LIMS-1836: Improvements to reprocessing

api/config_sample.php

@@ -406,6 +406,34 @@
     $dials_rest_jwt = "";
     $dials_rest_url_rings = false;
 
+    # Upstream reprocessing pipelines, by beamline type
+    $upstream_reprocessing_pipelines = array(
+        'sm' => array(
+            array('NAME' => 'Xia2 DIALS', 'VALUE' => 'xia2-dials'),
+            array('NAME' => 'Xia2 DIALS aimless', 'VALUE' => 'xia2-dials-aimless'),
+        ),
+        'default' => array(
+            array('NAME' => 'Xia2 DIALS', 'VALUE' => 'xia2-dials'),
+            array('NAME' => 'Xia2 3dii', 'VALUE' => 'xia2-3dii'),
+            array('NAME' => 'Fast DP', 'VALUE' => 'fast_dp'),
+            array('NAME' => 'autoPROC', 'VALUE' => 'autoPROC'),
+        ),
+    );
+
+    # Downstream reprocessing pipelines, by beamline type
+    $downstream_reprocessing_pipelines = array(
+        'sm' => array(
+            array('NAME' => 'shelxt', 'VALUE' => 'trigger-shelxt'),
+        ),
+        'default' => array(
+            array('NAME' => 'Dimple', 'VALUE' => 'trigger-dimple'),
+            array('NAME' => 'Fast EP', 'VALUE' => 'trigger-fastep'),
+            array('NAME' => 'Big EP', 'VALUE' => 'trigger-bigep'),
+            array('NAME' => 'MrBUMP', 'VALUE' => 'trigger-mrbump'),
+        ),
+    );
+
+
     # Add a button to upload file to CCP4 cloud
     #$ccp4_cloud_upload_url = 'https://data.cloud.ccp4.ac.uk/api/data/<%=USERNAME%>/<%=FACILITYNAME%>/<%=IMAGEPREFIX%>_<%=DATACOLLECTIONNUMBER%>/upload';
 ?>

api/index.php

@@ -73,8 +73,8 @@ function setupApplication($mode): Slim
             $valid_components, $enabled_container_types, $synchweb_version, $redirects,
             $shipping_service_app_url, $use_shipping_service_redirect, $use_shipping_service_redirect_incoming_shipments,
             $dials_rest_url_rings, $closed_proposal_link, $ccp4_cloud_upload_url,
-            $only_staff_can_assign, $industrial_prop_codes, $prop_codes_data_deleted, $container_types_with_parents,
-            $bl_capacity;
+            $only_staff_can_assign, $industrial_prop_codes, $upstream_reprocessing_pipelines, $downstream_reprocessing_pipelines,
+            $prop_codes_data_deleted, $container_types_with_parents, $bl_capacity;
         $app->contentType('application/json');
         $options = $app->container['options'];
         $app->response()->body(json_encode(array(
@@ -97,16 +97,18 @@ function setupApplication($mode): Slim
             'valid_components' => $valid_components,
             'enabled_container_types' => $enabled_container_types,
             'synchweb_version' => $synchweb_version,
+            'redirects' => $redirects,
             'shipping_service_app_url' => $use_shipping_service_redirect || $use_shipping_service_redirect_incoming_shipments ? $shipping_service_app_url : null,
             'shipping_service_app_url_incoming' => $use_shipping_service_redirect_incoming_shipments ? $shipping_service_app_url : null,
-            'closed_proposal_link' => $closed_proposal_link,
             'dials_rest_url_rings' => $dials_rest_url_rings,
+            'closed_proposal_link' => $closed_proposal_link,
             'ccp4_cloud_upload_url' => $ccp4_cloud_upload_url,
-            'redirects' => $redirects,
             'only_staff_can_assign' => $only_staff_can_assign,
-            'container_types_with_parents' => $container_types_with_parents,
             'industrial_prop_codes' => $industrial_prop_codes,
+            'upstream_reprocessing_pipelines' => $upstream_reprocessing_pipelines,
+            'downstream_reprocessing_pipelines' => $downstream_reprocessing_pipelines,
             'prop_codes_data_deleted' => $prop_codes_data_deleted ?? array(),
+            'container_types_with_parents' => $container_types_with_parents,
             'bl_capacity' => $bl_capacity,
         )));
     });

api/src/Page/Sample.php

@@ -17,8 +17,8 @@ class Sample extends Page
         's' => '\w+',
         'prop' => '\w+\d+',
         'term' => '\w+',
-        'pid' => '\d+',
-        'sid' => '\d+',
+        'pid' => '-?\d+',
+        'sid' => '-?\d+',
         'ssid' => '\d+',
         'cid' => '\d+',
         'crid' => '\d+',

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

@@ -100,6 +100,10 @@ define(['backbone', 'marionette', 'views/dialog',
             this.model.set('PIPELINENAME', this.ui.pipeline.find('option:selected').text())
             var btns = this.buttons
             var warning = ''
+            if (!this.model.get('PIPELINENAME')) {
+                warning = ' No pipelines available'
+                btns = this.disabledButtons
+            }
             if (['MrBUMP', 'Dimple'].includes(this.model.get('PIPELINENAME')) && this.type.includes('autoPROC')) {
                 warning = ' Cannot rerun ' + this.model.get('PIPELINENAME') + ' on ' + this.type + ' results'
                 btns = this.disabledButtons
@@ -112,15 +116,15 @@ define(['backbone', 'marionette', 'views/dialog',
                 warning = ' Cannot run Dimple as no PDBs defined'
                 btns = this.disabledButtons
             }
-            if (this.model.get('PIPELINENAME') === 'MrBUMP' && this.model.get('HASSEQ') === 'No') {
+            if (this.model.get('PIPELINENAME') === 'MrBUMP' && (this.model.get('HASSEQ') === 'No' || !this.model.get('HASSEQ'))) {
                 warning = ' Cannot run MrBUMP as no sequence defined'
                 btns = this.disabledButtons
             }
             if (this.model.get('PIPELINENAME') === 'Fast EP' && (!this.model.get('ANOMALOUSSCATTERER'))) {
                 warning = ' Cannot run Fast EP as no anomalous scatterer defined'
                 btns = this.disabledButtons
             }
-            if (this.model.get('PIPELINENAME') === 'Big EP' && this.model.get('HASSEQ') === 'No') {
+            if (this.model.get('PIPELINENAME') === 'Big EP' && (this.model.get('HASSEQ') === 'No' || !this.model.get('HASSEQ'))) {
                 warning = ' Cannot run Big EP as no sequence defined'
                 btns = this.disabledButtons
             }
@@ -155,7 +159,7 @@ define(['backbone', 'marionette', 'views/dialog',
 
 
         initialize: function(options) {
-            this.proteins = new Proteins(null, { queryParams: { sid: options.model.get('BLSAMPLEID') } })
+            this.proteins = new Proteins(null, { queryParams: { sid: options.model.get('BLSAMPLEID') || -1 } })
             this._ready = this.proteins.fetch()
             this._ready.done(this.doOnReady.bind(this))
             this.scalingid = options.scalingid
@@ -169,24 +173,23 @@ define(['backbone', 'marionette', 'views/dialog',
         },
 
         onRender: function() {
-
-            this.pipelines = new Pipelines([
-                { NAME: 'Dimple', VALUE: 'trigger-dimple' },
-                { NAME: 'Fast EP', VALUE: 'trigger-fastep' },
-                { NAME: 'Big EP', VALUE: 'trigger-bigep' },
-                { NAME: 'MrBUMP', VALUE: 'trigger-mrbump' },
-            ])
-
-            this.ui.pipeline.html(this.pipelines.opts())           
+            const dspls = app.options.get('downstream_reprocessing_pipelines')
+            if (dspls) {
+                const pls = dspls[app.type] ?? dspls['default'];
+                this.pipelines = new Pipelines(pls)
+                this.ui.pipeline.html(this.pipelines.opts())
+            }
         },
-        
+
         doOnReady: function() {
             var protein = this.proteins.at(0)
-            var self = this
-            _.each(['ACRONYM','PROTEINID','HASSEQ','PDBS','ANOMALOUSSCATTERER'], function(k) {
-                self.model.set(k, protein.get(k))
-            })
-            this.pdbs = new PDBs(null, { pid: this.model.get('PROTEINID') })
+            if (protein) {
+                var self = this
+                _.each(['ACRONYM','PROTEINID','HASSEQ','PDBS','ANOMALOUSSCATTERER'], function(k) {
+                    self.model.set(k, protein.get(k))
+                })
+            }
+            this.pdbs = new PDBs(null, { pid: this.model.get('PROTEINID') || -1 })
             this.pdbs.fetch().done(this.updatePipeline.bind(this))
             this.collection = new IDDataCollections()
             if (this.model) {

client/src/js/modules/dc/views/reprocess2.js

@@ -102,7 +102,7 @@ define(['backbone', 'marionette', 'views/dialog',
 
 
         selectAll: function(e) {
-            e.preventDefault()
+            if (e) e.preventDefault()
 
             var si = parseInt(this.model.get('SI'))
             var ni = parseInt(this.model.get('NUMIMG'))
@@ -148,6 +148,20 @@ define(['backbone', 'marionette', 'views/dialog',
             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())
+
+            // check .distl element has been created before selecting all
+            const callback = (mutationList, observer) => {
+                for (const mutation of mutationList) {
+                    for (const node of mutation.addedNodes) {
+                        if (node.nodeType === Node.ELEMENT_NODE && node.querySelector('.distl')) {
+                            this.selectAll()
+                            observer.disconnect()
+                        }
+                    }
+                }
+            }
+            const observer = new MutationObserver(callback)
+            observer.observe(document.getElementById("dialog"), { childList: true, subtree: true })
         },
 
         toggleSG: function(e) {
@@ -247,6 +261,12 @@ define(['backbone', 'marionette', 'views/dialog',
             sm: 'input[name=sm]',
             indexingMethod: 'select[name=method]',
             absorptionLevel: 'select[name=absorption_level]',
+            a: 'input[name=a]',
+            b: 'input[name=b]',
+            c: 'input[name=c]',
+            al: 'input[name=alpha]',
+            be: 'input[name=beta]',
+            ga: 'input[name=gamma]',
         },
 
         buttons: {
@@ -259,6 +279,7 @@ define(['backbone', 'marionette', 'views/dialog',
             'click a.opt': 'toggleOpts',
             'click @ui.ind': 'toggleIndividual',
             'change @ui.pipeline': 'updatePipeline',
+            'change @ui.indexingMethod': 'updateIndexingMethod',
             'click a.multicrystal': 'closeDialog',
         },
 
@@ -276,11 +297,40 @@ define(['backbone', 'marionette', 'views/dialog',
             }
         },
 
+        updateIndexingMethod: function() {
+            if (this.ui.indexingMethod.val() == 'real_space_grid_search') {
+                const st = this.ui.ind.is(':checked')
+                if (st) {
+                    let eachHasCell = true
+                    this.distlview.children.each(function(v) {
+                        if (!v.ui.a.val() || !v.ui.b.val() || !v.ui.c.val() ||
+                                !v.ui.al.val() || !v.ui.be.val() || !v.ui.ga.val()) {
+                            v.ui.cell.show()
+                            eachHasCell = false
+                        }
+                    })
+                    if (!eachHasCell) {
+                        app.alert({ message: 'Real Space Grid Search requires unit cell to be populated' })
+                        this.ui.indexingMethod.val('')
+                    }
+                } else {
+                    if (!this.ui.a.val() || !this.ui.b.val() || !this.ui.c.val() ||
+                            !this.ui.al.val() || !this.ui.be.val() || !this.ui.ga.val()) {
+                        app.alert({ message: 'Real Space Grid Search requires unit cell to be populated' })
+                        this.ui.indexingMethod.val('')
+                        this.ui.cell.show()
+                    }
+                }
+            }
+        },
+
         toggleIndividual: function(e) {
-            var st = this.ui.ind.is(':checked')
+            const st = this.ui.ind.is(':checked')
             st ? this.ui.mul.hide() : this.ui.mul.show()
+            if (st) this.ui.cell.hide()
             this.distlview.children.each(function(v) {
                 v.setInd(st)
+                if (!st) v.ui.cell.hide()
             })
         },
 
@@ -309,7 +359,7 @@ define(['backbone', 'marionette', 'views/dialog',
             var s = this.collection.where({ selected: true })
 
             if (!s.length) {
-                app.alert({ message: 'Please selected some data sets to integrate' })
+                app.alert({ message: 'Please select some data sets to integrate' })
                 return
             }
 
@@ -530,18 +580,16 @@ define(['backbone', 'marionette', 'views/dialog',
         },
 
         onRender: function() {
-            this.ui.opts.hide()
+            if (app.type != 'sm') this.ui.opts.hide()
             this.ui.cell.hide()
-            this.$el.find('span input[type="text"]').css('width', '50px')
-
-            this.pipelines = new Pipelines([
-                { NAME: 'Xia2 DIALS', VALUE: 'xia2-dials' },
-                { NAME: 'Xia2 3dii', VALUE: 'xia2-3dii' },
-                { NAME: 'Fast DP', VALUE: 'fast_dp' },
-                { NAME: 'autoPROC', VALUE: 'autoPROC' },
-            ])
+            this.$el.find('span input[type="text"]').css('width', '55px')
 
-            this.ui.pipeline.html(this.pipelines.opts())
+            const uspls = app.options.get('upstream_reprocessing_pipelines')
+            if (uspls) {
+                const pls = uspls[app.type] ?? uspls['default'];
+                this.pipelines = new Pipelines(pls)
+                this.ui.pipeline.html(this.pipelines.opts())
+            }
 
             this.indexingMethods = new IndexingMethods([
                 { NAME: '-', VALUE: '' },
@@ -578,6 +626,7 @@ define(['backbone', 'marionette', 'views/dialog',
             var nm = model.clone()
             nm.set('CID', this.collection.length+1)
             this.collection.add(nm)
+            this.toggleIndividual()
         },
 
         setCell: function(view, ap) {

client/src/js/modules/types/sm/dc/dc.js

@@ -7,9 +7,7 @@ define([
     return DCItemView.extend({
         apStatusItem: APStatusItem,
         template: Template,
-
         setProcessingVars: function() {},
-
     })
 
 })

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

@@ -11,8 +11,8 @@
         <span class="multi form">
             | 
             Pipeline :<select name="pipeline"></select>
-            High Res :<input type="text" name="res" /> &#197;
-            Low Res :<input type="text" name="lowres" /> &#197; |
+            High Res :<input type="text" name="res" placeholder="eg 1.5" /> &#197;
+            Low Res :<input type="text" name="lowres" placeholder="eg 40" /> &#197; |
             <a href="#" class="button sgm">Space Group / Cell</a> 
             <!-- Comments: <input type="text" name="comments" class="full" /> -->
         </span>

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

@@ -7,8 +7,8 @@ <h1 class="clearfix">
 
 <div class="ind data_collection">
     Pipeline <select name="pipeline"></select>
-    High Res <input type="text" name="res" /> &#197;
-    Low Res <input type="text" name="lowres" /> &#197; |
+    High Res <input type="text" name="res" placeholder="eg 1.5" /> &#197;
+    Low Res <input type="text" name="lowres" placeholder="eg 40" /> &#197; |
     <a href="#" class="button sg">Space Group / Cell</a> <br />
 </div>
 

client/src/js/templates/mc/datacollections.html

@@ -29,8 +29,8 @@ <h1>Data Collections for <%-VISIT%></h1>
         <label>&beta; <input type="text" name="beta" /></label>
         <label>&gamma; <input type="text" name="gamma" /></label>
 
-        <label>High Res <input type="text" name="res" /> &#197;</label>
-        <label>Low Res <input type="text" name="lowres" /> &#197;</label>
+        <label>High Res <input type="text" name="res" placeholder="eg 1.5" /> &#197;</label>
+        <label>Low Res <input type="text" name="lowres" placeholder="eg 40" /> &#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>