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LIMS-1537: Add more options to reprocessing #876

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LIMS-1537: Add more options to reprocessing #876

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c84e503
LIMS-1536: Add more options to reprocessing
Dec 9, 2024
1a38020
Merge branch 'master' into improvement/LIMS-1537/add-more-options-for…
ndg63276 Jan 9, 2025
8171b0e
LIMS-1537: Fix colour on successful submission
Jan 14, 2025
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43 changes: 40 additions & 3 deletions client/src/js/modules/dc/views/reprocess2.js
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,8 @@ define(['backbone', 'marionette', 'views/dialog',
ind: 'div.ind',
pipeline: 'select[name=pipeline]',
res: 'input[name=res]',
sg: 'select[name=SG]'
lowres: 'input[name=lowres]',
sg: 'input[name=SG]'
},

events: {
Expand All @@ -71,13 +72,18 @@ define(['backbone', 'marionette', 'views/dialog',

'change @ui.pipeline': 'updatePipeline',
'change @ui.res': 'updateRes',
'change @ui.lowres': 'updateLowRes',
},


updateRes: function() {
this.model.set('RES', this.ui.res.val())
},

updateLowRes: function() {
this.model.set('LOWRES', this.ui.lowres.val())
},

updatePipeline: function() {
this.model.set('PIPELINE', this.ui.pipeline.val())
},
Expand Down Expand Up @@ -139,6 +145,7 @@ define(['backbone', 'marionette', 'views/dialog',
this.ui.ind.hide()
this.$el.find('ul').addClass('half')
this.$el.find('li input[type="text"]').css('width', '25%')
this.$el.find('div input[type="text"]').css('width', '50px')
this.ui.pipeline.html(this.getOption('pipelines').opts())
this.model.set('PIPELINE', this.ui.pipeline.val())
},
Expand Down Expand Up @@ -172,7 +179,7 @@ define(['backbone', 'marionette', 'views/dialog',
this.ui.be.val(c['CELL_BE']).trigger('change')
this.ui.ga.val(c['CELL_GA']).trigger('change')

this.ui.sg.val(a['SG']).trigger('change')
this.ui.sg.val(a.get('SG')).trigger('change')
}
},

Expand Down Expand Up @@ -213,6 +220,12 @@ define(['backbone', 'marionette', 'views/dialog',
}, KVCollection))


var AbsorptionLevels = Backbone.Collection.extend(_.extend({
keyAttribute: 'NAME',
valueAttribute: 'VALUE',
}, KVCollection))


return ReprocessView = DialogView.extend({
template: template,
dialog: true,
Expand All @@ -233,6 +246,7 @@ define(['backbone', 'marionette', 'views/dialog',
sg: 'select[name=sg]',
sm: 'input[name=sm]',
indexingMethod: 'select[name=method]',
absorptionLevel: 'select[name=absorption_level]',
},

buttons: {
Expand Down Expand Up @@ -287,7 +301,7 @@ define(['backbone', 'marionette', 'views/dialog',
},

xia2params: function() {
return ['cc_half', 'isigma', 'misigma', 'sigma_strong', 'method']
return ['cc_half', 'isigma', 'misigma', 'sigma_strong', 'method', 'absorption_level']
},

integrate: function(e) {
Expand Down Expand Up @@ -327,6 +341,12 @@ define(['backbone', 'marionette', 'views/dialog',
PARAMETERVALUE: sw.get('RES')
}))

if (sw.get('LOWRES')) reprocessingparams.add(new ReprocessingParameter({
PROCESSINGJOBID: reprocessing.get('PROCESSINGJOBID'),
PARAMETERKEY: 'd_max',
PARAMETERVALUE: sw.get('LOWRES')
}))

var hascell = true
var cell = []
_.each(['CELL_A', 'CELL_B', 'CELL_C', 'CELL_ALPHA', 'CELL_BETA', 'CELL_GAMMA'], function(f, i) {
Expand Down Expand Up @@ -416,6 +436,13 @@ define(['backbone', 'marionette', 'views/dialog',
PARAMETERVALUE: res
}))

var lowres = self.$el.find('input[name=lowres]').val()
if (lowres) reprocessingparams.add(new ReprocessingParameter({
PROCESSINGJOBID: reprocessing.get('PROCESSINGJOBID'),
PARAMETERKEY: 'd_max',
PARAMETERVALUE: lowres
}))

var hascell = true
var cell = []
_.each(['a', 'b', 'c', 'alpha', 'beta', 'gamma'], function(f, i) {
Expand Down Expand Up @@ -505,6 +532,7 @@ define(['backbone', 'marionette', 'views/dialog',
onRender: function() {
this.ui.opts.hide()
this.ui.cell.hide()
this.$el.find('span input[type="text"]').css('width', '50px')

this.pipelines = new Pipelines([
{ NAME: 'Xia2 DIALS', VALUE: 'xia2-dials' },
Expand All @@ -524,6 +552,15 @@ define(['backbone', 'marionette', 'views/dialog',

this.ui.indexingMethod.html(this.indexingMethods.opts())

this.absorptionLevels = new AbsorptionLevels([
{ NAME: '-', VALUE: '' },
{ NAME: 'Low', VALUE: 'low' },
{ NAME: 'Medium', VALUE: 'medium' },
{ NAME: 'High', VALUE: 'high' },
])

this.ui.absorptionLevel.html(this.absorptionLevels.opts())

// asynchronously load space groups into the select menu
this.showSpaceGroups()

Expand Down
27 changes: 25 additions & 2 deletions client/src/js/modules/mc/views/datacollections.js
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,12 @@ define(['backbone', 'marionette',
}, KVCollection))


var AbsorptionLevels = Backbone.Collection.extend(_.extend({
keyAttribute: 'NAME',
valueAttribute: 'VALUE',
}, KVCollection))


return Marionette.LayoutView.extend({
className: 'content',
template: template,
Expand All @@ -63,6 +69,7 @@ define(['backbone', 'marionette',
wait: '.wait',
pipeline: 'select[name=pipeline]',
indexingMethod: 'select[name=method]',
absorptionLevel: 'select[name=absorption_level]',
opts: 'div.options',
sm: 'input[name=sm]',
sg: 'select[name=sg]',
Expand Down Expand Up @@ -94,7 +101,7 @@ define(['backbone', 'marionette',
},

xia2params: function() {
return ['cc_half', 'isigma', 'misigma', 'sigma_strong', 'method']
return ['cc_half', 'isigma', 'misigma', 'sigma_strong', 'method', 'absorption_level']
},

integrate: function(e) {
Expand Down Expand Up @@ -127,6 +134,13 @@ define(['backbone', 'marionette',
PARAMETERVALUE: res
}))

var lowres = self.$el.find('input[name=lowres]').val()
if (lowres) reprocessingparams.add(new ReprocessingParameter({
PROCESSINGJOBID: reprocessing.get('PROCESSINGJOBID'),
PARAMETERKEY: 'd_max',
PARAMETERVALUE: lowres
}))

var hascell = true
var cell = []
_.each(['a', 'b', 'c', 'alpha', 'beta', 'gamma'], function(f, i) {
Expand Down Expand Up @@ -179,7 +193,7 @@ define(['backbone', 'marionette',
var reprocessingsweeps = new ReprocessingImageSweeps(sweeps)
reprocessingsweeps.save()

app.alert({ message: '1 reprocessing job successfully submitted'})
app.message({ message: '1 reprocessing job successfully submitted'})
self._enqueue({ PROCESSINGJOBID: reprocessing.get('PROCESSINGJOBID') })
},

Expand Down Expand Up @@ -252,6 +266,15 @@ define(['backbone', 'marionette',
])

this.ui.indexingMethod.html(this.indexingMethods.opts())

this.absorptionLevels = new AbsorptionLevels([
{ NAME: '-', VALUE: '' },
{ NAME: 'Low', VALUE: 'low' },
{ NAME: 'Medium', VALUE: 'medium' },
{ NAME: 'High', VALUE: 'high' },
])

this.ui.absorptionLevel.html(this.absorptionLevels.opts())
},

setCell: function(view, ap) {
Expand Down
5 changes: 4 additions & 1 deletion client/src/js/templates/dc/reprocess.html
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@
<span class="multi form">
|
Pipeline :<select name="pipeline"></select>
High Res :<input type="text" name="res" /> &#197; |
High Res :<input type="text" name="res" /> &#197;
Low Res :<input type="text" name="lowres" /> &#197; |
<a href="#" class="button sgm">Space Group / Cell</a>
<!-- Comments: <input type="text" name="comments" class="full" /> -->
</span>
Expand All @@ -36,7 +37,9 @@
<label>Unmerged &lt;I/sigI&gt; :<input type="text" name="isigma" /></label>
<label>Merged &lt;I/sigI&gt; :<input type="text" name="misigma" /></label>
<label>Spot Finding Threshold :<input type="text" name="sigma_strong" /></label>
<br /><br />
<label>Indexing Method: <select name="method"></select></label>
<label>Absorption Level: <select name="absorption_level"></select></label>
</div>


Expand Down
3 changes: 2 additions & 1 deletion client/src/js/templates/dc/reprocess_dc.html
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,8 @@ <h1 class="clearfix">

<div class="ind data_collection">
Pipeline <select name="pipeline"></select>
High Res <input type="text" name="res" /> &#197; |
High Res <input type="text" name="res" /> &#197;
Low Res <input type="text" name="lowres" /> &#197; |
<a href="#" class="button sg">Space Group / Cell</a> <br />
</div>

Expand Down
4 changes: 3 additions & 1 deletion client/src/js/templates/mc/datacollections.html
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,8 @@ <h1>Data Collections for <%-VISIT%></h1>
<label>&beta; <input type="text" name="beta" /></label>
<label>&gamma; <input type="text" name="gamma" /></label>

<label>High Resolution <input type="text" name="res" /></label>
<label>High Res <input type="text" name="res" /> &#197;</label>
<label>Low Res <input type="text" name="lowres" /> &#197;</label>

<a href="#" class="button integrate" title="Integrate the selected data collections"><i class="fa fa-cog"></i> Integrate</a>
<a href="#" class="button opt">Xia2 Options</a>
Expand All @@ -41,6 +42,7 @@ <h1>Data Collections for <%-VISIT%></h1>
<label>Merged &lt;I/sigI&gt; :<input type="text" name="misigma" /></label>
<label>Spot Finding Threshold :<input type="text" name="sigma_strong" /></label>
<label>Indexing Method: <select name="method"></select></label>
<label>Absorption Level: <select name="absorption_level"></select></label>
</div>

<div class="dcs"></div>
Expand Down
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