Merge branch 'main' into full-test-suite

seek4science · Nov 9, 2023 · 8fb0352 · 8fb0352
2 parents 935d2d6 + 4d0808b
commit 8fb0352
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diff --git a/Gemfile b/Gemfile
@@ -18,7 +18,7 @@ gem 'RedCloth', '>=4.3.0'
 gem 'simple-spreadsheet-extractor', '~> 0.18.0'
 gem 'open4'
 gem 'sample-template-generator', '~>0.7'
-gem 'rmagick', '4.2.5'
+gem 'rmagick', '5.3.0'
 gem 'rest-client', '~>2.0'
 gem 'factory_bot', '~> 6.2.1'
 gem 'bio', '~> 1.5.1'

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -544,6 +544,7 @@ GEM
       rack
       rake (>= 0.8.1)
     pg (1.3.1)
+    pkg-config (1.5.5)
     pothoven-attachment_fu (3.3.2)
     pr_geohash (1.0.0)
     private_address_check (0.5.0)
@@ -729,7 +730,8 @@ GEM
       nokogiri
     rexml (3.2.5)
     rfc-822 (0.4.1)
-    rmagick (4.2.5)
+    rmagick (5.3.0)
+      pkg-config (~> 1.4)
     ro-bundle (0.3.0)
       addressable (~> 2.8.0)
       json (~> 2.3.0)
@@ -1066,7 +1068,7 @@ DEPENDENCIES
   responders
   rest-client (~> 2.0)
   rfc-822
-  rmagick (= 4.2.5)
+  rmagick (= 5.3.0)
   ro-bundle (~> 0.3.0)
   ro-crate (~> 0.5.1)
   rspec-rails (~> 5.1)

diff --git a/app/assets/javascripts/controlled_vocabs.js.erb b/app/assets/javascripts/controlled_vocabs.js.erb
@@ -215,7 +215,7 @@ CVTerms = {
                 CVTerms.disableAddTermButton('<%= I18n.t('controlled_vocabs.add_new_term_disabled_reason') %>');
                 var link = $j('a#selected-ols-link');
                 link.text(selected.text);
-                link.attr('href', 'https://www.ebi.ac.uk/ols/ontologies/' + selected.value);
+                link.attr('href', '<%= Ebi::OlsClient::ROOT_URL %>/ontologies/' + selected.value);
             }
         });
 

diff --git a/app/assets/javascripts/sample_types.js b/app/assets/javascripts/sample_types.js
@@ -72,12 +72,10 @@ var SampleTypes = {
     attributeTypeChanged: function (e, resetSelection=true) {
         //check if it is a controlled vocab, and change the state of the controlled vocab selector if need be
         var use_cv = $j(this).find(':selected').data('use-cv');
-				var is_ontology = $j(this).find(':selected').data('is-ontology');
         var cv_element = $j(this).siblings('.controlled-vocab-block');
         if (use_cv) {
 					var cv_selection = cv_element.find('.controlled-vocab-selection');
 					cv_selection.find('option').show();
-					cv_selection.find(`option[data-is-ontology="${!is_ontology}"]`).hide();
 					if (resetSelection) cv_selection.find('option:selected').prop("selected", false);
           cv_element.show();
         }

diff --git a/app/assets/javascripts/single_page/dynamic_table.js.erb b/app/assets/javascripts/single_page/dynamic_table.js.erb
@@ -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 {
@@ -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)

diff --git a/app/assets/javascripts/single_page/index.js.erb b/app/assets/javascripts/single_page/index.js.erb
@@ -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) {

diff --git a/app/assets/javascripts/templates.js b/app/assets/javascripts/templates.js
@@ -45,7 +45,8 @@ Templates.init = function (elem) {
     },
     { title: "PID", width: "10%" },
     { title: "pos" },
-    { title: "isa_tag_id" },
+    { title: "ISA Tag ID", width: "10%" },
+    { title: "ISA Tag", width: "10%" },
     {
       title: "Remove",
       width: "5%",
@@ -89,7 +90,7 @@ function loadTemplates(data) {
 
   $j.each(Object.keys(categorized), (i, key) => {
     const elem = $j(`<optgroup label=${key}></optgroup>`);
-    
+
     $j.each(categorized[key], (j, sub_item) => {
       elem.append(
         $j(`<option>${sub_item.title}</option>`).attr("value", sub_item.template_id).text(key.title)
@@ -119,13 +120,14 @@ Templates.mapData = (data) =>
     item.is_title,
     item.pid,
     item.pos,
-    item.isa_tag_id
+    item.isa_tag_id,
+    item.isa_tag_title
   ]);
 
 function loadFilterSelectors(data) {
   $j.each($j("select[id^='templates_']"), (i, elem) => {
     const key = elem.getAttribute("data-key");
-    
+
     // Gets the set of values to choose from per data-key
     let dt = [...new Set(data.map((item) => item[key]))];
     // If the key == level => options should be filtered out, depending on the 'field_name' context.
@@ -136,7 +138,7 @@ function loadFilterSelectors(data) {
       } else if(Templates.context.field_name === 'source_sample_type'){
         dt = dt.filter(lvl => lvl === "study source")
       } else if(Templates.context.field_name === 'sample_type') {
-        dt = dt.filter(lvl => lvl === "assay")
+        dt = dt.filter(lvl => ["assay - material", "assay - data file"].includes(lvl))
       }
       $j(elem).find("option").remove(); // Removes all options, even the first, i.e. "not selected"
     }
@@ -159,6 +161,42 @@ function loadFilterSelectors(data) {
   });
 }
 
+function get_filtered_isa_tags(level) {
+  var result;
+  $j.ajax({
+    type: 'POST',
+    async: false,
+    url: '/templates/filter_isa_tags_by_level',
+    data: {level: level},
+    dataType: 'json',
+    success: function(res) {
+      result = res.result;
+    },
+    error: function (errMsg) {
+      alert(`Couldn't find valid ISA Tags because of the following error:\n${errMsg}`);
+      result = [];
+    }
+  });
+  return result;
+}
+
+function updateIsaTagSelect(template_level, attribute_row) {
+  const isa_tags = get_filtered_isa_tags(template_level);
+
+  // Remove all options first, except blank one
+  $j(attribute_row).find('select[data-attr="isa_tag_title"] option:not([value=""])').each(function() {
+    $j(this).remove();
+  });
+
+  // Append filtered option to a new attribute row
+  $j.each(isa_tags, function (i, tag) {
+    $j(attribute_row).find('select[data-attr="isa_tag_title"]').append($j('<option>', {
+      value: tag.value,
+      text: tag.text
+    }));
+  });
+}
+
 const applyTemplate = () => {
   const id = $j("#source_select").find(":selected").val();
   const data = templates.find((t) => t.template_id == id);
@@ -170,10 +208,17 @@ const applyTemplate = () => {
   const attribute_table = "#attribute-table" + suffix;
   const attribute_row = "#new-attribute-row" + suffix;
   const addAttributeRow = "#add-attribute-row" + suffix;
+  updateIsaTagSelect(data.level, attribute_row);
 
   $j(`${attribute_table} tbody`).find("tr:not(:last)").remove();
   SampleTypes.unbindSortable();
-  // Make sure default sorted attributes are added to the table 
+
+  // Set template group, level and organism
+  $j('#template_organism').val(data.organism);
+  $j('#template_level').val(data.level);
+  $j('#template_parent_id').val(data.template_id);
+
+  // Make sure default sorted attributes are added to the table
   Templates.table.order([9, "asc"]).draw();
   $j.each(Templates.table.rows().data(), (i, row) => {
     var newRow = $j(`${attribute_row} tbody`).clone().html();
@@ -197,6 +242,8 @@ const applyTemplate = () => {
     $j(newRow).find(".sample-type-is-title").prop("checked", row[7]);
     $j(newRow).find('[data-attr="pid"]').val(row[8]);
     $j(newRow).find('[data-attr="isa_tag_id"]').val(row[10]);
+    $j(newRow).find('[data-attr="isa_tag_title"]').val(row[10]);
+    $j(newRow).find('[data-attr="isa_tag_title"]').attr('disabled', true);
 
     // Show the CV block if cv_id is not empty
     if (row[4]) $j(newRow).find(".controlled-vocab-block").show();
@@ -238,7 +285,7 @@ const updateTypeSelect = function(field_name) {
   } else if (field_name === 'source_sample_type') {
 		$j("#templates_type_select").val("study source").change();
   } else if(field_name === 'sample_type') {
-    $j("#templates_type_select").val("assay").change();
+    $j("#templates_type_select").val("assay - material").change();
   } else {
     $j("#templates_type_select option").first().change();
   }

diff --git a/app/assets/stylesheets/application.css b/app/assets/stylesheets/application.css
@@ -45,5 +45,5 @@
 *= require jquery.splitter/jquery.splitter
 *= require select2.min
 *= require select2.bootstrap.min
-*= require linked_custom_metadata
+*= require linked_extended_metadata
 */