Merge pull request #750 from DiamondLightSource/pre-release/2024-R1.4

Pre release/2024 r1.4
DiamondLightSource · Apr 2, 2024 · 0701128 · 0701128
2 parents 6d7bd13 + ea029f5
commit 0701128
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Showing 8 changed files with 773 additions and 53 deletions.
diff --git a/api/src/Page/DC.php b/api/src/Page/DC.php
@@ -976,7 +976,7 @@ function _data_collections($single = null)
 
             // Data collections
             if ($dc['TYPE'] == 'data') {
-                $nf = array(1 => array('AXISSTART'), 2 => array('RESOLUTION', 'TRANSMISSION', 'AXISRANGE'), 4 => array('WAVELENGTH', 'EXPOSURETIME'));
+                $nf = array(1 => array('AXISSTART', 'CHISTART', 'PHI', 'OVERLAP'), 2 => array('RESOLUTION', 'TRANSMISSION', 'AXISRANGE', 'TOTALDOSE'), 4 => array('WAVELENGTH', 'EXPOSURETIME'));
 
                 $dc['DIRFULL'] = $dc['DIR'];
                 $dc['DIR'] = preg_replace('/.*\/' . $this->arg('prop') . '-' . $dc['VN'] . '\//', '', $dc['DIR']);

diff --git a/api/src/Page/Sample.php b/api/src/Page/Sample.php
@@ -122,6 +122,7 @@ class Sample extends Page
         'UNQUEUE' => '\d',
         'nodata' => '\d',
         'notcompleted' => '\d',
+        'filter' => '\w+',
 
         // external is a flag to indicate this protein/sample has a user office system id
         // whereas externalid is the actual reference
@@ -594,6 +595,17 @@ function _queue_all_sub_samples()
 
         $args = array($this->proposalid, $this->arg('cid'), $this->arg('cid'), $this->arg('cid'));
         $where = ' AND c.containerid=:2 AND cq2.completedtimestamp IS NULL';
+
+        if ($this->has_arg('filter')) {
+            $filters = array(
+                'manual' => " AND ss.source='manual'",
+                'auto' => " AND ss.source='auto'",
+                'point' => " AND dp.experimentkind='SAD'",
+                'region' => " AND dp.experimentkind='MESH'",
+            );
+            $where .= $filters[$this->arg('filter')];
+        }
+
         $first_inner_select_where = ' AND s.containerid=:3';
         $second_inner_select_where = ' AND s.containerid=:4';
 
@@ -1715,12 +1727,24 @@ function _proteins()
 
         // Only display original UAS approved proteins (not clones which have the same externalId)
         if ($this->has_arg('original') && $this->arg('original') == 1) {
-            $group = 'pr.externalId';
-            $order .= ', pr.bltimeStamp DESC';
+            $where .= ' AND pr.proteintype = "ORIGIN:UAS"';
         }
 
         if ($this->has_arg('sort_by')) {
-            $cols = array('NAME' => 'pr.name', 'ACRONYM' => 'pr.acronym', 'MOLECULARMASS' => 'pr.molecularmass', 'HASSEQ' => "CASE WHEN sequence IS NULL THEN 'No' ELSE 'Yes' END");
+            $cols = array(
+                'NAME' => 'pr.name',
+                'ACRONYM' => 'pr.acronym',
+                'MOLECULARMASS' => 'pr.molecularmass',
+                'DENSITY' => 'pr.density',
+                'SEQUENCE' => 'pr.sequence',
+                'SAFETYLEVEL' => 'pr.safetylevel',
+                'HASSEQ' => "CASE WHEN sequence IS NULL THEN 'No' ELSE 'Yes' END",
+                'PDBS' => 'pdbs',
+                'CONCENTRATIONTYPE' => 'concentrationtype',
+                'COMPONENTTYPE' => 'componenttype',
+                'DCOUNT' => 'dcount',
+                'SCOUNT' => 'scount'
+            );
             $dir = $this->has_arg('order') ? ($this->arg('order') == 'asc' ? 'ASC' : 'DESC') : 'ASC';
             if (array_key_exists($this->arg('sort_by'), $cols))
                 $order = $cols[$this->arg('sort_by')] . ' ' . $dir;
@@ -1736,56 +1760,23 @@ function _proteins()
                                 HEX(pr.externalid) as externalid,
                                 pr.density,
                                 count(php.proteinid) as pdbs,
-                                pr.safetylevel
+                                pr.safetylevel,
+                                count(dc.datacollectionid) as dcount,
+                                count(b.blsampleid) as scount
 
                                 FROM protein pr
                                 LEFT OUTER JOIN concentrationtype ct ON ct.concentrationtypeid = pr.concentrationtypeid
                                 LEFT OUTER JOIN componenttype cmt ON cmt.componenttypeid = pr.componenttypeid
                                 LEFT OUTER JOIN protein_has_pdb php ON php.proteinid = pr.proteinid
-                                /*LEFT OUTER JOIN crystal cr ON cr.proteinid = pr.proteinid
+                                LEFT OUTER JOIN crystal cr ON cr.proteinid = pr.proteinid
                                 LEFT OUTER JOIN blsample b ON b.crystalid = cr.crystalid
-                                LEFT OUTER JOIN datacollection dc ON b.blsampleid = dc.blsampleid*/
+                                LEFT OUTER JOIN datacollection dc ON b.blsampleid = dc.blsampleid
                                 INNER JOIN proposal p ON p.proposalid = pr.proposalid
                                 $join
                                 WHERE $where
                                 GROUP BY $group
                                 ORDER BY $order", $args);
 
-        $ids = array();
-        $wcs = array();
-        foreach ($rows as $r) {
-            array_push($ids, $r['PROTEINID']);
-            array_push($wcs, 'pr.proteinid=:' . sizeof($ids));
-        }
-
-        $dcs = array();
-        $scs = array();
-
-        if (sizeof($ids)) {
-            $dcst = $this->db->pq('SELECT pr.proteinid, count(dc.datacollectionid) as dcount FROM datacollection dc INNER JOIN blsample s ON s.blsampleid=dc.blsampleid INNER JOIN crystal cr ON cr.crystalid = s.crystalid INNER JOIN protein pr ON pr.proteinid = cr.proteinid WHERE ' . implode(' OR ', $wcs) . ' GROUP BY pr.proteinid', $ids);
-
-
-            foreach ($dcst as $d) {
-                $dcs[$d['PROTEINID']] = $d['DCOUNT'];
-            }
-
-            $scst = $this->db->pq('SELECT pr.proteinid, count(s.blsampleid) as scount FROM blsample s INNER JOIN crystal cr ON cr.crystalid = s.crystalid INNER JOIN protein pr ON pr.proteinid = cr.proteinid WHERE ' . implode(' OR ', $wcs) . ' GROUP BY pr.proteinid', $ids);
-
-            foreach ($scst as $d) {
-                $scs[$d['PROTEINID']] = $d['SCOUNT'];
-            }
-        }
-
-        foreach ($rows as &$r) {
-            $dcount = array_key_exists($r['PROTEINID'], $dcs) ? $dcs[$r['PROTEINID']] : 0;
-            $r['DCOUNT'] = $dcount;
-            $scount = array_key_exists($r['PROTEINID'], $scs) ? $scs[$r['PROTEINID']] : 0;
-            $r['SCOUNT'] = $scount;
-
-            if ($this->has_arg('pid'))
-                $r['SEQUENCE'] = $this->db->read($r['SEQUENCE']);
-        }
-
         if ($this->has_arg('pid')) {
             if (sizeof($rows))
                 $this->_output($rows[0]);

diff --git a/api/src/Page/Shipment.php b/api/src/Page/Shipment.php
@@ -729,8 +729,7 @@ function _add_prop_dewar()
             $this->_error('No dewar specified');
         if (!$this->has_arg('PROPOSALID'))
             $this->_error('No proposal specified');
-        if (!$this->has_arg('LABCONTACTID'))
-            $this->_error('No lab contact specified');
+        $lc = $this->has_arg('LABCONTACTID') ? $this->arg('LABCONTACTID') : null;
 
         $chk = $this->db->pq("SELECT dewarregistryid 
               FROM dewarregistry_has_proposal
@@ -739,7 +738,7 @@ function _add_prop_dewar()
             $this->_error('That dewar is already registered to that proposal');
 
         $this->db->pq("INSERT INTO dewarregistry_has_proposal (dewarregistryid,proposalid,personid,labcontactid) 
-              VALUES (:1,:2,:3,:4)", array($this->arg('DEWARREGISTRYID'), $this->arg('PROPOSALID'), $this->user->personId, $this->arg('LABCONTACTID')));
+              VALUES (:1,:2,:3,:4)", array($this->arg('DEWARREGISTRYID'), $this->arg('PROPOSALID'), $this->user->personId, $lc));
 
         $this->_output(array('DEWARREGISTRYHASPROPOSALID' => $this->db->id()));
     }