Merge branch 'feature-sc/3907-require-files' into 'dev'

Files are required to submit new samples

Closes #3907

See merge request !613

browser/js/database.js

@@ -372,8 +372,17 @@ Database.prototype = {
         if ($option.attr('required_files') == "1"){
             $(".file_2").hide();
             $(".upload_file").val("");
+            $(".upload_field").each(function() {
+                $(this).prop("required", false);
+            });
         }else{
             $(".file_2").show();
+            if ($(".is_editing").length == 0) {
+                // Not editing a sample, but creating new ones
+                $(".upload_field").each(function() {
+                    $(this).prop("required", true);
+                });
+            }
         }
     },
 

browser/js/form_builder.js

@@ -351,6 +351,8 @@ FileFormBuilder.prototype.build_file_field = function(id, hidden) {
     var i = this.build_input('upload_' + id, 'upload_field', 'file'+id, 'file', 'file');
     if (this.source) {
         i.disabled = true;
+    } else {
+        i.required = true;
     }
     i.title = "(.fa, .fastq, .fa.gz, .fastq.gz, .clntab)";
     d.appendChild(i);

server/web2py/applications/vidjil/views/partial/file/form.html

@@ -12,6 +12,9 @@
             value="{{if 'id' in file:}}{{=file['id']}}{{pass}}" >
         <input type="hidden" id="sample_set_id" name="sample_set_id" value="{{if "sample_set_id" in request.vars:}}{{=request.vars["sample_set_id"]}}{{pass}}" >
         <input type="hidden" id="sample_type" name="sample_type" value="{{=sample_type}}" />
+        {{if isEditing:}}
+          <input type="hidden" id="is_editing" name="is_editing" value="1" />
+        {{pass}}
     </div>
 
     <div class="field_div">
@@ -19,6 +22,8 @@
             <input class="upload_field form-control" id="file_upload_1_{{=i}}" type="file"
             {{if network_source:}}
                 disabled
+            {{elif not isEditing:}}
+                required
             {{pass}}
                 onchange="db.upload_file_onChange('file_filename_{{=i}}', this.value)"
                 title="first file for this sample (.fa, .fastq, .fa.gz, .fastq.gz, .clntab)"
@@ -28,6 +33,8 @@
             <input class="upload_field form-control" id="file_upload_2_{{=i}}" type="file"
             {{if network_source:}}
                 disabled
+            {{elif not isEditing:}}
+                required
             {{pass}}
                 title="second file for this sample (.fa, .fastq, .fa.gz, .fastq.gz)"
             >

server/web2py/applications/vidjil/views/sample_set/index.html

@@ -94,6 +94,7 @@
     display: inline-block;" title="running pre_processs"></i>{{pass}} 
                         {{if row.sequence_file.pre_process_flag == "WAIT" :}}[queued]{{pass}} 
                         {{if row.sequence_file.pre_process_flag == "FAILED" :}}[failed] <span class="button" onclick="db.call('file/restart_pre_process', {sequence_file_id: {{=row.sequence_file.id}}})">try again</span>{{pass}}
+                        {{ if has_pre_process and row.sequence_file.pre_process_flag is None and row.sequence_file.data_file2 is None: }}<span title="All the files have not been properly received. Please edit the sample to reupload them.">[missing file]</span>{{pass}}
                         {{if row.sequence_file.pre_process_id != None :}} {{=pre_process_list[row.sequence_file.pre_process_id]}} {{pass}}
                      </td>
 		    {{if auth.is_admin():}}
@@ -136,7 +137,7 @@
                      <td></td><td></td><td></td><td></td>
                    {{pass}}
                    <td>
-                   {{if row.sequence_file.data_file != None and ( row.results_file.id == None or ( status != "RUNNING" and status != "QUEUED" and status != "ASSIGNED") ):}}
+                   {{if row.sequence_file.data_file != None and ( row.results_file.id == None or ( status != "RUNNING" and status != "QUEUED" and status != "ASSIGNED") ) and (not has_pre_process or row.sequence_file.pre_process_flag in ("COMPLETED", "FAILED")) :}}
                        {{if auth.can_process_sample_set(request.vars['id']) and (config_id > 0 and auth.can_use_config(config_id)) :}}
                            <span class="pointer" onclick="db.call('default/run_request', { 'sequence_file_id' : '{{=row.sequence_file.id}}', 'sample_set_id' : {{=request.vars["id"]}}, 'config_id' : {{=config_id}} } )"><i class="icon-cog-2" title="Run the selected configuration for this file"></i></span>
                        {{pass}}