LIMS-1759: Add pages to create and view ligands (#957)

* LIMS-1759: Add pages to add/view/list ligands, add PDBS, and add to samples

* LIMS-1759: Add ligands to samples in plates

* LIMS-1759: Fix bug where ligands were added multiple times

* LIMS-1759: Fix error with too few args

---------

Co-authored-by: Mark Williams <[email protected]>

Author: ndg63276

api/src/Database/Type/MySQL.php

@@ -135,6 +135,10 @@ class MySQL extends DatabaseParent {
         'BLSampleImageAutoScoreClass',
         'BLSampleImage_has_AutoScoreClass',
 
+        'Ligand',
+        'BLSample_has_Ligand',
+        'Ligand_has_PDB',
+
         // Queuing
         'ContainerQueueSample',
         'ContainerQueue',

api/src/Page/DC.php

@@ -19,6 +19,7 @@ class DC extends Page
         'aid' => '\d+',
         'pjid' => '\d+',
         'pid' => '\d+',
+        'lid' => '\d+',
         'h' => '\d\d',
         'dmy' => '\d\d\d\d\d\d\d\d',
         'ssid' => '\d+',
@@ -259,6 +260,16 @@ function _data_collections($single = null)
                 array_push($args, $this->arg('pid'));
             }
 
+            # Ligands
+        } else if ($this->has_arg('lid')) {
+            $info = $this->db->pq("SELECT ligandid FROM ligand l WHERE l.ligandid=:1", array($this->arg('lid')));
+
+            foreach (array('dc', 'es', 'r', 'xrf') as $i => $t) {
+                $extj[$i] .= " INNER JOIN blsample_has_ligand bhl ON bhl.blsampleid = smp.blsampleid";
+                $sess[$i] = 'bhl.ligandid=:' . (sizeof($args) + 1);
+                array_push($args, $this->arg('lid'));
+            }
+
             # Processing job
         } else if ($this->has_arg('PROCESSINGJOBID')) {
             $info = $this->db->pq('SELECT processingjobid 

api/src/Page/Proposal.php

@@ -37,6 +37,7 @@ class Proposal extends Page
         'SHIPPINGID' => '\d+',
         'LABCONTACTID' => '\d+',
         'DATACOLLECTIONID' => '\d+',
+        'LIGANDID' => '\d+',
 
         // proposal
         'PROPOSALCODE' => '\w+',
@@ -900,6 +901,7 @@ function _lookup()
             'SHIPPINGID' => 'sh.shippingid',
             'LABCONTACTID' => 'lc.labcontactid',
             'DATACOLLECTIONID' => 'dc.datacollectionid',
+            'LIGANDID' => 'l.ligandid',
         );
 
         $field = null;
@@ -958,6 +960,7 @@ function _lookup()
                 LEFT OUTER JOIN container c ON c.dewarid = d.dewarid
 
                 LEFT OUTER JOIN labcontact lc ON lc.proposalid = p.proposalid
+                LEFT OUTER JOIN ligand l ON l.proposalid = p.proposalid
                 $where
             ", $args);
 

api/src/Page/Sample.php

@@ -21,6 +21,7 @@ class Shipment extends Page
         'sid' => '\d+',
         'lcid' => '\d+',
         'pid' => '\d+',
+        'lid' => '\d+',
         'iid' => '\d+',
 
 
@@ -2276,6 +2277,14 @@ function _get_all_containers()
             array_push($args, $this->arg('pid'));
         }
 
+        if ($this->has_arg('lid')) {
+            $join .= ' LEFT OUTER JOIN blsample_has_ligand bhl ON bhl.blsampleid = s.blsampleid';
+            $where .= ' AND bhl.ligandid=:' . (sizeof($args) + 1);
+            $totalQuery->joinClause("LEFT OUTER JOIN blsample s ON s.containerid = c.containerid");
+            $totalQuery->joinClause("LEFT OUTER JOIN blsample_has_ligand bhl ON bhl.blsampleid = s.blsampleid");
+            array_push($args, $this->arg('lid'));
+        }
+
         if ($this->has_arg('assigned')) {
             $where .= " AND d.dewarstatus LIKE 'processing' AND c.samplechangerlocation > 0";
             $totalQuery->joinClause("INNER JOIN dewar d ON d.dewarid = c.dewarid");

api/src/Page/Shipment.php

@@ -0,0 +1,58 @@
+define(['underscore', 'backbone.paginator', 'models/ligand'], function(_, PageableCollection, Ligand) {
+    
+    return PageableCollection.extend({
+        model: Ligand,
+        mode: 'server',
+        url: '/sample/ligands',
+            
+        state: {
+            pageSize: 15,
+        },
+            
+        parseState: function(r, q, state, options) {
+            return { totalRecords: r.total }
+        },
+            
+        parseRecords: function(r, options) {
+            return r.data
+        },
+
+        initialize: function(collection, options) {
+            this.fetched = false
+            this.on('sync', this.setFetched, this)
+            if (options && options.pmodel) {
+                this.pmodel = options.pmodel
+                this.listenTo(this, 'change add remove', this._update_ligand_ids)
+                this.listenTo(this.pmodel, 'sync', this._add_ligands)
+                this._add_ligands()
+            }
+        },
+
+        setFetched: function() {
+          if (this.fetched) return
+          this.fetched = true
+          this.trigger('reset')
+        },
+
+        _update_ligand_ids: function() {
+            var ligs = this.slice(0)
+            var flds = { 
+                LIGANDIDS: _.map(ligs, function(m) { return m.get('LIGANDID') }),
+                LIGANDNAMES: _.map(ligs, function(m) { return m.get('NAME') }),
+            }
+            this.pmodel.set(flds)
+        },
+
+        _add_ligands: function() {
+            var ids = this.pmodel.get('LIGANDIDS') || []
+            var nas = this.pmodel.get('LIGANDNAMES') || []
+            var ligs = _.map(ids, function(id, i) { 
+                return { 
+                    LIGANDID: id, 
+                    NAME: nas[i],
+                }
+            })
+            this.reset(ligs)
+        },
+    })
+})

client/src/js/collections/ligands.js

@@ -0,0 +1,35 @@
+define(['backbone', 'markdown'], function(Backbone, markdown) {
+    
+    return Backbone.Model.extend({
+        idAttribute: 'LIGANDID',
+        urlRoot: '/sample/ligands',
+        
+        validation: {
+            NAME: {
+                required: true,
+                pattern: 'wwdash',
+            },
+            SMILES: {
+                required: false,
+                pattern: 'smiles'
+            },
+            LIBRARYNAME: {
+                required: false,
+                pattern: 'wwdash',
+            },
+            LIBRARYBATCHNUMBER: {
+                required: false,
+                pattern: 'wwdash',
+            },
+            PLATEBARCODE: {
+                required: false,
+                pattern: 'wwdash',
+            },
+            SOURCEWELL: {
+                required: false,
+                pattern: 'wwdash',  
+            },
+        },
+    })
+    
+})

client/src/js/models/ligand.js

@@ -1,6 +1,6 @@
-define(['backbone', 'collections/components', 
+define(['backbone', 'collections/components', 'collections/ligands',
     'utils/experimentkinds',
-    'utils/radiationsensitivity'], function(Backbone, Components, EXP, RS) {
+    'utils/radiationsensitivity'], function(Backbone, Components, Ligands, EXP, RS) {
 
     return Backbone.Model.extend({
         idAttribute: 'BLSAMPLEID',
@@ -10,6 +10,7 @@ define(['backbone', 'collections/components',
         initialize: function(attrs, options) {
             var addPrimary = (options && options.addPrimary) || (this.collection && this.collection.state.addPrimary)
             this.set('components', new Components(null, { pmodel: this, addPrimary: addPrimary }))
+            this.set('ligands', new Ligands(null, { pmodel: this }))
             this.updateScreeningOptions()
 
             this.listenTo(this, 'change:EXPERIMENTKIND', this.updateExpKind)
@@ -105,6 +106,8 @@ define(['backbone', 'collections/components',
             INITIALSAMPLEGROUP: '',
             COMPONENTIDS: [],
             COMPONENTAMOUNTS: [],
+            LIGANDIDS: [],
+            LIGANDNAMES: [],
             X: null,
             Y: null,
             Z: null,

client/src/js/models/sample.js

@@ -2,10 +2,13 @@ define(['backbone', 'modules/samples/models/pdb'], function(Backbone, PDB) {
 
     return Backbone.Collection.extend({
         model: PDB,
-        url: function() { return '/sample/pdbs'+(this.pid ? '/pid/'+this.pid : '') },
+        url: function() { return '/sample/pdbs'+(this.pid ? '/pid/'+this.pid : '')+(this.lid ? '/lid/'+this.lid : '') },
 
         initialize: function(models, options) {
-            if (options) this.pid = options.pid
+            if (options) {
+                this.pid = options.pid
+                this.lid = options.lid
+            }
         },
 
         opts: function() {
@@ -14,4 +17,4 @@ define(['backbone', 'modules/samples/models/pdb'], function(Backbone, PDB) {
 
     })
 
-})
+})

client/src/js/modules/samples/collections/pdbs.js

@@ -0,0 +1,71 @@
+<template>
+  <section>
+    <marionette-view
+      v-if="ready"
+      :key="$route.fullPath"
+      :options="options"
+      :fetch-on-load="true"
+      :mview="mview"
+      :breadcrumbs="bc"
+    />
+  </section>
+</template>
+
+<script>
+import MarionetteView from 'app/views/marionette/marionette-wrapper.vue'
+import AddLigandView from 'modules/samples/views/ligandadd'
+import Ligand from 'models/ligand'
+// Allow us to map store values to local computed properties
+import { mapGetters } from 'vuex'
+
+export default {
+    name: 'LigandAddWrapper',
+    components: {
+        'marionette-view': MarionetteView
+    },
+    data: function() {
+        return {
+            ready: false,
+            mview: null,
+            model: null,
+            bc : [],
+            title: '' // Used as a data property so we can report errors ok
+        }
+    },
+    computed: {
+        // Don't need to pass any options - it's a plain view
+        options: function() {
+            return {
+                model: this.model
+            }
+        },
+        ...mapGetters('proposal', {
+            proposalType: 'currentProposalType'
+        })
+    },
+    created: function() {
+        this.title = 'Ligand'
+
+        this.bc = [{ title: this.title+'s', url: '/'+this.title.toLowerCase()+'s' }]
+
+        // Are we allowed to add?
+        if (!this.checkPermissions()) return
+
+        this.bc.push({ title: 'Add '+this.title })
+
+        this.mview = AddLigandView
+
+        // We have no need to wait for proposal lookups here
+        this.ready = true
+    },
+    methods: {
+        checkPermissions: function() {
+            if (app.proposal && app.proposal.get('ACTIVE') != 1) {
+                app.alert({ title: 'Proposal Not Active', message: 'This proposal is not active so new '+this.title+'s cannot be added'} )
+                return false
+            }
+            return true
+        },
+    }
+}
+</script>