Merge pre-release/2025-R5.2 into master (#1008)

* LIMS-1957: Fix fault report URLs for beamlines with hyphens (#997)

* LIMS-1952: Add select all button to multicrystal page (#999)

* LIMS-1951: Fix reprocessing on Auto Processing Status Summary page (#996)

* LIMS-1753: View of all inspection images for a plate (#980)

* LIMS-598: Show Anode maps if attached (#995)

* LIMS-1951: Fix link to Multi Crystal reprocessing

Author: ndg63276

api/src/Downstream/DownstreamProcessing.php

@@ -113,7 +113,7 @@ function _get_attachments(
         }
 
         $rows = $this->db->pq(
-            "SELECT appa.filename, appa.filepath, appa.filetype, CONCAT(appa.filepath, '/', appa.filename) as file
+            "SELECT appa.autoprocprogramattachmentid, appa.filename, appa.filepath, appa.filetype, CONCAT(appa.filepath, '/', appa.filename) as file
             FROM autoprocprogramattachment appa
             WHERE appa.autoprocprogramid = :1 $where
             ORDER BY appa.importancerank,appa.filename",

api/src/Downstream/Type/Dimple.php

@@ -121,6 +121,7 @@ function results() {
         }
 
         $dat['ANODE_PEAKS'] = $this->_get_anode_peaks($this->process['PARAMETERS']['scaling_id']);
+        $dat['ANODE_MODEL'] = $this->_get_anode_model();
 
         $results = new DownstreamResult($this);
         $results->data = $dat;
@@ -199,4 +200,12 @@ function _get_anode_peaks($scaling_id) {
         }
         return array('TABLE' => $peaks, 'PLOT' => $plot);
     }
+
+    function _get_anode_model() {
+        $model = $this->_get_attachments('anode.html');
+        if ($model) {
+            return $model['AUTOPROCPROGRAMATTACHMENTID'];
+        }
+        return;
+    }
 }

api/src/Page/Imaging.php

@@ -611,12 +611,25 @@ function _get_inspection_images()
             array_push($args, $this->arg('sid'));
         }
 
-        $images = $this->db->pq("SELECT i.containerid, si.containerinspectionid, ROUND(TIMESTAMPDIFF('HOUR', min(i2.bltimestamp), i.bltimestamp)/24,1) as delta, si.blsampleimageid, si.blsampleid, si.micronsperpixelx, si.micronsperpixely, si.blsampleimagescoreid, si.comments, TO_CHAR(si.bltimestamp, 'DD-MM-YYYY HH24:MI') as bltimestamp, sc.name as scorename, sc.score, sc.colour as scorecolour, max.maxscore, scorecolours.colour as maxscorecolour
+        $order = 'i.bltimestamp';
+
+        if ($this->has_arg('sort_by')) {
+            $cols = array(
+                'BLTIMESTAMP' => 'i.bltimestamp',
+                'LOCATION' => 'b.location+0'
+            );
+            $dir = $this->has_arg('order') ? ($this->arg('order') == 'asc' ? 'ASC' : 'DESC') : 'ASC';
+            if (array_key_exists($this->arg('sort_by'), $cols))
+                $order = $cols[$this->arg('sort_by')] . ' ' . $dir;
+        }
+
+        $images = $this->db->pq("SELECT i.containerid, si.containerinspectionid, ROUND(TIMESTAMPDIFF('HOUR', min(i2.bltimestamp), i.bltimestamp)/24,1) as delta, si.blsampleimageid, si.blsampleid, si.micronsperpixelx, si.micronsperpixely, si.blsampleimagescoreid, si.comments, TO_CHAR(si.bltimestamp, 'DD-MM-YYYY HH24:MI') as bltimestamp, sc.name as scorename, sc.score, sc.colour as scorecolour, max.maxscore, scorecolours.colour as maxscorecolour, b.location
               FROM blsampleimage si
               LEFT OUTER JOIN blsampleimagescore sc ON sc.blsampleimagescoreid = si.blsampleimagescoreid
               INNER JOIN containerinspection i ON i.containerinspectionid = si.containerinspectionid
               LEFT OUTER JOIN containerinspection i2 ON i.containerid = i2.containerid
 
+              INNER JOIN blsample b ON b.blsampleid = si.blsampleid
               INNER JOIN container c ON c.containerid = i.containerid
               INNER JOIN dewar d ON d.dewarid = c.dewarid
               INNER JOIN shipping s ON s.shippingid = d.shippingid
@@ -631,7 +644,7 @@ function _get_inspection_images()
 
               WHERE p.proposalid = :1 $where
               GROUP BY i.containerid, si.containerinspectionid, i.bltimestamp, si.blsampleimageid, si.blsampleid, si.micronsperpixelx, si.micronsperpixely, si.blsampleimagescoreid, si.comments, TO_CHAR(si.bltimestamp, 'DD-MM-YYYY HH24:MI'), sc.name, sc.score, sc.colour
-              ORDER BY i.bltimestamp", $args);
+              ORDER BY $order", $args);
 
 
         if ($this->has_arg('imid')) {

client/src/css/partials/_base.scss

@@ -21,6 +21,13 @@ body {
     }
 }
 
+body.dialog-open {
+    overflow: hidden;
+    position: fixed;
+    width: 100%;
+    height: 100%;
+}
+
 a {
     color: $link-color;
 

client/src/css/partials/_mc.scss

@@ -132,3 +132,7 @@ span.run_state {
 .yAxis .tickLabel.selected {
     font-weight: bold;
 }
+
+span.cells {
+    cursor: pointer;
+}

client/src/css/partials/_utility.scss

@@ -72,6 +72,10 @@
     flex: 0 0 auto
 }
 
+.wrap {
+    flex-wrap: wrap;
+}
+
 /* TODO: If we can ever get rid of this class, we can also remove the
    work-around in plotly support which needs to circumvent it */
 .active {

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

@@ -41,7 +41,7 @@ define(['marionette',
             e.preventDefault()
 
             if (app.dialog.currentView instanceof ReprocessView) app.dialog.currentView.collection.add(this.model)
-            else app.dialog.show(new ReprocessView({ model: this.model, visit: this.model.get('VISIT') }))
+            else app.dialog.show(new ReprocessView({ model: this.model, visit: this.column.get('visit') }))
         }
 
     })
@@ -50,7 +50,6 @@ define(['marionette',
         initialize: function(options) {
             APItemCell.__super__.initialize.call(this,options)
             this.listenTo(this.model, 'change reset', this.render, this)
-            this.template = '<i class="fa fa-spin fa-spinner"></i>'
         },
 
         render: function() {
@@ -65,15 +64,16 @@ define(['marionette',
                     '<i class="fa icon red fa-times alt="Failed"></i>']
 
             var label = this.column.get('program')
-            this.$el.html(_.template(this.template))
             if (this.model.get('APLOADED') == true) {
-                var ap = res[this.column.get('group')][label]
-                var ress = {}
-                _.each(ap, function(a) {
-                    if (!(a in ress)) ress[a] = 0
-                    ress[a]++
-                })
-                this.$el.html(_.map(ress, function(c, st) { return c > 1 ? '<span class="count">'+c+'x</span> '+val[st] : val[st]}))
+                if (this.column.get('group') in res) {
+                    var ap = res[this.column.get('group')][label]
+                    var ress = {}
+                    _.each(ap, function(a) {
+                        if (!(a in ress)) ress[a] = 0
+                        ress[a]++
+                    })
+                    this.$el.html(_.map(ress, function(c, st) { return c > 1 ? '<span class="count">'+c+'x</span> '+val[st] : val[st]}))
+                }
             }
             this.delegateEvents();
             return this;
@@ -99,7 +99,7 @@ define(['marionette',
             ]
 
             this.columns.push.apply(this.columns, [
-                { label: '', cell: RPCell, template: '<a href="#" class="reprocess button button-notext" title="Reprocess"><i class="fa fa-cog"></i> <span>Reprocess</span></a>', editable: false },
+                { label: '', cell: RPCell, template: '<a href="#" class="reprocess button button-notext" title="Reprocess"><i class="fa fa-cog"></i> <span>Reprocess</span></a>', editable: false, visit: this.model.get('VISIT') },
                 { label: '', cell: APCell, template: '<a href="/dc/visit/'+this.model.escape('VISIT')+'/id/<%-ID%>" class="button button-notext dll" title="Open data collection"><i class="fa fa-arrow-right"></i> <span>Open data collection</span></a>', editable: false },
             ])
 
@@ -119,7 +119,7 @@ define(['marionette',
 
         updateColumns: function() {
             var states = this.statuses.pluck('STATES')
-            var group_names = _.keys(states[0])
+            var group_names = _.chain(states).map(_.keys).flatten().uniq().value();
             var groups = {}
             _.each(group_names, function(group) {
                 groups[group] = _.unique(_.map(states, function(state) { return _.keys(state[group]) }).flat())
@@ -159,4 +159,4 @@ define(['marionette',
             this.wrap.show(this.table)
         }
     })
-})
+})

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

@@ -11,7 +11,7 @@ define(['marionette',
     'modules/dc/views/apstatusitem',
     'modules/dc/views/apmessagestatusitem',
     'modules/dc/views/apmessages',
-    'modules/dc/views/reprocess2',
+    'modules/dc/views/reprocess',
     'modules/dc/views/dcbase',
     'templates/dc/dc.html', 'backbone-validation'], function(Marionette, 
       DialogView, TabView, DCDISTLView, 

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

@@ -13,6 +13,7 @@ define([
             rstats_div: '.rstats_div',
             blob: '.blobs img',
             blobs: '.blobs',
+            viewer: '.viewer',
         },
 
         showBlob: function() {
@@ -31,6 +32,12 @@ define([
 
             this.ui.blob.hide()
 
+            if (this.model.get('ANODE_MODEL')) {
+                this.ui.viewer.attr('href', app.apiurl+'/download/ap/attachments/' + this.model.get('ANODE_MODEL') + '/dl/2');
+            } else {
+                this.ui.viewer.hide()
+            }
+
             if (this.model.get('BLOBS') > 0) {
                 this.blob = new XHRImage()
                 this.blob.onload = this.showBlob.bind(this)
@@ -44,10 +51,10 @@ define([
                 this.ui.rstats.width(0.25*(this.options.holderWidth-14))
                 this.ui.plot.width(0.42*(this.options.holderWidth-14))
                 this.ui.plot.height(this.ui.plot.width()*0.41-80)
-                this.ui.rstats_div.height(this.ui.plot.width()*0.41-80)
+                this.ui.rstats_div.height(this.ui.plot.height())
             }
 
-            this.ui.blobs.css('min-height', this.ui.plot.width()*0.41-80)
+            this.ui.blobs.css('min-height', this.ui.plot.height())
 
             var data = [{ data: this.model.get('PLOTS').FVC, label: 'Rfree vs. Cycle' },
                         { data: this.model.get('PLOTS').RVC, label: 'R vs. Cycle' }]
@@ -56,8 +63,9 @@ define([
 
             const anodePeaks = this.model.get('ANODE_PEAKS');
             if (anodePeaks && anodePeaks.TABLE && anodePeaks.TABLE.length > 0) {
-                this.ui.plot_anode.width(0.42 * (this.options.holderWidth - 14))
-                this.ui.plot_anode.height(this.ui.plot.width() * 0.41 - 80)
+                this.ui.plot_anode.width(this.ui.plot.width())
+                this.ui.plot_anode.height(this.ui.plot.height())
+                this.ui.blobs.css('min-height', this.ui.plot.height() + this.ui.plot_anode.height())
 
                 var anode_data = [{ data: anodePeaks.PLOT, label: 'Peak Height (sig)' }]
                 var anode_pl = $.extend({}, utils.default_plot, { series: { lines: { show: true }}});