LIMS-1550: Add 'Mark Dispensing' button to plate well view

api/src/Database/Type/MySQL.php

@@ -75,6 +75,7 @@ class MySQL extends DatabaseParent {
         'DewarReport',
         'CourierTermsAccepted',
 
+        'BLSamplePosition',
         'BLSubSample',
         'PDB',
         'Protein_has_PDB',

api/src/Page/Sample.php

@@ -93,8 +93,8 @@ class Sample extends Page
         'scid' => '\d+-\d+',
 
         'BLSAMPLEID' => '\d+',
-        'X' => '\d+(.\d+)?',
-        'Y' => '\d+(.\d+)?',
+        'X' => '\d*(.\d+)?',
+        'Y' => '\d*(.\d+)?',
         'Z' => '\d+(.\d+)?',
         'X2' => '\d+(.\d+)?',
         'Y2' => '\d+(.\d+)?',
@@ -799,6 +799,9 @@ private function get_sub_samples_query($where, $first_inner_select_where = '', $
                 po2.posx as x2,
                 po2.posy as y2,
                 po2.posz as z2,
+                bsp.posx as dispensex,
+                bsp.posy as dispensey,
+                bsp.posz as dispensez,
                 IF(cqs.containerqueuesampleid IS NOT NULL AND cqs.containerqueueid IS NULL, 1, 0) as readyforqueue,
                 cq.containerqueueid,
                 count(distinct IF(dc.overlap != 0,
@@ -824,7 +827,7 @@ private function get_sub_samples_query($where, $first_inner_select_where = '', $
                 INNER JOIN shipping sh ON sh.shippingid = d.shippingid
                 INNER JOIN proposal p ON p.proposalid = sh.proposalid
 
-
+                LEFT OUTER JOIN blsampleposition bsp ON bsp.blsampleid = s.blsampleid
                 LEFT OUTER JOIN containerqueuesample cqs ON cqs.blsubsampleid = ss.blsubsampleid
                 LEFT OUTER JOIN containerqueue cq ON cqs.containerqueueid = cq.containerqueueid AND cq.completedtimestamp IS NULL
 
@@ -1903,11 +1906,12 @@ function _update_sample()
         if (!$this->has_arg('sid'))
             $this->_error('No sampleid specified');
 
-        $samp = $this->db->pq("SELECT b.blsampleid, pr.proteinid,cr.crystalid,dp.diffractionplanid 
+        $samp = $this->db->pq("SELECT b.blsampleid, pr.proteinid,cr.crystalid,dp.diffractionplanid,bsp.blsamplepositionid
               FROM blsample b 
               INNER JOIN crystal cr ON cr.crystalid = b.crystalid 
               INNER JOIN protein pr ON pr.proteinid = cr.proteinid 
               LEFT OUTER JOIN diffractionplan dp on dp.diffractionplanid = b.diffractionplanid 
+              LEFT OUTER JOIN blsampleposition bsp ON bsp.blsampleid = b.blsampleid AND bsp.positiontype='dispensing'
               WHERE pr.proposalid = :1 AND b.blsampleid = :2", array($this->proposalid, $this->arg('sid')));
 
         if (!sizeof($samp))
@@ -1980,6 +1984,34 @@ function _update_sample()
                 }
             }
         }
+
+        if ($this->has_arg('X') && $this->has_arg('Y')) {
+            $z = $this->has_arg('Z') ? $this->arg('Z') : null;
+            $pid = $samp['BLSAMPLEPOSITIONID'];
+            if ($this->arg('X') == '' && $this->arg('Y') == '') {
+                if (!empty($pid)) {
+                    $this->db->pq(
+                        "UPDATE blsampleposition SET posx=null, posy=null, posz=null, recordtimestamp=CURRENT_TIMESTAMP WHERE blsamplepositionid=:1",
+                        array($pid)
+                    );
+                }
+            } else {
+                if (empty($pid)) {
+                    $this->db->pq(
+                        "INSERT INTO blsampleposition (blsampleid, posx, posy, posz, positiontype, recordtimestamp)
+                        VALUES (:1, :2, :3, :4, 'dispensing', CURRENT_TIMESTAMP) RETURNING blsamplepositionid INTO :id",
+                        array($this->arg('sid'), $this->arg('X'), $this->arg('Y'), $z)
+                    );
+                    $pid = $this->db->id();
+                } else {
+                    $this->db->pq(
+                        "UPDATE blsampleposition SET posx=:1, posy=:2, posz=:3, recordtimestamp=CURRENT_TIMESTAMP WHERE blsamplepositionid=:4",
+                        array($this->arg('X'), $this->arg('Y'), $z, $pid)
+                    );
+                }
+            }
+            $this->_output(array('BLSAMPLEPOSITIONID' => $pid));
+        }
     }
 
 

client/src/js/models/sample.js

@@ -18,11 +18,17 @@ define(['backbone', 'collections/components',
             this.listenTo(this, 'change:RADIATIONSENSITIVITY', this.updateRadSen)
             this.updateRadSen()
 
+            this.listenTo(this, 'change:X', this.updatePosition)
+
             this.listenTo(this, 'change', this.updateHasData)
             this.updateHasData()
 
         },
 
+        updatePosition: function() {
+            this.save(this.changedAttributes(), { patch: true })
+        },
+
         updateHasData: function() {
             var hasData = this.get('DC') > 0 || this.get('GR') > 0 || this.get('SC') > 0
             if (hasData !== this.get('HASDATA')) this.set('HASDATA', hasData)
@@ -98,7 +104,10 @@ define(['backbone', 'collections/components',
             VOLUME: '',
             INITIALSAMPLEGROUP: '',
             COMPONENTIDS: [],
-            COMPONENTAMOUNTS: []
+            COMPONENTAMOUNTS: [],
+            X: null,
+            Y: null,
+            Z: null,
         },
 
         validation: {
@@ -225,6 +234,15 @@ define(['backbone', 'collections/components',
                 required: false,
                 pattern: 'word'
             },
+            X: {
+                required: false
+            },
+            Y: {
+                required: false
+            },
+            Z: {
+                required: false
+            },
 
             COMPONENTAMOUNTS: function(from_ui, attr, all_values) {
                 var values = all_values.components.pluck('ABUNDANCE')

client/src/js/modules/imaging/views/imageviewer.js

@@ -2,6 +2,7 @@ define(['marionette',
     'backbone',
     'modules/imaging/collections/inspectionimagescores',
 
+    'models/sample',
     'models/subsample',
     'collections/subsamples',
 
@@ -18,7 +19,7 @@ define(['marionette',
     'backbone-validation',
     ], function(Marionette,
         Backbone,
-        ImageScores, Subsample, Subsamples, ImageHistory, InspectionImage, Attachments,
+        ImageScores, Sample, Subsample, Subsamples, ImageHistory, InspectionImage, Attachments,
         Editable, utils, XHRImage, HeatMap,
         template) {
 
@@ -175,6 +176,10 @@ define(['marionette',
                     },
                 })
             }
+
+            if (this.add_dispensing) {
+                this.editDispensing(x, y)
+            }
         },
 
         setAddSubsample: function(state) {
@@ -184,7 +189,21 @@ define(['marionette',
         setAddSubsampleRegion: function(state) {
             this.add_region = state
         },
-
+
+        setAddDispensing: function(state) {
+            this.add_dispensing = state
+        },
+
+        deleteDispensing: function() {
+            this.editDispensing('', '')
+        },
+
+        editDispensing: function(x, y) {
+            var s = new Sample({ BLSAMPLEID: this.model.get('BLSAMPLEID') })
+            s.set({ X: x, Y: y })
+            this.trigger('finishdispensing')
+            this.subsamples.fetch()
+        },
 
         remSubsample: function() {
             this.draw()
@@ -204,6 +223,7 @@ define(['marionette',
         initialize: function(options) {
             this.add_object = false
             this.add_region = false
+            this.add_dispensing = false
 
             this.plotObjects = _.debounce(this.plotObjects, 200)
             this.drawDebounce = _.debounce(this.draw, 10)
@@ -1004,6 +1024,18 @@ define(['marionette',
             this.ctx.fillStyle = options.o.get('isSelected') ? 'turquoise' : options.o.get('SOURCE') === 'auto' ? 'darkblue' : 'red'
             this.ctx.font = parseInt(14*m)+'px Arial'
             this.ctx.fillText(parseInt(options.o.get('RID'))+1,x-(m*15), y-(m*6))
+
+            if (options.o.get('DISPENSEX') && options.o.get('DISPENSEY')) {
+                var disx = parseInt(options.o.get('DISPENSEX'))
+                var disy = parseInt(options.o.get('DISPENSEY'))
+                this.ctx.strokeStyle = 'white'
+                this.ctx.beginPath()
+                this.ctx.arc(disx, disy, 50, 0, 2*Math.PI)
+                this.ctx.stroke()
+                this.ctx.fillStyle = 'white'
+                this.ctx.fillText('D',disx-5*m, disy+5*m)
+                this.ctx.closePath()
+            }
         },
 
         drawBeam: function(o) {

client/src/js/modules/shipment/views/containerplate.js

@@ -242,6 +242,8 @@ define(['marionette',
             add: '.add_image',
             ads: 'a.add_point',
             adr: 'a.add_region',
+            addis: 'a.add_dispensing',
+            deldis: 'a.del_dispensing',
 
             drop: '.dropimage',
             prog: '.progress',
@@ -275,6 +277,8 @@ define(['marionette',
             'change @ui.ins': 'selectInspection',
             'click @ui.ads': 'setAddSubsamplePoint',
             'click @ui.adr': 'setAddSubsampleRegion',
+            'click @ui.addis': 'setAddDispensing',
+            'click @ui.deldis': 'deleteDispensing',
             'click a.add_inspection': 'showAddInspection',
             'click a.view_sched': 'showViewSchedule',
             'click @ui.play': 'playInspection',
@@ -483,16 +487,24 @@ define(['marionette',
                 this.ui.ads.removeClass('button-highlight')
                 this.image.setAddSubsample(false)
                 this.ui.ads.find('span').text('Mark Point')
+                this.ui.ads.find('i').removeClass('fa-times').addClass('fa-plus')
 
             } else {
                 this.ui.ads.addClass('button-highlight')
                 this.image.setAddSubsample(true)
                 this.ui.ads.find('span').text('Finish')
+                this.ui.ads.find('i').removeClass('fa-plus').addClass('fa-times')
             }
 
             this.ui.adr.removeClass('button-highlight')
+            this.ui.addis.removeClass('button-highlight')
             this.image.setAddSubsampleRegion(false)
+            this.image.setAddDispensing(false)
             this.ui.adr.find('span').text('Mark Region')
+            this.ui.adr.find('i').removeClass('fa-times').addClass('fa-plus')
+            this.ui.addis.find('span').text('Mark Dispensing')
+            this.ui.addis.find('i').removeClass('fa-times').addClass('fa-plus')
+            this.ui.deldis.hide()
         },
 
 
@@ -503,16 +515,59 @@ define(['marionette',
                 this.ui.adr.removeClass('button-highlight')
                 this.image.setAddSubsampleRegion(false)
                 this.ui.adr.find('span').text('Mark Region')
+                this.ui.adr.find('i').removeClass('fa-times').addClass('fa-plus')
 
             } else {
                 this.ui.adr.addClass('button-highlight')
                 this.image.setAddSubsampleRegion(true)
                 this.ui.adr.find('span').text('Finish')
+                this.ui.adr.find('i').removeClass('fa-plus').addClass('fa-times')
             }
 
             this.ui.ads.removeClass('button-highlight')
+            this.ui.addis.removeClass('button-highlight')
             this.image.setAddSubsample(false)
+            this.image.setAddDispensing(false)
             this.ui.ads.find('span').text('Mark Point')
+            this.ui.ads.find('i').removeClass('fa-times').addClass('fa-plus')
+            this.ui.addis.find('span').text('Mark Dispensing')
+            this.ui.addis.find('i').removeClass('fa-times').addClass('fa-plus')
+            this.ui.deldis.hide()
+        },
+
+        setAddDispensing: function(e) {
+            if (e) e.preventDefault()
+
+            if (this.ui.addis.hasClass('button-highlight')) {
+                this.ui.addis.removeClass('button-highlight')
+                this.image.setAddDispensing(false)
+                this.ui.addis.find('span').text('Mark Dispensing')
+                this.ui.addis.find('i').removeClass('fa-times').addClass('fa-plus')
+                this.ui.deldis.hide()
+
+            } else {
+                this.ui.addis.addClass('button-highlight')
+                this.image.setAddDispensing(true)
+                this.ui.addis.find('span').text('Cancel')
+                this.ui.addis.find('i').removeClass('fa-plus').addClass('fa-times')
+                if (this.subsamples.length && this.subsamples.findWhere({ BLSAMPLEID: this.getSample() }).get('DISPENSEX')) {
+                    this.ui.deldis.show()
+                }
+            }
+
+            this.ui.ads.removeClass('button-highlight')
+            this.ui.adr.removeClass('button-highlight')
+            this.image.setAddSubsample(false)
+            this.image.setAddSubsampleRegion(false)
+            this.ui.ads.find('span').text('Mark Point')
+            this.ui.ads.find('i').removeClass('fa-times').addClass('fa-plus')
+            this.ui.adr.find('span').text('Mark Region')
+            this.ui.adr.find('i').removeClass('fa-times').addClass('fa-plus')
+        },
+
+        deleteDispensing: function(e) {
+            e.preventDefault()
+            this.image.deleteDispensing()
         },
 
 
@@ -905,12 +960,14 @@ define(['marionette',
                 this.listenTo(this.image, 'image:prev', this.prevImage, this)
                 this.listenTo(this.image, 'image:first', this.firstImage, this)
                 this.listenTo(this.image, 'image:last', this.lastImage, this)
+                this.listenTo(this.image, 'finishdispensing', this.setAddDispensing, this)
 
                 if (this.getOption('params').iid) this.ui.ins.val(this.getOption('params').iid)
                 this.selectInspection()
 
                 this.ui.prog.hide()
                 this.ui.prog.progressbar({ value: 0 })
+                this.ui.deldis.hide()
 
                 this.img.show(this.image)
                 this.sten.show(new ImageHistoryView({ historyimages: this.startendimages, embed: true }))

client/src/js/templates/shipment/containerplateimage.html

@@ -89,6 +89,8 @@ <h2>Marked Sub Samples</h2>
             <div class="ra">
                 <a href="#" class="button add_point"><i class="fa fa-plus"></i> <span>Mark Point</span></a>
                 <a href="#" class="button add_region"><i class="fa fa-plus"></i> <span>Mark Region</span></a>
+                <a href="#" class="button add_dispensing"><i class="fa fa-plus"></i> <span>Mark Dispensing</span></a>
+                <a href="#" class="button del_dispensing"><i class="fa fa-trash"></i> <span>Delete</span></a>
             </div>
             <div class="subs"></div>
         </div>