXGN::Stock::RelatedStocks->new({dbic_schema => $schema, stock_id =>$stock_id}); + my $result = $progenies->get_plot_plant_related_seedlots(); + my @stocks; + foreach my $r (@$result){ + my ($transaction_type, $stock_type, $stock_id, $stock_name) = @$r; + push @stocks, [$transaction_type, $stock_type, qq{$stock_name}, $stock_name]; + } + + $c->stash->{rest}={data=>\@stocks}; +} + + sub get_stock_datatables_genotype_data : Chained('/stock/get_stock') :PathPart('datatables/genotype_data') : ActionClass('REST') { } sub get_stock_datatables_genotype_data_GET { @@ -2277,7 +2346,7 @@ sub stock_additional_file_upload :Chained('/stock/get_stock') PathPart('upload_a $c->stash->{rest} = {error=>$result->{error}}; $c->detach(); } - + $c->stash->{rest} = { success => 1, file_id => $result->{file_id} }; } @@ -2294,11 +2363,11 @@ sub get_accession_additional_file_uploaded :Chained('/stock/get_stock') PathPart my @file_array; my %file_info; - my $q = "SELECT file_id, m.create_date, p.sp_person_id, p.username, basename, dirname, filetype + my $q = "SELECT file_id, m.create_date, p.sp_person_id, p.username, basename, dirname, filetype FROM phenome.stock_file - JOIN metadata.md_files using(file_id) + JOIN metadata.md_files using(file_id) LEFT JOIN metadata.md_metadata as m using(metadata_id) - LEFT JOIN sgn_people.sp_person as p ON (p.sp_person_id=m.create_person_id) + LEFT JOIN sgn_people.sp_person as p ON (p.sp_person_id=m.create_person_id) WHERE stock_id=? and m.obsolete = 0 and metadata.md_files.filetype='accession_additional_file_upload' ORDER BY file_id ASC"; my $h = $c->dbc->dbh()->prepare($q); diff --git a/lib/SGN/Controller/AJAX/Trial.pm b/lib/SGN/Controller/AJAX/Trial.pm index 23b3ef2716..00336020b0 100644 --- a/lib/SGN/Controller/AJAX/Trial.pm +++ b/lib/SGN/Controller/AJAX/Trial.pm @@ -1255,7 +1255,9 @@ sub upload_multiple_trial_designs_file_POST : Args(0) { if ($trial_design->{'harvest_date'}){ $trial_info_hash{harvest_date} = $trial_design->{'harvest_date'}; } - + if ($trial_design->{'transplanting_date'}){ + $trial_info_hash{transplanting_date} = $trial_design->{'transplanting_date'}; + } my $trial_create = CXGN::Trial::TrialCreate->new(\%trial_info_hash); my $current_save = $trial_create->save_trial(); diff --git a/lib/SGN/Controller/AJAX/TrialMetadata.pm b/lib/SGN/Controller/AJAX/TrialMetadata.pm index cc45676369..00cd91cfcd 100644 --- a/lib/SGN/Controller/AJAX/TrialMetadata.pm +++ b/lib/SGN/Controller/AJAX/TrialMetadata.pm @@ -4901,6 +4901,188 @@ sub update_trial_design_type_POST : Args(0) { } + +# +# GET TRIAL PLOT ORDERS +# Get the ordered plots of one or more trials based on the requested ordering parameters +# Arguments: +# - trial_ids: array of trial ids +# - type: plot order file type ('planting', 'harvest', or 'harvestmaster') +# - order: the order to traverse the plots ('by_col_serpentine', 'by_col_zigzag', 'by_row_serpentine', 'by_row_zigzag') +# - start: the corner of the trial layout to start the traversal ('bottom_left', 'top_left', 'top_right', 'bottom_right') +# - top_border: set to true to include a top border +# - right_border: set to true to include a right border +# - bottom_border: set to true to include a bottom border +# - left_border: set to true to include a left border +# - gaps: set to true to include gaps / missing plots +# - hm_pltid: property to use as the harvestmaster PLTID (default: 'plot_id') +# - hm_range: property to use as the harvestmaster range (default: 'row_number') +# - hm_row: property to use as the harvestmaster row (default: 'col_number') +# +sub get_trial_plot_order : Path('/ajax/breeders/trial_plot_order') : Args(0) { + my $self = shift; + my $c = shift; + my $schema = $c->dbic_schema('Bio::Chado::Schema'); + my @trial_ids = split(',', $c->req->param('trial_ids') || ''); + my $type = $c->req->param('type') || 'planting'; + my $order = $c->req->param('order') || 'by_row_zigzag'; + my $start = $c->req->param('start') || 'bottom_left'; + my $top_border = $c->req->param('top_border') || 'false'; + my $right_border = $c->req->param('right_border') || 'false'; + my $bottom_border = $c->req->param('bottom_border') || 'false'; + my $left_border = $c->req->param('left_border') || 'false'; + my $gaps = $c->req->param('gaps') || 'false'; + my $hm_pltid = $c->req->param('hm_pltid') || 'plot_id'; + my $hm_range = $c->req->param('hm_range') || 'row_number'; + my $hm_row = $c->req->param('hm_row') || 'col_number'; + + # Check parameters + if ( scalar(@trial_ids) eq 0 ) { + $c->stash->{rest} = { error => "No trial_ids provided!" }; + return; + } + if ( $type ne 'planting' && $type ne 'harvest' && $type ne 'harvestmaster' ) { + $c->stash->{rest} = { error => "Unrecognized type!" }; + return; + } + if ( ( $order !~ /by_col/ && $order !~ /by_row/ ) || ( $order !~ /serpentine/ && $order !~ /zigzag/ ) ) { + $c->stash->{rest} = { error => "Unrecognized order!" }; + return; + } + if ( ( $start !~ /bottom/ && $start !~ /top/ ) || ( $start !~ /left/ && $start !~ /right/ ) ) { + $c->stash->{rest} = { error => "Unrecognized start!" }; + return; + } + my %borders = ( + top => $top_border eq 'true' || 0, + right => $right_border eq 'true' || 0, + bottom => $bottom_border eq 'true' || 0, + left => $left_border eq 'true' || 0 + ); + + # Get the sorted plots + my $results = CXGN::Trial->get_sorted_plots($schema, \@trial_ids, $order, $start, \%borders, $gaps eq 'true' || 0); + + # Return error message, if set + if ( !defined $results->{error} && !defined $results->{plots} ) { + $results->{error} = "An unknown error occurred"; + } + if ( defined $results->{error} ) { + $c->stash->{rest} = { error => $results->{error} }; + return; + } + + # Generate CSV file + my $filename; + my @data; + if ( $type eq 'planting' || $type eq 'harvest' ) { + $filename = $type . "_order.csv"; + my $col = $type . "_order"; + + # Add CSV headers + my @headers = ($col, "type", "location_name", "trial_name", "plot_number", "plot_name", "accession_name", "seedlot_name", "row_number", "col_number", "rep_number", "block_number", "is_a_control"); + push(@data, \@headers); + + # Add plot rows + my $plots = $results->{plots}; + foreach (@$plots) { + if ( $_->{type} eq 'plot' ) { + my @d = ( + $_->{order}, + $_->{type}, + "\"$_->{location_name}\"", + $_->{trial_name}, + $_->{plot_number}, + $_->{plot_name}, + $_->{accession_name}, + $_->{seedlot_name}, + $_->{row_number}, + $_->{col_number}, + $_->{rep_number}, + $_->{block_number}, + $_->{is_a_control} + ); + push(@data, \@d); + } + else { + my @d = ( + $_->{order}, + $_->{type}, + "", # location + "", # trial + "", # plot number + "", # plot name + "", # accession + "", # seedlot + $_->{row_number}, + $_->{col_number}, + "", # rep + "", # block + "", # control + ); + push(@data, \@d); + } + } + } + + elsif ( $type eq 'harvestmaster' ) { + $filename = "harvest_master.csv"; + + # Add CSV headers + my @headers = ("PLTID", "Range", "Row", "type", "location_name", "trial_name", "plot_number", "plot_name", "accession_name", "seedlot_name", "rep_number", "block_number", "is_a_control"); + push(@data, \@headers); + + # Add plot rows + my $plots = $results->{plots}; + foreach (@$plots) { + if ( $_->{type} eq 'plot' ) { + my @d = ( + $_->{$hm_pltid}, + $_->{$hm_range}, + $_->{$hm_row}, + $_->{type}, + "\"$_->{location_name}\"", + $_->{trial_name}, + $_->{plot_number}, + $_->{plot_name}, + $_->{accession_name}, + $_->{seedlot_name}, + $_->{rep_number}, + $_->{block_number}, + $_->{is_a_control} + ); + push(@data, \@d); + } + else { + my @d = ( + $_->{type}, + $_->{$hm_range}, + $_->{$hm_row}, + $_->{type}, + "", # location + "", # trial + "", # plot number + "", # plot name + "", # accession + "", # seedlot + "", # rep + "", # block + "", # control + ); + push(@data, \@d); + } + } + + } + + # Return the generated file + $c->res->content_type('text/csv'); + $c->res->headers->push_header("Content-disposition', 'attachment; filename=\"$filename\""); + $c->res->body( join("\n", map { $_ = join(",", @{$_}) } @data) ); + return; +} + + # # GET LINKED FIELD TRIALS # Get additional field trials that share the same physical field (to display together in the plot layout tool) diff --git a/lib/SGN/Controller/AJAX/VectorConstruct.pm b/lib/SGN/Controller/AJAX/VectorConstruct.pm index e714439399..6a4eee4c80 100644 --- a/lib/SGN/Controller/AJAX/VectorConstruct.pm +++ b/lib/SGN/Controller/AJAX/VectorConstruct.pm @@ -21,6 +21,7 @@ use Data::Dumper; use JSON; use SGN::Model::Cvterm; use CXGN::Stock::Vector; +use CXGN::Stock::Vector::ParseUpload; use Try::Tiny; use Encode; use JSON::XS qw | decode_json |; @@ -279,6 +280,7 @@ sub verify_vectors_file_POST : Args(0) { my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado'); my $upload = $c->req->upload('new_vectors_upload_file'); my $do_fuzzy_search = $user_role eq 'curator' && !$c->req->param('fuzzy_check_upload_vectors') ? 0 : 1; + my $autogenerate_uniquename = !$c->req->param('autogenerate_uniquename') ? 0 : 1; if ($user_role ne 'curator' && !$do_fuzzy_search) { $c->stash->{rest} = {error=>'Only a curator can add vectors without using the fuzzy search!'}; @@ -316,7 +318,7 @@ sub verify_vectors_file_POST : Args(0) { unlink $upload_tempfile; my @editable_vector_props = split ',', $c->config->{editable_vector_props}; - my $parser = CXGN::Stock::ParseUpload->new(chado_schema => $schema, filename => $archived_filename_with_path, editable_stock_props=>\@editable_vector_props, do_fuzzy_search=>$do_fuzzy_search); + my $parser = CXGN::Stock::Vector::ParseUpload->new(chado_schema => $schema, filename => $archived_filename_with_path, editable_stock_props=>\@editable_vector_props, do_fuzzy_search=>$do_fuzzy_search, autogenerate_uniquename=>$autogenerate_uniquename); $parser->load_plugin('VectorsXLS'); my $parsed_data = $parser->parse(); @@ -414,6 +416,35 @@ sub verify_vectors_fuzzy_options_POST : Args(0) { } +sub get_new_vector_uniquename : Path('/ajax/get_new_vector_uniquename') : ActionClass('REST') { } + +sub get_new_vector_uniquename_GET : Args(0) { + my ($self, $c) = @_; + my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado'); + + my $stock_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'vector_construct', 'stock_type')->cvterm_id(); + + my $stocks = $schema->resultset("Stock::Stock")->search({ + type_id => $stock_type_id, + }); + + my $id; + my $max=0; + while (my $r = $stocks->next()) { + $id = $r->uniquename; + if ($id =~ m/T[0-9]+/){ + $id =~ s/T//; + if($max < $id){ + $max = $id; + } + } + } + $max += 1; + #Vector construct has letter T before autogenerated number. + $c->stash->{rest} = [ "T". $max]; +} + + sub _parse_list_from_json { my $c = shift; my $list_json = shift; diff --git a/mason/analyses/detail.mas b/mason/analyses/detail.mas index 61a4fb7ad5..1f9d4e033b 100644 --- a/mason/analyses/detail.mas +++ b/mason/analyses/detail.mas @@ -52,7 +52,7 @@ $has_col_and_row_numbers % $layout_buttons = '

   This experiment does not have spatial layout info!

'; % } -<& /page/detail_page_2_col_section.mas, trial_id => $analysis_id, info_section_title => "

Field Layout Tools and Phenotype Heatmap

", info_section_subtitle => $subtitle, buttons_html => $layout_buttons, icon_class => "glyphicon glyphicon-th", info_section_id => "pheno_heatmap" &> +<& /page/detail_page_2_col_section.mas, trial_id => $analysis_id, has_col_and_row_numbers => $has_col_and_row_numbers, info_section_title => "

Field Layout Tools and Phenotype Heatmap

", info_section_subtitle => $subtitle, buttons_html => $layout_buttons, icon_class => "glyphicon glyphicon-th", info_section_id => "pheno_heatmap" &> <& /page/detail_page_2_col_section.mas, trial_id => $analysis_id, info_section_title => "

Analysis Tools

", info_section_subtitle => 'Run analyses', icon_class => "glyphicon glyphicon-signal", info_section_id => "analysis_page_analysis_tools" &> diff --git a/mason/breeders_toolbox/add_vectors_dialogs.mas b/mason/breeders_toolbox/add_vectors_dialogs.mas index 1d392ee582..e46b4b1685 100644 --- a/mason/breeders_toolbox/add_vectors_dialogs.mas +++ b/mason/breeders_toolbox/add_vectors_dialogs.mas @@ -52,6 +52,12 @@ $editable_stock_props_definitions Note: Use the fuzzy search to match similar names to prevent uploading of duplicate vectors. Fuzzy searching is much slower than regular search. Only a curator can disable the fuzzy search. +
+
+
+ +
+
diff --git a/mason/breeders_toolbox/seedlots_section.mas b/mason/breeders_toolbox/seedlots_section.mas index 0a2923f8f9..2265f31691 100644 --- a/mason/breeders_toolbox/seedlots_section.mas +++ b/mason/breeders_toolbox/seedlots_section.mas @@ -15,12 +15,11 @@ $stock_type => undef <&| /page/info_section.mas, id=>'related_seedlots_to_accessions', title => 'Seedlots of this '.ucfirst($stock_type), collapsible=>1, collapsed=>1, subtitle=>"" &>
-
+
-
<&| /page/info_section.mas, title => 'Copy Seedlots to a List', collapsible=>1, collapsed=>1, subtitle=>'Copy the seedlot names showing in table to a new or exisiting list'&>
@@ -38,6 +37,11 @@ jQuery(document).ready(function(){ jQuery('#related_seedlots_to_accessions_onswitch').one("click", function(){ var seedlots_table = jQuery('#seedlots_of_accession_table').DataTable({ + 'destroy' : true, + 'ordering' : false, + 'processing': true, + 'serverSide': true, + 'lengthMenu': [10,20,50,100,1000], 'ajax': { 'url': '/ajax/breeders/seedlots', 'data': function(d) { % if ($stock_type eq 'accession'){ @@ -53,24 +57,28 @@ jQuery(document).ready(function(){ { title: "Contents", "data": "contents_html" }, { title: "Seedlot Location", "data": "location" }, { title: "Count", "data": "count" }, + { title: "Weight(g)", "data": "weight_gram" }, + { title: "Box Name", "data": "box" }, + { title: "Quality", "data": "seedlot_quality" }, + { title: "", "data": "seedlot_stock_uniquename"} ], - "fnInitComplete": function(oSettings, json) { - //console.log(json); - if (!isLoggedIn()) { - jQuery('#accession_seedlots_to_list_menu').html("

Please login to use lists!

"); - } else { - var html = ""; - for(var i=0; i undef % $layout_buttons = '

   This experiment does not have spatial layout info!

'; % } -<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, info_section_title => "

Field Layout Tools and Phenotype Heatmap

", info_section_subtitle => $subtitle, buttons_html => $layout_buttons, icon_class => "glyphicon glyphicon-th", info_section_id => "pheno_heatmap" &> +<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, has_col_and_row_numbers => $has_col_and_row_numbers, info_section_title => "

Field Layout Tools and Phenotype Heatmap

", info_section_subtitle => $subtitle, buttons_html => $layout_buttons, icon_class => "glyphicon glyphicon-th", info_section_id => "pheno_heatmap" &> <& /page/detail_page_2_col_section.mas, trial_id => $trial_id, trial_name => $trial_name, info_section_title => "

Experimental Design

", info_section_subtitle => 'View and add experimental design information. Add plant entries and tissue sample entries.', buttons_html => ' ', icon_class => "glyphicon glyphicon-list-alt", info_section_id => "trial_design_section", has_plant_entries => $has_plant_entries, has_subplot_entries => $has_subplot_entries, has_tissue_sample_entries => $has_tissue_sample_entries, trial_stock_type => $trial_stock_type &> diff --git a/mason/breeders_toolbox/trial/phenotype_heatmap.mas b/mason/breeders_toolbox/trial/phenotype_heatmap.mas index 9e9b513f31..9d009e98ac 100644 --- a/mason/breeders_toolbox/trial/phenotype_heatmap.mas +++ b/mason/breeders_toolbox/trial/phenotype_heatmap.mas @@ -2,6 +2,7 @@ $trial_id $stockref => undef $data_level => 'plot' +$has_col_and_row_numbers => undef <& /util/import_css.mas, paths => ['fieldmap/leaflet-search.min.css', 'fieldmap/leaflet.css'] &> @@ -47,7 +48,6 @@ $data_level => 'plot' overflow: auto; /*overflow: scroll;*/ display: none; - margin: 10px; transition: all 1s ease-in-out; } @@ -158,29 +158,6 @@ $data_level => 'plot'

-
-
- - -
- -
- - -
- -
-
@@ -227,7 +204,82 @@ $data_level => 'plot'
+% if ( $has_col_and_row_numbers ) { +
+

Download Plot Order

+
+
+ + +
+
+ + +
+
+ + +
+
+
+ + +
+
+ + +
+
+
+ +
+ +
+
+% }
loading...
@@ -852,19 +904,49 @@ jQuery(document).ready( function() { FieldMap.load(); }); + jQuery("#plot_download_type").change(() => { + let type = jQuery("#plot_download_type").val(); + if ( type === 'harvestmaster' ) { + jQuery("#plot_download_harvestmaster_options").show(); + } + else { + jQuery("#plot_download_harvestmaster_options").hide(); + } + }); + + jQuery("#hm_range").change(() => { + let range = jQuery("#hm_range").val(); + jQuery("#hm_row").val(range === 'row_number' ? 'col_number' : 'row_number'); + }); + jQuery("#hm_row").change(() => { + let row = jQuery("#hm_row").val(); + jQuery("#hm_range").val(row === 'row_number' ? 'col_number' : 'row_number'); + }); + jQuery("#plot_download_button").click(() => { let type = jQuery("#plot_download_type").val(); let order = jQuery("#plot_download_order").val(); + let start = jQuery("#plot_download_start").val(); let include_borders = jQuery("#plot_download_borders").is(":checked"); + let include_gaps = jQuery("#plot_download_gaps").is(":checked"); if ( !type || type === '' ) { alert("Please select a type"); return; } if ( !order || order === '' ) { - alert("Please select a plot layout"); + alert("Please select a plot order"); return; } - FieldMap.get_plot_order(type, order, include_borders) + if ( !start || start === '' ) { + alert("Please select a starting plot"); + return; + } + let additional_properties = { + hm_pltid: jQuery("#hm_pltid").val(), + hm_range: jQuery("#hm_range").val(), + hm_row: jQuery("#hm_row").val() + } + FieldMap.get_plot_order(type, order, start, include_borders, include_gaps, additional_properties); }); jQuery("#invert_row_checkmark").change(function() { diff --git a/mason/breeders_toolbox/trial/trial_details.mas b/mason/breeders_toolbox/trial/trial_details.mas index b57c8c7298..b7639da8a7 100644 --- a/mason/breeders_toolbox/trial/trial_details.mas +++ b/mason/breeders_toolbox/trial/trial_details.mas @@ -218,7 +218,7 @@ $latest_trial_activity => undef
Plot Width (m) -
+
% if ($plot_width) { % print "$plot_width"; % } else { @@ -229,7 +229,7 @@ $latest_trial_activity => undef
Plot Length (m) -
+
% if ($plot_length) { % print "$plot_length"; % } else { @@ -240,7 +240,7 @@ $latest_trial_activity => undef
Field Size (ha) -
+
% if ($field_size) { % print "$field_size"; % } else { @@ -251,7 +251,7 @@ $latest_trial_activity => undef
Trial Will Be Genotyped -
+
% if ($field_trial_is_planned_to_be_genotyped) { % print "$field_trial_is_planned_to_be_genotyped"; % } else { @@ -262,7 +262,7 @@ $latest_trial_activity => undef
Trial Will Be In Crosses -
+
% if ($field_trial_is_planned_to_cross) { % print "$field_trial_is_planned_to_cross"; % } else { diff --git a/mason/breeders_toolbox/trial/trial_upload_dialogs.mas b/mason/breeders_toolbox/trial/trial_upload_dialogs.mas index 0a5415a197..71dd2136fa 100644 --- a/mason/breeders_toolbox/trial/trial_upload_dialogs.mas +++ b/mason/breeders_toolbox/trial/trial_upload_dialogs.mas @@ -687,6 +687,7 @@ $design_types => () Trials may be uploaded in an Excel file (.xls or .xlsx)
Multiple Trial Designs: +
Header:
The first row (header) must contain the following, which is an expansion of the single trial design header: @@ -734,7 +735,7 @@ $design_types => ()
  • breeding_program (The name of breeding program that managed the trial, must exist in the database.)
  • location (The name or abbreviation of the location where the trial was held, must exist in the database.)
  • year (The year the trial was held.)
    • -
  • transplanting_date(The transplanting_date of the trial was conducted.)
  • +
  • design_type (The shorthand for the design type, must exist in the database. Possible values include CRD (Completely Randomized Design), RCBD (Randomized Complete Block Design), RRC (Resolvable Row-Column), DRRC (Doubly-Resolvable Row-Column), ARC (Augmented Row-Column), Alpha (Alpha Lattice Design), Lattice (Lattice Design), Augmented (Augmented Design), MAD (Modified Augmented Design), greenhouse (undesigned Nursery/Greenhouse), splitplot (Split Plot), p-rep (Partially Replicated), Westcott (Westcott Design))
  • description (Additional text with any other relevant information about the trial.)
  • plot_name (Must be unique across entire database. It is often a concatenation of the trial name and the plot number.)
    • @@ -750,6 +751,7 @@ $design_types => ()
  • plot_length (plot length in meters)
  • field_size (field size in hectares)
  • planting_date (Date of Planting in YYYY-MM-DD format)
    • +
  • transplanting_date(The transplanting_date of the trial was conducted. Date in YYYY-MM-DD format))
  • harvest_date (Date of Harvest in YYYY-MM-DD format)
  • is_a_control (type 1 in this field if the plot is a control, otherwise 0 or leave blank. generally you will have accessions that are controls, so you should indicate the plots that that accession is in as a control.)
  • rep_number (replicate number, must be numeric)
    • diff --git a/mason/page/detail_page_2_col_section.mas b/mason/page/detail_page_2_col_section.mas index 23c8cfe0f7..5b2ec0e84a 100644 --- a/mason/page/detail_page_2_col_section.mas +++ b/mason/page/detail_page_2_col_section.mas @@ -54,6 +54,7 @@ $trial_owner => undef $phenotypes_fully_uploaded => undef $user_can_modify => undef $latest_trial_activity => undef +$has_col_and_row_numbers => undef #Specific to stock detail page $type_name => undef @@ -161,7 +162,7 @@ $analytics_protocol_result_summary => {}
    % if ($info_section_id eq 'pheno_heatmap'){ - <& /breeders_toolbox/trial/phenotype_heatmap.mas, trial_id => $trial_id, data_level => $data_level &> + <& /breeders_toolbox/trial/phenotype_heatmap.mas, trial_id => $trial_id, data_level => $data_level, has_col_and_row_numbers => $has_col_and_row_numbers &> % } #End pheno_heatmap % if ($info_section_id eq 'trial_design_section'){ <& /breeders_toolbox/trial/design_section.mas, trial_id => $trial_id, trial_name => $trial_name, has_subplot_entries => $has_subplot_entries, has_plant_entries => $has_plant_entries, has_tissue_sample_entries => $has_tissue_sample_entries, design_name => $design_name, trial_stock_type => $trial_stock_type &> diff --git a/mason/search/vectors.mas b/mason/search/vectors.mas index e3093f547c..02cb3d8767 100644 --- a/mason/search/vectors.mas +++ b/mason/search/vectors.mas @@ -167,7 +167,7 @@ my $stock_type_select = simple_selectbox_html( - + @@ -231,7 +231,7 @@ my $stock_type_select = simple_selectbox_html( stockprop_extra_columns_view[selected_property] = 1; stockprop_extra_columns_view_array.push(selected_property); - var table_header_html = '
    Stock NameVector Name Stock Type Organism Synonyms
    '; + var table_header_html = '
    Stock NameStock TypeOrganismSynonymsSubmitters
    '; for (var i=0; i' + stockprop_extra_columns_view_array[i] + ''; } @@ -253,7 +253,7 @@ my $stock_type_select = simple_selectbox_html( var index = stockprop_extra_columns_view_array.indexOf(selected_property); stockprop_extra_columns_view_array.splice(index, 1); - var table_header_html = '
    Vector NameStock TypeOrganismSynonymsSubmitters
    '; + var table_header_html = '
    Stock NameStock TypeOrganismSynonymsSubmitters
    '; for (var i=0; i' + stockprop_extra_columns_view_array[i] + ''; } diff --git a/mason/stock/add_vector.mas b/mason/stock/add_vector.mas index 758bb5d1d3..551f235c0b 100644 --- a/mason/stock/add_vector.mas +++ b/mason/stock/add_vector.mas @@ -31,6 +31,15 @@ $editable_stock_props_definitions => {}
    +
    + +
    + +
    + +
    +
    @@ -38,12 +47,10 @@ $editable_stock_props_definitions => {}
    -
    - +
    - +
    @@ -59,12 +66,6 @@ $editable_stock_props_definitions => {} -
    - -
    - -
    -
    @@ -78,7 +79,7 @@ $editable_stock_props_definitions => {}
    - +
    @@ -144,7 +145,7 @@ function handleSubmit() { const data = {}; dataForm.forEach((value, key) => (data[key] = value)); - + console.log(data); jQuery.ajax({ type: 'POST', data: {'data': JSON.stringify([data])}, @@ -156,24 +157,33 @@ function handleSubmit() { error: function(response) { alert( 'An Error occured while storing vectors.'); } - }); - - console.log(data); - + }); } - - diff --git a/mason/stock/index.mas b/mason/stock/index.mas index a9753ca662..bf2c754f04 100644 --- a/mason/stock/index.mas +++ b/mason/stock/index.mas @@ -246,7 +246,7 @@ function jqueryStuff() { alternate_ghosted_delete_button => '' &> - +


    @@ -260,13 +260,13 @@ function jqueryStuff() { <&| /page/info_section.mas, title => "Released variety name", subtitle=>$released_variety_link, is_subsection => 1 &> <& /stock/stockprops.mas, stock_id =>$stock_id, - form_div_id => 'released_variety_link', + form_div_id => 'released_variety_link', props => ['released_variety_name'], div_name => 'released_variety_name', edit_privs => $edit_privs, subset => ['released_variety_name'], editable => ['released_variety_name'] &> - +
    @@ -278,18 +278,22 @@ function jqueryStuff() { - + <&| /page/info_section.mas, title => "Navigator" , collapsible=> 1, collapsed=>0 &> % my $subtitle = $edit_privs ? "" : ""; % my $props_subtitle = $edit_privs ? "" : ""; +% if ($type_name eq 'plot' || $type_name eq 'plant' || $type_name eq 'subplot' || $type_name eq 'tissue_sample') { + <& /page/detail_page_2_col_section.mas, stock_id => $stock_id, info_section_title => "

    Related Stocks

    ", info_section_subtitle => 'View any accession, plot, plant, and/or tissue_sample that are linked to this stock.', icon_class => "glyphicon glyphicon-retweet", info_section_id => "stock_related_stock_section", stock_uniquename => $uniquename, type_name => $type_name &> +% } + % if ($type_name ne 'vector_construct' ){ <& /page/detail_page_2_col_section.mas, stock_id => $stock_id, type_name => $type_name, stockref => $stockref, buttons_html => $subtitle.$props_subtitle, info_section_title => "

    Additional Info

    ", info_section_subtitle => 'View and edit additional properties such as synonyms, editors, and all types of properties.', icon_class => "glyphicon glyphicon-info-sign", info_section_id => "stock_additional_info_section", stockprops => $stockprops, edit_privs => $edit_privs, editable_stock_props => \@editable_stock_props, editor_link => $editor_link_table, source_dbs => \%source_dbs, locus_add_uri => $locus_add_uri, new_locus_link => $new_locus_link, allele_div => $allele_div, is_owner => $is_owner &> % } else { <& /page/detail_page_2_col_section.mas, stock_id => $stock_id, type_name => $type_name, stockref => $stockref, buttons_html => $subtitle.$props_subtitle, info_section_title => "

    Additional Info

    ", info_section_subtitle => 'View and edit additional properties such as synonyms, editors, and all types of properties.', icon_class => "glyphicon glyphicon-info-sign", info_section_id => "stock_additional_info_section", stockprops => $stockprops, edit_privs => $edit_privs, editable_stock_props => \@editable_vector_props, editor_link => $editor_link_table, source_dbs => \%source_dbs, locus_add_uri => $locus_add_uri, new_locus_link => $new_locus_link, allele_div => $allele_div, is_owner => $is_owner &> -% } +% } % if ($type_name eq 'accession' || $type_name eq 'plant' || $type_name eq 'plot' || $type_name eq 'subplot' || $type_name eq 'tissue_sample'){ <& /page/detail_page_2_col_section.mas, stock_id => $stock_id, info_section_title => "

    Experiment Usage

    ", info_section_subtitle => 'View experiments that this stock has been used in.', icon_class => "glyphicon glyphicon-leaf", info_section_id => "stock_trials_section" &> @@ -313,9 +317,9 @@ function jqueryStuff() { % } <& /page/detail_page_2_col_section.mas, stock_id => $stock_id, info_section_title => "

    Sequencing Status

    ", info_section_subtitle => 'View and edit sequencing status info for this stock.', icon_class => "glyphicon glyphicon-inbox", info_section_id => "stock_sequencing_status_section", buttons_html => "$sequencing_status_button", map_html => $map_html &> - + - + <& /page/detail_page_2_col_section.mas, stock_id => $stock_id, info_section_title => "

    Genotype Marker Data

    ", info_section_subtitle => 'View and download phenotypic data for this stock.', icon_class => "glyphicon glyphicon-map-marker", info_section_id => "stock_genotypes_section", map_html => $map_html &> % } @@ -334,9 +338,9 @@ function jqueryStuff() { <& /page/detail_page_2_col_section.mas, stock_id => $stock_id, info_section_title => "

    Pedigree

    ", info_section_subtitle => 'View and edit pedigree information.', icon_class => "glyphicon glyphicon-random", info_section_id => "stock_pedigree_section", buttons_html => $add_parent_link.$remove_parent_link, has_pedigree => $has_pedigree, info_section_collapsed => 0 &> + <& /page/detail_page_2_col_section.mas, stock_id => $stock_id, info_section_title => "

    Related Stocks

    ", info_section_subtitle => 'View any plots, plants, tissue_sample, and/or accessions that are linked to this stock.', icon_class => "glyphicon glyphicon-retweet", info_section_id => "stock_related_stock_section", stock_uniquename => $uniquename, type_name => $type_name &> % } - <& /page/detail_page_2_col_section.mas, stock_id => $stock_id, info_section_title => "

    Related Stocks

    ", info_section_subtitle => 'View any plots, plants, tissue_sample, and/or accessions that are linked to this stock.', icon_class => "glyphicon glyphicon-retweet", info_section_id => "stock_related_stock_section", stock_uniquename => $uniquename, type_name => $type_name &> <& /page/detail_page_2_col_section.mas, stock_id => $stock_id, info_section_title => "

    Images

    ", info_section_subtitle => 'View and add images of this stock and of related stocks.', icon_class => "glyphicon glyphicon-camera", info_section_id => "stock_images_section", image_ids => $image_ids, related_image_ids => $related_image_ids, dbh => $dbh, buttons_html => qq|Add new imageCompare Images| &> diff --git a/mason/stock/related_stock.mas b/mason/stock/related_stock.mas index 3c2fb86a91..fe2b3a922c 100644 --- a/mason/stock/related_stock.mas +++ b/mason/stock/related_stock.mas @@ -6,16 +6,15 @@ $stock_type => undef % if ($stock_type eq 'accession' || $stock_type eq 'plant' || $stock_type eq 'plot' || $stock_type eq 'subplot' || $stock_type eq 'tissue_sample'){ - - <&| /page/info_section.mas, id=>'related_stocks_in_trial', title => 'Related stocks in trials', collapsible=>1, collapsed=>1 &> + <&| /page/info_section.mas, id=>'related_stocks_in_trial', title => 'Related stocks in trial', collapsible=>1, collapsed=>1 &>
    Vector NameStock TypeOrganismSynonymsSubmitters
    - + @@ -30,12 +29,64 @@ $stock_type => undef
    - % } -% if ($stock_type eq 'accession'){ +% if ($stock_type eq 'plot' || $stock_type eq 'plant'){ + <&| /page/info_section.mas, id=>'related_seedlots', title => 'Related seedlots', collapsible=>1, collapsed=>1 &> +
    +
    +
    + + + + + + + + + +
    +
    +
    + <&| /page/info_section.mas, title => 'Copy Stocks to a List', collapsible=>1, collapsed=>1, subtitle=>'Copy the seedlot names showing in table to a new or exisiting list'&> +
    +
    + + +
    + +% } + +% if ($stock_type eq 'accession') { <& /breeders_toolbox/seedlots_section.mas, stock_id=>$stock_id, stock_type=>$stock_type, stock_uniquename=>$stock_uniquename &> +% } + +% if ($stock_type eq 'accession' || $stock_type eq 'plant' || $stock_type eq 'plot' || $stock_type eq 'subplot'){ + + <&| /page/info_section.mas, id=>'related_stock_tissues', title => 'Related tissue samples', collapsible=>1, collapsed=>1 &> +
    +
    +
    + + + + + + + +
    TypeName
    +
    +
    + +
    + <&| /page/info_section.mas, title => 'Copy Stocks to a List', collapsible=>1, collapsed=>1, subtitle=>'Copy the stock names showing in table to a new or exisiting list'&> +
    +
    + + +
    + % } @@ -121,33 +172,6 @@ $stock_type => undef % } -% if ($stock_type eq 'accession' || $stock_type eq 'plant' || $stock_type eq 'plot' || $stock_type eq 'subplot' || $stock_type eq 'tissue_sample'){ - - <&| /page/info_section.mas, id=>'related_stock_tissues', title => 'Related stocks for tissue sample', collapsible=>1, collapsed=>1 &> -
    -
    -
    - - - - - - - -
    NameType
    -
    -
    - -
    - <&| /page/info_section.mas, title => 'Copy Stocks to a List', collapsible=>1, collapsed=>1, subtitle=>'Copy the stock names showing in table to a new or exisiting list'&> -
    -
    - - -
    - - -% }