Merge pre-release/2025-R3.3 into master (#954)

* LIMS-1550: Add 'Mark Dispensing' button to plate well view (#869)

* LIMS-167: Dont default to mx type for calendar/logistics views (#942)

* LIMS-1716: Multicrystal processing only shows one DC per group (#938)

* LIMS-1718: Display cluster info on multiplex jobs (#937)

* LIMS-1752: Create view for Ligand Fit pipeline (#943)

Author: ndg63276

api/src/Database/Type/MySQL.php

@@ -75,6 +75,7 @@ class MySQL extends DatabaseParent {
         'DewarReport',
         'CourierTermsAccepted',
 
+        'BLSamplePosition',
         'BLSubSample',
         'PDB',
         'Protein_has_PDB',

api/src/Downstream/Type/LigandFit.php

@@ -0,0 +1,73 @@
+<?php
+
+namespace SynchWeb\Downstream\Type;
+
+use SynchWeb\Downstream\DownstreamPlugin;
+use SynchWeb\Downstream\DownstreamResult;
+
+class LigandFit extends DownstreamPlugin {
+    var $has_images = true;
+    var $friendlyname = 'LigandFit';
+    var $has_mapmodel = array(1, 0);
+
+    function _get_ligandfit_results_json() {
+        $appid = array($this->autoprocprogramid);
+        $filepath = $this->db->pq(
+            "SELECT app.filePath, app.filename from autoprocprogramattachment app where autoprocprogramid = :1 and filename like '%.json' ",
+            $appid
+        );
+        return $filepath;
+    }
+
+    function _get_ligandfit_results_png() {
+        $appid = array($this->autoprocprogramid);
+        $filepath = $this->db->pq(
+            "SELECT app.filepath, app.filename from autoprocprogramattachment app where autoprocprogramid = :1 and filename like '%.png' ",
+            $appid
+        );
+        return $filepath;
+    }
+
+    function _get_model_appaid() {
+        $appid = array($this->autoprocprogramid);
+        $filepath = $this->db->pq(
+            "SELECT app.autoprocprogramattachmentid from autoprocprogramattachment app where autoprocprogramid = :1 and filename like '%.html' ",
+            $appid
+        );
+        if (sizeof($filepath)) {
+            return $filepath[0]["AUTOPROCPROGRAMATTACHMENTID"];
+        } else {
+            return;
+        }
+    }
+
+    function results() {
+        $json_filepath = $this->_get_ligandfit_results_json();
+        if (sizeof($json_filepath)) {
+            $json_path = $json_filepath[0]["FILEPATH"] . "/" . $json_filepath[0]["FILENAME"] ;
+            $json_data = file_get_contents($json_path);
+        } else {
+            $json_data = "[]";
+        }
+        $dat = array();
+        $appaid = $this->_get_model_appaid();
+        $dat['BLOBS'] = $appaid ? 1 : 0;
+        $dat['MODEL_APPAID'] = $appaid;
+        $dat['SOLUTIONS'] = json_decode($json_data);
+        $dat['PARENTAUTOPROCPROGRAM'] = $this->process['PROCESSINGCOMMENTS'];
+
+        $results = new DownstreamResult($this);
+        $results->data = $dat;
+
+        return $results;
+    }
+
+    function images($n = 0) {
+        $png = $this->_get_ligandfit_results_png();
+        if (sizeof($png)) {
+            return $png[0]["FILEPATH"] . "/" . $png[0]["FILENAME"];
+        } else {
+            return;
+        }
+    }
+}

api/src/Page/DC.php

@@ -37,6 +37,7 @@ class DC extends Page
         'PERSONID' => '\d+',
         'AUTOPROCPROGRAMMESSAGEID' => '\d+',
         'PROCESSINGJOBID' => '\d+',
+        'expandgroups' => '\d',
         'debug' => '\d',
         'sgid' => '\d+'
     );
@@ -381,7 +382,7 @@ function _data_collections($single = null)
         }
 
         # Set Count field
-        if ($this->has_arg('dcg') || $this->has_arg('PROCESSINGJOBID') || $this->has_arg('sgid')) {
+        if ($this->has_arg('dcg') || $this->has_arg('PROCESSINGJOBID') || $this->has_arg('sgid') || $this->has_arg('expandgroups')) {
             $count_field = 'dc.datacollectionid';
         } else {
             $count_field = 'distinct dc.datacollectiongroupid';
@@ -616,6 +617,9 @@ function _data_collections($single = null)
                     IFNULL(max(dc.rotationaxis), 'Omega') as rotationaxis,
                     dc.detector2theta";
             $groupby = "GROUP BY dc.datacollectiongroupid";
+            if ($this->has_arg('expandgroups')) {
+                $groupby = "GROUP BY dc.datacollectionid";
+            }
         }
 
         // We don't want to remove duplicates, since if two counts are equal, one might go uncounted

api/src/Page/Processing.php

@@ -978,6 +978,7 @@ private function _autoprocessing_query_builder($where, $group, $order = '') {
             (SELECT COUNT(api1.autoprocintegrationid) FROM autoprocintegration api1 WHERE api1.autoprocprogramid = app.autoprocprogramid) as imagesweepcount,
             app.processingstatus,
             app.processingmessage,
+            app.processingenvironment,
             count(distinct pjis.datacollectionid) as dccount,
             max(pjis.processingjobid) as processingjobid,
             (SELECT IFNULL(blsg.name, bls.name) FROM processingjobparameter pjp
@@ -1059,6 +1060,9 @@ private function _format_auto_processing_result($table_rows, $messages_result) {
                         if ($row['GROUPNAME']) {
                             $value .= ' ('.$row['GROUPNAME'].')';
                         }
+                        if ($row['PROCESSINGENVIRONMENT'] && strpos($row['PROCESSINGENVIRONMENT'], 'cluster=') !== false) {
+                            $value .= ' ('.$row['PROCESSINGENVIRONMENT'].')';
+                        }
                     }
 
 

api/src/Page/Proposal.php

@@ -389,7 +389,11 @@ function _get_visits($visit = null, $output = true)
         }
 
         if ($this->has_arg('ty')) {
-            $beamlines = $this->_get_beamlines_from_type($this->arg('ty'));
+            if ($this->arg('ty') == 'calendar') {
+                $beamlines = $this->_get_beamlines_from_type($this->ty);
+            } else {
+                $beamlines = $this->_get_beamlines_from_type($this->arg('ty'));
+            }
 
             if (!empty($beamlines)) {
                 $bls = implode("', '", $beamlines);

api/src/Page/Sample.php

@@ -93,8 +93,8 @@ class Sample extends Page
         'scid' => '\d+-\d+',
 
         'BLSAMPLEID' => '\d+',
-        'X' => '\d+(.\d+)?',
-        'Y' => '\d+(.\d+)?',
+        'X' => '\d*(.\d+)?',
+        'Y' => '\d*(.\d+)?',
         'Z' => '\d+(.\d+)?',
         'X2' => '\d+(.\d+)?',
         'Y2' => '\d+(.\d+)?',
@@ -799,6 +799,9 @@ private function get_sub_samples_query($where, $first_inner_select_where = '', $
                 po2.posx as x2,
                 po2.posy as y2,
                 po2.posz as z2,
+                bsp.posx as dispensex,
+                bsp.posy as dispensey,
+                bsp.posz as dispensez,
                 IF(cqs.containerqueuesampleid IS NOT NULL AND cqs.containerqueueid IS NULL, 1, 0) as readyforqueue,
                 cq.containerqueueid,
                 count(distinct IF(dc.overlap != 0,
@@ -824,7 +827,7 @@ private function get_sub_samples_query($where, $first_inner_select_where = '', $
                 INNER JOIN shipping sh ON sh.shippingid = d.shippingid
                 INNER JOIN proposal p ON p.proposalid = sh.proposalid
 
-
+                LEFT OUTER JOIN blsampleposition bsp ON bsp.blsampleid = s.blsampleid
                 LEFT OUTER JOIN containerqueuesample cqs ON cqs.blsubsampleid = ss.blsubsampleid
                 LEFT OUTER JOIN containerqueue cq ON cqs.containerqueueid = cq.containerqueueid AND cq.completedtimestamp IS NULL
                 
@@ -1903,11 +1906,12 @@ function _update_sample()
         if (!$this->has_arg('sid'))
             $this->_error('No sampleid specified');
 
-        $samp = $this->db->pq("SELECT b.blsampleid, pr.proteinid,cr.crystalid,dp.diffractionplanid 
+        $samp = $this->db->pq("SELECT b.blsampleid, pr.proteinid,cr.crystalid,dp.diffractionplanid,bsp.blsamplepositionid
               FROM blsample b 
               INNER JOIN crystal cr ON cr.crystalid = b.crystalid 
               INNER JOIN protein pr ON pr.proteinid = cr.proteinid 
               LEFT OUTER JOIN diffractionplan dp on dp.diffractionplanid = b.diffractionplanid 
+              LEFT OUTER JOIN blsampleposition bsp ON bsp.blsampleid = b.blsampleid AND bsp.positiontype='dispensing'
               WHERE pr.proposalid = :1 AND b.blsampleid = :2", array($this->proposalid, $this->arg('sid')));
 
         if (!sizeof($samp))
@@ -1980,6 +1984,34 @@ function _update_sample()
                 }
             }
         }
+
+        if ($this->has_arg('X') && $this->has_arg('Y')) {
+            $z = $this->has_arg('Z') ? $this->arg('Z') : null;
+            $pid = $samp['BLSAMPLEPOSITIONID'];
+            if ($this->arg('X') == '' && $this->arg('Y') == '') {
+                if (!empty($pid)) {
+                    $this->db->pq(
+                        "UPDATE blsampleposition SET posx=null, posy=null, posz=null, recordtimestamp=CURRENT_TIMESTAMP WHERE blsamplepositionid=:1",
+                        array($pid)
+                    );
+                }
+            } else {
+                if (empty($pid)) {
+                    $this->db->pq(
+                        "INSERT INTO blsampleposition (blsampleid, posx, posy, posz, positiontype, recordtimestamp)
+                        VALUES (:1, :2, :3, :4, 'dispensing', CURRENT_TIMESTAMP) RETURNING blsamplepositionid INTO :id",
+                        array($this->arg('sid'), $this->arg('X'), $this->arg('Y'), $z)
+                    );
+                    $pid = $this->db->id();
+                } else {
+                    $this->db->pq(
+                        "UPDATE blsampleposition SET posx=:1, posy=:2, posz=:3, recordtimestamp=CURRENT_TIMESTAMP WHERE blsamplepositionid=:4",
+                        array($this->arg('X'), $this->arg('Y'), $z, $pid)
+                    );
+                }
+            }
+            $this->_output(array('BLSAMPLEPOSITIONID' => $pid));
+        }
     }
 
 

api/src/Page/Shipment.php

@@ -1677,7 +1677,11 @@ function _get_dewars()
         }
 
         if ($this->has_arg('ty')) {
-            $bls_tmp = $this->_get_beamlines_from_type($this->arg('ty'));
+            if ($this->arg('ty') == 'overview') {
+                $bls_tmp = $this->_get_beamlines_from_type($this->ty);
+            } else {
+                $bls_tmp = $this->_get_beamlines_from_type($this->arg('ty'));
+            }
             if (!empty($bls_tmp)) {
                 $bls = implode("', '", $bls_tmp);
                 $where .= " AND se.beamlinename IN ('$bls')";

client/src/css/partials/_content.scss

@@ -1082,6 +1082,11 @@ li:last-child .visit_users {
         width: 40.5%;
         height: 300px;
 
+        &.map {
+            width: 30%;
+            height: auto;
+        }
+
         &.image-third {
             width: 32.4%;
 

client/src/js/models/sample.js

@@ -18,11 +18,17 @@ define(['backbone', 'collections/components',
             this.listenTo(this, 'change:RADIATIONSENSITIVITY', this.updateRadSen)
             this.updateRadSen()
 
+            this.listenTo(this, 'change:X', this.updatePosition)
+
             this.listenTo(this, 'change', this.updateHasData)
             this.updateHasData()
 
         },
 
+        updatePosition: function() {
+            this.save(this.changedAttributes(), { patch: true })
+        },
+
         updateHasData: function() {
             var hasData = this.get('DC') > 0 || this.get('GR') > 0 || this.get('SC') > 0
             if (hasData !== this.get('HASDATA')) this.set('HASDATA', hasData)
@@ -98,7 +104,10 @@ define(['backbone', 'collections/components',
             VOLUME: '',
             INITIALSAMPLEGROUP: '',
             COMPONENTIDS: [],
-            COMPONENTAMOUNTS: []
+            COMPONENTAMOUNTS: [],
+            X: null,
+            Y: null,
+            Z: null,
         },
 
         validation: {
@@ -225,6 +234,15 @@ define(['backbone', 'collections/components',
                 required: false,
                 pattern: 'word'
             },
+            X: {
+                required: false
+            },
+            Y: {
+                required: false
+            },
+            Z: {
+                required: false
+            },
 
             COMPONENTAMOUNTS: function(from_ui, attr, all_values) {
                 var values = all_values.components.pluck('ABUNDANCE')

client/src/js/modules/calendar/views/calendar-view.vue

@@ -244,7 +244,7 @@ export default {
           all: 1,
         }
 
-        if (app.staff) queryParams.ty = this.proposalType
+        if (app.staff) queryParams.ty = 'calendar'
         if (this.selectedBeamline !== 'all') queryParams.bl = this.selectedBeamline
 
         const visitsCollection = new Visits(null, {