Merge pre-release/2024-R5.1 into master (#859)

* LIMS-139: link multiplex results to sample or sample group (#816)

* LIMS-1454: Show non-automatic downstream processing (#837)

* LIMS-1462: Show characterizations on Screenings tab (#844)

* LIMS-1467: Allow lab contacts to have spaces in their names (#843)

* LIMS-1489: Update message when trying to queue containers in uploaded shipments (#847)

Author: ndg63276

api/src/Page/Contact.php

@@ -9,8 +9,8 @@ class Contact extends Page
 {
 
         public static $arg_list = array('CARDNAME' => '([\w\s\-])+',
-                              'FAMILYNAME' => '([\w\-])+',
-                              'GIVENNAME' => '([\w\-])+',
+                              'FAMILYNAME' => '([\w\s\-])+',
+                              'GIVENNAME' => '([\w\s\-])+',
                               'PHONENUMBER' => '.*',
                               'EMAILADDRESS' => '.*',
                               'LABNAME' => '([\w\s\-])+',

api/src/Page/DC.php

@@ -121,11 +121,11 @@ function _data_collections($single = null)
 
                 $where = '';
                 if ($this->arg('t') == 'sc')
-                    $where = ' AND (dc.overlap != 0 OR ifnull(et.name, dcg.experimenttype) = "Screening")';
+                    $where = ' AND (dc.overlap != 0 OR ifnull(et.name, dcg.experimenttype) in ("Screening", "Characterization"))';
                 else if ($this->arg('t') == 'gr')
                     $where = ' AND dc.axisrange = 0';
                 else if ($this->arg('t') == 'fc')
-                    $where = ' AND dc.overlap = 0 AND dc.axisrange > 0 AND dc.numberOfImages > 1 AND ifnull(et.name, dcg.experimenttype) != "Screening"';
+                    $where = ' AND dc.overlap = 0 AND dc.axisrange > 0 AND dc.numberOfImages > 1 AND ifnull(et.name, dcg.experimenttype) not in ("Screening", "Characterization")';
             } else if ($this->arg('t') == 'edge') {
                 $where2 = '';
             } else if ($this->arg('t') == 'mca') {
@@ -139,11 +139,11 @@ function _data_collections($single = null)
                 $where2 = " AND es.comments LIKE '%_FLAG_%'";
                 $where4 = " AND xrf.comments LIKE '%_FLAG_%'";
             } else if ($this->arg('t') == 'ap') {
-                $where = ' AND app.processingstatus = 1';
+                $where = " AND ifnull(et.name, dcg.experimenttype) not in ('Screening', 'Characterization') AND app.processingstatus = 1";
                 $extj[0] .= "INNER JOIN autoprocintegration ap ON dc.datacollectionid = ap.datacollectionid
                         INNER JOIN autoprocprogram app ON app.autoprocprogramid = ap.autoprocprogramid";
             } else if ($this->arg('t') == 'ph') {
-                $where = " AND app.processingstatus = 1 AND app.processingprograms in ('big_ep', 'fast_ep')";
+                $where = " AND ifnull(et.name, dcg.experimenttype) not in ('Screening', 'Characterization') AND app.processingstatus = 1 AND app.processingprograms in ('big_ep', 'fast_ep')";
                 $extj[0] .= "INNER JOIN processingjob pj ON dc.datacollectionid = pj.datacollectionid
                         INNER JOIN autoprocprogram app ON app.processingjobid = pj.processingjobid";
             } else if ($this->arg('t') == 'err') {

api/src/Page/Processing.php

@@ -141,7 +141,7 @@ function _autoproc_status($where, $ids) {
                 INNER JOIN processingjob pj ON pj.datacollectionid = dc.datacollectionid
                 INNER JOIN autoprocprogram app ON pj.processingjobid = app.processingjobid
                 LEFT OUTER JOIN autoprocintegration api ON api.autoprocprogramid = app.autoprocprogramid
-                WHERE $where AND api.autoprocintegrationid IS NULL AND pj.automatic = 1
+                WHERE $where AND api.autoprocintegrationid IS NULL
                     AND app.processingprograms NOT IN ('$filter')",
             ),
             $ids
@@ -697,11 +697,17 @@ private function _autoprocessing_query_builder($where, $group, $order = '') {
             ap.refinedcell_alpha as cell_al,
             ap.refinedcell_beta as cell_be,
             ap.refinedcell_gamma as cell_ga, 
-            (SELECT COUNT(api1.autoprocintegrationid) FROM autoprocintegration api1 WHERE api1.autoprocprogramid =  app.autoprocprogramid) as imagesweepcount,
+            (SELECT COUNT(api1.autoprocintegrationid) FROM autoprocintegration api1 WHERE api1.autoprocprogramid = app.autoprocprogramid) as imagesweepcount,
             app.processingstatus,
             app.processingmessage,
             count(distinct pjis.datacollectionid) as dccount,
             max(pjis.processingjobid) as processingjobid,
+            (SELECT IFNULL(blsg.name, bls.name) FROM processingjobparameter pjp
+              LEFT OUTER JOIN blsample bls ON pjp.parametervalue = bls.blsampleid
+              LEFT OUTER JOIN blsamplegroup blsg ON pjp.parametervalue = blsg.blsamplegroupid
+              WHERE pjp.processingjobid = pj.processingjobid
+              AND pjp.parameterkey in ('sample_id', 'sample_group_id')
+            ) as groupname,
             pj.automatic";
 
         $from = "FROM autoprocintegration api";
@@ -751,7 +757,7 @@ private function _format_auto_processing_result($table_rows, $messages_result) {
             'cell_ga',
         );
         $resolution_data = array('rlow', 'rhigh');
-        $returned_keys = array('PROCESSINGJOBID', 'IMAGESWEEPCOUNT', 'DCCOUNT', 'TYPE', 'PROCESSINGSTATUS', 'PROCESSINGMESSAGE');
+        $returned_keys = array('PROCESSINGJOBID', 'IMAGESWEEPCOUNT', 'DCCOUNT', 'TYPE', 'PROCESSINGSTATUS', 'PROCESSINGMESSAGE', 'GROUPNAME');
 
         foreach($table_rows as &$row) {
             if (!array_key_exists($row['AUTOPROCPROGRAMID'], $formatted_result)) {
@@ -772,6 +778,9 @@ private function _format_auto_processing_result($table_rows, $messages_result) {
                             $prefix = preg_match('/multi/', $value) ? '' : 'multi-';
                             $value = $row['DCCOUNT'] . 'x ' . $prefix . $value;
                         }
+                        if ($row['GROUPNAME']) {
+                            $value .= ' ('.$row['GROUPNAME'].')';
+                        }
                     }
 
 

client/src/js/models/labcontact.js

@@ -14,11 +14,11 @@ define(['backbone'], function(Backbone) {
             },
             FAMILYNAME: {
                 required: true,
-                pattern: 'wwdash',
+                pattern: 'wwsdash',
             },
             GIVENNAME: {
                 required: true,
-                pattern: 'wwdash',
+                pattern: 'wwsdash',
             },
             PHONENUMBER: {
                 required: true,

client/src/js/modules/shipment/models/dispatch.js

@@ -24,12 +24,12 @@ define(['backbone'], function(Backbone) {
 
         GIVENNAME: {
             required: function () {return this.dispatchDetailsRequired},
-            pattern: 'wwdash',
+            pattern: 'wwsdash',
         },
 
         FAMILYNAME: {
             required: function () {return this.dispatchDetailsRequired},
-            pattern: 'wwdash',
+            pattern: 'wwsdash',
         },
 
         PHONENUMBER: {

client/src/js/modules/shipment/views/dispatch.js

@@ -276,6 +276,7 @@ define(['marionette', 'views/form',
             this.dispatchCountry = this.ui.country.val()
             this.ui.courierSection.show();
             this.ui.dispatchDetails.show();
+            this.model.visitRequired = true
             this.model.dispatchDetailsRequired = true
             this.ui.submit.show();
             if (
@@ -334,6 +335,7 @@ define(['marionette', 'views/form',
             ){
                 this.model.visitRequired = false
                 this.ui.dispatchDetails.hide()
+                this.model.dispatchDetailsRequired = false
                 this.ui.submit.text("Proceed")
                 this.ui.shippingadvice.html("<mark>On clicking 'Proceed' you will be redirected to the new Diamond shipping service to book the shipment. Please ensure all stages of the form are completed.</mark><br /><br />")
             }

client/src/js/modules/types/mx/shipment/views/mx-container-add.vue

@@ -94,6 +94,9 @@
                   v-model="QUEUEFORUDC"
                   name="Queue For UDC"
                 />
+                <span v-else-if="shippingSafetyLevel === null">
+                  Cannot queue container until shipment safety level is set
+                </span>
                 <span v-else>
                   Cannot queue containers in {{ shippingSafetyLevel }} shipments
                 </span>
@@ -663,7 +666,7 @@ export default {
 
         await this.$store.dispatch('samples/save', containerId)
         this.$store.commit('notifications/addNotification', {
-          message: `New Container created, click <a href=/containers/cid/${containerId}>here</a> to view it`,
+          message: `New Container created, click <a href=/containers/cid/${containerId}>here</a> to view it. Remember to add sequences and PDBs if needed.`,
           level: 'info',
           persist: true
         })

client/src/js/modules/types/mx/shipment/views/mx-container-view.vue

@@ -106,6 +106,9 @@
                   @click="onUnQueueContainer"
                 ><i class="fa fa-times" /> Unqueue</a>
               </span>
+              <span v-else-if="shippingSafetyLevel === null">
+                Cannot queue container until shipment safety level is set
+              </span>
               <span v-else-if="shippingSafetyLevel != 'Green'">
                 Cannot queue containers in {{ shippingSafetyLevel }} shipments
               </span>