LIMS-261: Allow download of PDB files (#857)

* LIMS-261: Allow download of PDB files

* LIMS-261: Use RCSB for links

* LIMS-261: Use EBI instead of RCSB

---------

Co-authored-by: Mark Williams <[email protected]>

Author: ndg63276

api/src/Page/Sample.php

@@ -195,6 +195,7 @@ class Sample extends Page
         array('/pdbs(/pid/:pid)', 'get', '_get_pdbs'),
         array('/pdbs', 'post', '_add_pdb'),
         array('/pdbs(/:pdbid)', 'delete', '_remove_pdb'),
+        array('/pdbs/download/:pdbid', 'get', '_download_pdb'),
 
         array('/concentrationtypes', 'get', '_concentration_types'),
         array('/componenttypes', 'get', '_component_types'),
@@ -2062,6 +2063,21 @@ function _get_pdbs()
         $this->_output($rows);
     }
 
+    # ------------------------------------------------------------------------
+    # Download a pdb file
+    function _download_pdb()
+    {
+        if (!$this->has_arg('pdbid'))
+            $this->_error('No PDB id specified');
+
+        $pdb = $this->db->pq("SELECT name, contents FROM pdb WHERE pdbid = :1", array($this->arg('pdbid')));
+        $pdb = $pdb[0];
+
+        header('Content-Type:text/plain');
+        header('Content-Disposition:attachment;filename='.$pdb['NAME']);
+        print $pdb['CONTENTS'];
+    }
+
     # ------------------------------------------------------------------------
     # Add a new pdb
     function _add_pdb()

client/src/js/modules/samples/views/pdbs.js

@@ -1,15 +1,28 @@
-define(['marionette'], function(Marionette) {
+define(['marionette', 'utils'], function(Marionette, utils) {
 
 
     var UserItem = Marionette.ItemView.extend({
-        template: _.template('<%-NAME%> <% if (CODE) { %>[CODE]<% } else { %>[File]<% } %> <span class="r"><a class="button button-notext delete" href="#"><i class="fa fa-times"></i> <span>Delete</span></a></span>'),
+        template: _.template(''),
         tagName: 'li',
         attributes: { 'data-testid': 'protein-pdb-list-item' },
         events: {
-            'click a.delete': 'deleteUser',
+            'click a.delete': 'deletePDB',
+            'click a.download': utils.signHandler,
         },
 
-        deleteUser: function(e) {
+        render: function() {
+            UserItem.__super__.render.call(this)
+            const linkButton = '<a class="button button-notext" href="https://www.ebi.ac.uk/pdbe/entry/pdb/'+this.model.get('CODE')+'"><i class="fa fa-link"></i> <span>EBI</span></a>'
+            const deleteButton = '<a class="button button-notext delete" href="#"><i class="fa fa-times"></i> <span>Delete</span></a>'
+            const downloadButton = '<a class="button button-notext download" href="'+app.apiurl+'/sample/pdbs/download/'+this.model.get('PDBID')+'"><i class="fa fa-download"></i> <span>Download</span></a>'
+            if (this.model.get('CODE')) {
+                this.$el.append(this.model.get('NAME')+' [Code] <span class="r">'+linkButton+' '+deleteButton+'</span>')
+            } else {
+                this.$el.append(this.model.get('NAME')+' [File] <span class="r">'+downloadButton+' '+deleteButton+'</span>')
+            }
+        },
+
+        deletePDB: function(e) {
             this.model.destroy()
         },
     })
@@ -30,4 +43,4 @@ define(['marionette'], function(Marionette) {
     })
 
 
-})
+})