Merge pre-release/2024-R3.1 into master (#797)

* LIMS-595: Change Sample Changers/Containers/Stage to Pucks for i15/i15-1 (xpdf) (#579) * LIMS-67: Fix 2 slow queries on imaging admin dashboard (#751) * LIMS-1334: Allow selection of plate samples already in a group (#778) * LIMS-1246: Allow users with all_dewars permission to view all shipments (#752) * LIMS-1351: Switch to simpler arrows (#787) * LIMS-1343: Interface changes based on reviewer suggestions from Conexs paper (#783) * LIMS-1170: Dont use thumbnails for crystal snapshots (#784)
DiamondLightSource · Jul 3, 2024 · da53c52 · da53c52
1 parent a968b04
commit da53c52
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Showing 42 changed files with 181 additions and 151 deletions.
diff --git a/api/src/Page.php b/api/src/Page.php
@@ -366,6 +366,9 @@ function auth($require_staff)
                     {
                         if (sizeof(array_intersect($vis, $this->visits)))
                             $auth = True;
+                        if ($this->user->hasPermission('all_dewars'))
+                            // allow to see anything without an id or a visit
+                            $auth = True;
                     }
 
                     // No id or visit, anyone ok to view

diff --git a/api/src/Page/DC.php b/api/src/Page/DC.php
@@ -1082,14 +1082,8 @@ function _chk_image()
             $images = array();
             foreach (array('X1', 'X2', 'X3', 'X4') as $j => $im) {
                 array_push($images, file_exists($dc[$im]) ? 1 : 0);
-                if ($im == 'X1') {
-                    $ext = pathinfo($dc[$im], PATHINFO_EXTENSION);
-                    $thumb = str_replace('.' . $ext, 't.' . $ext, $dc[$im]);
-                    if ($this->staff && $this->has_arg('debug'))
-                        $debug['snapshot_thumb'] = array('file' => $thumb, 'exists' => file_exists($thumb) ? 1 : 0);
-                    if (file_exists($thumb))
-                        $sn = 1;
-                }
+                if ($im == 'X1' && file_exists($dc[$im]))
+                    $sn = 1;
                 unset($dc[$im]);
             }
 

diff --git a/api/src/Page/Image.php b/api/src/Page/Image.php
@@ -22,13 +22,13 @@ class Image extends Page
             'thresh' => '\d',
         );
 
-        public static $dispatch = array(array('/id/:id(/f/:f)(/n/:n)', 'get', '_xtal_image'),
+        public static $dispatch = array(array('/id/:id(/n/:n)', 'get', '_xtal_image'),
                               array('/diff/id/:id(/f/:f)(/n/:n)', 'get', '_diffraction_image'),
                               array('/di/id/:id(/thresh/:thresh)(/n/:n)', 'get', '_diffraction_viewer'),
                               array('/cam/bl/:bl(/n/:n)', 'get', '_forward_webcam'),
                               array('/oav/bl/:bl(/n/:n)', 'get', '_forward_oav'),
                               array('/fa/fid/:id', 'get', '_fault_attachment'),
-                              array('/ai/visit/:visit/aid/:aid(/n/:n)(/f/:f)', 'get', '_action_image'),
+                              array('/ai/visit/:visit/aid/:aid(/n/:n)', 'get', '_action_image'),
                               array('/dr/:drid', 'get', '_dewar_report_image'),
                               array('/cr/:crid', 'get', '_container_report_image'),
                             );
@@ -121,8 +121,6 @@ function _action_image() {
                 INNER JOIN proposal p ON s.proposalid = p.proposalid 
                 WHERE r.robotactionid=:1 AND CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) LIKE :2", array($this->arg('aid'), $this->arg('visit')));
 
-            //print_r($image);
-
             if (!sizeof($image)) return;
             else $image = $image[0];
 
@@ -133,10 +131,9 @@ function _action_image() {
             if ($n < sizeof($images)) {
                 $this->_browser_cache();
                 $ext = pathinfo($images[$n], PATHINFO_EXTENSION);
-                $file = $this->has_arg('f') ? $images[$n] : str_replace('.'.$ext, 't.'.$ext, $images[$n]);
-                if (file_exists($file)) {
+                if (file_exists($images[$n])) {
                     $this->app->contentType('image/'.$ext);
-                    readfile($file);
+                    readfile($images[$n]);
                 } else {
                     $this->_error('Not found', 'That image is no longer available');
                 }
@@ -161,11 +158,10 @@ function _xtal_image() {
             if ($n < sizeof($images)) {
                 $ext = pathinfo($images[$n], PATHINFO_EXTENSION);
 
-                $file = $this->has_arg('f') ? $images[$n] : str_replace('.'.$ext, 't.'.$ext, $images[$n]);
-                if (file_exists($file)) {
+                if (file_exists($images[$n])) {
                     $this->_browser_cache();
                     $this->app->contentType('image/'.$ext);
-                    readfile($file);
+                    readfile($images[$n]);
 
                 } else {
                     $this->_error('Not found', 'That image is no longer available');

diff --git a/api/src/Page/Imaging.php b/api/src/Page/Imaging.php
@@ -407,8 +407,15 @@ function _get_inspections()
                 'STATE' => 'i.state',
                 'SCHEDULECOMPONENTID' => 'i.schedulecomponentid',
                 'MANUAL' => 'i.manual',
-                'IMAGESSCORED' => 'imagesscored',
                 'CONTAINER' => 'c.code',
+                'CONTAINERID' => 'i.containerid',
+                'PROP' => 'prop',
+                'VISIT_NUMBER' => 'ses.visit_number',
+                'CONTAINERINSPECTIONID' => 'i.containerinspectionid',
+                'INSPECTIONTYPE' => 'inspectiontype',
+                'DURATION' => 'duration',
+                'DWELL' => 'dwell',
+                'AGE' => 'age',
             );
             $dir = $this->has_arg('order') ? ($this->arg('order') == 'asc' ? 'ASC' : 'DESC') : 'ASC';
             if (array_key_exists($this->arg('sort_by'), $cols))
@@ -439,11 +446,30 @@ function _get_inspections()
             $extc = ", ROUND(TIMESTAMPDIFF('MINUTE', min(i2.bltimestamp), i.bltimestamp)/(60*24),1) as delta, CONCAT(CONCAT(CONCAT(CONCAT(TO_CHAR(i.bltimestamp, 'HH24:MI DD-MM-YYYY'), ' (+'), ROUND(TIMESTAMPDIFF('HOUR', case when min(i2.bltimestamp) is not null then min(i2.bltimestamp) else i.bltimestamp end, i.bltimestamp)/24,1)), 'd) '), (case when i.manual=1 then '[Manual]' else (case when i.schedulecomponentid is null then '[Adhoc]' else '' end) end)) as title";
         }
 
-        $inspections = $this->db->paginate("SELECT ROUND(TIMESTAMPDIFF('HOUR', i.bltimestamp, CURRENT_TIMESTAMP)/24,1) as age, ROUND(TIMESTAMPDIFF('MINUTE', i.scheduledtimestamp, i.bltimestamp)/(24*60),2) as dwell, c.code as container, CONCAT(p.proposalcode, p.proposalnumber) as prop, TO_CHAR(min(im.modifiedtimestamp), 'DD-MM-YYYY HH24:MI') as imagesscoredtimestamp, case when count(im.blsampleimageid) > 0 then 1 else 0 end as imagesscored,
-                TO_CHAR(i.scheduledtimestamp, 'DD-MM-YYYY HH24:MI') as scheduledtimestamp, sc.offset_hours, i.priority, i.state, i.schedulecomponentid, i.manual, img.name as imager, it.name as inspectiontype, i.containerinspectionid, i.containerid, i.inspectiontypeid, i.temperature, TO_CHAR(i.bltimestamp, 'DD-MM-YYYY HH24:MI') as bltimestamp, i.imagerid, CONCAT(p.proposalcode, p.proposalnumber, '-', ses.visit_number) as visit, ses.visit_number, TIMESTAMPDIFF('MINUTE', i.bltimestamp, i.completedtimestamp) as duration $extc
+        $inspections = $this->db->paginate("SELECT ROUND(TIMESTAMPDIFF('HOUR', i.bltimestamp, CURRENT_TIMESTAMP)/24,1) as age,
+                ROUND(TIMESTAMPDIFF('MINUTE', i.scheduledtimestamp, i.bltimestamp)/(24*60),2) as dwell,
+                c.code as container,
+                CONCAT(p.proposalcode, p.proposalnumber) as prop,
+                TO_CHAR(i.scheduledtimestamp, 'DD-MM-YYYY HH24:MI') as scheduledtimestamp,
+                sc.offset_hours,
+                i.priority,
+                i.state,
+                i.schedulecomponentid,
+                i.manual,
+                img.name as imager,
+                it.name as inspectiontype,
+                i.containerinspectionid,
+                i.containerid,
+                i.inspectiontypeid,
+                i.temperature,
+                TO_CHAR(i.bltimestamp, 'DD-MM-YYYY HH24:MI') as bltimestamp,
+                i.imagerid,
+                CONCAT(p.proposalcode, p.proposalnumber, '-', ses.visit_number) as visit,
+                ses.visit_number,
+                TIMESTAMPDIFF('MINUTE', i.bltimestamp, i.completedtimestamp) as duration
+                $extc
                 FROM containerinspection i
                 LEFT OUTER JOIN schedulecomponent sc ON sc.schedulecomponentid = i.schedulecomponentid
-                LEFT OUTER JOIN blsampleimage im ON im.containerinspectionid = i.containerinspectionid AND im.blsampleimagescoreid IS NOT NULL
                 INNER JOIN inspectiontype it ON it.inspectiontypeid = i.inspectiontypeid
                 INNER JOIN container c ON c.containerid = i.containerid
                 LEFT OUTER JOIN imager img ON img.imagerid = i.imagerid
@@ -456,6 +482,13 @@ function _get_inspections()
                 GROUP BY i.containerinspectionid
                 ORDER BY $order", $args);
 
+        foreach ($inspections as &$i) {
+            $args = array($i['CONTAINERINSPECTIONID']);
+            $scored = $this->db->pq("SELECT case when count(im.blsampleimageid) > 0 then 1 else 0 end as imagesscored
+                FROM blsampleimage im
+                WHERE im.containerinspectionid=:1 AND im.blsampleimagescoreid IS NOT NULL", $args);
+            $i['IMAGESSCORED'] = $scored[0]['IMAGESSCORED'];
+        }
 
         if ($this->has_arg('iid')) {
             if (!sizeof($inspections))

diff --git a/api/src/Page/Proposal.php b/api/src/Page/Proposal.php
@@ -170,6 +170,8 @@ function _get_proposals($id = null)
                 $where .= " AND (shp.personid=:" . (sizeof($args) + 1) . " OR s.beamlinename in ('" . implode("','", $bls) . "'))";
                 array_push($args, $this->user->personId);
             }
+        } else if ($this->user->hasPermission('all_dewars')) {
+            // allow to see shipments on all proposals
         } else {
             $where = " INNER JOIN session_has_person shp ON shp.sessionid = s.sessionid  " . $where;
             $where .= " AND shp.personid=:" . (sizeof($args) + 1);
@@ -921,6 +923,8 @@ function _lookup()
 
                 $where .= " AND ses.beamlinename in ('" . implode("','", $bls) . "')";
             }
+        } else if ($field == 'SHIPPINGID' && $this->user->hasPermission('all_dewars')) {
+            // allow to see shipments
         } else {
             $where = " INNER JOIN session_has_person shp ON shp.sessionid = ses.sessionid  " . $where;
             $where .= " AND shp.personid=:" . (sizeof($args) + 1);

diff --git a/api/src/Page/Shipment.php b/api/src/Page/Shipment.php
@@ -1973,7 +1973,7 @@ function _get_all_containers()
         array_push($args, $start);
         array_push($args, $end);
 
-        $order = 'c.bltimestamp DESC';
+        $order = 'c.containerid DESC';
 
         if ($this->has_arg('ty')) {
             if ($this->arg('ty') == 'todispose') {

diff --git a/client/src/js/app/components/header.vue b/client/src/js/app/components/header.vue
@@ -50,7 +50,6 @@
       </router-link>
     </div>
     <div
-      v-if="isStaff"
       class="tw-flex"
     >
       <!-- Only show those links with correct permission -->

diff --git a/client/src/js/modules/assign/views/assign.js b/client/src/js/modules/assign/views/assign.js
@@ -301,6 +301,7 @@ define(['marionette', 'backbone', 'views/pages',
         templateHelpers: function() {
             return {
                 VISIT: this.getOption('visit').toJSON(),
+                APP_TYPE: app.type,
             }
         },
 

diff --git a/client/src/js/modules/assign/views/selectvisit.js b/client/src/js/modules/assign/views/selectvisit.js
@@ -19,7 +19,13 @@ define(['marionette', 'templates/assign/selectvisit.html'], function(Marionette,
         className: 'content',
         childView: VisitView,
         childViewContainer: 'ul.visits',
-        emptyView: EmptyView
+        emptyView: EmptyView,
+
+        templateHelpers: function() {
+            return {
+                APP_TYPE: app.type,
+            }
+        },
 
     })
 

diff --git a/client/src/js/modules/dc/views/gridplot.js b/client/src/js/modules/dc/views/gridplot.js
@@ -158,9 +158,9 @@ define(['jquery', 'marionette',
                     opts.push('<option value='+i+'>Image '+i+'</option>')
                     if (i === 1) {
                         // show button to view image full size
-                        this.ui.sns.append('<a class="button" href="'+app.apiurl+'/image/id/'+this.getOption('ID')+'/f/1/n/'+i+'"><i class="fa fa-arrows"></a>')
+                        this.ui.sns.append('<a class="button" href="'+app.apiurl+'/image/id/'+this.getOption('ID')+'/n/'+i+'"><i class="fa fa-arrows"></a>')
                     } else {
-                        this.ui.sns.append('<a class="hidden" href="'+app.apiurl+'/image/id/'+this.getOption('ID')+'/f/1/n/'+i+'"></a>')
+                        this.ui.sns.append('<a class="hidden" href="'+app.apiurl+'/image/id/'+this.getOption('ID')+'/n/'+i+'"></a>')
                     }
                 }
             }
@@ -171,7 +171,7 @@ define(['jquery', 'marionette',
 
         loadImage: function() {
             var n = this.ui.ty3.val()
-            this.snapshot.load(app.apiurl+'/image/id/'+this.getOption('ID')+'/f/1/n/'+n)
+            this.snapshot.load(app.apiurl+'/image/id/'+this.getOption('ID')+'/n/'+n)
         },
 
         toggleFluo: function() {
@@ -270,7 +270,7 @@ define(['jquery', 'marionette',
                 if (m.get('SNS')[this.getOption('snapshotId')] && !this.hasSnapshot) {
                     this.snapshotLoading = true
                     this.$el.addClass('loading')
-                    this.snapshot.load(app.apiurl+'/image/id/'+this.getOption('ID')+'/f/1')
+                    this.snapshot.load(app.apiurl+'/image/id/'+this.getOption('ID'))
                 }
             }
         },

diff --git a/client/src/js/modules/dc/views/imagestatusitem.js b/client/src/js/modules/dc/views/imagestatusitem.js
@@ -69,7 +69,7 @@ define(['marionette',
                 var sns = ''
                 for (var i = 1; i < this.model.get('SNS').length; i++) {
                     if (this.model.get('SNS')[i]) {
-                        sns += ('<a href="'+app.apiurl+'/image/id/'+id+'/f/1/n/'+(i+1)+'" title="Crystal Snapshot '+(i+1)+'"></a>')
+                        sns += ('<a href="'+app.apiurl+'/image/id/'+id+'/n/'+(i+1)+'" title="Crystal Snapshot '+(i+1)+'"></a>')
                     }
                 }
 
@@ -91,4 +91,4 @@ define(['marionette',
         },
     })
 
-})
+})
diff --git a/client/src/js/modules/samples/components/sample-group-create-and-edit.vue b/client/src/js/modules/samples/components/sample-group-create-and-edit.vue
@@ -71,6 +71,7 @@
             v-else-if="selectedContainerType.NAME && selectedContainerType.NAME.toLowerCase() !== 'puck'"
             :container-type="selectedContainerType"
             :valid-samples="validSamples"
+            :manually-selected-samples="manuallySelectedSamples"
             :container-identifier="selectedContainerName"
             color-attribute="VALID"
             added-color-attribute="ADDED"
@@ -218,11 +219,14 @@ export default {
     validSamples() {
       if (this.selectedContainerId) {
         const selectedContainer = this.selectedSamplesInGroups[this.selectedContainerId] || []
-        const difference = differenceBy(selectedContainer, this.selectedContainerAddedSamples, 'BLSAMPLEID')
-        return [...this.selectedContainerAddedSamples, ...difference]
+        const uniqueSelectedContainer = uniqBy(selectedContainer.concat(this.selectedContainerAddedSamples), 'BLSAMPLEID')
+        return uniqueSelectedContainer
       }
 
       return []
+    },
+    manuallySelectedSamples() {
+      return this.selectedSamplesInGroups[this.selectedContainerId] || []
     }
   },
   created: function () {

diff --git a/client/src/js/modules/shipment/components/plate-view.vue b/client/src/js/modules/shipment/components/plate-view.vue
@@ -76,6 +76,10 @@ export default {
       type: Array,
       default: () => ([])
     },
+    manuallySelectedSamples: {
+      type: Array,
+      default: () => ([])
+    },
     addedColorAttribute: {
       type: String,
       default: ''
@@ -425,7 +429,7 @@ export default {
         }
       }
       else {
-        if (this.selectedDrops.includes(itemsWithSample[0])) {
+        if (this.manuallySelectedSamples.some(e => Number(e.LOCATION) === itemsWithSample[0])) {
           this.$emit('unselect-cell', itemsWithSample)
           this.currentSelectedDropIndex = -1
         }
@@ -625,4 +629,4 @@ export default {
 .pointer {
   cursor: pointer
 }
-</style>
+</style>
diff --git a/client/src/js/modules/shipment/views/shipment.js b/client/src/js/modules/shipment/views/shipment.js
@@ -146,26 +146,32 @@ define(['marionette',
 
         showDewar: function(did, force) {
             if (did == this.lastDewarID && !force) return
-
             this.$el.find('.dewar_name').text(this.dewars.findWhere({ DEWARID: did }).get('CODE'))
-            if (app.proposal && app.proposal.get('ACTIVE') == '1') this.$el.find('.add_container').html('<a class="button" data-testid="shipment-add-container" href="/containers/add/did/'+did+'"><i class="fa fa-plus"></i> Add Container</a>')
+            if (app.proposal && app.proposal.get('ACTIVE') == '1') {
+                if (app.type == "xpdf"){
+                    this.$el.find('.add_container').html('<a class="button" data-testid="shipment-add-container" href="/containers/add/did/'+did+'"><i class="fa fa-plus"></i> Add Puck</a>')
+                    this.$el.find('.add-container-small').prop('title', 'Click to add a puck')
+                    this.$el.find('.add-container-text').text('Add Puck')
+                } else {
+                    this.$el.find('.add_container').html('<a class="button" data-testid="shipment-add-container" href="/containers/add/did/'+did+'"><i class="fa fa-plus"></i> Add Container</a>')
+                }
+            }
             this.dewarcontent.dewarID = did
             this.dewarcontent.fetch()
             this.dewarhistory.id = did
             this.dewarhistory.fetch()
 
             var d = this.dewars.findWhere({ DEWARID: did })
-            if (d && (d.get('TRACKINGNUMBERTOSYNCHROTRON') || d.get('TRACKINGNUMBERTOSYNCHROTRON'))) {
+            if (d && (d.get('TRACKINGNUMBERTOSYNCHROTRON') || d.get('TRACKINGNUMBERFROMSYNCHROTRON'))) {
                 this.dewartracking.queryParams.DEWARID = did
                 this.dewartracking.fetch()
 
             } else {
                 this.dewartracking.ORIGIN = 'N/A'
                 this.dewartracking.DESTINATION = 'N/A'
                 this.dewartracking.reset()
-
-            this.lastDewarID = did
             }
+            this.lastDewarID = did
         },
 
         refreshDewar: function() {