LIMS-2233: Add xia2.multiplex reprocessing

api/src/Authentication/Type/OIDC.php

@@ -44,9 +44,9 @@ private function getUser($token)
         global $sso_user_key;
 
         $ch = curl_init();
-        curl_setopt($ch, CURLOPT_URL, $this->getProviderConfig()->userinfo_endpoint);
-        curl_setopt($ch, CURLOPT_HEADER, 0);
-        curl_setopt($ch, CURLOPT_HTTPHEADER, array('Authorization: Bearer ' . $token));
+        curl_setopt($ch, CURLOPT_URL, $this->getProviderConfig()->introspection_endpoint);
+        curl_setopt($ch, CURLOPT_POSTFIELDS, array('token' => $token));
+        curl_setopt($ch, CURLOPT_HTTPHEADER, array('Authorization: Basic ' . $this->getProviderConfig()->b64ClientCreds));
         curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
         $response = curl_exec($ch);
         curl_close($ch);

api/src/Page/Process.php

@@ -12,7 +12,7 @@ class Process extends Page
             'PROCESSINGJOBID' => '\d+',
             'DATACOLLECTIONID' => '\d+',
             'SCALINGID' => '\d+',
-            'DISPLAYNAME' => '([\w\s\-])+',
+            'DISPLAYNAME' => '[\w\s\-.\(\)\=]+',
             'COMMENTS' => '.*',
 
             'PROCESSINGJOBIMAGESWEEPID' => '\d+',

client/src/js/modules/dc/views/autointegration.js

@@ -9,6 +9,7 @@ define(['marionette',
     'modules/dc/views/autoprocattachments',
     'modules/dc/views/apmessages',
     'modules/dc/views/downstreamreprocess',
+    'modules/dc/views/multiplexreprocess.js',
 
     'views/log',
     'views/table',
@@ -17,7 +18,7 @@ define(['marionette',
     'templates/dc/dc_autoproc.html'], function(Marionette, Backbone, Backgrid, TabView,
         AutoProcAttachments, AutoIntegrations, 
         RDPlotView, AIPlotsView, AutoProcAttachmentsView, APMessagesView, 
-        DownstreamView,
+        DownstreamView, MultiplexView,
         LogView, TableView, table,
         utils, template) {
 
@@ -34,6 +35,11 @@ define(['marionette',
             'click a.apattach': 'showAttachments',
             'click a.downstream': 'downstream',
             'click .dll': utils.signHandler,
+            'click @ui.multiplex': 'multiplexReprocessing',
+        },
+
+        ui: {
+            multiplex: '.multiplex',
         },
 
         regions: {
@@ -42,6 +48,15 @@ define(['marionette',
 
         onRender: function() {
             this.messages.show(new APMessagesView({ messages: new Backbone.Collection(this.model.get('MESSAGES')), embed: true }))
+            if (this.model.get('TYPE').toLowerCase().includes('cluster') || !this.model.get('TYPE').toLowerCase().includes('multiplex')) {
+                this.ui.multiplex.hide()
+            }
+        },
+
+        multiplexReprocessing: function(e) {
+            if (e) e.preventDefault()
+            app.dialog.show(new MultiplexView({ model: this.getOption('templateHelpers').PARENT, scalingid: this.model.get('SCALINGID'), type: this.model.get('TYPE')}))
+
         },
 
         showAttachments: function(e) {

client/src/js/modules/dc/views/multiplexreprocess.js

@@ -0,0 +1,213 @@
+define(['backbone', 'marionette', 'views/dialog',
+    'collections/spacegroups',
+    'models/reprocessing',
+    'models/reprocessingparameter',
+    'collections/reprocessingparameters',
+    'utils/kvcollection',
+    'templates/dc/multiplex.html'
+], function(Backbone, Marionette, DialogView,
+        Spacegroups,
+        Reprocessing,
+        ReprocessingParameter,
+        ReprocessingParameters,
+        KVCollection, 
+        template
+        ) {
+
+    const FilteringMethods = Backbone.Collection.extend(_.extend({
+        keyAttribute: 'NAME',
+        valueAttribute: 'VALUE',
+    }, KVCollection))
+
+    return ReprocessView = DialogView.extend({
+        template: template,
+        dialog: true,
+        className: 'rp content',
+        dOptions: {
+            width: '1000px',
+        },
+
+        ui: {
+            fields: 'input, select',
+            sg: 'select[name=sg]',
+            res: 'input[name=res]',
+            opts: 'div.options',
+            filteringMethod: 'select[name=method]',
+            sdcutoff: 'input[name=sdcutoff]',
+            cchalf: 'input[name=cchalf]',
+            groupsize: 'input[name=groupsize]',
+        },
+
+        buttons: {
+            Submit: 'submit',
+            Close: 'closeDialog',
+        },
+
+        events: {
+            'input @ui.fields': 'onFieldChanged',
+            'change @ui.fields': 'onFieldChanged',
+            'click a.opt': 'toggleOpts',
+            'change @ui.cchalf': 'updateCCHalf',
+            'change @ui.filteringMethod': 'updateFilteringMethod',
+        },
+
+        templateHelpers: function() {
+            return {
+                TYPE: this.getOption('type')
+            }
+        },
+
+        toggleOpts: function(e) {
+            e.preventDefault()
+            this.ui.opts.slideToggle()
+        },
+
+        updateCCHalf: function() {
+            const enabled = this.ui.cchalf.is(':checked')
+            if (enabled) {
+                this.ui.filteringMethod.prop('disabled', false).val('image_group')
+                this.ui.sdcutoff.prop('disabled', false)
+                this.ui.groupsize.prop('disabled', false)
+            } else {
+                this.ui.sdcutoff.prop('disabled', true).val('')
+                this.ui.filteringMethod.prop('disabled', true).val('')
+                this.ui.groupsize.prop('disabled', true).val('')
+            }
+        },
+
+        updateFilteringMethod: function() {
+            const val = this.ui.filteringMethod.val()
+            if (val === 'dataset') {
+                this.ui.groupsize.prop('disabled', true).val('')
+            } else {
+                this.ui.groupsize.prop('disabled', false)
+            }
+        },
+
+        submit: async function(e) {
+            e.preventDefault()
+            this._disableSubmitButton()
+            const reprocessing = new Reprocessing({
+                DATACOLLECTIONID: this.model.get('ID'),
+                RECIPE: 'trigger-multiplex',
+                DISPLAYNAME: this.type,
+            })
+
+            try {
+                await reprocessing.save()
+                const jobId = reprocessing.get('PROCESSINGJOBID')
+                const reprocessingparams = new ReprocessingParameters()
+
+                reprocessingparams.add(new ReprocessingParameter({
+                    PROCESSINGJOBID: jobId,
+                    PARAMETERKEY: 'scaling_id',
+                    PARAMETERVALUE: this.scalingid
+                }));
+
+                const res = this.ui.res.val()
+                if (res) reprocessingparams.add(new ReprocessingParameter({
+                    PROCESSINGJOBID: jobId,
+                    PARAMETERKEY: 'd_min',
+                    PARAMETERVALUE: res
+                }))
+
+                const sg = this.ui.sg.val().replace(/\s/g, '')
+                if (sg) reprocessingparams.add(new ReprocessingParameter({
+                    PROCESSINGJOBID: jobId,
+                    PARAMETERKEY: 'spacegroup',
+                    PARAMETERVALUE: sg
+                }))
+
+                const cchalf = this.ui.cchalf.prop('checked')
+                if (cchalf) reprocessingparams.add(new ReprocessingParameter({
+                    PROCESSINGJOBID: jobId,
+                    PARAMETERKEY: 'apply_cchalf_filtering',
+                    PARAMETERVALUE: 1
+                }))
+
+                const method = this.ui.filteringMethod.val()
+                if (method) reprocessingparams.add(new ReprocessingParameter({
+                    PROCESSINGJOBID: jobId,
+                    PARAMETERKEY: 'cchalf_filtering_method',
+                    PARAMETERVALUE: method
+                }))
+
+                const sdcutoff = this.ui.sdcutoff.val()
+                if (sdcutoff) reprocessingparams.add(new ReprocessingParameter({
+                    PROCESSINGJOBID: jobId,
+                    PARAMETERKEY: 'sd_cutoff',
+                    PARAMETERVALUE: sdcutoff
+                }))
+
+                const groupsize = this.ui.groupsize.val()
+                if (groupsize) reprocessingparams.add(new ReprocessingParameter({
+                    PROCESSINGJOBID: jobId,
+                    PARAMETERKEY: 'image_group_size',
+                    PARAMETERVALUE: groupsize
+                }))
+
+                await reprocessingparams.save()
+                this._enqueue({ PROCESSINGJOBID: reprocessing.get('PROCESSINGJOBID') })
+                app.message({ message: 'Multiplex reprocessing job successfully submitted'})
+
+            } catch {
+                app.alert({ message: 'Something went wrong starting that reprocessing run' })
+            }
+
+        },
+
+        onFieldChanged: function() {
+            this._enableSubmitButton();
+        },
+
+        _disableSubmitButton: function() {
+            var btn = $('.ui-dialog-buttonpane button:contains("Submit")')
+            btn.addClass('submitted').button('disable').button('option', 'label', 'Submitted!')
+            this.resetTimeout = setTimeout(() => {
+                this._enableSubmitButton()
+            }, 5000)
+        },
+
+        _enableSubmitButton: function() {
+            var btn = $('.ui-dialog-buttonpane button.submitted')
+            btn.removeClass('submitted').button('enable').button('option', 'label', 'Submit')
+            clearTimeout(this.resetTimeout);
+        },
+
+        _enqueue: function(options) {
+            Backbone.ajax({
+                url: app.apiurl+'/process/enqueue',
+                method: 'POST',
+                data: {
+                    PROCESSINGJOBID: options.PROCESSINGJOBID,
+                },
+            })
+        },
+
+        initialize: function(options) {
+            this.scalingid = options.scalingid
+            this.type = options.type
+            this.title = 'Rerun multiplex processing - ' + this.type
+            this.filteringMethods = new FilteringMethods([
+                { NAME: 'image_group', VALUE: 'image_group' },
+                { NAME: 'dataset', VALUE: 'dataset' },
+            ])
+            this.spacegroups = new Spacegroups(null, { state: { pageSize: 9999 } })
+            this.listenTo(this.spacegroups, 'sync', this.populateSpacegroups)
+            this.spacegroups.fetch()
+        },
+
+        onRender: function() {
+            this.ui.opts.hide()
+            this.ui.filteringMethod.html(this.filteringMethods.opts())
+            this.ui.filteringMethod.prop('disabled', true).val('')
+            this.ui.sdcutoff.prop('disabled', true)
+            this.ui.groupsize.prop('disabled', true)
+        },
+
+        populateSpacegroups: function() {
+            this.ui.sg.html('<option value=""> - </option>'+this.spacegroups.opts())
+        }
+
+    })
+})

client/src/js/templates/dc/dc_autoproc.html

@@ -13,6 +13,7 @@
     <% } else { %>
 
     <p class="r downloads">
+        <a class="multiplex button" href="#"><i class="fa fa-cog"></i> Multiplex Reprocessing</a>
         <% if (IMAGESWEEPCOUNT > 1) { %>
             <span><%=IMAGESWEEPCOUNT%> image sweeps</span>
         <% } %>

client/src/js/templates/dc/multiplex.html

@@ -0,0 +1,18 @@
+<div class="data_collection">
+    <span class="multi form">
+        <label>Space Group: <select name="sg"></select></label>
+        High Res :<input type="text" name="res" placeholder="eg 1.5" /> &#197;
+    </span>
+    <a href="#" class="button opt">Filtering Options</a>
+    <br />
+</div>
+
+<div class="options data_collection">
+    <label>Apply &Delta;CC&half;<input type="checkbox" name="cchalf" value="0" /></label>
+    <br /><br />
+    <label>Method: <select name="method"></select></label>
+    <label>Standard deviation cutoff: <input type="text" name="sdcutoff" placeholder="eg 3" /></label>
+    <label>Image group size: <input type="text" name="groupsize" placeholder="eg 50" /></label>
+</div>
+
+