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LIMS-1550: Add 'Mark Dispensing' button to plate well view #869

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LIMS-1550: Add 'Mark Dispensing' button to plate well view #869

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0b7e49b
LIMS-1550: Add 'Mark Dispensing' button to plate well view
Nov 29, 2024
5dafe3b
LIMS-1550: Dont throw an error if no subsamples exist
Nov 29, 2024
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40 changes: 36 additions & 4 deletions api/src/Page/Sample.php
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Original file line number Diff line number Diff line change
Expand Up @@ -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+)?',
Expand Down Expand Up @@ -792,6 +792,9 @@ private function get_sub_samples_query($where, $first_inner_select_where = '', $
po2.posx as x2,
po2.posy as y2,
po2.posz as z2,
po3.posx as dispensex,
po3.posy as dispensey,
po3.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,
Expand All @@ -817,7 +820,7 @@ 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 position po3 ON po3.positionid = s.positionid
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

Expand Down Expand Up @@ -1895,7 +1898,7 @@ 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,b.positionid
FROM blsample b
INNER JOIN crystal cr ON cr.crystalid = b.crystalid
INNER JOIN protein pr ON pr.proteinid = cr.proteinid
Expand Down Expand Up @@ -1972,6 +1975,35 @@ function _update_sample()
}
}
}

if ($this->has_arg('X') && $this->has_arg('Y')) {
$z = $this->has_arg('Z') ? $this->arg('Z') : null;
$pid = $samp['POSITIONID'];
if ($this->arg('X') == '' && $this->arg('Y') == '') {
if (!empty($pid)) {
$this->db->pq(
"UPDATE position SET posx=null, posy=null, posz=null, recordtimestamp=CURRENT_TIMESTAMP WHERE positionid=:1",
array($pid)
);
}
} else {
if (empty($pid)) {
$this->db->pq(
"INSERT INTO position (positionid, posx, posy, posz, recordtimestamp)
VALUES (s_position.nextval, :1, :2, :3, CURRENT_TIMESTAMP) RETURNING positionid INTO :id",
array($this->arg('X'), $this->arg('Y'), $z)
);
$pid = $this->db->id();
$this->db->pq("UPDATE blsample SET positionid=:1 WHERE blsampleid=:2", array($pid, $samp['BLSAMPLEID']));
} else {
$this->db->pq(
"UPDATE position SET posx=:1, posy=:2, posz=:3, recordtimestamp=CURRENT_TIMESTAMP WHERE positionid=:4",
array($this->arg('X'), $this->arg('Y'), $z, $pid)
);
}
}
$this->_output(array('POSITIONID' => $pid));
}
}


Expand Down
20 changes: 19 additions & 1 deletion client/src/js/models/sample.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -98,7 +104,10 @@ define(['backbone', 'collections/components',
VOLUME: '',
INITIALSAMPLEGROUP: '',
COMPONENTIDS: [],
COMPONENTAMOUNTS: []
COMPONENTAMOUNTS: [],
X: null,
Y: null,
Z: null,
},

validation: {
Expand Down Expand Up @@ -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')
Expand Down
36 changes: 34 additions & 2 deletions client/src/js/modules/imaging/views/imageviewer.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ define(['marionette',
'backbone',
'modules/imaging/collections/inspectionimagescores',

'models/sample',
'models/subsample',
'collections/subsamples',

Expand All @@ -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) {

Expand Down Expand Up @@ -175,6 +176,10 @@ define(['marionette',
},
})
}

if (this.add_dispensing) {
this.editDispensing(x, y)
}
},

setAddSubsample: function(state) {
Expand All @@ -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()
Expand All @@ -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)
Expand Down Expand Up @@ -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) {
Expand Down
47 changes: 46 additions & 1 deletion client/src/js/modules/shipment/views/containerplate.js
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Original file line number Diff line number Diff line change
Expand Up @@ -243,6 +243,8 @@ 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',
Expand Down Expand Up @@ -272,6 +274,8 @@ 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',
Expand Down Expand Up @@ -488,8 +492,12 @@ define(['marionette',
}

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.addis.find('span').text('Mark Dispensing')
this.ui.deldis.hide()
},


Expand All @@ -508,8 +516,43 @@ define(['marionette',
}

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.addis.find('span').text('Mark Dispensing')
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.deldis.hide()

} else {
this.ui.addis.addClass('button-highlight')
this.image.setAddDispensing(true)
this.ui.addis.find('span').text('Cancel')
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.adr.find('span').text('Mark Region')
},

deleteDispensing: function(e) {
e.preventDefault()
this.image.deleteDispensing()
},


Expand Down Expand Up @@ -539,7 +582,7 @@ define(['marionette',
var i = this.inspectionimages.at(n)
if (this.caching && i) {
var xhr = new XHRImage()
console.log('caching', i.urlFor('hd'))
//console.log('caching', i.urlFor('hd'))
xhr.load(i.urlFor('full'), function() {
self.plateView.drawPlate()

Expand Down Expand Up @@ -890,12 +933,14 @@ 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 }))
Expand Down
2 changes: 2 additions & 0 deletions client/src/js/templates/shipment/containerplateimage.html
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,8 @@ <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>
Expand Down
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