Merge pre-release/2026-R2.4 into master

api/src/Downstream/BigEPPhasing.php

@@ -12,7 +12,7 @@ class BigEPPhasing extends DownstreamPlugin {
     function results() {
         $dat = array();
 
-        if (array_key_exists('program_id', $this->process['PARAMETERS'])) {
+        if (array_key_exists('scaling_id', $this->process['PARAMETERS'])) {
             $parent = $this->_lookup_parent_autoproc();
             if ($parent) {
                 $dat['PARENTAUTOPROCPROGRAM'] = $parent['PROCESSINGPROGRAMS'];

api/src/Downstream/DownstreamProcessing.php

@@ -288,6 +288,7 @@ function legacy() {
         $resp['TYPE'] = $this->friendlyname;
         $resp['PROCESS'] = $this->process;
         $resp['MESSAGES'] = $this->process['MESSAGES'];
+        $resp['DCID'] = $this->process['DCID'];
         $resp['FEATURES'] = array(
             'MAPMODEL' => $this->has_mapmodel,
             'IMAGES' => $this->has_images,

api/src/Page/Exp.php

@@ -141,7 +141,7 @@ class Exp extends Page
             array('/plans/detectors/:DATACOLLECTIONPLANHASDETECTORID', 'patch', '_dp_update_detector'),
             array('/plans/detectors/:DATACOLLECTIONPLANHASDETECTORID', 'delete', '_dp_remove_detector'),
 
-            array('/setup', 'get', '_get_beamline_setups'),
+            array('/setup(/:BEAMLINESETUPID)', 'get', '_get_beamline_setups'),
             array('/setup', 'post', '_add_beamline_setup'),
             array('/setup/:BEAMLINESETUPID', 'patch', '_update_beamline_setup'),
 
@@ -164,7 +164,7 @@ function _detectors()
             array_push($args, $this->arg('BEAMLINENAME'));
         }
 
-        $tot = $this->db->pq("SELECT count(d.detectorid) as tot
+        $tot = $this->db->pq("SELECT count(distinct d.detectorid) as tot
             FROM detector d
             LEFT OUTER JOIN beamlinesetup bls ON bls.detectorid = d.detectorid
             WHERE $where", $args);
@@ -177,10 +177,24 @@ function _detectors()
             'd.detectorid ASC'
         );
 
-        $rows = $this->db->paginate("SELECT d.detectorid, d.detectortype, d.detectormanufacturer, d.detectorserialnumber, d.sensorthickness, d.detectormodel, d.detectorpixelsizehorizontal, d.detectorpixelsizevertical, d.detectordistancemin, d.detectordistancemax, d.density, d.composition, concat(d.detectormanufacturer,' ',d.detectormodel, ' (',d.detectortype,')') as description, d.detectormaxresolution, d.detectorminresolution, count(distinct dc.datacollectionid) as dcs, count(distinct bls.beamlinesetupid) as blsetups, (SELECT count(distinct dphd.detectorid) FROM DataCollectionPlan_has_Detector dphd WHERE dphd.detectorid = d.detectorid) as dps, GROUP_CONCAT(distinct bls.beamlinename) as beamlines, d.numberofpixelsx, d.numberofpixelsy, d.detectorrollmin, d.detectorrollmax
+        $rows = $this->db->paginate("SELECT d.detectorid, d.detectortype, d.detectormanufacturer, d.detectorserialnumber, d.sensorthickness, d.detectormodel, d.detectorpixelsizehorizontal, d.detectorpixelsizevertical, d.detectordistancemin, d.detectordistancemax, d.density, d.composition, d.detectormaxresolution, d.detectorminresolution, d.numberofpixelsx, d.numberofpixelsy, d.detectorrollmin, d.detectorrollmax,
+            concat(d.detectormanufacturer,' ',d.detectormodel, ' (', ifnull(d.detectortype, ''), ')') as description,
+            count(distinct bls.beamlinesetupid) as blsetups,
+            GROUP_CONCAT(distinct bls.beamlinename) as beamlines,
+            COALESCE(datacollections.dcs, 0) as dcs,
+            COALESCE(datacollectionplans.dps, 0) as dps
             FROM detector d
-            LEFT OUTER JOIN datacollection dc ON dc.detectorid = d.detectorid
             LEFT OUTER JOIN beamlinesetup bls ON bls.detectorid = d.detectorid
+            LEFT JOIN (
+                SELECT detectorid, COUNT(datacollectionid) as dcs
+                FROM datacollection
+                GROUP BY detectorid
+            ) datacollections ON datacollections.detectorid = d.detectorid
+            LEFT JOIN (
+                SELECT detectorid, COUNT(DISTINCT detectorid) as dps
+                FROM DataCollectionPlan_has_Detector
+                GROUP BY detectorid
+            ) datacollectionplans ON datacollectionplans.detectorid = d.detectorid
             WHERE $where
             GROUP BY d.detectorid
             ORDER BY $order", $args);
@@ -925,4 +939,4 @@ function _get_experiment_types()
 
         $this->_output(array('total' => count($rows), 'data' => $rows));
     }
-}
+}

api/src/Page/Processing.php

@@ -799,7 +799,7 @@ function _get_downstreams($dcid = null, $aid = null) {
         }
 
         $downstreams = $this->db->pq(
-            "SELECT app.autoprocprogramid, app.processingprograms, pj.automatic, 
+            "SELECT app.autoprocprogramid, app.processingprograms, pj.automatic, pj.datacollectionid as dcid,
                     app.processingstatus, app.processingmessage,
                     app.processingstarttime, app.processingendtime, pj.recipe, pj.comments as processingcomments,
                     dc.imageprefix as dcimageprefix, dc.imagedirectory as dcimagedirectory, 

api/src/Page/Sample.php

@@ -1966,15 +1966,19 @@ function _ligands()
             array_push($args, $this->arg('lid'));
         }
 
-        $tot = $this->db->pq("SELECT count(distinct l.ligandid) as tot FROM ligand l INNER JOIN proposal p ON p.proposalid = l.proposalid WHERE $where", $args);
-        $tot = intval($tot[0]['TOT']);
-
         if ($this->has_arg('s')) {
             $st = sizeof($args) + 1;
-            $where .= " AND l.name LIKE CONCAT('%',:" . $st . ", '%')";
-            array_push($args, $this->arg('s'));
+            $where .= " AND (
+                l.name LIKE CONCAT('%',:" . $st . ", '%')
+                OR l.libraryname LIKE CONCAT('%',:" . ($st + 1) . ", '%')
+                OR l.librarybatchnumber LIKE CONCAT('%',:" . ($st + 2) . ", '%')
+                OR l.platebarcode LIKE CONCAT('%',:" . ($st + 3) . ", '%')
+            )";
+            array_push($args, $this->arg('s'), $this->arg('s'), $this->arg('s'), $this->arg('s'));
         }
 
+        $tot = $this->db->pq("SELECT count(distinct l.ligandid) as tot FROM ligand l WHERE $where", $args);
+        $tot = intval($tot[0]['TOT']);
 
         $start = 0;
         $pp = $this->has_arg('per_page') ? $this->arg('per_page') : 15;
@@ -1990,12 +1994,18 @@ function _ligands()
         array_push($args, $end);
 
         $order = 'l.ligandid DESC';
-
         $group = 'l.ligandid';
 
         if ($this->has_arg('sort_by')) {
             $cols = array(
                 'NAME' => 'l.name',
+                'SMILES' => 'l.smiles',
+                'LIBRARYNAME' => 'l.libraryname',
+                'LIBRARYBATCHNUMBER' => 'l.librarybatchnumber',
+                'PLATEBARCODE' => 'l.platebarcode',
+                'SOURCEWELL' => 'l.sourcewell',
+                'SCOUNT' => 'scount',
+                'DCOUNT' => 'dcount',
             );
             $dir = $this->has_arg('order') ? ($this->arg('order') == 'asc' ? 'ASC' : 'DESC') : 'ASC';
             if (array_key_exists($this->arg('sort_by'), $cols))
@@ -2006,7 +2016,6 @@ function _ligands()
                                 COUNT(DISTINCT dc.datacollectionid) AS dcount,
                                 COUNT(DISTINCT b.blsampleid) AS scount
                                 FROM ligand l
-                                INNER JOIN proposal p ON p.proposalid = l.proposalid
                                 LEFT OUTER JOIN ligand_has_pdb lhp ON lhp.ligandid = l.ligandid
                                 LEFT OUTER JOIN blsample_has_ligand bhl ON bhl.ligandid = l.ligandid
                                 LEFT OUTER JOIN blsample b ON b.blsampleid = bhl.blsampleid
@@ -2081,29 +2090,51 @@ function _add_ligand()
     {
         if (!$this->has_arg('prop'))
             $this->_error('No proposal specified');
-        if (!$this->has_arg('NAME'))
-            $this->_error('No ligand name');
 
-        $smiles = $this->has_arg('SMILES') ? $this->arg('SMILES') : '';
+        $ligs = array();
+        $lids = array();
+
         $libname = $this->has_arg('LIBRARYNAME') ? $this->arg('LIBRARYNAME') : null;
         $libbatch = $this->has_arg('LIBRARYBATCHNUMBER') ? $this->arg('LIBRARYBATCHNUMBER') : null;
         $barcode = $this->has_arg('PLATEBARCODE') ? $this->arg('PLATEBARCODE') : null;
-        $well = $this->has_arg('SOURCEWELL') ? $this->arg('SOURCEWELL') : null;
 
-        $chk = $this->db->pq("SELECT name FROM ligand
-              WHERE proposalid=:1 AND name=:2", array($this->proposalid, $this->arg('NAME')));
-        if (sizeof($chk))
-            $this->_error('That ligand name already exists in this proposal');
+        $json = $this->request['json'] ?? null;
+        if ($json && is_array($json)) {
 
-        $this->db->pq(
-            'INSERT INTO ligand (proposalid,name,smiles,libraryname,librarybatchnumber,platebarcode,sourcewell)
-              VALUES (:1,:2,:3,:4,:5,:6,:7) RETURNING ligandid INTO :id',
-            array($this->proposalid, $this->arg('NAME'), $smiles, $libname, $libbatch, $barcode, $well)
-        );
+            foreach ($json as $row) {
+                if (isset($row->NAME)) {
+                    $name = $row->NAME;
+                    $smiles = isset($row->SMILES) ? $row->SMILES : null;
+                    $well = isset($row->SOURCEWELL) ? $row->SOURCEWELL : null;
+                    array_push($ligs, array($this->proposalid, $name, $smiles, $libname, $libbatch, $barcode, $well));
+                }
+            }
+        } else {
+            if (!$this->has_arg('NAME'))
+                $this->_error('No ligand name');
+
+            $smiles = $this->has_arg('SMILES') ? $this->arg('SMILES') : null;
+            $well = $this->has_arg('SOURCEWELL') ? $this->arg('SOURCEWELL') : null;
 
-        $lid = $this->db->id();
+            array_push($ligs, array($this->proposalid, $this->arg('NAME'), $smiles, $libname, $libbatch, $barcode, $well));
+
+            $chk = $this->db->pq("SELECT name FROM ligand
+                  WHERE proposalid=:1 AND name=:2", array($this->proposalid, $this->arg('NAME')));
+            if (sizeof($chk))
+                $this->_error('That ligand name already exists in this proposal');
+        }
+
+        foreach ($ligs as $lig) {
+            $this->db->pq(
+                'INSERT INTO ligand (proposalid,name,smiles,libraryname,librarybatchnumber,platebarcode,sourcewell)
+                VALUES (:1,:2,:3,:4,:5,:6,:7) RETURNING ligandid INTO :id',
+                $lig
+            );
+
+            array_push($lids, $this->db->id());
+        }
 
-        $this->_output(array('LIGANDID' => $lid));
+        $this->_output(array('LIGANDIDS' => $lids));
     }
 
     # ------------------------------------------------------------------------

api/src/Page/Shipment.php

@@ -538,10 +538,11 @@ function _add_history()
                 $email_location = $dewar_complete_email_locations[$last_location];
                 $send_return_email = preg_match($email_location, strtolower($this->arg('LOCATION')));
             }
-            // If dewar status is dispatch-requested - don't change it.
+            // If dewar status is dispatch-requested or dispatch-booked - don't change it.
             // This way the dewar can be moved between storage locations and keep the record that a user requested the dispatch
             // Default status is 'at-facility'
-            $dewarstatus = strtolower($dew['DEWARSTATUS']) == 'dispatch-requested' ? 'dispatch-requested' : 'at facility';
+            $status = strtolower($dew['DEWARSTATUS']);
+            $dewarstatus = ($status == 'dispatch-requested' || $status == 'dispatch-booked') ? $status : 'at facility';
             $dewarlocation = $this->arg('LOCATION');
 
         } else {

client/package.json

@@ -82,6 +82,7 @@
     "jquery.flot.tooltip": "^0.9.0",
     "lodash-es": "^4.17.21",
     "markdown": "^0.5.0",
+    "papaparse": "^5.4.1",
     "plotly.js": "^1.52.2",
     "portal-vue": "2.1.7",
     "promise": "^8.0.3",

client/src/files/ligand_template.csv

@@ -0,0 +1 @@
+Name,SMILES,Well

client/src/js/collections/detectors.js

@@ -9,7 +9,7 @@ define(['backbone.paginator', 'models/detector', 'utils/kvcollection'], function
         valueAttribute: 'DETECTORID',
 
         state: {
-            pageSize: 5,
+            pageSize: 9999,
         },
 
         parseState: function(r, q, state, options) {

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

@@ -97,7 +97,7 @@ define(['backbone', 'marionette',
             var mapButton = null
             if (this.getOption('links')) {
                 var links = [
-                    '<a class="view button" href="/dc/map/id/'+this.getOption('DCID')+'/aid/'+this.model.get('AID')+'"><i class="fa fa-search"></i> Map / Model Viewer</a>',
+                    '<a class="view button" href="/dc/map/id/'+this.model.get('DCID')+'/aid/'+this.model.get('AID')+'"><i class="fa fa-search"></i> Map / Model Viewer</a>',
                     '<a class="pattach button" href="#"><i class="fa fa-files-o"></i> Logs &amp; Files</a>',
                     '<a class="dll button" href="'+app.apiurl+'/download/ap/archive/'+this.model.get('AID')+'"><i class="fa fa-cloud-download"></i> Download Zip</a>',
                 ]

client/src/js/modules/fault/views/list.js

@@ -5,7 +5,7 @@ define(['marionette', 'modules/fault/views/filters', 'views/table', 'utils/table
         argument: 'FAULTID',
     })
 
-    
+
     return Marionette.LayoutView.extend({
         className: 'content',
         template: _.template('<h1>Faults</h1><% if (app.user_can(\'fault_add\')) { %><div class="r"><a class="button add" href="/faults/add"><i class="fa fa-plus"></i> Add Fault Report</a></div><% } %><div class="filters"></div><div class="wrapper"></div>'),
@@ -14,6 +14,7 @@ define(['marionette', 'modules/fault/views/filters', 'views/table', 'utils/table
         search: true,
 
         initialize: function(options) {
+            const params = this.getOption('params') || {}
             var columns = [
                 { name: 'TITLE', label: 'Title', cell: table.HTMLCell, editable: false },
                 { name: 'STARTTIME', label: 'Time', cell: 'string', editable: false },
@@ -26,23 +27,23 @@ define(['marionette', 'modules/fault/views/filters', 'views/table', 'utils/table
                 { name: 'NAME', label: 'Reporter', cell: 'string', editable: false },
 
             ]
-            
+
             if (app.mobile()) {
                 _.each([3,4,5,6,8], function(v) {
                     columns[v].renderable = false
                 })
             }
+
+            this.table = new TableView({ collection: options.collection, columns: columns, tableClass: 'proposals', filter: 's', search: params.s, loading: true, backgrid: { row: ClickableRow, emptyText: 'No faults found' } })
 
-            this.table = new TableView({ collection: options.collection, columns: columns, tableClass: 'proposals', filter: 's', search: options.params.s, loading: true, backgrid: { row: ClickableRow, emptyText: 'No faults found' } })
-
-            if (this.getOption('filters')) this.filters = new FilterView({ collection: options.collection, params: this.getOption('params') })
+            if (this.getOption('filters')) this.filters = new FilterView({ collection: options.collection, params: params })
         },
-                                          
+
         onRender: function() {
             this.wrap.show(this.table)
             if (this.getOption('filters')) this.flts.show(this.filters)
         },
-          
+
         onShow: function() {
             this.table.focusSearch()
         },

client/src/js/modules/imaging/views/admin/params.js

@@ -180,6 +180,11 @@ define(['marionette',
 
 
     var DetectorsLimitsCellStatic = Backgrid.Cell.extend({
+        initialize: function(options) {
+            Backgrid.Cell.prototype.initialize.apply(this, arguments)
+            this.listenTo(this.model, 'sync change', this.render)
+        },
+
         render: function() {
             this.$el.empty()
             if (!this.model.isNew()) {
@@ -238,9 +243,17 @@ define(['marionette',
             console.log('model changed', arguments)
             // Changed Attributes are not being detected correctly.
             // Therefore we can crudely set all parameters to enforce a PATCH request
-            if (!m.isNew()) m.save(_.clone(m.attributes), { patch: true })
-        },
 
+            if (!m.isNew()) {
+                m.save(_.clone(m.attributes), {
+                    patch: true,
+                    wait: true,
+                    success: function() {
+                        m.fetch()
+                    }
+                });
+            }
+        },
 
 
         onRender: function() {
@@ -297,4 +310,4 @@ define(['marionette',
     })
 
 
-})
+})

client/src/js/modules/samples/routes.js

@@ -58,6 +58,10 @@ app.addInitializer(function() {
     app.navigate('/ligands/lid/'+lid)
   })
 
+  app.on('ligands:viewall', function() {
+    app.navigate('/ligands')
+  })
+
   app.on('phases:view', function(pid) {
     app.navigate('/phases/pid/'+pid)
   })