Merge pre-release/2025-R3.2 into master (#949)

* LIMS-1758: Fix slowness with plates with lots of subsamples (#941)

* LIMS-1758: Fix slowness with plates with lots of samples

* LIMS-1758: Remove unnecessary change

* LIMS-1758: Remove unnecessary whitespace

* LIMS-1758: Do large updates in chunks

* LIMS-1758: Use native JS

---------

Co-authored-by: Mark Williams <mark.williams@diamond.ac.uk>

* LIMS-1715: Clear sessionId from containers if a dewar transfer is requested (#939)

* LIMS-1715: Clear sessionId from containers if a dewar transfer is requested

* LIMS-1715: Clear sessionId from containers if a dewar transfer is requested

---------

Co-authored-by: Mark Williams <mark.williams@diamond.ac.uk>

* LIMS-1714: Populate Dewar.dewarRegistryId (#936)

Co-authored-by: Mark Williams <mark.williams@diamond.ac.uk>

* LIMS-1701: Make Xray Centring results an openable table (#935)

Co-authored-by: Mark Williams <mark.williams@diamond.ac.uk>

* LIMS-1642: Fix search when clicking x on search bars (#909)

Co-authored-by: Mark Williams <mark.williams@diamond.ac.uk>

* LIMS-1639: List most common screens at the top of the list (#928)

Co-authored-by: Mark Williams <mark.williams@diamond.ac.uk>

* LIMS-1777: Fix download of autoprocessing attachments on sm beamlines (#947)

Co-authored-by: Mark Williams <mark.williams@diamond.ac.uk>

---------

Co-authored-by: Mark Williams <mark.williams@diamond.ac.uk>

Author: ndg63276

api/src/Page/DC.php

@@ -1508,20 +1508,25 @@ function _grid_xrc()
         $info = $this->db->pq("SELECT dc.datacollectiongroupid, dc.datacollectionid,
                 xrc.xraycentringtype as method, xrcr.xraycentringresultid,
                 xrcr.centreofmassx as x, xrcr.centreofmassy as y, xrcr.centreofmassz as z,
-                xrcr.totalcount
+                xrcr.totalcount,
+                xrcr.boundingboxmaxx-xrcr.boundingboxminx as sizex,
+                xrcr.boundingboxmaxy-xrcr.boundingboxminy as sizey,
+                xrcr.boundingboxmaxz-xrcr.boundingboxminz as sizez,
+                s.blsampleid, s.name
                 FROM datacollection dc
                 INNER JOIN xraycentring xrc ON xrc.datacollectiongroupid = dc.datacollectiongroupid
                 INNER JOIN xraycentringresult xrcr ON xrcr.xraycentringid = xrc.xraycentringid
-                WHERE dc.datacollectionid = :1 ", array($this->arg('id')));
+                LEFT JOIN blsample s ON xrcr.blsampleid = s.blsampleid
+                WHERE dc.datacollectionid = :1
+                ORDER BY xrcr.totalcount desc", array($this->arg('id')));
 
         if (!sizeof($info))
             $this->_output(array('total' => 0, 'data' => array()));
         else {
             foreach ($info as &$i) {
                 foreach ($i as $k => &$v) {
-                    if ($k == 'METHOD')
-                        continue;
-                    $v = round(floatval($v), 2);
+                    if ($k == 'X' || $k == 'Y' || $k == 'Z')
+                        $v = number_format($v, 1);
                 }
             }
             $this->_output(array('total' => sizeof($info), 'data' => $info));

api/src/Page/Imaging.php

@@ -866,11 +866,12 @@ function _get_screens()
             array_push($args, $this->arg('scid'));
         }
 
-        $screens = $this->db->pq("SELECT ct.name as containertypeid, IFNULL(ct.capacity, 96) as capacity, CONCAT(p.proposalcode, p.proposalnumber) as prop, s.global, s.name, s.screenid, s.proposalid, count(distinct sg.screencomponentgroupid) as groups, count(distinct sc.screencomponentid) as components
+        $screens = $this->db->pq("SELECT ct.name as containertypeid, IFNULL(ct.capacity, 96) as capacity, CONCAT(p.proposalcode, p.proposalnumber) as prop, s.global, s.name, s.screenid, s.proposalid, count(distinct sg.screencomponentgroupid) as groups, count(distinct sc.screencomponentid) as components, COUNT(DISTINCT c.containerid) AS cnt
               FROM screen s
               LEFT OUTER JOIN screencomponentgroup sg ON sg.screenid = s.screenid
               LEFT OUTER JOIN screencomponent sc ON sc.screencomponentgroupid = sg.screencomponentgroupid
               LEFT OUTER JOIN containertype ct ON ct.containertypeid = s.containertypeid
+              LEFT OUTER JOIN container c ON c.screenId = s.screenid
               INNER JOIN proposal p ON p.proposalid = s.proposalid
               WHERE $where
               GROUP BY CONCAT(p.proposalcode, p.proposalnumber), s.global, s.name, s.screenid, s.proposalid", $args);

api/src/Page/Shipment.php

@@ -38,7 +38,7 @@ class Shipment extends Page
 
         // Dewar Fields
         'CODE' => '([\w\-])+',
-        'FACILITYCODE' => '([\w\-])+',
+        'FACILITYCODE' => '([\w\-])*',
         'NEWFACILITYCODE' => '([\w\-])+',
         'TRACKINGNUMBERTOSYNCHROTRON' => '\w*',
         'TRACKINGNUMBERFROMSYNCHROTRON' => '\w*',
@@ -957,6 +957,11 @@ function _transfer_dewar()
 
         // Update dewar status to transfer-requested to keep consistent with history
         $this->db->pq("UPDATE dewar set dewarstatus='transfer-requested' WHERE dewarid=:1", array($this->arg('DEWARID')));
+        // Remove sessionId from containers and unqueue any pucks, so it doesnt look like a finished UDC dewar
+        $this->db->pq("UPDATE container set sessionid=NULL WHERE dewarid=:1", array($this->arg('DEWARID')));
+        $this->db->pq("DELETE cq from containerqueue cq
+                        INNER JOIN container c ON c.containerid = cq.containerid
+                        WHERE dewarid=:1", array($this->arg('DEWARID')));
 
         if ($this->has_arg('NEXTVISIT')) {
             $sessions = $this->db->pq(
@@ -1729,7 +1734,7 @@ function _get_dewars()
             CONCAT(p.proposalcode, p.proposalnumber, '-', se2.visit_number) as udcfirstexperiment,
             r.labcontactid, se.beamlineoperator as localcontact, se.beamlinename,
             TO_CHAR(se.startdate, 'HH24:MI DD-MM-YYYY') as firstexperimentst, d.firstexperimentid,
-            s.shippingid, s.shippingname, d.facilitycode, count(c.containerid) as ccount,
+            s.shippingid, s.shippingname, IFNULL(r.facilitycode, d.facilitycode) as facilitycode, count(c.containerid) as ccount,
             (case when se.visit_number > 0 then (CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number)) else '' end) as exp,
             d.code, d.barcode, d.storagelocation, d.dewarstatus, d.dewarid,
             d.trackingnumbertosynchrotron, d.trackingnumberfromsynchrotron, d.externalShippingIdFromSynchrotron,
@@ -1741,11 +1746,11 @@ function _get_dewars()
               INNER JOIN proposal p ON p.proposalid = s.proposalid
               LEFT OUTER JOIN blsession se ON d.firstexperimentid = se.sessionid
               LEFT OUTER JOIN blsession se2 ON c.sessionid = se2.sessionid
-              LEFT OUTER JOIN dewarregistry r ON r.facilitycode = d.facilitycode
+              LEFT OUTER JOIN dewarregistry r ON r.dewarregistryid = d.dewarregistryid
               LEFT OUTER JOIN labcontact lc ON s.sendinglabcontactid = lc.labcontactid
               LEFT OUTER JOIN person pe ON lc.personid = pe.personid
               WHERE $where 
-              GROUP BY CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number), r.labcontactid, se.beamlineoperator, TO_CHAR(se.startdate, 'HH24:MI DD-MM-YYYY'), (case when se.visit_number > 0 then (CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number)) else '' end),s.shippingid, s.shippingname, d.code, d.barcode, d.storagelocation, d.dewarstatus, d.dewarid,  d.trackingnumbertosynchrotron, d.trackingnumberfromsynchrotron, d.facilitycode, d.firstexperimentid
+              GROUP BY CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number), r.labcontactid, se.beamlineoperator, TO_CHAR(se.startdate, 'HH24:MI DD-MM-YYYY'), (case when se.visit_number > 0 then (CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number)) else '' end),s.shippingid, s.shippingname, d.code, d.barcode, d.storagelocation, d.dewarstatus, d.dewarid,  d.trackingnumbertosynchrotron, d.trackingnumberfromsynchrotron, facilitycode, d.firstexperimentid
               ORDER BY $order", $args);
 
         if ($this->has_arg('did')) {
@@ -1779,6 +1784,7 @@ function _add_dewar()
         $to = $this->has_arg('TRACKINGNUMBERTOSYNCHROTRON') ? $this->arg('TRACKINGNUMBERTOSYNCHROTRON') : '';
         $from = $this->has_arg('TRACKINGNUMBERFROMSYNCHROTRON') ? $this->arg('TRACKINGNUMBERFROMSYNCHROTRON') : '';
         $fc = $this->has_arg('FACILITYCODE') ? $this->arg('FACILITYCODE') : '';
+        $drid = $this->_get_dewarregistryid($fc);
         $wg = $this->has_arg('WEIGHT') ? $this->arg('WEIGHT') : $dewar_weight;
         $exp = null;
         $source = $this->has_arg('SOURCE') ? $this->arg('SOURCE') : null;
@@ -1789,9 +1795,9 @@ function _add_dewar()
         }
 
         $this->db->pq(
-            "INSERT INTO dewar (dewarid,code,trackingnumbertosynchrotron,trackingnumberfromsynchrotron,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,weight,source)
-              VALUES (s_dewar.nextval,:1,:2,:3,:4,CURRENT_TIMESTAMP,'opened',:5,:6,:7,IFNULL(:8,CURRENT_USER)) RETURNING dewarid INTO :id",
-            array($this->arg('CODE'), $to, $from, $this->arg('SHIPPINGID'), $exp, $fc, $wg, $source)
+            "INSERT INTO dewar (dewarid,code,trackingnumbertosynchrotron,trackingnumberfromsynchrotron,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,dewarregistryid,weight,source)
+              VALUES (s_dewar.nextval,:1,:2,:3,:4,CURRENT_TIMESTAMP,'opened',:5,:6,:7,:8,IFNULL(:9,CURRENT_USER)) RETURNING dewarid INTO :id",
+            array($this->arg('CODE'), $to, $from, $this->arg('SHIPPINGID'), $exp, $fc, $drid, $wg, $source)
         );
 
         $id = $this->db->id();
@@ -1937,6 +1943,9 @@ function _update_dewar()
                     } else {
                         $this->_output(1);
                     }
+                } else if ($f === 'FACILITYCODE') {
+                    $drid = $this->_get_dewarregistryid($this->arg($f));
+                    $this->db->pq("UPDATE dewar SET $f=:1, dewarregistryid=:2 WHERE dewarid=:3", array($this->arg($f), $drid, $this->arg('did')));
                 } else {
                     $this->db->pq("UPDATE dewar SET $f=:1 WHERE dewarid=:2", array($this->arg($f), $this->arg('did')));
                     $this->_output(array($f => $this->arg($f)));
@@ -3141,11 +3150,12 @@ function _add_shipment()
                 for ($i = 0; $i < $this->arg('DEWARS'); $i++) {
                     $fc = $i < sizeof($this->arg('FCODES')) ? $fcs[$i] : '';
                     $n = $fc ? $fc : ('Dewar' . ($i + 1));
+                    $drid = $this->_get_dewarregistryid($fc);
 
                     $this->db->pq(
-                        "INSERT INTO dewar (dewarid,code,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,weight,source)
-                          VALUES (s_dewar.nextval,:1,:2,CURRENT_TIMESTAMP,'opened',:3,:4,:5,IFNULL(:6,CURRENT_USER)) RETURNING dewarid INTO :id",
-                        array($n, $sid, $exp, $fc, $dewar_weight, $source)
+                        "INSERT INTO dewar (dewarid,code,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,dewarregistryid,weight,source)
+                          VALUES (s_dewar.nextval,:1,:2,CURRENT_TIMESTAMP,'opened',:3,:4,:5,:6,IFNULL(:7,CURRENT_USER)) RETURNING dewarid INTO :id",
+                        array($n, $sid, $exp, $fc, $drid, $dewar_weight, $source)
                     );
 
                     $id = $this->db->id();
@@ -3165,6 +3175,17 @@ function _add_shipment()
         $this->_output(array('SHIPPINGID' => $sid));
     }
 
+    function _get_dewarregistryid($fc)
+    {
+        $drid = null;
+        if ($fc) {
+            $dr = $this->db->pq("SELECT dewarregistryid FROM dewarregistry where facilitycode=:1", array($fc));
+            if (sizeof($dr))
+                $drid = $dr[0]['DEWARREGISTRYID'];
+        }
+        return $drid;
+    }
+
     function _get_default_dewar()
     {
         if ($this->has_arg('visit')) {

client/src/js/modules/dc/collections/gridxrc.js

@@ -0,0 +1,16 @@
+define(['backbone'], function(Backbone) {
+
+  return Backbone.Collection.extend({
+
+    url: function() { return '/dc/grid/xrc/' + this.id },
+
+    initialize: function(options) {
+      this.id = options.id
+    },
+
+    parse: function(r) {
+      return r.data
+    },
+  })
+
+})

client/src/js/modules/dc/models/gridxrc.js

@@ -154,7 +154,7 @@ define(['marionette',
             var iCatProposalRootURL = this.getICatProposalRootUrl(proposalID);
 
             this.isIndustry = this.hasIndustryPrefix(proposalID); // ! FIXME: Naive check.
-            this.isPurgedSession = options.dcPurgedProcessedData !== "0";
+            this.isPurgedSession = (options && options.dcPurgedProcessedData) ? (options.dcPurgedProcessedData !== "0") : false;
 
             var columns = [
                 { name: 'FILENAME', label: 'File', cell: 'string', editable: false },

client/src/js/modules/dc/views/autoprocattachments.js

@@ -10,7 +10,7 @@ define(['marionette',
     'modules/dc/views/dccomments', 
     'modules/dc/views/attachments',
     'modules/dc/views/apstatusitem',
-    'modules/dc/models/gridxrc',
+    'modules/dc/views/gridxrc',
     'templates/dc/grid.html', 'backbone-validation'], 
     function(Marionette, DCBase, TabView, AddToProjectView, Editable, Backbone, ImageViewer, GridPlot, 
       DialogView, DCCommentsView, AttachmentsView, APStatusItem, GridXRC,
@@ -22,6 +22,7 @@ define(['marionette',
     apStatusItem: APStatusItem,
 
     events: {
+      'click .holder h1.xrc': 'loadXRC',
       'click @ui.zoom': 'toggleZoom'
     },
 
@@ -136,24 +137,16 @@ define(['marionette',
             }
 
             if (state >= 2) {
-                this.xrc = new GridXRC({ id: this.model.get('ID') })
-                this.xrc.fetch({
-                    success: this.showXRC.bind(this)
-                })
+                this.xrc = new GridXRC({ id: this.model.get('ID'), el: this.$el.find('div.xrc') })
             }
         }
     },
 
-    showXRC: function() {
-        var xrcs = this.xrc.get('data')
-        var t = ''
-        for (var i = 0; i < xrcs.length; i++) {
-            t += ' - Crystal '+(i+1)+': X Pos '+xrcs[i]['X']+' Y Pos '+xrcs[i]['Y']+' Z Pos '+xrcs[i]['Z']+' Strength '+xrcs[i]['TOTALCOUNT']
-        }
-        if (xrcs.length > 0) {
-            this.ui.holder.prepend('Method: '+xrcs[0]['METHOD']+t)
+    loadXRC: function(e) {
+        if (!this.xrc) {
+            this.xrc = new GridXRC({ id: this.model.get('ID'), el: this.$el.find('div.xrc') })
         } else {
-            this.ui.holder.prepend('Found no diffraction')
+            this.xrc.$el.slideToggle()
         }
     },
 

client/src/js/modules/dc/views/grid.js

@@ -0,0 +1,49 @@
+define(['marionette',
+    'modules/dc/collections/gridxrc',
+    'views/table',
+    'utils/table'], function(Marionette, GridXRC, TableView, table) {
+
+    var linkIfSample = function(data) {
+        if (data.BLSAMPLEID) {
+            return '<a href="/samples/sid/'+data.BLSAMPLEID+'"><i class="fa fa-search"></i> '+data.NAME+'</a>'
+        } else {
+            return ''
+        }
+    }
+
+    return Marionette.LayoutView.extend({
+        template: _.template('<div class="summary"></div>'),
+        regions: {
+            summary: '.summary',
+        },
+
+        initialize: function(options) {
+            this.collection = new GridXRC({ id: options.id })
+            this.collection.fetch().done(this.render.bind(this))
+        },
+
+        onRender: function() {
+            this.summary.show(new TableView({
+                className: 'ui-tabs-panel',
+                noTableHolder: true,
+                collection: this.collection,
+                columns: [
+                    { label: 'Sample', cell: table.TemplateCell, template: d=>linkIfSample(d), editable: false },
+                    { name: 'METHOD', label: 'Method', cell: 'string', editable: false },
+                    { name: 'TOTALCOUNT', label: 'Strength', cell: 'string', editable: false },
+                    { name: 'X', label: 'Pos X (Boxes)', cell: 'string', editable: false },
+                    { name: 'Y', label: 'Pos Y (Boxes)', cell: 'string', editable: false },
+                    { name: 'Z', label: 'Pos Z (Boxes)', cell: 'string', editable: false },
+                    { name: 'SIZEX', label: 'Size X (Boxes)', cell: 'string', editable: false },
+                    { name: 'SIZEY', label: 'Size Y (Boxes)', cell: 'string', editable: false },
+                    { name: 'SIZEZ', label: 'Size Z (Boxes)', cell: 'string', editable: false },
+                ],
+                pages: false,
+                backgrid: {
+                    emptyText: 'No xray centring results available for this data collection',
+                },
+            }))
+        },
+    })
+
+})

client/src/js/modules/dc/views/gridxrc.js

@@ -604,9 +604,11 @@ define(['marionette',
         },
 
         calcZoom: function() {
-            var min = this.ui.canvas.width() < this.ui.canvas.height() ? this.ui.canvas.width()/this.width : this.ui.canvas.height()/this.height
-            this.ui.zoom.slider('option', 'min', 100*min)
-            this.onZoomChange()
+            if (this.ui.zoom.hasClass('ui-slider')) {
+                var min = this.ui.canvas.width() < this.ui.canvas.height() ? this.ui.canvas.width()/this.width : this.ui.canvas.height()/this.height
+                this.ui.zoom.slider('option', 'min', 100*min)
+                this.onZoomChange()
+            }
         },
 
         clampOffsets: function() {