Merge branch 'hotfix-s/3213-edit-with-preprocess' into 'dev'

Resolve "Éditer un sample qui possède un pre-process empêche de relancer une analyse dessus"

Closes #3213

See merge request !216

server/web2py/applications/vidjil/controllers/file.py

@@ -236,6 +236,10 @@ def submit():
             reupload = True
             fid = int(f["id"])
             sequence_file = db.sequence_file[fid]
+            if f['filename'] == '':
+                # If we don't reupload a new file
+                file_data.pop('pre_process_flag')
+            
             db.sequence_file[fid] = file_data
             #remove previous membership
             db( db.sample_set_membership.sequence_file_id == fid).delete()
@@ -298,6 +302,10 @@ def submit():
     
 def form_response(data):
     source_module_active = hasattr(defs, 'FILE_SOURCE') and hasattr(defs, 'FILE_TYPES')
+    network_source = source_module_active and (data['action'] != 'edit'     \
+                                               or len(data['file']) == 0    \
+                                               or data['file'][0].network)
+      # should be true only when we want to use the network view
     response.view = 'file/form.html'
     upload_group_ids = [int(gid) for gid in get_upload_group_ids(auth)]
     group_ids = get_involved_groups()
@@ -309,6 +317,7 @@ def form_response(data):
            sample_type = data['sample_type'],
            errors = data['errors'],
            source_module_active = source_module_active,
+           network_source = network_source,
            group_ids = group_ids,
            upload_group_ids = upload_group_ids,
            isEditing = data['action']=='edit')

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

@@ -7,22 +7,26 @@
    <h3>Add samples</h3>
    {{ pass }}
 
+   {{ required_files = 1 }}
     {{ if source_module_active: }}
         <span>file source: </span>
         <label for="source_computer">my computer</label>
-        <input type="radio" id="source_computer" name="source" value="computer" onchange="db.toggle_file_source()"/>
+        <input type="radio" id="source_computer" name="source" value="computer" onchange="db.toggle_file_source()" {{ if not network_source: }} checked="checked" {{pass}}/>
         <label for="source_nfs">network</label>
-        <input type="radio" id="source_nfs" name="source" value="nfs" onchange="db.toggle_file_source()" checked="checked" />        
+        <input type="radio" id="source_nfs" name="source" value="nfs" onchange="db.toggle_file_source()" {{if network_source:}} checked="checked" {{pass}} />
         <p></p>
     {{pass}}
-    <div {{if source_module_active:}} hidden {{pass}}>
+    <div {{if network_source:}} hidden {{pass}}>
         <h3>Pre-process scenario</h3>
         If you have two R1/R2 files per sample, please select an appropriate pre-process :
-        <select id="pre_process" name="pre_process" onChange="db.pre_process_onChange(this)" {{if source_module_active:}} disabled {{pass}}>
+        <select id="pre_process" name="pre_process" onChange="db.pre_process_onChange(this)" {{if network_source:}} disabled {{pass}}>
             <option required_files="1" value="0">no pre-process (1 file per sample)</option>
             {{for row in pre_process_list :}}
                 <option title="{{=row["info"]}}" required_files="{{=row["file"]}}" value="{{=row["id"]}}"
-                    {{if 'file_id' in request.vars and row["id"]==files[0].pre_process_id :}}selected{{pass}}>
+                    {{if 'file_id' in request.vars and row["id"]==files[0].pre_process_id :}}
+			selected
+			{{ required_files=row["file"]}}
+			{{pass}}>
                     {{=row["id"]}} &ndash; {{=row["name"]}}
                 </option>
             {{pass}}

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

@@ -15,18 +15,18 @@
     </div>
 
     <div class="field_div">
-        <div id="file_field_1_{{=i}}" class="field_div file_1" {{if source_module_active:}} style="display: none" {{pass}}>
+        <div id="file_field_1_{{=i}}" class="field_div file_1" {{if network_source:}} style="display: none" {{pass}}>
             <input class="upload_field form-control" id="file_upload_1_{{=i}}" type="file"
-            {{if source_module_active:}}
+            {{if network_source:}}
                 disabled
             {{pass}}
                 onchange="db.upload_file_onChange('file_filename_{{=i}}', this.value)"
                 title="first file for this sample (.fa, .fastq, .fa.gz, .fastq.gz, .clntab)"
             >
         </div>
-        <div id="file_2_{{=i}}" class="field_div file_2" style="display: none">
+        <div id="file_2_{{=i}}" class="field_div file_2" {{if required_files < 2:}}style="display: none"{{pass}}>
             <input class="upload_field form-control" id="file_upload_2_{{=i}}" type="file"
-            {{if source_module_active:}}
+            {{if network_source:}}
                 disabled
             {{pass}}
                 title="second file for this sample (.fa, .fastq, .fa.gz, .fastq.gz)"
@@ -34,7 +34,7 @@
         </div>
         <div id="jstree_field_{{=i}}"
             class="field_div jstree_field form-control"
-            {{if not source_module_active:}} style="display: none;" {{pass}}
+            {{if not network_source:}} hidden {{pass}}
             data-index={{=i}}
             onclick="db.display_jstree(this.dataset.index)">
             <span class="button2">browse</span>