Merge tag '0.21.2' into release/0.21

app/assets/javascripts/components/cdx_select_autocomplete.js.jsx

@@ -1,21 +1,31 @@
 var CdxSelectAutocomplete = React.createClass({
+  getInitialState: function () {
+    return {
+      options: null,
+    };
+  },
+
   render: function () {
     return (<Select
+      ref={this.setSelectRef}
       className={this.props.className}
       name={this.props.name}
       value={this.props.value}
       placeholder={this.props.placeholder}
       searchable={true}
       clearable={true}
-      asyncOptions={this.asyncOptions.bind(this)}
+      asyncOptions={this.asyncOptions}
+      value={this.props.value || ""}
+      onChange={this.onChange}
     />);
   },
 
   asyncOptions: function (query, callback) {
-    if (!query || /^\s*$/.test(query)) {
-      return callback(null, []);
-    }
+    query = query.trim();
+    if (!query) return callback(null, []);
 
+    var autoselect = this.props.autoselect;
+    var prepareOptions = this.props.prepareOptions;
     var url = this.props.url;
     url += (url.includes("?") ? "&query=" : "?query=") + encodeURIComponent(query);
 
@@ -24,15 +34,31 @@ var CdxSelectAutocomplete = React.createClass({
       url: url,
 
       success: function (options) {
+        if (prepareOptions) {
+          options = prepareOptions.call(null, options);
+        }
         callback(null, {
           options: options,
           complete: options.size < 10,
         });
-      },
+        if (autoselect && options.length === 1 && options[0].value === query) {
+          this.selectRef.setValue(query);
+        }
+      }.bind(this),
 
       error: function (_, error) {
         callback(error);
       },
     })
   },
+
+  onChange: function (value, options) {
+    if (this.props.onSelect) {
+      this.props.onSelect.call(null, value, options);
+    }
+  },
+
+  setSelectRef: function (ref) {
+    this.selectRef = ref;
+  }
 });

app/assets/javascripts/components/samples_selector.js.jsx

@@ -0,0 +1,102 @@
+var SamplesSelector = React.createClass({
+  getInitialState: function () {
+    return {
+      samples: this.props.samples,
+    };
+  },
+
+  render: function () {
+    return (<div className="samples-selector">
+      {this.renderTitle()}
+      {this.state.samples.map(this.renderSample)}
+
+      <a className="add-samples" href="#" onClick={this.addSample}>
+        <div className="add-samples">
+          <div className="icon-circle-plus icon-blue icon-margin"></div>
+          <div className="add-sample-link">ADD SAMPLE</div>
+        </div>
+      </a>
+    </div>);
+  },
+
+  renderTitle() {
+    var samples = this.state.samples;
+    if (!samples.length) return;
+
+    var count = samples.reduce(function (a, e) {
+      return e.uuid ? a + 1 : a;
+    }, 0);
+
+    return (<div className="samples-count">
+      <div className="title">{count}&nbsp;{count == 1 ? "sample" : "samples"}</div>
+    </div>);
+  },
+
+  renderSample(sample, index) {
+    if (sample.uuid) {
+      function removeSample(event) {
+        this.removeSample(event, index);
+      }
+      return (<div className="batches-samples" key={"samples-selector-" + index}>
+        <div className="samples-row">
+          <div className="samples-item">{sample.uuid}</div>
+          <div className="samples-row-actions">
+            <input type="hidden" name={this.props.name + "[" + index + "]"} value={sample.uuid}/>
+            <span>{sample.batch_number}</span>
+            <a href="#" onClick={removeSample.bind(this)} title="Remove this sample">
+              <i className="icon-close icon-gray bigger"></i>
+            </a>
+          </div>
+        </div>
+      </div>);
+    } else {
+      function selectSample(_, options) {
+        this.selectSample(index, options && options[0]);
+      }
+      return (<div className="batches-samples" key={"samples-selector-" + index}>
+        <div className="samples-row">
+          <CdxSelectAutocomplete
+            className={this.props.className}
+            url={this.props.url}
+            placeholder={this.props.placeholder}
+            value={sample.uuid}
+            prepareOptions={this.prepareOptions}
+            autoselect={true}
+            onSelect={selectSample.bind(this)}
+          />
+        </div>
+      </div>);
+    }
+  },
+
+  prepareOptions: function (options) {
+    return options.map(function (option) {
+      option.value = option.uuid;
+      option.label = option.uuid + " (" + option.batch_number + ")";
+      return option;
+    });
+  },
+
+  addSample: function (event) {
+    event.preventDefault();
+
+    var samples = this.state.samples;
+    samples.push({ uuid: "" });
+    this.setState({ samples: samples });
+  },
+
+  selectSample: function (index, sample) {
+    var samples = this.state.samples;
+    samples[index] = sample;
+    this.setState({ samples: samples });
+  },
+
+  removeSample: function (event, index) {
+    event.preventDefault();
+
+    var samples = this.state.samples;
+    samples.splice(index, 1);
+
+    this.setState({ samples: samples });
+  },
+});

app/assets/stylesheets/_batches.scss

@@ -69,6 +69,11 @@
   align-items: center;
   min-height: 40px;
 }
+.samples-row-actions {
+  display: flex;
+  align-items: center;
+  gap: 10px;
+}
 
 .transfer-data {
   color: black;

app/assets/stylesheets/_sprites.scss

@@ -67,6 +67,9 @@
     color: inherit;
   }
 
+  &.bigger {
+    font-size: 24px;
+  }
   &.medium {
     font-size: 35px;
   }

app/controllers/boxes_controller.rb

@@ -1,5 +1,6 @@
 class BoxesController < ApplicationController
   before_action :load_box, except: %i[index new create bulk_destroy]
+  helper_method :samples_data
 
   def index
     @can_create = has_access?(@navigation_context.institution, CREATE_INSTITUTION_BOX)
@@ -59,6 +60,7 @@ def create
 
     @box_form = BoxForm.build(@navigation_context, box_params)
     @box_form.batches = check_access(load_batches, READ_BATCH)
+    @box_form.samples = check_access(load_samples, READ_SAMPLE)
 
     if @box_form.valid?
       @box_form.build_samples
@@ -106,13 +108,31 @@ def load_batches
       .where(uuid: @box_form.batch_uuids.values.reject(&:blank?))
   end
 
+  def load_samples
+    Sample
+      .within(@navigation_context.entity, @navigation_context.exclude_subsites)
+      .find_all_by_any_uuid(@box_form.sample_uuids.values.reject(&:blank?))
+  end
+
   def box_params
     if Rails::VERSION::MAJOR == 5 && Rails::VERSION::MINOR == 0
       params.require(:box).permit(:purpose, :media).tap do |allowed|
-        allowed[:batch_uuids] = params[:box][:batch_uuids].permit!
+        allowed[:batch_uuids] = params[:box][:batch_uuids].try(&:permit!)
+        allowed[:sample_uuids] = params[:box][:sample_uuids].try(&:permit!)
       end
     else
-      params.require(:box).permit(:purpose, :media, batch_uuids: {})
+      params.require(:box).permit(:purpose, :media, batch_uuids: {}, sample_uuids: [])
+    end
+  end
+
+  def samples_data(samples)
+    # NOTE: duplicates the samples/autocomplete template (but returns an
+    # Array<Hash> instead of rendering to a JSON String)
+    samples.map do |sample|
+      {
+        uuid: sample.uuid,
+        batch_number: sample.batch_number,
+      }
     end
   end
 end

app/controllers/samples_controller.rb

@@ -25,6 +25,20 @@ def index
       .preload(:batch, :sample_identifiers)
   end
 
+  def autocomplete
+    samples = Sample
+      .where(institution: @navigation_context.institution)
+      .within(@navigation_context.entity, @navigation_context.exclude_subsites)
+
+    samples = samples.without_qc if params[:qc] == "0"
+
+    @samples = check_access(samples, READ_SAMPLE)
+      .joins(:sample_identifiers)
+      .autocomplete(params[:query])
+      .limit(10)
+      .preload(:batch)
+  end
+
   def edit_or_show
     sample = Sample.find(params[:id])
 

app/controllers/transfer_packages_controller.rb

@@ -95,14 +95,14 @@ def confirm
     return unless authorize_resource(confirmation_resource(transfer_package), UPDATE_BOX)
 
     if transfer_package.confirmed?
-      flash[:info] = "Transfer had already been confirmed."
-      redirect_to transfer_package
+      flash[:notice] = "Transfer had already been confirmed."
+      redirect_to transfer_packages_path
       return
     end
 
     transfer_package.confirm!
-    flash[:success] = "Transfer has been confirmed."
-    redirect_to transfer_package
+    flash[:notice] = "Transfer has been confirmed."
+    redirect_to transfer_packages_path
   end
 
   def unblind

app/helpers/cdx_form_helper.rb

@@ -78,12 +78,35 @@ def form_actions(&block)
     end
   end
 
-  private
+  def fields_for(record_name, record_object = nil, fields_options = {}, &block)
+    if record_object.nil? && @object.respond_to?(record_name)
+      record_object = @object.send(record_name)
+    end
+
+    super(record_name, record_object, objectify_options(fields_options)) do |form|
+      # Clear errors that are handeld in the nested form
+      form.errors_to_show.each do |nested_key|
+        errors_to_show.delete("#{record_name}.#{nested_key}".to_sym)
+      end
+
+      block.call(form)
+
+      @template.concat form.form_errors
+    end
+  end
+
+  def has_error?(attr_name)
+    errors_to_show.include?(attr_name.to_sym)
+  end
+
+  protected
 
   def errors_to_show
     @errors_to_show ||= @object.errors.keys
   end
 
+  private
+
   def error_messages_to_show
     Hash[errors_to_show.map do |attribute|
       messages = @object.errors.full_messages_for(attribute)

app/models/box.rb

@@ -95,7 +95,7 @@ def blind_attributes
       %i[concentration concentration_formula replicate]
     when "Variants"
       %i[batch_number virus_lineage]
-    when "Challenge"
+    when "Challenge", "Other"
       %i[batch_number concentration concentration_formula replicate virus_lineage]
     else
       []