Merge pre-release/2025-R2.1 into master (#920)

* LIMS-1646: Show 'Use Facility Account' button for EU dewar dispatch (#910)

* LIMS-1622: Add units and decimal places to visit summary page (#911)

* LIMS-1605: Remove jquery-touchswipe library (#895)

* LIMS-1496: Fix offset grid scan heatmaps in Safari (#896)

* LIMS-1389 - Add upload to ccp4 cloud button (#901)

* LIMS-538: Remove the 'Centring Method' column from creating an MX container (#908)

* LIMS-128: Add plate view to queue container page (#900)

Author: ndg63276

api/config_sample.php

@@ -379,4 +379,7 @@
     $dials_rest_url = "";
     $dials_rest_jwt = "";
     $dials_rest_url_rings = false;
+
+    # Add a button to upload file to CCP4 cloud
+    #$ccp4_cloud_upload_url = 'https://data.cloud.ccp4.ac.uk/api/data/<%=USERNAME%>/<%=FACILITYNAME%>/<%=IMAGEPREFIX%>_<%=DATACOLLECTIONNUMBER%>/upload';
 ?>

api/index.php

@@ -72,7 +72,7 @@ function setupApplication($mode): Slim
             $dhl_enable, $scale_grid, $scale_grid_end_date, $preset_proposal, $timezone,
             $valid_components, $enabled_container_types, $synchweb_version, $redirects,
             $shipping_service_app_url, $use_shipping_service_redirect, $use_shipping_service_redirect_incoming_shipments,
-            $dials_rest_url_rings, $closed_proposal_link;
+            $dials_rest_url_rings, $closed_proposal_link, $ccp4_cloud_upload_url;
         $app->contentType('application/json');
         $options = $app->container['options'];
         $app->response()->body(json_encode(array(
@@ -97,6 +97,7 @@ function setupApplication($mode): Slim
             'shipping_service_app_url_incoming' => $use_shipping_service_redirect_incoming_shipments ? $shipping_service_app_url : null,
             'closed_proposal_link' => $closed_proposal_link,
             'dials_rest_url_rings' => $dials_rest_url_rings,
+            'ccp4_cloud_upload_url' => $ccp4_cloud_upload_url,
             'redirects' => $redirects
         )));
     });

api/src/Page/Processing.php

@@ -16,16 +16,10 @@ class Processing extends Page {
 
         array('/downstream/:id', 'get', '_downstream'),
         array('/downstream/images/:aid(/n/:n)', 'get', '_downstream_images'),
-        array(
-            '/downstream/mapmodel/:aid(/n/:n)',
-            'get',
-            '_downstream_mapmodel',
-        ),
-        array(
-            '/multiplex_jobs/groups/:blSampleGroupId',
-            'get',
-            '_get_latest_multiplex_job_result'
-        ),
+        array('/downstream/mapmodel/:aid(/n/:n)', 'get', '_downstream_mapmodel'),
+        array('/multiplex_jobs/groups/:blSampleGroupId', 'get', '_get_latest_multiplex_job_result'),
+
+        array('/upload', 'post', '_upload_to_cloud'),
     );
 
     public static $arg_list = array(
@@ -44,6 +38,10 @@ class Processing extends Page {
         'rmeas' => '[\d\.]+',
         'cchalf' => '[\d\.]+',
         'ccanom' => '[\d\.]+',
+        'username' => '(\w|\s|\-|\.)+',
+        'cloudrunid' => '(\w|\-)+',
+        'AUTOPROCPROGRAMATTACHMENTID' => '\d+',
+        'DATACOLLECTIONFILEATTACHMENTID' => '\d+',
     );
 
     /**
@@ -66,6 +64,80 @@ function _map_status($status) {
         }
     }
 
+    function _make_curl_file($file){
+        $mime = mime_content_type($file);
+        $info = pathinfo($file);
+        $name = $info['basename'];
+        $output = new \CURLFile($file, $mime, $name);
+        return $output;
+    }
+
+    function _upload_to_cloud() {
+        global $facility_name, $facility_short, $ccp4_cloud_upload_url;
+        if (!$this->has_arg('AUTOPROCPROGRAMATTACHMENTID') && !$this->has_arg('DATACOLLECTIONFILEATTACHMENTID')) {
+            $this->_error('No file specified');
+        }
+        if (!$this->has_arg('username')) {
+            $this->_error('No username specified');
+        }
+        if (!$this->has_arg('cloudrunid')) {
+            $this->_error('No cloudrun id specified');
+        }
+        if ($this->has_arg('AUTOPROCPROGRAMATTACHMENTID')) {
+            $select = ", concat(appa.filepath, '/', appa.filename) as filefullpath";
+            $join = "INNER JOIN processingjob pj ON dc.datacollectionid = pj.datacollectionid
+                INNER JOIN autoprocprogram app ON pj.processingjobid = app.processingjobid
+                INNER JOIN autoprocprogramattachment appa ON app.autoprocprogramid = appa.autoprocprogramid";
+            $where = "WHERE appa.autoprocprogramattachmentid=:1";
+            $args = array($this->arg('AUTOPROCPROGRAMATTACHMENTID'));
+        } else if ($this->has_arg('DATACOLLECTIONFILEATTACHMENTID')) {
+            $select = ", dcfa.filefullpath";
+            $join = "INNER JOIN datacollectionfileattachment dcfa ON dc.datacollectionid = dcfa.datacollectionid";
+            $where = "WHERE dcfa.datacollectionfileattachmentid=:1";
+            $args = array($this->arg('DATACOLLECTIONFILEATTACHMENTID'));
+        }
+        $dc = $this->db->pq(
+            "SELECT dc.imageprefix, dc.datacollectionnumber, concat(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit
+                $select
+                FROM datacollection dc
+                INNER JOIN blsession s ON dc.sessionid = s.sessionid
+                INNER JOIN proposal p ON s.proposalid = p.proposalid
+                $join
+                $where",
+            $args);
+        $dc = $dc[0];
+        $dc['USERNAME'] = $this->arg('username');
+        $dc['FACILITYNAME'] = strtolower(preg_replace( '/[\W]/', '', $facility_name));
+        $dc['FACILITYSHORT'] = strtolower(preg_replace( '/[\W]/', '', $facility_short));
+        $url = preg_replace_callback('/<%=(\w+)%>/',
+            function($mat) use ($dc) {
+                if (array_key_exists($mat[1], $dc)) {
+                    return $dc[$mat[1]];
+                }
+            },
+            $ccp4_cloud_upload_url);
+        $ch = curl_init($url);
+        $headers = array('cloudrun_id: '.$this->arg('cloudrunid'));
+        $data = array('file' => $this->_make_curl_file($dc['FILEFULLPATH']));
+        curl_setopt_array(
+            $ch,
+            array(
+                CURLOPT_RETURNTRANSFER => TRUE,
+                CURLOPT_HTTPHEADER => $headers,
+                CURLOPT_TIMEOUT => 10,
+                CURLOPT_POST => TRUE,
+                CURLOPT_POSTFIELDS => $data,
+            )
+        );
+        $result = json_decode(curl_exec($ch));
+        curl_close($ch);
+        if (isset($result->error)) {
+            $this->_error($result);
+        } else {
+            $this->_output($result);
+        }
+    }
+
     function _screening_status($where, $ids) {
         $screenings = $this->db->pq(
             "SELECT dc.datacollectionid, sc.programversion, so.indexingsuccess, so.strategysuccess, so.alignmentsuccess
@@ -420,13 +492,16 @@ function _results_for_visit() {
         // Set number of decimal places
         $nf = array(
             0 => array('ENERGY'),
+            1 => array(
+                'OVERALLCOMPLETENESS', 'INNERCOMPLETENESS', 'OUTERCOMPLETENESS',
+                'ANOMOVERALLCOMPLETENESS', 'ANOMINNERCOMPLETENESS', 'ANOMOUTERCOMPLETENESS',
+            ),
             2 => array(
-                'RESOLUTION', 'INNERRMEAS', 'OUTERCCHALF', 'INNERCCANOM',
+                'RESOLUTION', 'OUTERCCHALF', 'INNERCCANOM',
                 'CELL_A', 'CELL_B', 'CELL_C', 'CELL_AL', 'CELL_BE', 'CELL_GA',
                 'OVERALLRHIGH', 'OVERALLRLOW', 'INNERRHIGH', 'INNERRLOW', 'OUTERRHIGH', 'OUTERRLOW',
-                'OVERALLCOMPLETENESS', 'INNERCOMPLETENESS', 'OUTERCOMPLETENESS',
-                'ANOMOVERALLCOMPLETENESS', 'ANOMINNERCOMPLETENESS', 'ANOMOUTERCOMPLETENESS'
-            )
+            ),
+            3 => array('INNERRMEAS'),
         );
 
         foreach ($nf as $nff => $cols) {

api/src/Page/Sample.php

@@ -596,7 +596,7 @@ function _queue_all_sub_samples()
             $this->_error('No containerid specified');
         }
 
-        $args = array($this->proposalid, $this->arg('cid'), $this->arg('cid'), $this->arg('cid'));
+        $args = array($this->proposalid, $this->arg('cid'));
         $where = ' AND c.containerid=:2 AND cq2.completedtimestamp IS NULL';
 
         if ($this->has_arg('filter')) {
@@ -609,8 +609,14 @@ function _queue_all_sub_samples()
             $where .= $filters[$this->arg('filter')];
         }
 
-        $first_inner_select_where = ' AND s.containerid=:3';
-        $second_inner_select_where = ' AND s.containerid=:4';
+        if ($this->has_arg('LOCATION')) {
+            $where .= ' AND s.location=:' . (sizeof($args) + 1);
+            array_push($args, $this->arg('LOCATION'));
+        }
+
+        $first_inner_select_where = ' AND s.containerid=:' . (sizeof($args) + 1);
+        $second_inner_select_where = ' AND s.containerid=:' . (sizeof($args) + 2);
+        array_push($args, $this->arg('cid'), $this->arg('cid'));
 
         $this->db->wait_rep_sync(true);
         $ss_query_string = $this->get_sub_samples_query($where, $first_inner_select_where, $second_inner_select_where);
@@ -1311,8 +1317,8 @@ function _handle_update_sample_full($a, $sid)
         $blSampleId = $samp['BLSAMPLEID'];
 
         $this->db->pq(
-            "UPDATE blsample set name=:1,comments=:2,code=:3,volume=:4,packingfraction=:5,dimension1=:6,dimension2=:7,dimension3=:8,shape=:9,looptype=:10 WHERE blsampleid=:11",
-            array($a['NAME'], $a['COMMENTS'], $a['CODE'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'], $blSampleId)
+            "UPDATE blsample set name=:1,comments=:2,code=:3,volume=:4,packingfraction=:5,dimension1=:6,dimension2=:7,dimension3=:8,shape=:9,looptype=:10,smiles=:11 WHERE blsampleid=:12",
+            array($a['NAME'], $a['COMMENTS'], $a['CODE'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'], $a['SMILES'], $blSampleId)
         );
 
         if (array_key_exists('PROTEINID', $a)) {
@@ -1480,6 +1486,7 @@ function _prepare_sample_args($s = null)
             'LOOPTYPE',
             'ENERGY',
             'USERPATH',
+            'SMILES',
             'SCREENINGMETHOD',
             'SCREENINGCOLLECTVALUE',
             'SAMPLEGROUP',
@@ -1537,8 +1544,8 @@ function _do_add_sample($s)
         }
 
         $this->db->pq(
-            "INSERT INTO blsample (blsampleid,crystalid,diffractionplanid,containerid,location,comments,name,code,blsubsampleid,screencomponentgroupid,volume,packingfraction,dimension1,dimension2,dimension3,shape,looptype,source) VALUES (s_blsample.nextval,:1,:2,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14,:15,:16,IFNULL(:17,CURRENT_USER)) RETURNING blsampleid INTO :id",
-            array($crysid, $did, $a['CONTAINERID'], $a['LOCATION'], $a['COMMENTS'], $a['NAME'], $a['CODE'], $a['BLSUBSAMPLEID'], $a['SCREENCOMPONENTGROUPID'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'], $a['SOURCE'])
+            "INSERT INTO blsample (blsampleid,crystalid,diffractionplanid,containerid,location,comments,name,code,blsubsampleid,screencomponentgroupid,volume,packingfraction,dimension1,dimension2,dimension3,shape,looptype,smiles,source) VALUES (s_blsample.nextval,:1,:2,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14,:15,:16,:17,IFNULL(:18,CURRENT_USER)) RETURNING blsampleid INTO :id",
+            array($crysid, $did, $a['CONTAINERID'], $a['LOCATION'], $a['COMMENTS'], $a['NAME'], $a['CODE'], $a['BLSUBSAMPLEID'], $a['SCREENCOMPONENTGROUPID'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'], $a['SMILES'], $a['SOURCE'])
         );
         $sid = $this->db->id();
 

client/package-lock.json

@@ -81,7 +81,6 @@
     "jquery": "^1.12.4",
     "jquery-color": "^3.0.0-alpha.1",
     "jquery-flot-resize": "^1.0.0",
-    "jquery-touchswipe": "^1.6.19",
     "jquery-ui": "^1.12.1",
     "jquery-ui-timepicker-addon": "^1.6.3",
     "jquery.flot": "^0.8.3",

client/package.json

@@ -226,3 +226,7 @@ input[name=gap] {
     text-align: center;
     box-sizing: content-box;
 }
+
+.plate-max-width {
+    max-width: 700px;
+}

client/src/css/partials/_imaging.scss

@@ -97,6 +97,10 @@
     font-weight: bold;
 }
 
+.u {
+    text-decoration: underline;
+}
+
 .nowrap {
     white-space: nowrap;
 }

client/src/css/partials/_utility.scss

@@ -39,6 +39,7 @@ const INITIAL_SAMPLE_STATE = {
   SCREENINGCOLLECTVALUE: '',
   THEORETICALDENSITY: '',
   SHAPE: '',
+  SMILES: '',
   SPACEGROUP: '',
   SYMBOL: '',
   USERPATH: '',

client/src/js/app/store/modules/store.samples.js

@@ -3,15 +3,17 @@ define(['marionette',
     'views/table', 
     'collections/attachments', 
     'views/log',
+    'views/cloudupload',
     'utils'], 
-    function(Marionette, Backgrid, TableView, attachments, LogView, utils) {
+    function(Marionette, Backgrid, TableView, attachments, LogView, CloudUploadView, utils) {
 
 
     var OptionsCell = Backgrid.Cell.extend({
         events: {
             'click a.dl': utils.signHandler,
             'click a.rsv': 'closeDialog',
             'click a.vatlog': 'showLog',
+            'click a.vatupload': 'showCloudUpload',
         },
 
         closeDialog: function() {
@@ -30,6 +32,11 @@ define(['marionette',
             })
         },
 
+        showCloudUpload: function(e) {
+            e.preventDefault()
+            app.dialog.show(new CloudUploadView({ model: this.model, collection: this.model.collection }))
+        },
+
         render: function() {
             // This was using an 'id' passed into the column as the dcid (getOption('id')).
             // However, this is not present when loading attachments from a data collection group
@@ -46,6 +53,10 @@ define(['marionette',
                 this.$el.append('<a href="/dc/rsv/id/'+dcid+'" class="button rsv"><i class="fa fa-search"></i> Reciprocal Space Viewer</a>')
             }
 
+            if (app.options.get('ccp4_cloud_upload_url') && this.model.get('FILETYPE') == 'params') {
+                this.$el.append('<a class="vatupload button" href="#"><i class="fa fa-cloud-upload"></i> CCP4 Cloud</a>')
+            }
+
             return this
         }
     })