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Issue 1558 hide unauthorized cells in dynamic table (#1620)
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* Remove MIAPPE stuff from ISA Study from

* Add appropriate message if no templates are stored in the DB.

* substitute sources by input. Is more clear.

* Make unauthorized samples hidden.

* Prevent to download the table when it has errors

* Improve the error message when no sample is selected.

* Change alert message

* Filter out samples with hidden inputs and completely hidden samples
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@kdp-cloud
kdp-cloud authored Nov 8, 2023
1 parent 58adc18 commit fb4803b
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Showing 6 changed files with 127 additions and 82 deletions.
13 changes: 10 additions & 3 deletions app/assets/javascripts/single_page/dynamic_table.js.erb
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,14 @@ const handleSelect = (e) => {
if (c.multi_link) {
data = data && Array.isArray(data) ? data : [data];
data = data[0]?.id ? data : [];
const existingOptions = data.map((e) => `<option selected="selected" title="ID: ${e.id}" value="${e.id}">${e.title}</option>`).join("");
const existingOptions = data.map((e) => {
isHiddenInput = (e.title == '#HIDDEN')
if (isHiddenInput) {
return `<option selected="selected" title="ID: hidden" value="hidden">hidden</option>`
} else {
return `<option selected="selected" title="ID: ${e.id}" value="${e.id}">${e.title}</option>`
}
}).join("");
if (options.readonly) {
return data.map((e) => `<span title="ID: ${e.id}" class="badge">${e.title}</span>`).join(" ");
} else {
Expand All @@ -61,15 +68,15 @@ const handleSelect = (e) => {
const linkedSamples = retrieveLinkedSamples(url);
const linkedSampleIds = linkedSamples.map((ls) => ls.id);
const unLinkedSamples = data.reduce(function(filtered, sample) {
if(!linkedSampleIds.includes(parseInt(sample.id))){
if(!linkedSampleIds.includes(parseInt(sample.id)) && sample.title != '#HIDDEN'){
filtered.push(sample);
}
return filtered;
}, []);
const hasUnlinkedSamples = unLinkedSamples.length > 0 ? true : false;
const extraClass = hasUnlinkedSamples ? 'select2__error' : '';
const titleText = hasUnlinkedSamples ? `Sample(s) '${unLinkedSamples.map(uls => uls.title).join(', ')}' not recognised as sources. Please correct this issue!` : '';
const titleText = hasUnlinkedSamples ? `Sample(s) '${unLinkedSamples.map(uls => uls.title).join(', ')}' not recognised as input. Please correct this issue!` : '';

return objectInputTemp
.replace(/_NAME_/g, objectInputName)
Expand Down
111 changes: 64 additions & 47 deletions app/assets/javascripts/single_page/index.js.erb
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Original file line number Diff line number Diff line change
Expand Up @@ -207,61 +207,78 @@ async function batchDeleteSample(sampleTypes) {
// Posts the content of the dynamic table to the single_pages_controller,
// which generates an excel workbook based on a template.
async function exportToExcel(tableName, studyId, assayId, sampleTypeId) {
const headerRow = $j(`table[id=${tableName}] thead tr`)["0"];
const headerRow = $j(`table[id=${tableName}] thead tr`)["0"];

// Cells from the table body => Each row = array
// For some reason they contain null values, which should be filtered out
let bodyCells = $j(`table[id=${tableName}]`).DataTable().data().toArray().map(subarray => subarray.filter(function(el){return el != null}));
// Cells from the table body => Each row = array
// For some reason they contain null values, which should be filtered out
let bodyCells = $j(`table[id=${tableName}]`).DataTable().data().toArray().map(subarray => subarray.filter(function(el){return el != null}));

// Return array of table header cells from headerRow
let headerCells = [];
$j.each(headerRow.cells, function (i, v) {
headerCells.push(v.textContent);
});
// Checks whether the dynamic table has errors
// The excel export will be aborted as long as the dynamic table has errors
hasErrorcells = $j(`table[id=${tableName}]`).find('select.select2__error').size() > 0
if (hasErrorcells) {
alert('It appears this sample table has some errors. Please correct the errors in the current sample table and try downloading again.');
return;
}

// Construct the 'struct' of the table data
let data = [];
for (let i = 0; i < bodyCells.length; i++) {
const row = bodyCells[i];
// If a row has been checked / unchecked,
// the datatable body gets one extra hidden cell at index 1,
// compared to the table header. This has to be removed.
if (row.length !== headerCells.length)row.splice(1,1);
let obj = {};
for (let j = 0; j < headerCells.length; j++) {
const attr = headerCells[j];
const val = row[j];
// Return array of table header cells from headerRow
let headerCells = [];
$j.each(headerRow.cells, function (i, v) {
headerCells.push(v.textContent);
});

// The source inputs are wrapped in an object and must be unwrapped first
// And then packaged as a single element
if(j === 0) {
obj["selected"] = (val === "") ? false : val;
} else {
obj[attr] = val;
}
if(obj.selected) data.push(obj);
// Construct the 'struct' of the table data
let data = [];
for (let i = 0; i < bodyCells.length; i++) {
const row = bodyCells[i];
// If a row has been checked / unchecked,
// the datatable body gets one extra hidden cell at index 1,
// compared to the table header. This has to be removed.
if (row.length !== headerCells.length)row.splice(1,1);
let obj = {};
let hasHiddenInputs = false;
for (let j = 0; j < headerCells.length; j++) {
const attr = headerCells[j];
const val = row[j];

// Check whether sample has one or more hidden Inputs or if sample is completely hidden
if (attr.toLowerCase().includes('input')) {
if (Array.isArray(val)){
hasHiddenInputs = val.some(input => input.title === '#HIDDEN'); // Sample has hidden inputs
} else {
hasHiddenInputs = val === '#HIDDEN'; // Sample is completely hidden
}
}

// Use ajax for POST request with table data in the body
// If succes => Redirect to download path for retrieving excel file
$j.ajax({
type: 'POST',
url: '<%= export_to_excel_single_pages_path() %>',
data: { sample_data: JSON.stringify(data),
sample_type_id: JSON.stringify(sampleTypeId),
study_id: JSON.stringify(studyId),
assay_id: JSON.stringify(assayId),
},
success: function(response) {
downloadUrl = `<%= download_samples_excel_single_pages_path() %>?uuid=${response.uuid}`;
window.location.href = downloadUrl;
},
error: function(response) {
alert(`Failed to export through excel!\nStatus: ${response.status}\nError: ${JSON.stringify(response.error().statusText)}`);
}
});
// The source inputs are wrapped in an object and must be unwrapped first
// And then packaged as a single element
if(j === 0) {
obj["selected"] = (val === "") ? false : val;
} else {
obj[attr] = val;
}
}
if (!hasHiddenInputs) data.push(obj);
}

// Use ajax for POST request with table data in the body
// If succes => Redirect to download path for retrieving excel file
$j.ajax({
type: 'POST',
url: '<%= export_to_excel_single_pages_path() %>',
data: { sample_data: JSON.stringify(data),
sample_type_id: JSON.stringify(sampleTypeId),
study_id: JSON.stringify(studyId),
assay_id: JSON.stringify(assayId),
},
success: function(response) {
downloadUrl = `<%= download_samples_excel_single_pages_path() %>?uuid=${response.uuid}`;
window.location.href = downloadUrl;
},
error: function(response) {
alert(`Failed to export through excel!\nStatus: ${response.status}\nError: ${JSON.stringify(response.error().statusText)}`);
}
});
}

async function batchUpdateSample(sampleTypes) {
Expand Down
6 changes: 4 additions & 2 deletions app/controllers/single_pages_controller.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,9 @@ def download_samples_excel
@project = @study.projects.first
@samples = Sample.where(id: sample_ids)&.authorized_for(:view)&.sort_by(&:id)

raise 'Nothing to export to Excel.' if @samples.nil? || @samples == [] || sample_type_id.nil?
if @samples.nil? || @samples == [] || sample_type_id.nil?
raise 'Nothing to export to Excel. Please select samples in the table and try downloading the table again.'
end

@sample_type = SampleType.find(sample_type_id)

Expand Down Expand Up @@ -114,7 +116,7 @@ def download_samples_excel
def export_to_excel
cache_uuid = UUID.new.generate
id_label = "#{Seek::Config.instance_name} id"
sample_ids = JSON.parse(params[:sample_data]).map { |sample| sample[id_label] unless sample[id_label] == '#HIDDEN' }
sample_ids = JSON.parse(params[:sample_data]).map { |sample| sample[id_label] }
sample_type_id = JSON.parse(params[:sample_type_id])
study_id = JSON.parse(params[:study_id])
assay_id = JSON.parse(params[:assay_id])
Expand Down
30 changes: 25 additions & 5 deletions app/helpers/dynamic_table_helper.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -31,14 +31,34 @@ def link_sequence(sample_type)

def dt_rows(sample_type)
sample_type.samples.map do |s|
if s.can_view?
['', s.id, s.uuid] +
JSON(s.json_metadata).values
else
['', '#HIDDEN', '#HIDDEN'] +
if s.can_view?
sanitized_json_metadata = hide_unauthorized_inputs(JSON(s.json_metadata))
['', s.id, s.uuid] +
sanitized_json_metadata.values
else
['', '#HIDDEN', '#HIDDEN'] +
Array.new(JSON(s.json_metadata).length, '#HIDDEN')
end
end
end

def hide_unauthorized_inputs(json_metadata)
input_key = json_metadata.keys.detect { |jmdk| jmdk.downcase.include? 'input' }

unless input_key.nil?
json_metadata[input_key] = json_metadata[input_key].map do |input|
input_exists = Sample.where(id: input['id']).any?
if !input_exists
input
elsif Sample.find(input['id']).can_view?
input
else
{ 'id' => input['id'], 'type' => input['type'], 'title' => '#HIDDEN' }
end
end
end

json_metadata
end

def dt_cols(sample_type)
Expand Down
38 changes: 23 additions & 15 deletions app/views/isa_studies/_form.html.erb
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@

<div id="investigation_collection" class="hidden">
<%= render :partial=>"studies/investigation_list",:locals=>{study:@isa_study.study, :investigations=>Investigation.all.select {|i|current_user.person.member_of? i.projects}} -%>
</div>
</div>

<div class="form-group">
<%= study_fields.label "Study position" -%><br/>
Expand All @@ -42,48 +42,56 @@
<%= render partial: 'projects/implicit_project_selector', locals: { action: action,
select_id: '#study_investigation_id',
parents: Investigation.authorized_for('edit') } %>
<%= folding_panel("Define #{t(:sample_type)} for Source") do %>
<%= render partial: 'sample_types_form', locals: {f: f, sample_type: @isa_study.source, id_suffix: "_source_sample_type", action: action } if @isa_study.source %>
<% end %>
<%= folding_panel(t(:sop).pluralize) do %>
<p class="help-block">The following <%= t(:sop).pluralize %> are associated with this <%= t(:study) %>:</p>

<%= study_fields.fancy_multiselect :sops, { other_projects_checkbox: true, name: "isa_study[study][sop_ids]" } %>
<% end %>
<%= folding_panel("Define #{t(:sample_type)} for Sample") do %>
<%= render partial: 'sample_types_form', locals: {f: f, sample_type: @isa_study.sample_collection, id_suffix: "_sample_collection_sample_type", action: action } if @isa_study.sample_collection %>
<% end %>
<% end -%>
<% end -%>
<%= form_submit_buttons(@isa_study.study) %>

<script>
const templates = <%= load_templates().to_json.html_safe %>
const initTemplateModal = function(field_name) {
Templates.context.description_elem = `#isa_study_${field_name}_description`
Templates.context.suffix = "_" + field_name
Templates.context.field_name = field_name
showTemplateModal()
if (templates.length > 0) {
Templates.context.description_elem = `#isa_study_${field_name}_description`
Templates.context.suffix = "_" + field_name
Templates.context.field_name = field_name
showTemplateModal()
}else{
if (confirm("No templates available for this project. Click 'OK' to create a project specific template or 'cancel' to close this window.")){
window.open('/templates/new')
}
}
}

$j(document).ready(function () {
$j(document).ready(function () {
const urlSearchParams = new URLSearchParams(window.location.search);
const params = Object.fromEntries(urlSearchParams.entries());
const investigation_id = params["investigation_id"]
// Prevent setting the hidden field on redirect (query string parameters are missing)
if(investigation_id) {
$j("#isa_study_study_investigation_id").val(investigation_id);
$j("#isa_study_study_investigation_id").val(investigation_id);
$j("#study_investigation_id").val(investigation_id).change();
}
}

Templates.init($j('#template-attributes'));
});
if (templates.length > 0) {
Templates.init($j('#template-attributes'));
}
});
</script>
11 changes: 1 addition & 10 deletions app/views/isa_studies/new.html.erb
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Original file line number Diff line number Diff line change
Expand Up @@ -6,20 +6,11 @@
</span>
<h1>New <%=t('isa_study')%></h1>

<% if show_batch_miappe_button? %>
<h4>Upload studies from file:</h4>
<%= link_to "MIAPPE Study batch upload", batch_uploader_studies_path, class: "btn btn-primary" %>
<div>
<%= link_to "Download MIAPPE template here", asset_path('batch_upload_template/MIAPPE Study batch template.zip', skip_pipeline: true) %>
</div>
<h4>Or create a study with the form:</h4>
<% end %>
<%= render :partial => "templates/template_modal" -%>

<div class="show_basic">
<%= form_for @isa_study do |f| %>
<%= render :partial => "form", :locals => { :f => f, :action=>:new } -%>
<% end -%>
</div>
<% end -%>
<% end -%>

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