Merge pre-release/2024-R4.3 into master (#842)

* LIMS-1368: Fix incorrectly summed dose for DC groups when filtered (#803)

* LIMS-1099: Limit what can be done with red proteins (#827)

* LIMS-14: Show a direct link to the autoprocessing log (#805)

* LIMS-1422: Reprocessing dialog edits the end value unpredictably (#819)

* LIMS-1424: Show visit for each container if set (#828)

* LIMS-1425: Show samples with no processing as grey (#820)

api/src/Page/DC.php

@@ -440,7 +440,7 @@ function _data_collections($single = null)
                     dc.c2lens,
                     dc.objaperture,
                     dc.magnification,
-                    dc.totalexposeddose as totaldose,
+                    dose.total as totaldose,
                     CAST(dc.totalabsorbeddose AS DECIMAL(5, 2)) as totalabsdose,
                     d.detectorpixelsizehorizontal,
                     d.detectorpixelsizevertical,
@@ -574,7 +574,7 @@ function _data_collections($single = null)
                     max(dc.c2lens) as c2lens,
                     max(dc.objaperture) as objaperture,
                     max(dc.magnification) as magnification,
-                    sum(dc.totalabsorbeddose) as totaldose,
+                    dose.total as totaldose,
                     CAST(dc.totalabsorbeddose AS DECIMAL(5, 2)) as totalabsdose,
                     max(d.detectormanufacturer) as detectormanufacturer,
                     max(d.detectormodel) as detectormodel,
@@ -660,6 +660,9 @@ function _data_collections($single = null)
                 SELECT $extcg $fields 
                 FROM datacollection dc
                 INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid
+                INNER JOIN (
+                    select datacollectiongroupid, sum(totalabsorbeddose) as total from datacollection group by datacollectiongroupid) dose
+                    ON dc.datacollectiongroupid = dose.datacollectiongroupid
                 INNER JOIN blsession ses ON ses.sessionid = dcg.sessionid
                 LEFT OUTER JOIN experimenttype et on dcg.experimenttypeid = et.experimenttypeid
                 $sample_joins[0]

api/src/Page/Download.php

@@ -56,6 +56,7 @@ class Download extends Page
 
         array('/ap/attachments(/:AUTOPROCPROGRAMATTACHMENTID)(/dl/:download)', 'get', '_get_autoproc_attachments'),
         array('/ap/archive/:AUTOPROCPROGRAMID', 'get', '_get_autoproc_archive'),
+        array('/ap/log/:AUTOPROCPROGRAMID', 'get', '_get_autoproc_log'),
     );
 
 
@@ -220,7 +221,7 @@ function __get_autoproc_attachments()
                 INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid
                 INNER JOIN blsession s ON s.sessionid = dcg.sessionid
                 WHERE s.proposalid=:1 $where
-                ORDER BY importancerank"
+                ORDER BY importancerank, filename"
         ), $args);
 
         return $rows;
@@ -413,6 +414,48 @@ function _get_attachment()
         }
     }
 
+    # ------------------------------------------------------------------------
+    # Get the most important log of an autoprocessing job
+    function _get_autoproc_log()
+    {
+
+        if (!$this->has_arg('prop')) {
+            $this->_error('No proposal specified');
+        }
+        $args = array($this->proposalid, $this->arg('AUTOPROCPROGRAMID'));
+
+        $rows = $this->db->union(array(
+            "SELECT app.autoprocprogramid, appa.filename, appa.filepath
+                FROM autoprocintegration api
+                INNER JOIN autoprocprogram app ON api.autoprocprogramid = app.autoprocprogramid
+                INNER JOIN autoprocprogramattachment appa ON appa.autoprocprogramid = app.autoprocprogramid
+                INNER JOIN datacollection dc ON dc.datacollectionid = api.datacollectionid
+                INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid
+                INNER JOIN blsession s ON s.sessionid = dcg.sessionid
+                WHERE s.proposalid=:1
+                AND app.autoprocprogramid=:2
+                AND appa.importancerank=1
+                AND appa.filetype='Log'",
+            "SELECT app.autoprocprogramid, appa.filename, appa.filepath
+                FROM autoprocprogram app
+                INNER JOIN processingjob pj on pj.processingjobid = app.processingjobid
+                INNER JOIN autoprocprogramattachment appa ON appa.autoprocprogramid = app.autoprocprogramid
+                INNER JOIN datacollection dc ON dc.datacollectionid = pj.datacollectionid
+                INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid
+                INNER JOIN blsession s ON s.sessionid = dcg.sessionid
+                WHERE s.proposalid=:1
+                AND app.autoprocprogramid=:2
+                AND appa.importancerank=1
+                AND appa.filetype='Log'"
+        ), $args);
+
+        if (!sizeof($rows)) {
+            return $this->_error('No log file found');
+        }
+        $this->_get_file($rows[0]['AUTOPROCPROGRAMID'], $rows[0]);
+
+    }
+
 
     # ------------------------------------------------------------------------
     # Get an archive of an autoproc

api/src/Page/Sample.php

@@ -1819,12 +1819,17 @@ function _distinct_proteins()
             $where .= ' AND pr.externalid IS NOT NULL';
         }
 
-        $has_safety_level = $this->has_arg('SAFETYLEVEL');
-        if ($has_safety_level && $this->arg('SAFETYLEVEL') === 'ALL') {
-            $where .= ' AND pr.safetyLevel IS NOT NULL';
-        } else if ($has_safety_level && $this->arg('SAFETYLEVEL') !== 'ALL') {
-            $where .= ' AND pr.safetyLevel=:' . (sizeof($args) + 1);
-            array_push($args, $this->arg('SAFETYLEVEL'));
+        if ($this->has_arg('SAFETYLEVEL')) {
+            if ($this->arg('SAFETYLEVEL') === 'ALL') {
+                $where .= ' AND pr.safetyLevel IS NOT NULL';
+            } else if (strtolower($this->arg('SAFETYLEVEL')) === 'yellow') {
+                $where .= " AND pr.safetyLevel in ('green','yellow')";
+            } else if (strtolower($this->arg('SAFETYLEVEL')) === 'red') {
+                $where .= " AND pr.safetyLevel in ('green','yellow','red')";
+            } else {
+                $where .= ' AND pr.safetyLevel=:' . (sizeof($args) + 1);
+                array_push($args, $this->arg('SAFETYLEVEL'));
+            }
         }
 
         if ($this->has_arg('term')) {

api/src/Page/Shipment.php

@@ -1626,7 +1626,7 @@ function _get_dewars()
                 $order = $cols[$this->arg('sort_by')] . ' ' . $dir;
         }
 
-        $dewars = $this->db->paginate("SELECT CONCAT(p.proposalcode, p.proposalnumber) as prop, CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number) as firstexperiment, r.labcontactid, se.beamlineoperator as localcontact, se.beamlinename, TO_CHAR(se.startdate, 'HH24:MI DD-MM-YYYY') as firstexperimentst, d.firstexperimentid, s.shippingid, s.shippingname, d.facilitycode, count(c.containerid) as ccount, (case when se.visit_number > 0 then (CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number)) else '' end) as exp, d.code, d.barcode, d.storagelocation, d.dewarstatus, d.dewarid,  d.trackingnumbertosynchrotron, d.trackingnumberfromsynchrotron, d.externalShippingIdFromSynchrotron, s.deliveryagent_agentname, d.weight, d.deliveryagent_barcode, GROUP_CONCAT(c.code SEPARATOR ', ') as containers, s.sendinglabcontactid, s.returnlabcontactid, pe.givenname, pe.familyname
+        $dewars = $this->db->paginate("SELECT CONCAT(p.proposalcode, p.proposalnumber) as prop, CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number) as firstexperiment, r.labcontactid, se.beamlineoperator as localcontact, se.beamlinename, TO_CHAR(se.startdate, 'HH24:MI DD-MM-YYYY') as firstexperimentst, d.firstexperimentid, s.shippingid, s.shippingname, d.facilitycode, count(c.containerid) as ccount, (case when se.visit_number > 0 then (CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number)) else '' end) as exp, d.code, d.barcode, d.storagelocation, d.dewarstatus, d.dewarid,  d.trackingnumbertosynchrotron, d.trackingnumberfromsynchrotron, d.externalShippingIdFromSynchrotron, s.deliveryagent_agentname, d.weight, d.deliveryagent_barcode, GROUP_CONCAT(c.code SEPARATOR ', ') as containers, s.sendinglabcontactid, s.returnlabcontactid, pe.givenname, pe.familyname, s.safetylevel as shippingsafetylevel
               FROM dewar d 
               LEFT OUTER JOIN container c ON c.dewarid = d.dewarid 
               INNER JOIN shipping s ON d.shippingid = s.shippingid 
@@ -1700,6 +1700,39 @@ function _add_dewar()
         $this->_output(array('DEWARID' => $id));
     }
 
+    # Check new safety level is ok
+    function _check_safety_level()
+    {
+        $ship = $this->db->pq("SELECT cq.containerqueueid, p.safetylevel FROM dewar d
+            LEFT OUTER JOIN container c on c.dewarid = d.dewarid
+            LEFT OUTER JOIN containerqueue cq on cq.containerid = c.containerid
+            LEFT OUTER JOIN blsample b ON b.containerid = c.containerid
+            LEFT OUTER JOIN crystal cr ON cr.crystalid = b.crystalid
+            LEFT OUTER JOIN protein p ON p.proteinid = cr.proteinid
+            WHERE d.shippingid = :1", array($this->arg('sid')));
+        if (strtolower($this->arg('SAFETYLEVEL')) == 'green') {
+            foreach ($ship as $s) {
+                if (strtolower($s['SAFETYLEVEL']) == 'yellow')
+                    $this->_error('Cannot set safety level to green as one or more samples are yellow.');
+                if (strtolower($s['SAFETYLEVEL']) == 'red')
+                    $this->_error('Cannot set safety level to green as one or more samples are red.');
+            }
+        } else if (strtolower($this->arg('SAFETYLEVEL')) == 'yellow') {
+            foreach ($ship as $s) {
+                if ($s['CONTAINERQUEUEID'] != null)
+                    $this->_error('Cannot set safety level to yellow as one or more containers are queued.');
+                if (strtolower($s['SAFETYLEVEL']) == 'red')
+                    $this->_error('Cannot set safety level to yellow as one or more samples are red.');
+            }
+        } else {
+            foreach ($ship as $s) {
+                if ($s['CONTAINERQUEUEID'] != null)
+                    $this->_error('Cannot set safety level to red as one or more containers are queued.');
+            }
+        }
+    }
+
+
     # Update shipment
     function _update_shipment()
     {
@@ -1721,6 +1754,9 @@ function _update_shipment()
                 if (in_array($f, array('DELIVERYAGENT_DELIVERYDATE', 'DELIVERYAGENT_SHIPPINGDATE'))) {
                     $fl = "TO_DATE(:1, 'DD-MM-YYYY')";
                 }
+                if ($f == 'SAFETYLEVEL') {
+                    $this->_check_safety_level();
+                }
 
                 $this->db->pq("UPDATE shipping SET $f=$fl WHERE shippingid=:2", array($this->arg($f), $this->arg('sid')));
 
@@ -2120,6 +2156,7 @@ function _get_all_containers()
         }
         // $this->db->set_debug(True);
         $rows = $this->db->paginate("SELECT round(TIMESTAMPDIFF('HOUR', min(ci.bltimestamp), CURRENT_TIMESTAMP)/24,1) as age, case when count(ci2.containerinspectionid) > 1 then 0 else 1 end as allow_adhoc, c.scheduleid, c.screenid, sc.name as screen, c.imagerid, i.temperature as temperature, i.name as imager, TO_CHAR(max(ci.bltimestamp), 'HH24:MI DD-MM-YYYY') as lastinspection, round(TIMESTAMPDIFF('HOUR', max(ci.bltimestamp), CURRENT_TIMESTAMP)/24,1) as lastinspectiondays, count(distinct ci.containerinspectionid) as inspections, CONCAT(p.proposalcode, p.proposalnumber) as prop, c.bltimestamp, c.samplechangerlocation, c.beamlinelocation, d.dewarstatus, c.containertype, c.capacity, c.containerstatus, c.containerid, c.code as name, d.code as dewar, sh.shippingname as shipment, d.dewarid, sh.shippingid, count(distinct s.blsampleid) as samples, cq.containerqueueid, TO_CHAR(cq.createdtimestamp, 'DD-MM-YYYY HH24:MI') as queuedtimestamp, CONCAT(p.proposalcode, p.proposalnumber, '-', ses.visit_number) as visit, ses.beamlinename, c.requestedreturn, c.requestedimagerid, c.comments, c.experimenttype, c.storagetemperature, c.barcode, reg.barcode as registry, reg.containerregistryid,
+                sh.safetylevel as shippingsafetylevel,
                 (SELECT sch.name FROM schedule sch WHERE sch.scheduleid = c.scheduleid) as schedule,
                 (SELECT i2.name FROM imager i2 WHERE i2.imagerid = c.requestedimagerid) as requestedimager,
                 (SELECT count(distinct ss.blsubsampleid) FROM blsubsample ss RIGHT OUTER JOIN blsample s2 ON s2.blsampleid = ss.blsampleid WHERE s2.containerid = c.containerid AND ss.source='manual') as subsamples,

client/src/js/models/shipment.js

@@ -18,6 +18,11 @@ define(['backbone'], function (Backbone) {
         pattern: 'fcode',
       },
 
+      FIRSTEXPERIMENTID: {
+        required: false,
+        pattern: 'number',
+      },
+
       REMOTEORMAILIN: {
         required: false,
       },

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

@@ -27,7 +27,7 @@ define(['marionette', 'modules/dc/models/distl', 'utils',
       },
 
       plotSelected: function(e, ranges) {
-          this.trigger('plot:select', Math.floor(ranges.xaxis.from), Math.ceil(ranges.xaxis.to))
+          this.trigger('plot:select', Math.round(ranges.xaxis.from), Math.round(ranges.xaxis.to))
       },
 
       plotUnselected: function(e) {
@@ -112,4 +112,4 @@ define(['marionette', 'modules/dc/models/distl', 'utils',
       }
   })       
 
-})
+})

client/src/js/modules/dc/views/reprocess2.js

@@ -110,13 +110,19 @@ define(['backbone', 'marionette', 'views/dialog',
             var si = parseInt(this.model.get('SI'))
             var ni = parseInt(this.model.get('NUMIMG'))
 
-            if (this.ui.st.val() > (si+ni-1)) this.ui.st.val(si+ni-1)
-            if (this.ui.st.val() < si) this.ui.st.val(si)
+            if (this.ui.st.val()) {
+                if (this.ui.st.val() > (si+ni-1)) this.ui.st.val(si+ni-1)
+                if (this.ui.st.val() < si) this.ui.st.val(si)
+            }
 
-            if (this.ui.en.val() > (si+ni-1)) this.ui.en.val(si+ni-1)
-            if (this.ui.en.val() < si) this.ui.en.val(si)
+            if (this.ui.en.val()) {
+                if (this.ui.en.val() > (si+ni-1)) this.ui.en.val(si+ni-1)
+                if (this.ui.en.val() < si) this.ui.en.val(si)
+            }
 
-            this.plotview.setSelection(parseInt(this.ui.st.val()), parseInt(this.ui.en.val()))
+            if (this.ui.st.val() && this.ui.en.val()) {
+                this.plotview.setSelection(parseInt(this.ui.st.val()), parseInt(this.ui.en.val()))
+            }
         },
 
         initialize: function(options) {
@@ -377,7 +383,7 @@ define(['backbone', 'marionette', 'views/dialog',
                 }, this)
 
                 $.when.apply($, reqs).done(function() {
-                    app.alert({ message: jobs+' reprocessing job(s) successfully submitted'})
+                    app.message({ message: jobs+' reprocessing job(s) successfully submitted'})
                     _.each(rps, function(rp) {
                         self._enqueue({ PROCESSINGJOBID: rp.get('PROCESSINGJOBID') })
                     })
@@ -463,7 +469,7 @@ define(['backbone', 'marionette', 'views/dialog',
                         reqs.push(reprocessingsweeps.save())
 
                         $.when.apply($, reqs).done(function() {
-                            app.alert({ message: '1 reprocessing job successfully submitted'})
+                            app.message({ message: '1 reprocessing job successfully submitted'})
                             self._enqueue({ PROCESSINGJOBID: reprocessing.get('PROCESSINGJOBID') })
                         })
                     },

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

@@ -250,7 +250,7 @@ define(['marionette', 'backbone', 'utils', 'backbone-validation'], function(Mari
 
                                 this.ctx.fillStyle = sample.get(this.rankOption.value)
                                     ? utils.rainbow(val/4) 
-                                    : (sample.get(this.rankOption.check) > 0 ? 'yellow' : '#dfdfdf')
+                                    : '#dfdfdf'
                                 this.ctx.fill()
 
                             } else {

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

@@ -200,7 +200,7 @@ define(['marionette',
 
             var edit = new Editable({ model: this.model, el: this.$el })
             edit.create('SHIPPINGNAME', 'textlong')
-            edit.create('SAFETYLEVEL', 'select', { data: {'Green': 'Green', 'Yellow':'Yellow', 'Red': 'Red'} })
+            edit.create('SAFETYLEVEL', 'select', { data: {'Green': 'Green', 'Yellow':'Yellow', 'Red': 'Red'}, alert: true, revert: true })
             edit.create('COMMENTS', 'textarea')
             edit.create('DELIVERYAGENT_AGENTNAME', 'text')
             edit.create('DELIVERYAGENT_AGENTCODE', 'text')

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

@@ -63,6 +63,7 @@ define(['marionette', 'views/form',
             'click a.add_lc': 'addLC',
             'click @ui.noexp': 'updateFirstExp',
             'click @ui.dynamic': 'updateDynamicSchedule',
+            'change select[name^=SAFETYLEVEL]': 'changeSafetyLevel',
         },
 
         ui: {
@@ -73,6 +74,8 @@ define(['marionette', 'views/form',
             noexp: 'input[name=noexp]',
             dynamic: 'input[name=DYNAMIC]', // A checkbox to indicate dynamic/remote mail-in scheduling
             comments: 'textarea[name=COMMENTS]', // We need this so we can prefill comments to aid users
+            safetylevel: 'select[name^=SAFETYLEVEL]',
+            udcresponsive: '.udcresponsive',
         },
 
         addLC: function(e) {
@@ -97,12 +100,24 @@ define(['marionette', 'views/form',
             app.alert({ message: 'Something went wrong registering this shipment, please try again'})
         },
 
+        changeSafetyLevel: function() {
+            if (this.ui.safetylevel.val() === 'Green') {
+                this.ui.udcresponsive.show()
+            } else {
+                this.ui.noexp.prop('checked', false)
+                this.updateFirstExp()
+                this.ui.dynamic.prop('checked', false)
+                this.updateDynamicSchedule()
+                this.ui.udcresponsive.hide()
+            }
+        },
+
         updateFirstExp: function() {
             if (this.ui.noexp.is(':checked')) {
                 this.ui.first.html('<option value=""> - </option>')
                 this.ui.dynamic.prop('checked', false)
             } else {
-                this.ui.first.html(this.visits.opts())
+                this.ui.first.html('<option value="!">Please select one</option>'+this.visits.opts())
             }
         },
 
@@ -121,7 +136,7 @@ define(['marionette', 'views/form',
                 }
             } else {
                 this.model.validation.REMOTEORMAILIN.required = false
-                this.ui.first.html(this.visits.opts())
+                this.ui.first.html('<option value="!">Please select one</option>'+this.visits.opts())
                 this.$el.find(".remoteform").hide()
                 if (industrial_visit) {
                     this.$el.find(".remoteormailin").hide()

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

@@ -128,7 +128,7 @@ export default {
         proteinsCollection.queryParams.external = 1
       }
 
-      proteinsCollection.queryParams.SAFETYLEVEL = 'ALL'
+      proteinsCollection.queryParams.SAFETYLEVEL = this.shippingSafetyLevel
 
       const result = await this.$store.dispatch('getCollection', proteinsCollection)
       this.proteins = result.toJSON()