Merge pre-release/2026-R2.5 into master

api/src/Page/Download.php

@@ -155,6 +155,7 @@ function _auto_processing_plots()
                     // If we are looking for a specific plot (by attachment id) then OK...
                     if ($this->has_arg('aid')) {
                         $r['PLOTLY'] = true;
+                        error_log('LIMS-2148 - Plotly used for autoprocprogramattachmentid ' . $this->arg('aid'));
                     } else {
                         // ..if not, we should remove this from the list of returned plots
                         // Autoprocessing results use the same bespoke format for charts

api/src/Page/Sample.php

@@ -177,6 +177,7 @@ class Sample extends Page
         array('/sub/:ssid', 'get', '_get_sub_sample'),
         array('/sub/:ssid', 'patch', '_update_sub_sample'),
         array('/sub/:ssid', 'put', '_update_sub_sample_full'),
+        array('/sub/cid/:cid', 'post', '_update_container_sub_samples'),
         array('/sub', 'post', '_add_sub_sample'),
         array('/sub/:ssid', 'delete', '_delete_sub_sample'),
         array('/sub/queue/cid/:cid', 'post', '_queue_all_sub_samples'),
@@ -638,13 +639,49 @@ function _queue_all_sub_samples()
 
         $this->db->wait_rep_sync(false);
 
+        if (!sizeof($subs))
+            $this->_error('No subsamples found');
+
+        $sub_ids = array_column($subs, 'BLSUBSAMPLEID');
+        $chunks = array_chunk($sub_ids, 500);
         $ret = array();
-        foreach ($subs as $sub) {
-            array_push($ret, array(
-                'BLSUBSAMPLEID' => $sub['BLSUBSAMPLEID'], 
-                'CONTAINERQUEUESAMPLEID' => $this->_do_pre_q_sample(array('BLSUBSAMPLEID' => $sub['BLSUBSAMPLEID']))));
+
+        if ($this->has_arg('UNQUEUE')) {
+            foreach ($chunks as $chunk) {
+                $placeholders = implode(',', array_fill(0, count($chunk), '?'));
+                $this->db->pq("DELETE FROM containerqueuesample
+                    WHERE containerqueueid IS NULL
+                    AND blsubsampleid IN ($placeholders)", $chunk);
+            }
+
+            $ret = array_map(function($id) {
+                return array('BLSUBSAMPLEID' => $id, 'CONTAINERQUEUESAMPLEID' => null);
+            }, $sub_ids);
+
+        } else {
+            foreach ($chunks as $chunk) {
+                $placeholders = implode(',', array_fill(0, count($chunk), '?'));
+                $this->db->pq("INSERT INTO containerqueuesample (blsubsampleid)
+                    SELECT ss.blsubsampleid
+                    FROM blsubsample ss
+                    INNER JOIN blsample s ON s.blsampleid = ss.blsampleid
+                    INNER JOIN container c ON c.containerid = s.containerid
+                    INNER JOIN dewar d ON d.dewarid = c.dewarid
+                    INNER JOIN shipping sh ON sh.shippingid = d.shippingid
+                    WHERE sh.proposalid = ?
+                    AND ss.blsubsampleid IN ($placeholders)",
+                    array_merge(array($this->proposalid), $chunk));
+
+                $chunk_ret = $this->db->pq("SELECT blsubsampleid, containerqueuesampleid
+                    FROM containerqueuesample
+                    WHERE blsubsampleid IN ($placeholders)
+                    AND containerqueueid IS NULL", $chunk);
+
+                $ret = array_merge($ret, $chunk_ret);
+            }
         }
         $this->_output($ret);
+
     }
 
     function _sub_samples()
@@ -960,6 +997,68 @@ function _update_sub_sample_full()
     }
 
 
+    function _update_container_sub_samples()
+    {
+        if (!$this->arg('cid'))
+            $this->_error('No container specified');
+
+        if (!$this->arg('EXPERIMENTKIND'))
+            $this->_error('No experiment kind provided');
+
+        $rows = $this->db->pq("SELECT DISTINCT ss.diffractionplanid
+            FROM blsubsample ss
+            INNER JOIN blsample s ON s.blsampleid = ss.blsampleid
+            INNER JOIN diffractionplan dp ON dp.diffractionplanid = ss.diffractionplanid
+            INNER JOIN containerqueuesample cqs ON cqs.blsubsampleid = ss.blsubsampleid
+            WHERE s.containerid=:1
+            AND dp.experimentkind=:2
+            AND ss.diffractionplanid IS NOT NULL
+            AND cqs.containerqueuesampleid IS NOT NULL
+            AND cqs.containerqueueid IS NULL",
+            array($this->arg('cid'), $this->arg('EXPERIMENTKIND')));
+
+        if (!sizeof($rows)) {
+            $this->_output(array('TOTAL_UPDATED' => 0));
+            return;
+        }
+
+        $all_ids = array_column($rows, 'DIFFRACTIONPLANID');
+        $set_args = array();
+        foreach (array(
+            'REQUIREDRESOLUTION', 'EXPERIMENTKIND', 'PREFERREDBEAMSIZEX', 'PREFERREDBEAMSIZEY',
+            'EXPOSURETIME', 'BOXSIZEX', 'BOXSIZEY', 'AXISSTART', 'AXISRANGE', 'NUMBEROFIMAGES',
+            'TRANSMISSION', 'ENERGY', 'MONOCHROMATOR'
+        ) as $f) {
+            array_push($set_args, $this->has_arg($f) ? $this->arg($f) : null);
+        }
+
+        $chunks = array_chunk($all_ids, 500);
+        $total_updated = 0;
+
+        foreach ($chunks as $chunk) {
+            $start_index = sizeof($set_args) + 1;
+            $placeholders = array();
+
+            foreach ($chunk as $index => $id) {
+                array_push($placeholders, ':' . ($start_index + $index));
+            }
+
+            $id_placeholders_list = implode(',', $placeholders);
+
+            $combined_args = array_merge($set_args, $chunk);
+
+            $this->db->pq("UPDATE diffractionplan
+                SET requiredresolution=:1, experimentkind=:2, preferredbeamsizex=:3, preferredbeamsizey=:4,
+                    exposuretime=:5, boxsizex=:6, boxsizey=:7, axisstart=:8, axisrange=:9,
+                    numberofimages=:10, transmission=:11, energy=:12, monochromator=:13
+                WHERE diffractionplanid IN ($id_placeholders_list)", $combined_args);
+
+            $total_updated += sizeof($chunk);
+        }
+
+        $this->_output(array('TOTAL_UPDATED' => $total_updated));
+    }
+
 
     function _add_sub_sample()
     {

api/src/Page/Shipment.php

@@ -2532,8 +2532,12 @@ function _get_all_containers()
                 'MANUAL' => 'queuedmanualsubsamples', 'AUTO' => 'queuedautosubsamples',
             );
             $dir = $this->has_arg('order') ? ($this->arg('order') == 'asc' ? 'ASC' : 'DESC') : 'ASC';
-            if (array_key_exists($this->arg('sort_by'), $cols))
+            if (array_key_exists($this->arg('sort_by'), $cols)) {
                 $order = $cols[$this->arg('sort_by')] . ' ' . $dir;
+                if ($this->arg('sort_by') == 'NAME') {
+                    $order .= ', c.containerid ' . $dir;
+                }
+            }
         }
         // $this->db->set_debug(True);
         $rows = $this->db->paginate("SELECT $select