LIMS-1458: Fix GitHub warnings (#841)

* LIMS-1458: Do not access attributes directly. Use set() and get() instead * LIMS-1458: Move function declaration to function body root * LIMS-1458: Do not access attributes directly. Use set() and get() instead * LIMS-1458: Unnecessary escape character * LIMS-1458: Empty block statement, Unnecessary semicolon * LIMS-1458: variable is already defined * LIMS-1458: variable is already defined * LIMS-1458: Do sorting on the server * Update client/src/js/modules/dc/views/reprocess2.js Co-authored-by: Guilherme Francisco <[email protected]> --------- Co-authored-by: Mark Williams <[email protected]> Co-authored-by: Guilherme Francisco <[email protected]>
DiamondLightSource · Dec 3, 2024 · 72c4ca6 · 72c4ca6
1 parent 6e51851
commit 72c4ca6
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Showing 27 changed files with 101 additions and 98 deletions.
diff --git a/api/src/Page/Cell.php b/api/src/Page/Cell.php
@@ -274,8 +274,8 @@ function _beamlines()
         $pdb = $this->db->pq("SELECT TO_CHAR(p.pdbdate, 'YYYY') as year, $replace as bl, count(p.pdbentryid) as count
                 FROM pdbentry p
                 WHERE p.pdbdate > TO_DATE('2010-05', 'YYYY-MM')
-                GROUP BY $replace, TO_CHAR(p.pdbdate, 'YYYY')
-                ORDER BY TO_CHAR(p.pdbdate, 'YYYY')");
+                GROUP BY bl, year
+                ORDER BY year, bl");
 
         $isp = $this->db->pq("SELECT TO_CHAR(p.pdbdate, 'YYYY') as year, CASE WHEN p.autoprocprogramid > 0 THEN UPPER(s.beamlinename) ELSE $replace END as bl, count(p.pdbentryid) as count
                 FROM pdbentry p
@@ -284,8 +284,8 @@ function _beamlines()
                 INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid
                 INNER JOIN blsession s ON s.sessionid = dcg.sessionid
                 WHERE p.pdbdate > TO_DATE('2010-05', 'YYYY-MM')
-                GROUP BY CASE WHEN p.autoprocprogramid > 0 THEN UPPER(s.beamlinename) ELSE $replace END, TO_CHAR(p.pdbdate, 'YYYY')
-                ORDER BY TO_CHAR(p.pdbdate, 'YYYY')");
+                GROUP BY bl, year
+                ORDER BY year, bl");
 
         foreach ($pdb as $i => &$s) {
             $s['COUNT'] = intval(($s['COUNT']));

diff --git a/client/src/js/models/protein.js b/client/src/js/models/protein.js
@@ -16,7 +16,7 @@ define(['backbone', 'markdown'], function(Backbone, markdown) {
         },
 
         refreshOptions: function() {
-            if (this.get('SEQUENCE')) this.attributes.SEQUENCEMD = markdown.toHTML(this.get('SEQUENCE'))
+            if (this.get('SEQUENCE')) this.set('SEQUENCEMD', markdown.toHTML(this.get('SEQUENCE')))
         },
 
         validation: {

diff --git a/client/src/js/models/visit.js b/client/src/js/models/visit.js
@@ -51,10 +51,10 @@ define(['backbone', 'backbone-validation', 'luxon'], function(Backbone, BackBone
     addDate: function() {
         var { DateTime } = luxon
 
-        this.attributes.ENISO = DateTime.fromISO(this.get('ENISO'), { zone: this.dateTimeZone })
-        this.attributes.STISO = DateTime.fromISO(this.get('STISO'), { zone: this.dateTimeZone })
-        this.attributes.LEN = Number(this.attributes.ENISO.diff(this.attributes.STISO)/(3600*1000)).toFixed(2);
-        this.attributes.VISITDETAIL = this.get('VISIT')+' ('+this.get('BL')+': '+this.get('ST')+')'
+        this.set('ENISO', DateTime.fromISO(this.get('ENISO'), { zone: this.dateTimeZone }))
+        this.set('STISO', DateTime.fromISO(this.get('STISO'), { zone: this.dateTimeZone }))
+        this.set('LEN', Number(this.get('ENISO').diff(this.get('STISO'))/(3600*1000)).toFixed(2))
+        this.set('VISITDETAIL', this.get('VISIT')+' ('+this.get('BL')+': '+this.get('ST')+')')
     },
 
     dateTimeZone: 'Europe/London'

diff --git a/client/src/js/modules/cell/views/beamlines.js b/client/src/js/modules/cell/views/beamlines.js
@@ -30,28 +30,27 @@ define(['marionette', 'utils',
                 })
 
                 var bl = []
+                var data = {}
                 _.each(bls, function(i, b) {
+                    data[b] = {}
                     bl.push(b)
                     ticks.push([bl.length-1, b])
+                    _.each(years, function(x, y) {
+                        data[b][y] = 0
+                    })
                 })
 
-                  _.each(this.model.get('data')[did], function(v, i) {
-                      var y = yrs.indexOf(v.YEAR)
-                      var b = bl.indexOf(v.BL)
-                      //console.log('d', y, b)
-                      d[y].data.push([b, v.COUNT])
-                  })
-
-                  function ascsort(a,b) {
-                      if (a[0] == b[0]) return 0
-                      else return (a[0] < b[0]) ? -1 : 1
-                  }
-
-                  _.each(d, function(d,i) {
-                      d.data.sort(ascsort)
-                  })
+                _.each(this.model.get('data')[did], function(v, i) {
+                    data[v.BL][v.YEAR] = v.COUNT
+                })
 
-                  console.log(d)
+                _.each(data, function(el, beamline) {
+                    _.each(el, function(count, year) {
+                        var y = yrs.indexOf(year)
+                        var b = bl.indexOf(beamline)
+                        d[y].data.push([b, count])
+                    })
+                })
 
                 var options = {
                     series: {

diff --git a/client/src/js/modules/dc/models/autointegration.js b/client/src/js/modules/dc/models/autointegration.js
@@ -13,13 +13,13 @@ define(['backbone'], function(Backbone){
             var shells = this.get('SHELLS')
             if (!shells) return
 
-            this.attributes.CLASS = { RMERGE: {}, RMEAS: {}, COMPLETENESS: {} }
+            this.set('CLASS', { RMERGE: {}, RMEAS: {}, COMPLETENESS: {} })
             _.each(['overall', 'innerShell', 'outerShell'], function(k) {
                 var c = shells[k] ? shells[k].COMPLETENESS : null
-                this.attributes.CLASS.COMPLETENESS[k] = c > 95 ? 'active' : (c > 80 ? 'minor' : 'inactive')
+                this.set('CLASS[COMPLETENESS[k]]', c > 95 ? 'active' : (c > 80 ? 'minor' : 'inactive'))
 
                 var r = shells[k] ? shells[k].RMEAS : null
-                this.attributes.CLASS.RMEAS[k] = r < 0.5 ? 'active' : (r < 0.6 ? 'minor' : 'inactive')
+                this.set('CLASS[RMEAS[k]]', r < 0.5 ? 'active' : (r < 0.6 ? 'minor' : 'inactive'))
             }, this)
         },
 

diff --git a/client/src/js/modules/dc/models/dccomment.js b/client/src/js/modules/dc/models/dccomment.js
@@ -27,11 +27,11 @@ define(['backbone', 'markdown'], function(Backbone, markdown) {
     },
 
     addDate: function() {
-        this.attributes.CREATETIMEISO = new Date(this.get('CREATETIME'))
-        this.attributes.MODTIMEISO = new Date(this.get('MODTIME'))
-        if (this.get('COMMENTS')) this.attributes.COMMENTSMD = markdown.toHTML(this.get('COMMENTS'))
+        this.set('CREATETIMEISO', new Date(this.get('CREATETIME')))
+        this.set('MODTIMEISO', new Date(this.get('MODTIME')))
+        if (this.get('COMMENTS')) this.set('COMMENTSMD', markdown.toHTML(this.get('COMMENTS')))
     }
 
   })
 
-})
+})
diff --git a/client/src/js/modules/dc/views/reprocess2.js b/client/src/js/modules/dc/views/reprocess2.js
@@ -162,8 +162,8 @@ define(['backbone', 'marionette', 'views/dialog',
             if (e) e.preventDefault()
 
             if (this.aps.length) {
-                var e = this.aps.at(0)
-                var c = e.get('CELL')
+                const a = this.aps.at(0)
+                const c = a.get('CELL')
 
                 this.ui.a.val(c['CELL_A']).trigger('change')
                 this.ui.b.val(c['CELL_B']).trigger('change')
@@ -172,7 +172,7 @@ 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(e['SG']).trigger('change')
+                this.ui.sg.val(a['SG']).trigger('change')
             }
         },
 
@@ -300,11 +300,11 @@ define(['backbone', 'marionette', 'views/dialog',
             }
 
             var self = this
+            var reqs = []
             // Integrate individually
             if (this.ui.ind.is(':checked')) {
                 var jobs = 0
 
-                var reqs = []
                 var rps = []
                 _.each(s, function(sw) {
                     var p = this.pipelines.findWhere({ VALUE: sw.get('PIPELINE') })
@@ -405,7 +405,6 @@ define(['backbone', 'marionette', 'views/dialog',
                     return
                 }
 
-                var reqs = []
                 reqs.push(reprocessing.save({}, {
                     success: function() {
                         var reprocessingparams = new ReprocessingParameters()

diff --git a/client/src/js/modules/dc/views/reprocessoverview.js b/client/src/js/modules/dc/views/reprocessoverview.js
@@ -53,29 +53,29 @@ define(['marionette',
             },
 
             render: function() {
-                var columns = [
+                var pcolumns = [
                    { name: 'PARAMETERKEY', label: 'Key', cell: 'string', editable: false },
                    { name: 'PARAMETERVALUE', label: 'Value', cell: 'string', editable: false },
                 ]
 
                 var ptable = new TableView({ 
                     collection: this.params, 
-                    columns: columns, 
+                    columns: pcolumns,
                     loading: false,
                     pages: false,
                     backgrid: { emptyText: 'No parameters found' },
                 })
 
                 this.$el.html(ptable.render().$el)
 
-                var columns = [
+                var scolumns = [
                    { label: 'Files', cell: table.TemplateCell, editable: false, template: '<a href="/dc/visit/<%-VISIT%>/id/<%-DATACOLLECTIONID%>"><%-IMAGEDIRECTORY%><%-IMAGEPREFIX%>_<%-DATACOLLECTIONNUMBER%></a>' },
                    { label: 'Image #', cell: table.TemplateCell, editable: false, template: '<%-STARTIMAGE%> - <%-ENDIMAGE%>' },
                 ]
 
                 var stable = new TableView({ 
                     collection: this.sweeps, 
-                    columns: columns, 
+                    columns: scolumns,
                     loading: false,
                     pages: false,
                     backgrid: { emptyText: 'No image sweeps found' },

diff --git a/client/src/js/modules/dc/views/samplechanger.js b/client/src/js/modules/dc/views/samplechanger.js
@@ -162,11 +162,11 @@ define(['marionette', 'utils/canvas', 'utils',
             // Draw Grid
             this.ctx.clearRect(0, 0, this.canvas.width, this.canvas.height)
             //this.ctx.drawImage(this.numbers, 0, 0, this.canvas.width, this.canvas.height)
-            for (var j = 0; j < this.sc; j++) {
+            for (var n = 0; n < this.sc; n++) {
                 this.ctx.fillStyle = '#000'
                 this.ctx.font = "11px Arial"
                 this.ctx.lineWidth = 1
-                this.ctx.fillText(j+1,10,this.sh*j+this.tpad+4);
+                this.ctx.fillText(n+1,10,this.sh*n+this.tpad+4);
             }
 
             for (var i = 0; i < this.positions; i++) {

diff --git a/client/src/js/modules/fault/models/component.js b/client/src/js/modules/fault/models/component.js
@@ -8,15 +8,15 @@ define(['backbone'], function(Backbone) {
         },
         initialize: function(options) {
             this.on('change', this._add_id, this)
-              this._add_id()
+            this._add_id()
         },
         urlRoot: '/fault/com',
         idAttribute: 'COMPONENTID',
 
         _add_id: function() {
-            this.attributes.ID = this.get('COMPONENTID')
+            this.set('ID', this.get('COMPONENTID'))
         },
 
     })
 
-})
+})
diff --git a/client/src/js/modules/fault/models/fault.js b/client/src/js/modules/fault/models/fault.js
@@ -22,11 +22,11 @@ define(['backbone', 'markdown', 'models/wfile'], function(Backbone, markdown, Fi
         },
 
         refreshOptions: function() {
-            this.attributes.RESOLVEDTEXT = this.resolvedOptions[this.get('RESOLVED')]
-            this.attributes.BEAMTIMELOSTTEXT = this.btlOptions[this.get('BEAMTIMELOST')]
+            this.set('RESOLVEDTEXT', this.resolvedOptions[this.get('RESOLVED')])
+            this.set('BEAMTIMELOSTTEXT', this.btlOptions[this.get('BEAMTIMELOST')])
 
-            if (this.get('DESCRIPTION')) this.attributes.DESCRIPTIONMD = markdown.toHTML(this.get('DESCRIPTION'))
-            if (this.get('RESOLUTION')) this.attributes.RESOLUTIONMD = markdown.toHTML(this.get('RESOLUTION'))
+            if (this.get('DESCRIPTION')) this.set('DESCRIPTIONMD', markdown.toHTML(this.get('DESCRIPTION')))
+            if (this.get('RESOLUTION')) this.set('RESOLUTIONMD', markdown.toHTML(this.get('RESOLUTION')))
         },
 
         validation: {

diff --git a/client/src/js/modules/fault/models/subcomponent.js b/client/src/js/modules/fault/models/subcomponent.js
@@ -8,12 +8,12 @@ define(['backbone'], function(Backbone) {
         },
         initialize: function(options) {
             this.on('change', this._add_id, this)
-              this._add_id()
+            this._add_id()
         },
         urlRoot: '/fault/scom',
         idAttribute: 'SUBCOMPONENTID',
         _add_id: function() {
-            this.attributes.ID = this.get('SUBCOMPONENTID')
+            this.set('ID', this.get('SUBCOMPONENTID'))
         },
     })
-})
+})
diff --git a/client/src/js/modules/fault/models/system.js b/client/src/js/modules/fault/models/system.js
@@ -13,8 +13,8 @@ define(['backbone'], function(Backbone) {
         urlRoot: '/fault/sys',
         idAttribute: 'SYSTEMID',
         _add_id: function() {
-            this.attributes.ID = this.get('SYSTEMID')
+            this.set('ID', this.get('SYSTEMID'))
         },
     })
 
-})
+})
diff --git a/client/src/js/modules/imaging/views/queuecontainer.js b/client/src/js/modules/imaging/views/queuecontainer.js
@@ -692,10 +692,11 @@ define(['marionette',
         },
 
         applyModel: function(modelParameter, isLimitedToSelected) {
+            var models = null
             if (isLimitedToSelected) {
-                var models = this.qsubsamples.where({ isGridSelected: true })
+                models = this.qsubsamples.where({ isGridSelected: true })
             } else {
-                var models = this.qsubsamples.fullCollection.toArray()
+                models = this.qsubsamples.fullCollection.toArray()
             }
             _.each(models, function(model) {
                 if (modelParameter.get('EXPERIMENTKIND') !== model.get('EXPERIMENTKIND')) return

diff --git a/client/src/js/modules/shipment/models/containerreport.js b/client/src/js/modules/shipment/models/containerreport.js
@@ -14,7 +14,7 @@ define(['backbone', 'markdown', 'models/wfile'], function(Backbone, markdown, Fi
         },
 
         refreshOptions: function() {
-            if (this.get('REPORT')) this.attributes.REPORTMD = markdown.toHTML(this.get('REPORT'))
+            if (this.get('REPORT')) this.set('REPORTMD', markdown.toHTML(this.get('REPORT')))
         },
 
         validation: {

diff --git a/client/src/js/modules/shipment/models/dewarreport.js b/client/src/js/modules/shipment/models/dewarreport.js
@@ -14,7 +14,7 @@ define(['backbone', 'markdown', 'models/wfile'], function(Backbone, markdown, Fi
         },
 
         refreshOptions: function() {
-            if (this.get('REPORT')) this.attributes.REPORTMD = markdown.toHTML(this.get('REPORT'))
+            if (this.get('REPORT')) this.set('REPORTMD', markdown.toHTML(this.get('REPORT')))
         },
 
         validation: {
@@ -37,4 +37,4 @@ define(['backbone', 'markdown', 'models/wfile'], function(Backbone, markdown, Fi
             }
         }
     }, File))
-})
+})
diff --git a/client/src/js/modules/shipment/views/containerregistry.js b/client/src/js/modules/shipment/views/containerregistry.js
@@ -116,7 +116,7 @@ define(['marionette',
                 this.listenTo(this.proposals, 'backgrid:selected', this.selectModel, this)
                 this.proposals.fetch()
 
-                var columns = [
+                var columns2 = [
                     { label: '', cell: 'select-row', headerCell: 'select-all', editable: false },
                     { name: 'PROPOSALCODE', label: 'Code', cell: 'string', editable: false },
                     { name: 'PROPOSALNUMBER', label: 'Number', cell: 'string', editable: false },
@@ -126,7 +126,7 @@ define(['marionette',
 
                 this.table2 = new TableView({
                     collection: this.proposals,
-                    columns: columns, tableClass: 'proposals', filter: 's', search: options.params.s, loading: true, noPageUrl: true, noSearchUrl: true,
+                    columns: columns2, tableClass: 'proposals', filter: 's', search: options.params.s, loading: true, noPageUrl: true, noSearchUrl: true,
                     backgrid: { emptyText: 'No proposals found' } 
                 })
 
@@ -175,4 +175,4 @@ define(['marionette',
         }
     })
 
-})
+})
diff --git a/client/src/js/modules/shipment/views/manifest.js b/client/src/js/modules/shipment/views/manifest.js
@@ -57,14 +57,14 @@ define(['marionette',
             var d = new Date()
             _.each([d.getFullYear(), d.getFullYear()-1], function(y) {
                 _.each(_.range(1,13), function(m) {
-                    var m = (m < 10 ? ('0'+m) : m)+'-'+y
+                    m = (m < 10 ? ('0'+m) : m)+'-'+y
                     this.ui.month.append('<option value="'+m+'">'+m+'</option>')
                 }, this)
             }, this)
 
 
-            var m = d.getMonth() +1
-            var cur = (m < 10 ? ('0'+m) : m)+'-'+d.getFullYear()
+            var mon = d.getMonth() +1
+            var cur = (mon < 10 ? ('0'+mon) : mon)+'-'+d.getFullYear()
             this.ui.month.val(cur)
 
             var columns = [
@@ -95,4 +95,4 @@ define(['marionette',
 
     })
 
-})
+})