LIMS-148: Improve staff imaging dashboard (#914)

ndg63276 · Mark Williams · gfrn · web-flow · commit 34f78636f950 · 2025-03-25T15:54:35.000Z
* LIMS-148: Improve staff imaging dashboard

* LIMS-148: Add highlighting of queued samples, show queued containers

* LIMS-148: Fix display of queued samples in queued containers

* LIMS-148: Allow sorting by no of subsamples

* LIMS-148: Dont break xpdf containers page

* LIMS-148: Use strict equality

Co-authored-by: Guilherme Francisco &lt;guilherme.de-freitas@diamond.ac.uk&gt;

---------

Co-authored-by: Mark Williams &lt;mark.williams@diamond.ac.uk&gt;
Co-authored-by: Guilherme Francisco &lt;guilherme.de-freitas@diamond.ac.uk&gt;
diff --git a/api/src/Page/Shipment.php b/api/src/Page/Shipment.php
@@ -2097,8 +2097,73 @@ function _get_all_containers()
             $totalQuery->joinClause("INNER JOIN shipping sh ON sh.shippingid = d.shippingid");
         }
 
+        $subsamples = '0 as queuedmanualsubsamples,
+                       0 as completedmanualsubsamples,
+                       0 as availablemanualsubsamples,
+                       0 as queuedautosubsamples,
+                       0 as completedautosubsamples,
+                       0 as availableautosubsamples,';
+
+        $manualsubsamples = "
+                (SELECT count(distinct ss.blsubsampleid) FROM blsubsample ss
+                    INNER JOIN blsample s2 ON s2.blsampleid = ss.blsampleid
+                    LEFT OUTER JOIN containerqueuesample cqs2 ON cqs2.blsubsampleid = ss.blsubsampleid
+                    LEFT OUTER JOIN containerqueue cq2 ON cq2.containerqueueid = cqs2.containerqueueid
+                    WHERE s2.containerid = c.containerid AND ss.source='manual'
+                    AND cqs2.containerqueuesampleid IS NOT NULL AND cq2.completedtimestamp IS NULL) as queuedmanualsubsamples,
+                (SELECT count(distinct ss.blsubsampleid) FROM blsubsample ss
+                    INNER JOIN blsample s2 ON s2.blsampleid = ss.blsampleid
+                    LEFT OUTER JOIN containerqueuesample cqs2 ON cqs2.blsubsampleid = ss.blsubsampleid
+                    LEFT OUTER JOIN containerqueue cq2 ON cq2.containerqueueid = cqs2.containerqueueid
+                    WHERE s2.containerid = c.containerid AND ss.source='manual'
+                    AND cq2.completedtimestamp IS NOT NULL) as completedmanualsubsamples,
+                (SELECT count(distinct ss.blsubsampleid) FROM blsubsample ss
+                    INNER JOIN blsample s2 ON s2.blsampleid = ss.blsampleid
+                    LEFT OUTER JOIN containerqueuesample cqs2 ON cqs2.blsubsampleid = ss.blsubsampleid
+                    WHERE s2.containerid = c.containerid AND ss.source='manual'
+                    AND cqs2.containerqueuesampleid IS NULL) as availablemanualsubsamples,";
+        $autosubsamples = "
+                (SELECT COUNT(DISTINCT CASE WHEN cqs3.containerqueuesampleid IS NOT NULL AND cq3.completedtimestamp IS NULL THEN ss3.blsubsampleid ELSE NULL END)
+                    FROM blsample s3
+                    LEFT JOIN (
+                        SELECT si.blsampleid, MAX(si.blsampleimageid) AS max_blsampleimageid
+                        FROM blsampleimage si
+                        GROUP BY si.blsampleid
+                    ) AS max_si ON s3.blsampleid = max_si.blsampleid
+                    LEFT JOIN blsubsample ss3 ON max_si.max_blsampleimageid = ss3.blsampleimageid AND ss3.source = 'auto'
+                    LEFT OUTER JOIN containerqueuesample cqs3 ON cqs3.blsubsampleid = ss3.blsubsampleid
+                    LEFT OUTER JOIN containerqueue cq3 ON cq3.containerqueueid = cqs3.containerqueueid
+                    WHERE s3.containerid = c.containerid
+                ) AS queuedautosubsamples,
+                (SELECT COUNT(DISTINCT CASE WHEN cq3.completedtimestamp IS NOT NULL THEN ss3.blsubsampleid ELSE NULL END)
+                    FROM blsample s3
+                    LEFT JOIN (
+                        SELECT si.blsampleid, MAX(si.blsampleimageid) AS max_blsampleimageid
+                        FROM blsampleimage si
+                        GROUP BY si.blsampleid
+                    ) AS max_si ON s3.blsampleid = max_si.blsampleid
+                    LEFT JOIN blsubsample ss3 ON max_si.max_blsampleimageid = ss3.blsampleimageid AND ss3.source = 'auto'
+                    LEFT OUTER JOIN containerqueuesample cqs3 ON cqs3.blsubsampleid = ss3.blsubsampleid
+                    LEFT OUTER JOIN containerqueue cq3 ON cq3.containerqueueid = cqs3.containerqueueid
+                    WHERE s3.containerid = c.containerid
+                ) AS completedautosubsamples,
+                (SELECT COUNT(DISTINCT CASE WHEN cqs3.containerqueuesampleid IS NULL THEN ss3.blsubsampleid ELSE NULL END)
+                    FROM blsample s3
+                    LEFT JOIN (
+                        SELECT si.blsampleid, MAX(si.blsampleimageid) AS max_blsampleimageid
+                        FROM blsampleimage si
+                        GROUP BY si.blsampleid
+                    ) AS max_si ON s3.blsampleid = max_si.blsampleid
+                    LEFT JOIN blsubsample ss3 ON max_si.max_blsampleimageid = ss3.blsampleimageid AND ss3.source = 'auto'
+                    LEFT OUTER JOIN containerqueuesample cqs3 ON cqs3.blsubsampleid = ss3.blsubsampleid
+                    WHERE s3.containerid = c.containerid
+                ) AS availableautosubsamples,";
+
 
         if ($this->has_arg('ty')) {
+            if ($this->arg('ty') != 'puck') {
+                $subsamples = $manualsubsamples . $autosubsamples;
+            }
             if ($this->arg('ty') == 'plate') {
                 $where .= " AND c.containertype NOT LIKE '%puck'";
             } else if ($this->arg('ty') == 'puck') {
@@ -2120,7 +2185,7 @@ function _get_all_containers()
             } else if ($this->arg('ty') == 'processing') {
                 $where .= " AND c.containerstatus = 'processing'";
             } else if ($this->arg('ty') == 'subsamples') {
-                $having .= " HAVING subsamples > 0";
+                $having .= " HAVING queuedmanualsubsamples+completedmanualsubsamples+availablemanualsubsamples > 0";
                 $subsamplesInTotal = ", count(distinct ss.blsubsampleid) as subsamples";
                 $totalQuery->joinClause("LEFT OUTER JOIN blsample s ON s.containerid = c.containerid");
                 $totalQuery->joinClause("LEFT OUTER JOIN blsubsample ss ON s.blsampleid = ss.blsampleid AND ss.source='manual'");
@@ -2180,16 +2245,18 @@ function _get_all_containers()
         }
 
         if ($this->has_arg('imager')) {
-            if ($this->arg('imager') == '1')
+            if ($this->arg('imager') == '1') {
                 $where .= ' AND c.imagerid IS NOT NULL';
-            else
+                $subsamples = $manualsubsamples . $autosubsamples;
+            } else
                 $where .= ' AND c.imagerid IS NULL AND c.requestedimagerid IS NULL';
         }
 
 
         if ($this->has_arg('iid')) {
             $where .= ' AND c.imagerid=:' . (sizeof($args) + 1);
             array_push($args, $this->arg('iid'));
+            $subsamples = $manualsubsamples . $autosubsamples;
         }
 
         if ($this->has_arg('CONTAINERREGISTRYID')) {
@@ -2202,22 +2269,30 @@ function _get_all_containers()
             array_push($args, $this->user->personId);
         }
 
-        $tot = $this->db->pq("SELECT count(distinct c.containerid) as tot 
-                $subsamplesInTotal
+        if ($this->has_arg('s')) {
+            $totalQuery->joinClause("INNER JOIN dewar d ON d.dewarid = c.dewarid");
+            $totalQuery->joinClause("INNER JOIN shipping sh ON sh.shippingid = d.shippingid");
+            $totalQuery->joinClause("INNER JOIN proposal p ON p.proposalid = sh.proposalid");
+            $searchfields = array('c.code', 'c.barcode', 'd.code', 'sh.shippingname', 'c.containertype', 'concat(p.proposalcode, p.proposalnumber)');
+            $conditions = array();
+            foreach ($searchfields as $sf) {
+                $st = sizeof($args) + 1;
+                array_push($conditions, $sf." LIKE CONCAT('%', :".$st.", '%')");
+                array_push($args, $this->arg('s'));
+            }
+            $where .= " AND (" . implode(" OR ", $conditions) . ")";
+        }
+
+        $tot = $this->db->pq("SELECT COUNT(*) as tot FROM
+                (SELECT $manualsubsamples
+                c.containerid
                 FROM container c 
                 {$totalQuery->getJoins()}
                 WHERE $where
-                $having", $args);
+                group by c.containerid
+                $having) as result", $args);
         $tot = sizeof($tot) ? intval($tot[0]['TOT']) : 0;
 
-        if ($this->has_arg('s')) {
-            $st = sizeof($args) + 1;
-            $where .= " AND (lower(c.code) LIKE lower(CONCAT(CONCAT('%',:" . $st . "), '%')) OR lower(c.barcode) LIKE lower(CONCAT(CONCAT('%',:" . ($st + 1) . "), '%')))";
-            array_push($args, $this->arg('s'));
-            array_push($args, $this->arg('s'));
-        }
-
-
         $pp = $this->has_arg('per_page') ? $this->arg('per_page') : 15;
         $pg = $this->has_arg('page') ? $this->arg('page') - 1 : 0;
         $start = $pg * $pp;
@@ -2242,9 +2317,13 @@ function _get_all_containers()
 
         if ($this->has_arg('sort_by')) {
             $cols = array(
-                'NAME' => 'c.code', 'DEWAR' => 'd.code', 'SHIPMENT' => 'sh.shippingname', 'SAMPLES' => 'count(s.blsampleid)', 'SHIPPINGID' => 'sh.shippingid', 'LASTINSPECTION' => 'max(ci.bltimestamp)', 'INSPECTIONS' => 'count(ci.containerinspectionid)',
+                'NAME' => 'c.code', 'DEWAR' => 'd.code', 'SHIPMENT' => 'sh.shippingname', 'SAMPLES' => 'count(distinct s.blsampleid)',
+                'SHIPPINGID' => 'sh.shippingid', 'LASTINSPECTION' => 'max(ci.bltimestamp)', 'INSPECTIONS' => 'count(distinct ci.containerinspectionid)',
                 'DCCOUNT' => 'COUNT(distinct dc.datacollectionid)', 'SUBSAMPLES' => 'subsamples',
-                'LASTQUEUECOMPLETED' => 'max(cq2.completedtimestamp)', 'QUEUEDTIMESTAMP' => 'max(cq.createdtimestamp)'
+                'LASTQUEUECOMPLETED' => 'max(cq2.completedtimestamp)', 'QUEUEDTIMESTAMP' => 'max(cq.createdtimestamp)',
+                'CONTAINERTYPE' => 'c.containertype', 'CONTAINERSTATUS' => 'c.containerstatus', 'LASTINSPECTIONDAYS' => 'lastinspectiondays',
+                'AGE' => 'age', 'VISIT' => 'visit', 'REQUESTEDIMAGER' => 'requestedimager', 'IMAGER' => 'imager',
+                'MANUAL' => 'queuedmanualsubsamples', 'AUTO' => 'queuedautosubsamples',
             );
             $dir = $this->has_arg('order') ? ($this->arg('order') == 'asc' ? 'ASC' : 'DESC') : 'ASC';
             if (array_key_exists($this->arg('sort_by'), $cols))
@@ -2256,6 +2335,7 @@ function _get_all_containers()
                 (SELECT sch.name FROM schedule sch WHERE sch.scheduleid = c.scheduleid) as schedule,
                 (SELECT i2.name FROM imager i2 WHERE i2.imagerid = c.requestedimagerid) as requestedimager,
                 (SELECT count(distinct ss.blsubsampleid) FROM blsubsample ss RIGHT OUTER JOIN blsample s2 ON s2.blsampleid = ss.blsampleid WHERE s2.containerid = c.containerid AND ss.source='manual') as subsamples,
+                $subsamples
                 (SELECT ses3.beamlinename FROM blsession ses3 WHERE d.firstexperimentid = ses3.sessionid) as firstexperimentbeamline,
                 (SELECT pp.name FROM processingpipeline pp WHERE c.prioritypipelineid = pp.processingpipelineid) as pipeline,
                 TO_CHAR(max(cq2.completedtimestamp), 'HH24:MI DD-MM-YYYY') as lastqueuecompleted, TIMESTAMPDIFF('MINUTE', max(cq2.completedtimestamp), max(cq2.createdtimestamp)) as lastqueuedwell,
diff --git a/client/src/js/modules/imaging/views/admin/dashboard.js b/client/src/js/modules/imaging/views/admin/dashboard.js
@@ -127,7 +127,7 @@ define(['marionette',
             this.ty = new FilterView({ collection: this.inspections, filters: filters, mobile: true, url: false, name: 'ty' })
             this.insf.show(this.ty)
 
-            this.ctrs.show(new ContainersView({ collection: this.containers, params: {}, barcode: true }))
+            this.ctrs.show(new ContainersView({ collection: this.containers, params: {}, imager: true }))
         },
         
     })
diff --git a/client/src/js/modules/shipment/views/containers.js b/client/src/js/modules/shipment/views/containers.js
@@ -48,9 +48,30 @@ define(['marionette',
         cookie: true,
     })
     
+    var CustomHeaderCell = Backgrid.HeaderCell.extend({
+        render: function() {
+            // Allow HTML in the column header
+            this.$el.html(this.column.get("label"));
+            return this;
+        }
+    });
+
+    var highlightQueued = function(data, auto) {
+        const queued = auto ? data.QUEUEDAUTOSUBSAMPLES : data.QUEUEDMANUALSUBSAMPLES;
+        const completed = auto ? data.COMPLETEDAUTOSUBSAMPLES : data.COMPLETEDMANUALSUBSAMPLES;
+        const available = auto ? data.AVAILABLEAUTOSUBSAMPLES : data.AVAILABLEMANUALSUBSAMPLES;
+        return (queued > 0 ? '<span class="minor">'+queued+'</span>' : queued)+' / '+completed+' / '+available;
+    }
+
+    var queuedCompleted = function(data) {
+        if (data.LASTQUEUECOMPLETED) { return data.LASTQUEUECOMPLETED }
+        if (data.CONTAINERQUEUEID) { return 'Queued' }
+        return null
+    }
+
     return Marionette.LayoutView.extend({
         className: 'content',
-        template: '<div><h1>Containers</h1><div class="filter type"></div><div class="filter"><ul><li><label><input type="checkbox" name="currentuser" /> My Containers</label></li></ul></div><div class="wrapper"></div></div>',
+        template: '<div><h1>Containers</h1><div class="filter"><span class="type"></span><span><ul><li><label><input type="checkbox" name="currentuser" /> My Containers</label></li></ul></span></div><div class="wrapper"></div></div>',
         regions: { wrap: '.wrapper', type: '.type' },
         
         ui: {
@@ -61,18 +82,19 @@ define(['marionette',
             'change @ui.cur': 'refresh'
         },
 
-        hiddenColumns: [1,2,5,6,9,10,11],
+        hiddenColumns: [1,2,5,6,7,10,11,12],
 
         columns: [
             { name: 'NAME', label: 'Name', cell: 'string', editable: false },
             { name: 'DEWAR', label: 'Dewar', cell: 'string', editable: false },
             { name: 'BARCODE', label: 'Barcode', cell: 'string', editable: false },
             { name: 'SHIPMENT', label: 'Shipment', cell: 'string', editable: false },
             { name: 'SAMPLES', label: '# Samples', cell: 'string', editable: false },
-            { name: 'SUBSAMPLES', label: '# Subsamples', cell: 'string', editable: false },
+            { name: 'MANUAL', label: '<button>Manual Subsamples<br>Queued / Complete / Avail</button>', cell: table.TemplateCell, template: d=>highlightQueued(d,false), editable: false, headerCell: CustomHeaderCell },
+            { name: 'AUTO', label: '<button>Auto Subsamples<br>Queued / Complete / Avail</button>', cell: table.TemplateCell, template: d=>highlightQueued(d,true), editable: false, headerCell: CustomHeaderCell },
             { name: 'CONTAINERTYPE', label: 'Type', cell: 'string', editable: false },
             { name: 'CONTAINERSTATUS', label: 'Status', cell: 'string', editable: false },
-            { name: 'LASTQUEUECOMPLETED', label: 'Completed', cell: 'string', editable: false },
+            { name: 'LASTQUEUECOMPLETED', label: 'Completed', cell: table.TemplateCell, template: queuedCompleted, editable: false },
             { name: 'INSPECTIONS', label: 'Inspections', cell: 'string', editable: false },
             { name: 'LASTINSPECTIONDAYS', label: 'Last (d)', cell: 'string', editable: false },
             { name: 'AGE', label: 'Age (d)', cell: 'string', editable: false },
@@ -86,7 +108,7 @@ define(['marionette',
             { id: 'queued', name: 'Queued'},
             { id: 'completed', name: 'Completed'},
             { id: 'processing', name: 'Processing'},
-            { id: 'subsamples', name: 'Has Subsamples'},
+            { id: 'subsamples', name: 'Has Manual Subsamples'},
         ],
 
         showImaging: true,
@@ -100,7 +122,9 @@ define(['marionette',
         },
 
         initialize: function(options) {
-            var filters = this.getOption('filters').slice(0)
+            this.imager = options.imager
+            // dont show Plates/Pucks/In Imager filters if in imager mode
+            var filters = this.getOption('filters').slice(this.imager ? 3 : 0)
             var columns = this.getOption('columns').slice(0)
             if (app.user_can('disp_cont') && !app.mobile() && this.getOption('showImaging')) {
                 columns.push({ name: 'VISIT', label: 'Visit', cell: 'string', editable: false })
@@ -111,12 +135,6 @@ define(['marionette',
                 filters.push({ id: 'todispose', name: 'To Dispose'})
             }
 
-            columns[2].renderable = false
-            if (options.barcode) {
-                columns[1].renderable = false
-                columns[2].renderable = true
-            }
-
             if (app.mobile()) {
                 _.each(this.getOption('hiddenColumns'), function(v) {
                     columns[v].renderable = false
@@ -141,12 +159,16 @@ define(['marionette',
         },
 
         updateCols: function(selected) {
-            var isPuck = (selected == null || selected == 'puck')
+            var isPuck = !this.imager && (selected === null || selected === 'puck')
 
             var dew = this.table.grid.columns.findWhere({ name: 'DEWAR' })
             var bc = this.table.grid.columns.findWhere({ name: 'BARCODE' })
+            var manual = this.table.grid.columns.findWhere({ name: 'MANUAL' })
+            var auto = this.table.grid.columns.findWhere({ name: 'AUTO' })
             dew.set('renderable', isPuck)
             bc.set('renderable', !isPuck)
+            if (manual) manual.set('renderable', !isPuck)
+            if (auto) auto.set('renderable', !isPuck)
         },
                                           
         onRender: function() {
@@ -158,4 +180,4 @@ define(['marionette',
         }
     })
 
-})
+})
