Merge pre-release/2026-R3.2 into master

api/src/Downstream/Type/Dimple.php

@@ -43,7 +43,7 @@ function results() {
             return;
         }
 
-        $lfs = $this->_get_attachments(null, null, 'refmac5_restr.log');
+        $lfs = $this->_get_attachments(null, null, 'refmac%_restr.log');
         if (sizeof($lfs)) {
             $lf = $lfs[0]['FILE'];
         } else {

api/src/Page/DC.php

@@ -1171,7 +1171,7 @@ function _dc_strategies($id)
         global $strat_align;
 
         $rows = $this->db->pq("SELECT s.programversion, s.comments,
-                st.rankingresolution as rankres,
+                st.rankingresolution as rankres, sssw.dosetotal, st.screeningstrategyid,
                 ssw.wedgenumber, ssw.chi, ssw.kappa, ssw.phi, ssw.comments as sswcomments,
                 sssw.subwedgenumber, sssw.axisstart as st, sssw.exposuretime as time, sssw.transmission as tran,
                 sssw.oscillationrange as oscran, sssw.resolution as res, sssw.numberofimages as nimg, sssw.rotationaxis,
@@ -1199,6 +1199,7 @@ function _dc_strategies($id)
                 $output[$t] = array('CELL' => array(), 'STRATS' => array());
 
             $r['ATRAN'] = $r['TRAN'] / 100.0 * $r['DCTRN'];
+            $r['ROTATION'] = $r['NIMG'] * $r['OSCRAN'];
             foreach ($nf as $nff => $cols) {
                 foreach ($cols as $c) {
                     $r[$c] = number_format($r[$c], $nff);

api/src/Page/Processing.php

@@ -9,7 +9,7 @@
 class Processing extends Page {
     public static $dispatch = array(
         array('/:id(/dcg/:dcg)', 'get', '_results'),
-        array('/visit/:visit(/csv/:csv)', 'get', '_results_for_visit'),
+        array('/summary(/group/:sgid)(/protein/:pid)(/visit/:visit)(/csv/:csv)', 'get', '_summary'),
         array('/status', 'post', '_statuses'),
 
         array('/messages/status', 'post', '_ap_message_status'),
@@ -27,6 +27,8 @@ class Processing extends Page {
         'id' => '\d+',
         'ids' => '\d+',
         'dcg' => '\d+',
+        'pid' => '\d+',
+        'sgid' => '\d+',
         'visit' => '\w+\d+-\d+',
         'map' => '\d+',
         'n' => '\d+',
@@ -382,24 +384,56 @@ function _statuses() {
         $this->_output($out);
     }
 
-    function _results_for_visit() {
-        if (!($this->has_arg('visit'))) {
-            $this->_error('No visit specified');
-        }
-        $pattern = '/([A-z]+)(\d+)-(\d+)/';
-        preg_match($pattern, $this->arg('visit'), $matches);
-        if (!sizeof($matches))
-            $this->_error('No such visit');
+    function _summary() {
+        $where = 'dc.overlap = 0 AND dc.axisrange > 0 AND app.processingstatus = 1';
+        $join = '';
+        if ($this->has_arg('visit')) {
+            $pattern = '/([A-z]+)(\d+)-(\d+)/';
+            preg_match($pattern, $this->arg('visit'), $matches);
+            if (!sizeof($matches))
+                $this->_error('No such visit');
+
+            $info = $this->db->pq("SELECT s.sessionid FROM blsession s
+                INNER JOIN proposal p ON (p.proposalid = s.proposalid)
+                WHERE p.proposalid=:1 AND p.proposalcode=:2 AND p.proposalnumber=:3 AND s.visit_number=:4",
+                array($this->proposalid, $matches[1], $matches[2], $matches[3])
+            );
 
-        $info = $this->db->pq("SELECT s.sessionid FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE p.proposalcode=:1 AND p.proposalnumber=:2 AND s.visit_number=:3", array($matches[1], $matches[2], $matches[3]));
+            if (!sizeof($info)) {
+                $this->_error('No such visit');
+            }
 
-        if (!sizeof($info)) {
-            $this->_error('No such visit');
-        }
+            $args = array($info[0]['SESSIONID']);
+            $where .= ' AND dc.sessionid=:1';
+        } else if ($this->has_arg('pid')) {
+            $info = $this->db->pq("SELECT pr.proteinid FROM protein pr
+                WHERE pr.proposalid=:1 AND pr.proteinid=:2",
+                array($this->proposalid, $this->arg('pid'))
+            );
+
+            if (!sizeof($info)) {
+                $this->_error('No such protein');
+            }
+
+            $args = array($info[0]['PROTEINID']);
+            $where .= ' AND c.proteinid=:1';
+            $join = 'INNER JOIN crystal c on smp.crystalid=c.crystalid';
+        } else if ($this->has_arg('sgid')) {
+            $info = $this->db->pq("SELECT blsg.blsamplegroupid FROM blsamplegroup blsg
+                WHERE blsg.proposalid=:1 AND blsg.blsamplegroupid=:2",
+                array($this->proposalid, $this->arg('sgid'))
+            );
 
-        $args = array($info[0]['SESSIONID']);
+            if (!sizeof($info)) {
+                $this->_error('No such sample group');
+            }
 
-        $where = 'dc.sessionid=:1 AND dc.overlap = 0 AND dc.axisrange > 0 AND app.processingstatus = 1';
+            $args = array($info[0]['BLSAMPLEGROUPID']);
+            $where .= ' AND bhb.blsamplegroupid=:1';
+            $join = 'INNER JOIN BLSampleGroup_has_BLSample bhb on smp.blsampleid=bhb.blsampleid';
+        } else {
+            $this->_error('No visit, protein or group specified');
+        }
 
         if ($this->has_arg('pipeline')) {
             $st = sizeof($args);
@@ -489,6 +523,7 @@ function _results_for_visit() {
         $jobs = $this->db->pq(
             "SELECT dc.datacollectionid as id,
                 CONCAT(dc.imageprefix, '_', dc.datacollectionnumber) as prefix,
+                CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit,
                 smp.name as sample,
                 smp.blsampleid,
                 ".self::EVTOA."/dc.wavelength as energy,
@@ -518,7 +553,10 @@ function _results_for_visit() {
                 apssinner.ccanomalous as innerccanom,
                 app.autoprocprogramid as aid
                 FROM datacollection dc
+                INNER JOIN blsession s ON dc.sessionid = s.sessionid
+                INNER JOIN proposal p ON s.proposalid = p.proposalid
                 LEFT OUTER JOIN blsample smp ON dc.blsampleid = smp.blsampleid
+                $join
                 INNER JOIN processingjob pj ON dc.datacollectionid = pj.datacollectionid
                 INNER JOIN autoprocprogram app ON pj.processingjobid = app.processingjobid
                 INNER JOIN autoproc ap ON app.autoprocprogramid=ap.autoprocprogramid
@@ -583,7 +621,14 @@ function _results_for_visit() {
 
         if ($this->has_arg('csv')) {
             $this->app->response->headers->set("Content-type", "text/csv");
-            Utils::setDispositionAttachment($this->app->response, $this->arg('visit') . "_summary.csv");
+            if ($this->has_arg('visit')) {
+                $filename = 'visit_' . $this->arg('visit') . "_summary.csv";
+            } else if ($this->has_arg('pid')) {
+                $filename = 'protein_' . $this->arg('pid') . "_summary.csv";
+            } else {
+                $filename = 'group_' . $this->arg('sgid') . "_summary.csv";
+            }
+            Utils::setDispositionAttachment($this->app->response, $filename);
             if (!empty($data)) {
                 print implode(',', array_keys($data[0])) . "\n";
             }

api/src/Page/Sample.php

@@ -2013,7 +2013,7 @@ function _distinct_proteins()
               LEFT OUTER JOIN concentrationtype ct ON ct.concentrationtypeid = pr.concentrationtypeid
               WHERE pr.acronym is not null AND $where
               GROUP BY ct.symbol, pr.acronym, pr.name, pr.global
-              ORDER BY lower(pr.acronym)", $args);
+              ORDER BY lower(pr.acronym), pr.proteinid", $args);
 
         $this->_output($rows);
     }