LIMS-2151: Allow summary page to be for visits/proteins/groups

api/src/Page/Processing.php

@@ -9,7 +9,7 @@
 class Processing extends Page {
     public static $dispatch = array(
         array('/:id(/dcg/:dcg)', 'get', '_results'),
-        array('/visit/:visit(/csv/:csv)', 'get', '_results_for_visit'),
+        array('/summary(/group/:sgid)(/protein/:pid)(/visit/:visit)(/csv/:csv)', 'get', '_summary'),
         array('/status', 'post', '_statuses'),
 
         array('/messages/status', 'post', '_ap_message_status'),
@@ -27,6 +27,8 @@ class Processing extends Page {
         'id' => '\d+',
         'ids' => '\d+',
         'dcg' => '\d+',
+        'pid' => '\d+',
+        'sgid' => '\d+',
         'visit' => '\w+\d+-\d+',
         'map' => '\d+',
         'n' => '\d+',
@@ -382,24 +384,56 @@ function _statuses() {
         $this->_output($out);
     }
 
-    function _results_for_visit() {
-        if (!($this->has_arg('visit'))) {
-            $this->_error('No visit specified');
-        }
-        $pattern = '/([A-z]+)(\d+)-(\d+)/';
-        preg_match($pattern, $this->arg('visit'), $matches);
-        if (!sizeof($matches))
-            $this->_error('No such visit');
+    function _summary() {
+        $where = 'dc.overlap = 0 AND dc.axisrange > 0 AND app.processingstatus = 1';
+        $join = '';
+        if ($this->has_arg('visit')) {
+            $pattern = '/([A-z]+)(\d+)-(\d+)/';
+            preg_match($pattern, $this->arg('visit'), $matches);
+            if (!sizeof($matches))
+                $this->_error('No such visit');
+
+            $info = $this->db->pq("SELECT s.sessionid FROM blsession s
+                INNER JOIN proposal p ON (p.proposalid = s.proposalid)
+                WHERE p.proposalid=:1 AND p.proposalcode=:2 AND p.proposalnumber=:3 AND s.visit_number=:4",
+                array($this->proposalid, $matches[1], $matches[2], $matches[3])
+            );
 
-        $info = $this->db->pq("SELECT s.sessionid FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE p.proposalcode=:1 AND p.proposalnumber=:2 AND s.visit_number=:3", array($matches[1], $matches[2], $matches[3]));
+            if (!sizeof($info)) {
+                $this->_error('No such visit');
+            }
 
-        if (!sizeof($info)) {
-            $this->_error('No such visit');
-        }
+            $args = array($info[0]['SESSIONID']);
+            $where .= ' AND dc.sessionid=:1';
+        } else if ($this->has_arg('pid')) {
+            $info = $this->db->pq("SELECT pr.proteinid FROM protein pr
+                WHERE pr.proposalid=:1 AND pr.proteinid=:2",
+                array($this->proposalid, $this->arg('pid'))
+            );
+
+            if (!sizeof($info)) {
+                $this->_error('No such protein');
+            }
+
+            $args = array($info[0]['PROTEINID']);
+            $where .= ' AND c.proteinid=:1';
+            $join = 'INNER JOIN crystal c on smp.crystalid=c.crystalid';
+        } else if ($this->has_arg('sgid')) {
+            $info = $this->db->pq("SELECT blsg.blsamplegroupid FROM blsamplegroup blsg
+                WHERE blsg.proposalid=:1 AND blsg.blsamplegroupid=:2",
+                array($this->proposalid, $this->arg('sgid'))
+            );
 
-        $args = array($info[0]['SESSIONID']);
+            if (!sizeof($info)) {
+                $this->_error('No such sample group');
+            }
 
-        $where = 'dc.sessionid=:1 AND dc.overlap = 0 AND dc.axisrange > 0 AND app.processingstatus = 1';
+            $args = array($info[0]['BLSAMPLEGROUPID']);
+            $where .= ' AND bhb.blsamplegroupid=:1';
+            $join = 'INNER JOIN BLSampleGroup_has_BLSample bhb on smp.blsampleid=bhb.blsampleid';
+        } else {
+            $this->_error('No visit, protein or group specified');
+        }
 
         if ($this->has_arg('pipeline')) {
             $st = sizeof($args);
@@ -489,6 +523,7 @@ function _results_for_visit() {
         $jobs = $this->db->pq(
             "SELECT dc.datacollectionid as id,
                 CONCAT(dc.imageprefix, '_', dc.datacollectionnumber) as prefix,
+                CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit,
                 smp.name as sample,
                 smp.blsampleid,
                 ".self::EVTOA."/dc.wavelength as energy,
@@ -518,7 +553,10 @@ function _results_for_visit() {
                 apssinner.ccanomalous as innerccanom,
                 app.autoprocprogramid as aid
                 FROM datacollection dc
+                INNER JOIN blsession s ON dc.sessionid = s.sessionid
+                INNER JOIN proposal p ON s.proposalid = p.proposalid
                 LEFT OUTER JOIN blsample smp ON dc.blsampleid = smp.blsampleid
+                $join
                 INNER JOIN processingjob pj ON dc.datacollectionid = pj.datacollectionid
                 INNER JOIN autoprocprogram app ON pj.processingjobid = app.processingjobid
                 INNER JOIN autoproc ap ON app.autoprocprogramid=ap.autoprocprogramid
@@ -583,7 +621,14 @@ function _results_for_visit() {
 
         if ($this->has_arg('csv')) {
             $this->app->response->headers->set("Content-type", "text/csv");
-            Utils::setDispositionAttachment($this->app->response, $this->arg('visit') . "_summary.csv");
+            if ($this->has_arg('visit')) {
+                $filename = 'visit_' . $this->arg('visit') . "_summary.csv";
+            } else if ($this->has_arg('pid')) {
+                $filename = 'protein_' . $this->arg('pid') . "_summary.csv";
+            } else {
+                $filename = 'group_' . $this->arg('sgid') . "_summary.csv";
+            }
+            Utils::setDispositionAttachment($this->app->response, $filename);
             if (!empty($data)) {
                 print implode(',', array_keys($data[0])) . "\n";
             }

api/src/Page/Sample.php

@@ -2010,7 +2010,7 @@ function _distinct_proteins()
               LEFT OUTER JOIN concentrationtype ct ON ct.concentrationtypeid = pr.concentrationtypeid
               WHERE pr.acronym is not null AND $where
               GROUP BY ct.symbol, pr.acronym, pr.name, pr.global
-              ORDER BY lower(pr.acronym)", $args);
+              ORDER BY lower(pr.acronym), pr.proteinid", $args);
 
         $this->_output($rows);
     }

client/src/css/partials/_content.scss

@@ -33,6 +33,7 @@
 
         &.nou {
             border-bottom: 0;
+            margin-bottom: 0;
         }
 
         &.center {

client/src/css/partials/_utility.scss

@@ -386,11 +386,19 @@ ul.ui-autocomplete {
     @apply tw-flex;
     @apply tw-flex-row;
     @apply tw-gap-2;
-    @apply tw-items-center;
+    @apply tw-items-baseline;
     border-bottom: 1px solid grey;
 
     h1 {
         padding: 0 !important;
         @apply tw-flex-grow;
+
+        &.no-grow {
+            @apply tw-flex-grow-0;
+        }
+    }
+
+    .xl {
+        @apply tw-text-xl;
     }
 }

client/src/js/app/views/marionette/marionette-wrapper.vue

@@ -18,7 +18,9 @@ export default {
     // If this component is used directly from another vue component this will not be called
     // Instead the parent vue component will need to load the model/collection data as required
     beforeRouteEnter: function(to, from, next) {
-        next(vm => vm.prefetchData())
+        next(vm => {
+            if (!vm.fetchOnLoad) vm.prefetchData()
+        })
     },
     props: {
         'mview': [Function, Promise], // The marionette view could be lazy loaded or static import 

client/src/js/collections/datacollectionsforvisit.js

@@ -4,25 +4,41 @@ define(['backbone.paginator', 'models/datacollectionsforvisit', 'utils/kvcollect
         model: DCs,
         mode: 'server',
         visit: null,
-        url: function() { return '/processing/visit/'+this.visit },
+        pid: null,
+        sgid: null,
+        url: function() {
+            if (this.pid) {
+                return '/processing/summary/protein/'+this.pid
+            } else if (this.visit) {
+                return '/processing/summary/visit/'+this.visit
+            } else {
+                return '/processing/summary/group/'+this.sgid
+            }
+        },
 
         initialize(collection, options) {
             if (options && options.queryParams && options.queryParams.visit) {
                 this.visit = options.queryParams.visit
             }
+            if (options && options.queryParams && options.queryParams.pid) {
+                this.pid = options.queryParams.pid
+            }
+            if (options && options.queryParams && options.queryParams.sgid) {
+                this.sgid = options.queryParams.sgid
+            }
         },
-                                          
+
         state: {
             pageSize: 15,
         },
-                                          
+
         parseState: function(r, q, state, options) {
             return { totalRecords: r.total }
         },
-      
+
         parseRecords: function(r, options) {
             return r.data
         },
-        
+
     }))
 })

client/src/js/collections/samplegroups.js

@@ -5,8 +5,9 @@
 define(['backbone',
   'backbone.paginator',
   'models/samplegroup',
-], function(Backbone, PageableCollection, SampleGroup) {
-  return PageableCollection.extend({
+  'utils/kvcollection',
+], function(Backbone, PageableCollection, SampleGroup, KVCollection) {
+  return PageableCollection.extend(_.extend({}, KVCollection, {
     model: SampleGroup,
     url: '/sample/groups',
 
@@ -23,5 +24,8 @@ define(['backbone',
     parseState: function(r) {
       return { totalRecords: r.total }
     },
-  })
+
+    keyAttribute: 'NAME',             // What the user sees in the dropdown list
+    valueAttribute: 'BLSAMPLEGROUPID', // The hidden ID submitted when selected
+  }))
 })

client/src/js/modules/dc/routes.js

@@ -42,6 +42,18 @@ application.addInitializer(function() {
       application.navigate('/dc/'+(visit ? ('visit/'+visit) : '') + '/ty/'+type+'/id/'+id)
   //   controller.dc_list(visit, null, null, null, type, id)
   })
+
+  application.on('visitsummary:show', function(visit) {
+    application.navigate('/dc/summary/visit/'+visit)
+  })
+
+  application.on('proteinsummary:show', function(pid) {
+    application.navigate('/dc/summary/protein/'+pid)
+  })
+
+  application.on('groupsummary:show', function(pid) {
+    application.navigate('/dc/summary/group/'+pid)
+  })
 })
 
 // appRoutes: {
@@ -110,12 +122,45 @@ let routes = [
       id: +route.params.id || null,
     }),
   },
+  {
+    path: '/dc/summary/protein/:pid([0-9]+)',
+    name: 'dc-summary-protein',
+    component: MarionetteView,
+    props: route => ({
+        mview: Summary,
+        fetchOnLoad: true,
+        pid: route.params.pid || '',
+        options: {
+          model: new Visit(),
+          collection: new DCVisit(null, {
+            queryParams: { pid: route.params.pid }
+          })
+        }
+    }),
+  },
+  {
+    path: '/dc/summary/group/:sgid([0-9]+)',
+    name: 'dc-summary-group',
+    component: MarionetteView,
+    props: route => ({
+        mview: Summary,
+        fetchOnLoad: true,
+        sgid: route.params.sgid || '',
+        options: {
+          model: new Visit(),
+          collection: new DCVisit(null, {
+            queryParams: { sgid: route.params.sgid }
+          })
+        }
+    }),
+  },
   {
     path: '/dc/summary/visit/:visit([a-zA-Z]{2}[0-9]+-[0-9]+)',
     name: 'dc-summary',
     component: MarionetteView,
     props: route => ({
         mview: Summary,
+        fetchOnLoad: true,
         visit: route.params.visit || '',
         options: {
           model: visitModel,