Merge release 2024-R3.2 into master (#810)

* LIMS-1319: Show dose for all data collection types (#791) * LIMS-954: Add ability to edit manufacturer serial no on dewars (#652) * LIMS-1276: Add printed date to shipping labels (#755) * LIMS-902: Clear sessionId from containers when requesting a dewar transfer (#673) * LIMS-277: Fix sample changer view scaling (#794) * LIMS-121: Allow use of VMXm Gridboxes and Cartridges (#732) * LIMS-1257: Allow population of source fields (#769) * LIMS-1382: Add message to users about using the shipping service (#801) --------- Co-authored-by: Mark Williams <[email protected]> Co-authored-by: Guilherme Francisco <[email protected]>
DiamondLightSource · Jul 23, 2024 · ed7962d · ed7962d
1 parent da53c52
commit ed7962d
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diff --git a/api/assets/pdf/shipment_label.php b/api/assets/pdf/shipment_label.php
@@ -8,12 +8,11 @@
             <ol>
                 <li><span class="bold">Dewar Label:</span> affix this label to your dewar which ensures it can be identified at all times at the facility</li>
                 <li><span class="bold">Outbound Address label:</span> To be attached to the outside of your transport container for shipment to facility</li>
-                <li><span class="bold">Return Address Label:</span> The return address for your shipment (Please include this in your shipment, e.g. put it behind the outward bound address or in the transport container)</li>
+                <li><span class="bold">Return Address Label:</span> The return address for your shipment (Please include this in your shipment, e.g. put it behind the outbound label or in the transport container)</li>
             </ol>
+            Please remove old paperwork immediately after you receive your dewar back from Diamond.
         </div>
 
-
-        <br />
         <br />
 
         <p class="ca bold red">1. Dewar Tracking Label</p>
@@ -49,10 +48,6 @@
                     <td class="grey px150">Safety Level</td>
                     <td><?php echo $ship['SAFETYLEVEL'] ?></td>
                 </tr>
-                <tr>
-                    <td class="grey px150">No. Parcels</td>
-                    <td><?php echo sizeof($dewars) ?></td>
-                </tr>
             </table>
 
             <table class="center px500">
@@ -68,6 +63,10 @@
                     <td class="grey px150">Local Contact</td>
                     <td><?php echo $d['BEAMLINEOPERATOR'] ?></td>
                 </tr>
+                <tr>
+                    <td class="grey px150">Printed on</td>
+                    <td><?php echo date('j M o') ?></td>
+                </tr>
             </table>
 
             <div class="float-left px150 title-wrapper">
@@ -79,7 +78,7 @@
                 <?php foreach(explode(',', $d['CONTAINERSBARCODE']) as $bar_code) { ?>
                     <div class="container-item"><?php echo strlen($bar_code) > 15 ? substr($bar_code,0,14).'+' : $bar_code ?></div>
                 <?php }?>
-                <?php if ($d['CONTAINERS'] > 10) { ?>
+                <?php if ($d['CONTAINERS'] > count(explode(',', $d['CONTAINERSBARCODE']))) { ?>
                     <div class="container-item"><?php echo " plus " . ($d['CONTAINERS'] - count(explode(',', $d['CONTAINERSBARCODE']))) . " more" ?></div>
                 <?php }?>
             </div>
@@ -158,6 +157,10 @@
                         <td class="grey px150">Local Contact</td>
                         <td><?php echo $d['BEAMLINEOPERATOR'] ?></td>
                     </tr>
+                    <tr>
+                        <td class="grey px150">Printed on</td>
+                        <td><?php echo date('j M o') ?></td>
+                    </tr>
                 </table>
 
                 <div class="left" style="width: 70px">FROM:</div>
@@ -250,6 +253,10 @@
                         <td class="grey px150">Transport Value</td>
                         <td><?php echo $d['TRANSPORTVALUE'] ?></td>
                     </tr>
+                    <tr>
+                        <td class="grey px150">Printed on</td>
+                        <td><?php echo date('j M o') ?></td>
+                    </tr>
                 </table>
 
                 <div class="left" style="width: 70px">FROM:</div>
@@ -267,4 +274,4 @@
         <?php endif; ?>
 
 
-    <?php endforeach; ?>
+    <?php endforeach; ?>
diff --git a/api/assets/pdf/styles.css b/api/assets/pdf/styles.css
@@ -123,7 +123,7 @@ table {
 }
 
 ol {
-    margin-left: 25px;
+    margin-left: 10px;
 }
 
 .bold {
@@ -185,4 +185,4 @@ ol {
 
 .float-left {
     float: left;
-}
+}
diff --git a/api/src/Page/PDF.php b/api/src/Page/PDF.php
@@ -159,7 +159,7 @@ function _shipment_label()
 
         $this->ship = $ship;
 
-        $this->dewars = $this->db->pq("SELECT bl.beamlinename, bl.beamlineoperator, TO_CHAR(bl.startdate, 'DD-MM-YYYY') as st, d.transportvalue, d.customsvalue, d.code, d.barcode, count(cq.containerqueueid) as auto, count(c.containerid) as containers, GROUP_CONCAT(COALESCE(cr.barCode, c.code) LIMIT 10) as containersBarCode
+        $this->dewars = $this->db->pq("SELECT bl.beamlinename, bl.beamlineoperator, TO_CHAR(bl.startdate, 'DD-MM-YYYY') as st, d.transportvalue, d.customsvalue, d.code, d.barcode, count(cq.containerqueueid) as auto, count(c.containerid) as containers, GROUP_CONCAT(COALESCE(cr.barCode, c.code) LIMIT 8) as containersBarCode
                 FROM dewar d 
                 LEFT OUTER JOIN blsession bl ON d.firstexperimentid = bl.sessionid 
                 LEFT OUTER JOIN container c ON c.dewarid = d.dewarid

diff --git a/api/src/Page/Sample.php b/api/src/Page/Sample.php
@@ -116,6 +116,7 @@ class Sample extends Page
         'MONOCHROMATOR' => '\w+',
         'PRESET' => '\d',
         'BEAMLINENAME' => '[\w\-]+',
+        'SOURCE' => '[\w\-]+',
 
         'queued' => '\d',
         'UNQUEUE' => '\d',
@@ -1342,8 +1343,10 @@ function _update_sample_components($initial, $final, $amounts, $crystalid)
 
     function _add_sample()
     {
-        if (!$this->has_arg('prop'))
-            $this->_error('No proposal specified');
+        if (!$this->has_arg('prop')) {
+            $this->_output(array());
+            return;
+        }
 
         // Register entire container
         if ($this->has_arg('collection')) {
@@ -1465,7 +1468,8 @@ function _prepare_sample_args($s = null)
             'SAMPLEGROUP',
             'STRATEGYOPTION',
             'MINIMUMRESOLUTION',
-            'INITIALSAMPLEGROUP'
+            'INITIALSAMPLEGROUP',
+            'SOURCE'
         ) as $f) {
             if ($s)
                 $a[$f] = array_key_exists($f, $s) ? $s[$f] : null;
@@ -1516,8 +1520,8 @@ function _do_add_sample($s)
         }
 
         $this->db->pq(
-            "INSERT INTO blsample (blsampleid,crystalid,diffractionplanid,containerid,location,comments,name,code,blsubsampleid,screencomponentgroupid,volume,packingfraction,dimension1,dimension2,dimension3,shape,looptype) VALUES (s_blsample.nextval,:1,:2,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14,:15,:16) RETURNING blsampleid INTO :id",
-            array($crysid, $did, $a['CONTAINERID'], $a['LOCATION'], $a['COMMENTS'], $a['NAME'], $a['CODE'], $a['BLSUBSAMPLEID'], $a['SCREENCOMPONENTGROUPID'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'])
+            "INSERT INTO blsample (blsampleid,crystalid,diffractionplanid,containerid,location,comments,name,code,blsubsampleid,screencomponentgroupid,volume,packingfraction,dimension1,dimension2,dimension3,shape,looptype,source) VALUES (s_blsample.nextval,:1,:2,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14,:15,:16,IFNULL(:17,CURRENT_USER)) RETURNING blsampleid INTO :id",
+            array($crysid, $did, $a['CONTAINERID'], $a['LOCATION'], $a['COMMENTS'], $a['NAME'], $a['CODE'], $a['BLSUBSAMPLEID'], $a['SCREENCOMPONENTGROUPID'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'], $a['SOURCE'])
         );
         $sid = $this->db->id();
 

diff --git a/api/src/Page/Shipment.php b/api/src/Page/Shipment.php
@@ -53,6 +53,7 @@ class Shipment extends Page
         'STATUS' => '[\w|\s|\-]+',
 
         'PURCHASEDATE' => '\d+-\d+-\d+',
+        'MANUFACTURERSERIALNUMBER' => '.*',
         'LABCONTACTID' => '\d+',
         'REPORT' => '.*',
 
@@ -126,6 +127,7 @@ class Shipment extends Page
         'PUCK' => '\d',
         'PROCESSINGPIPELINEID' => '\d+',
         'OWNERID' => '\d+',
+        'SOURCE' => '[\w\-]+',
 
         'CONTAINERREGISTRYID' => '\d+',
         'PROPOSALID' => '\d+',
@@ -620,7 +622,7 @@ function _dewar_registry()
         $args = array($this->proposalid);
         $where = 'p.proposalid=:1';
 
-        $fields = "r.dewarregistryid, max(CONCAT(p.proposalcode, p.proposalnumber)) as prop, r.facilitycode, TO_CHAR(r.purchasedate, 'DD-MM-YYYY') as purchasedate, ROUND(TIMESTAMPDIFF('DAY',r.purchasedate, CURRENT_TIMESTAMP)/30.42,1) as age, r.labcontactid, count(distinct d.dewarid) as dewars, GROUP_CONCAT(distinct CONCAT(p.proposalcode,p.proposalnumber) SEPARATOR ', ') as proposals, r.bltimestamp, TO_CHAR(max(d.bltimestamp),'DD-MM-YYYY') as lastuse, count(dr.dewarreportid) as reports";
+        $fields = "r.dewarregistryid, max(CONCAT(p.proposalcode, p.proposalnumber)) as prop, r.facilitycode, TO_CHAR(r.purchasedate, 'DD-MM-YYYY') as purchasedate, ROUND(TIMESTAMPDIFF('DAY',r.purchasedate, CURRENT_TIMESTAMP)/30.42,1) as age, r.labcontactid, count(distinct d.dewarid) as dewars, GROUP_CONCAT(distinct CONCAT(p.proposalcode,p.proposalnumber) SEPARATOR ', ') as proposals, r.bltimestamp, TO_CHAR(max(d.bltimestamp),'DD-MM-YYYY') as lastuse, count(dr.dewarreportid) as reports, r.manufacturerserialnumber";
         $group = "r.facilitycode";
 
         if ($this->has_arg('all') && $this->staff) {
@@ -712,7 +714,8 @@ function _add_dewar_registry()
         }
 
         $purchase = $this->has_arg('PURCHASEDATE') ? $this->arg('PURCHASEDATE') : '';
-        $this->db->pq("INSERT INTO dewarregistry (facilitycode, purchasedate, bltimestamp) VALUES (:1, TO_DATE(:2, 'DD-MM-YYYY'), SYSDATE)", array($fc, $purchase));
+        $serial = $this->has_arg('MANUFACTURERSERIALNUMBER') ? $this->arg('MANUFACTURERSERIALNUMBER') : '';
+        $this->db->pq("INSERT INTO dewarregistry (facilitycode, purchasedate, bltimestamp, manufacturerserialnumber) VALUES (:1, TO_DATE(:2, 'DD-MM-YYYY'), SYSDATE, :3)", array($fc, $purchase, $serial));
 
         $this->_output(array('FACILITYCODE' => $fc, 'DEWARREGISTRYID' => $this->db->id()));
     }
@@ -734,7 +737,7 @@ function _update_dewar_registry()
         else
             $dew = $dew[0];
 
-        $fields = array('PURCHASEDATE');
+        $fields = array('PURCHASEDATE', 'MANUFACTURERSERIALNUMBER');
         if ($this->staff)
             array_push($fields, 'NEWFACILITYCODE');
         foreach ($fields as $f) {
@@ -915,26 +918,25 @@ function _transfer_dewar()
         if (!$this->has_arg('LOCATION'))
             $this->_error('No location specified');
 
-        $dew = $this->db->pq("SELECT d.dewarid,s.shippingid
+        $dew = $this->db->pq("SELECT d.dewarid,s.shippingid,c.containerid
               FROM dewar d
               INNER JOIN shipping s ON s.shippingid = d.shippingid
               INNER JOIN proposal p ON p.proposalid = s.proposalid
+              LEFT JOIN container c ON d.dewarid = c.dewarid
               WHERE d.dewarid=:1 and p.proposalid=:2", array($this->arg('DEWARID'), $this->proposalid));
 
         if (!sizeof($dew))
             $this->_error('No such dewar');
-        else
-            $dew = $dew[0];
 
 
         $this->db->pq(
             "INSERT INTO dewartransporthistory (dewartransporthistoryid,dewarid,dewarstatus,storagelocation,arrivaldate) 
               VALUES (s_dewartransporthistory.nextval,:1,'transfer-requested',:2,CURRENT_TIMESTAMP) RETURNING dewartransporthistoryid INTO :id",
-            array($dew['DEWARID'], $this->arg('LOCATION'))
+            array($this->arg('DEWARID'), $this->arg('LOCATION'))
         );
 
         // Update dewar status to transfer-requested to keep consistent with history
-        $this->db->pq("UPDATE dewar set dewarstatus='transfer-requested' WHERE dewarid=:1", array($dew['DEWARID']));
+        $this->db->pq("UPDATE dewar set dewarstatus='transfer-requested' WHERE dewarid=:1", array($this->arg('DEWARID')));
 
         if ($this->has_arg('NEXTVISIT')) {
             $sessions = $this->db->pq(
@@ -947,7 +949,13 @@ function _transfer_dewar()
 
             $sessionId = !empty($sessions) ? $sessions[0]['SESSIONID'] : NULL;
 
-            $this->db->pq("UPDATE dewar SET firstexperimentid=:1 WHERE dewarid=:2", array($sessionId, $dew['DEWARID']));
+            $this->db->pq("UPDATE dewar SET firstexperimentid=:1 WHERE dewarid=:2", array($sessionId, $this->arg('DEWARID')));
+
+            if (is_null($sessionId)) {
+                foreach ($dew as $container) {
+                    $this->db->pq("UPDATE container SET sessionid=:1 WHERE containerid=:2", array($sessionId, $container['CONTAINERID']));
+                }
+            }
         }
 
         $email = new Email('dewar-transfer', '*** Dewar ready for internal transfer ***');
@@ -1550,16 +1558,17 @@ function _add_dewar()
         $fc = $this->has_arg('FACILITYCODE') ? $this->arg('FACILITYCODE') : '';
         $wg = $this->has_arg('WEIGHT') ? $this->arg('WEIGHT') : $dewar_weight;
         $exp = null;
+        $source = $this->has_arg('SOURCE') ? $this->arg('SOURCE') : null;
 
         if ($this->has_arg('FIRSTEXPERIMENTID')) {
             $experimentId = $this->arg('FIRSTEXPERIMENTID');
             $exp = !empty($experimentId) ? $this->arg('FIRSTEXPERIMENTID') : NULL;
         }
 
         $this->db->pq(
-            "INSERT INTO dewar (dewarid,code,trackingnumbertosynchrotron,trackingnumberfromsynchrotron,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,weight) 
-              VALUES (s_dewar.nextval,:1,:2,:3,:4,CURRENT_TIMESTAMP,'opened',:5,:6,:7) RETURNING dewarid INTO :id",
-            array($this->arg('CODE'), $to, $from, $this->arg('SHIPPINGID'), $exp, $fc, $wg)
+            "INSERT INTO dewar (dewarid,code,trackingnumbertosynchrotron,trackingnumberfromsynchrotron,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,weight,source)
+              VALUES (s_dewar.nextval,:1,:2,:3,:4,CURRENT_TIMESTAMP,'opened',:5,:6,:7,IFNULL(:8,CURRENT_USER)) RETURNING dewarid INTO :id",
+            array($this->arg('CODE'), $to, $from, $this->arg('SHIPPINGID'), $exp, $fc, $wg, $source)
         );
 
         $id = $this->db->id();
@@ -2185,11 +2194,12 @@ function _add_container()
         $crid = $this->has_arg('CONTAINERREGISTRYID') ? $this->arg('CONTAINERREGISTRYID') : null;
 
         $pipeline = $this->has_arg('PROCESSINGPIPELINEID') ? $this->arg('PROCESSINGPIPELINEID') : null;
+        $source = $this->has_arg('SOURCE') ? $this->arg('SOURCE') : null;
 
         $this->db->pq(
-            "INSERT INTO container (containerid,dewarid,code,bltimestamp,capacity,containertype,scheduleid,screenid,ownerid,requestedimagerid,comments,barcode,experimenttype,storagetemperature,containerregistryid,prioritypipelineid)
-              VALUES (s_container.nextval,:1,:2,CURRENT_TIMESTAMP,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14) RETURNING containerid INTO :id",
-            array($this->arg('DEWARID'), $this->arg('NAME'), $cap, $this->arg('CONTAINERTYPE'), $sch, $scr, $own, $rid, $com, $bar, $ext, $tem, $crid, $pipeline)
+            "INSERT INTO container (containerid,dewarid,code,bltimestamp,capacity,containertype,scheduleid,screenid,ownerid,requestedimagerid,comments,barcode,experimenttype,storagetemperature,containerregistryid,prioritypipelineid,source)
+              VALUES (s_container.nextval,:1,:2,CURRENT_TIMESTAMP,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14,IFNULL(:15,CURRENT_USER)) RETURNING containerid INTO :id",
+            array($this->arg('DEWARID'), $this->arg('NAME'), $cap, $this->arg('CONTAINERTYPE'), $sch, $scr, $own, $rid, $com, $bar, $ext, $tem, $crid, $pipeline, $source)
         );
 
         $cid = $this->db->id();
@@ -2665,6 +2675,7 @@ function _add_shipment()
         $rt = $this->has_arg('READYBYTIME') ? $this->arg('READYBYTIME') : null;
         $ct = $this->has_arg('CLOSETIME') ? $this->arg('CLOSETIME') : null;
         $loc = $this->has_arg('PHYSICALLOCATION') ? $this->arg('PHYSICALLOCATION') : null;
+        $source = $this->has_arg('SOURCE') ? $this->arg('SOURCE') : null;
 
         $hard_drive_enclosed = null;
         if ($this->has_arg('ENCLOSEDHARDDRIVE')) {
@@ -2727,9 +2738,9 @@ function _add_shipment()
         $extra = json_encode($extra_array);
 
         $this->db->pq(
-            "INSERT INTO shipping (shippingid, proposalid, shippingname, deliveryagent_agentname, deliveryagent_agentcode, deliveryagent_shippingdate, deliveryagent_deliverydate, bltimestamp, creationdate, comments, sendinglabcontactid, returnlabcontactid, shippingstatus, safetylevel, readybytime, closetime, physicallocation) 
-        VALUES (s_shipping.nextval,:1,:2,:3,:4,TO_DATE(:5,'DD-MM-YYYY'), TO_DATE(:6,'DD-MM-YYYY'),CURRENT_TIMESTAMP,CURRENT_TIMESTAMP,:7,:8,:9,'opened',:10, :11, :12, :13) RETURNING shippingid INTO :id",
-            array($this->proposalid, $this->arg('SHIPPINGNAME'), $an, $ac, $sd, $dd, $com, $this->arg('SENDINGLABCONTACTID'), $this->arg('RETURNLABCONTACTID'), $this->arg('SAFETYLEVEL'), $rt, $ct, $loc)
+            "INSERT INTO shipping (shippingid, proposalid, shippingname, deliveryagent_agentname, deliveryagent_agentcode, deliveryagent_shippingdate, deliveryagent_deliverydate, bltimestamp, creationdate, comments, sendinglabcontactid, returnlabcontactid, shippingstatus, safetylevel, readybytime, closetime, physicallocation, source)
+        VALUES (s_shipping.nextval,:1,:2,:3,:4,TO_DATE(:5,'DD-MM-YYYY'), TO_DATE(:6,'DD-MM-YYYY'),CURRENT_TIMESTAMP,CURRENT_TIMESTAMP,:7,:8,:9,'opened',:10, :11, :12, :13, IFNULL(:14,CURRENT_USER)) RETURNING shippingid INTO :id",
+            array($this->proposalid, $this->arg('SHIPPINGNAME'), $an, $ac, $sd, $dd, $com, $this->arg('SENDINGLABCONTACTID'), $this->arg('RETURNLABCONTACTID'), $this->arg('SAFETYLEVEL'), $rt, $ct, $loc, $source)
         );
 
         $sid = $this->db->id();
@@ -2756,9 +2767,9 @@ function _add_shipment()
                     $n = $fc ? $fc : ('Dewar' . ($i + 1));
 
                     $this->db->pq(
-                        "INSERT INTO dewar (dewarid,code,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,weight) 
-                          VALUES (s_dewar.nextval,:1,:2,CURRENT_TIMESTAMP,'opened',:3,:4,$dewar_weight) RETURNING dewarid INTO :id",
-                        array($n, $sid, $exp, $fc)
+                        "INSERT INTO dewar (dewarid,code,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,weight,source)
+                          VALUES (s_dewar.nextval,:1,:2,CURRENT_TIMESTAMP,'opened',:3,:4,:5,IFNULL(:6,CURRENT_USER)) RETURNING dewarid INTO :id",
+                        array($n, $sid, $exp, $fc, $dewar_weight, $source)
                     );
 
                     $id = $this->db->id();

diff --git a/client/src/images/block-4_no_labels_470x470.png b/client/src/images/block-4_no_labels_470x470.png
diff --git a/client/src/images/cartridge_no_labels_470x470.png b/client/src/images/cartridge_no_labels_470x470.png
diff --git a/client/src/images/gridbox_no_labels_470x470.png b/client/src/images/gridbox_no_labels_470x470.png
diff --git a/client/src/js/modules/dc/views/samplechanger.js b/client/src/js/modules/dc/views/samplechanger.js
@@ -69,7 +69,7 @@ define(['marionette', 'utils/canvas', 'utils',
             this.rpad = 0 //pad - 25
 
             var sw = 18
-            this.aspectratio = (sw/this.positions) - (this.positions <= 10 ? 0.3 : 0)
+            this.aspectratio = (this.positions <= 10 ? 1.5 : 0.4)
             this.contwidth = (this.positions * sw) + this.pad + this.rpad + 15
             console.log('sc width', this.contwidth, this.aspectratio)
             if (!this.getOption('fullScreen')) {
@@ -230,4 +230,4 @@ define(['marionette', 'utils/canvas', 'utils',
     })
 
 
-})
+})
diff --git a/client/src/js/modules/shipment/components/container-view-wrapper.vue b/client/src/js/modules/shipment/components/container-view-wrapper.vue
@@ -123,7 +123,8 @@ export default {
       // This is the current logic to determine the plate type
       // Anything other than Box, Puck or PCRStrip
       // TODO - get container types from data base
-      let is_plate = ['box', 'puck', 'pcrstrip', 'block-4', null].indexOf(containerType) == -1 && containerType.indexOf('puck') == -1
+      let puckTypes = ['cartridge', 'box', 'puck', 'pcrstrip', 'block-4']
+      let is_plate = containerType !== null && (!puckTypes.some(v => containerType.includes(v)))
 
       return is_plate
     },