Merge pull request #679 from DiamondLightSource/pre-release/2023-R4.2

* LIMS-222: Apply experimental parameters to all samples (#595) * LIMS-222: Apply experimental parameters to all samples * LIMS-222: Fix bug from renaming method * Use toArray instead of filter and make names better --------- Co-authored-by: Mark Williams <[email protected]> Co-authored-by: John Holt <[email protected]> * LIMS-210: Prevent double clicking to create multiple samples (#660) * LIMS-210: Prevent double clicking to create multiple samples * Use loading state to avoid double click --------- Co-authored-by: Mark Williams <[email protected]> Co-authored-by: John Holt <[email protected]> * LIMS-499: Make reciprocal space viewer more obvious (#653) Co-authored-by: Mark Williams <[email protected]> * LIMS-395: Display warning if no spots or incomplete PIA (#623) * LIMS-395: Display a warning on grid scans if no spots found or incomplete PIA results * LIMS-395: Use new XRC tables --------- Co-authored-by: Mark Williams <[email protected]> * LIMS-759: Show multipin samples and their sublocations (#648) Co-authored-by: Mark Williams <[email protected]> * LIMS-154: Enable display of all grid scan snapshots in full (#631) * LIMS-154: Enable display of all grid scan snapshots in full * Avoid overwriting globally scoped variable n Co-authored-by: Guilherme Francisco <[email protected]> --------- Co-authored-by: Mark Williams <[email protected]> Co-authored-by: Guilherme Francisco <[email protected]> * LIMS-952: Display xray centring results if running 3d xray centring (#647) * LIMS-952: Display xray centring results if running 3d xray centring * LIMS-952: Mark no results as xray centring failure * LIMS-952: Display message if no diffraction found --------- Co-authored-by: Mark Williams <[email protected]> * LIMS-862: Reset registered container after creating container (#628) Co-authored-by: Mark Williams <[email protected]> * LIMS-77: Link Lab Contacts to fedids (#622) * LIMS-77: Link Lab Contacts to fedids * Use Promise.all rather than $.when Co-authored-by: Guilherme Francisco <[email protected]> --------- Co-authored-by: Mark Williams <[email protected]> Co-authored-by: Guilherme Francisco <[email protected]> * Fix user data invocation tests * Revert "LIMS-759: Show multipin samples and their sublocations (#648)" This reverts commit 5ec00f1. --------- Co-authored-by: Mark W <[email protected]> Co-authored-by: Mark Williams <[email protected]> Co-authored-by: John Holt <[email protected]> Co-authored-by: Guilherme Francisco <[email protected]> Co-authored-by: NKatti2011 <[email protected]>
DiamondLightSource · Oct 5, 2023 · 7d6f57f · 7d6f57f
2 parents fa177c3 + feca5b6
commit 7d6f57f
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Showing 19 changed files with 324 additions and 86 deletions.
diff --git a/api/src/Database/Type/MySQL.php b/api/src/Database/Type/MySQL.php
@@ -202,6 +202,7 @@ class MySQL extends DatabaseParent {
         // Xray Centring
         'XrayCentring',
         'XrayCentringResult',
+        'XrayCentring',
 
         'BeamCalendar',
         'SpaceGroup',

diff --git a/api/src/Model/Services/UserData.php b/api/src/Model/Services/UserData.php
@@ -192,7 +192,7 @@ function getUsers($getCount, $isStaffMember, $stringMatch, $page, $sortBy = null
             }
         }
 
-        $rows = $this->db->paginate("SELECT $extc p.personid, p.givenname, p.familyname, CONCAT(p.givenname, ' ', p.familyname) as fullname, p.login, p.emailaddress, p.phonenumber, l.name as labname, l.address, l.city, '' as postcode, l.country
+        $rows = $this->db->paginate("SELECT $extc p.personid, p.givenname, p.familyname, CONCAT(p.givenname, ' ', p.familyname) as fullname, p.login, p.emailaddress, p.phonenumber, l.name as labname, l.address, l.city, l.postcode, l.country
                                FROM person p
                                LEFT OUTER JOIN proposalhasperson prhp ON prhp.personid = p.personid
                                LEFT OUTER JOIN labcontact lc ON lc.personid = p.personid
@@ -253,7 +253,7 @@ function getUsersForProposal($where, $getCount, $page, $sortBy, $proposalid, $cu
             }
         }
 
-        $extc = "p.personid, p.givenname, p.familyname, CONCAT(p.givenname, ' ', p.familyname) as fullname, p.login, p.emailaddress, p.phonenumber, l.name as labname, l.address, l.city, '' as postcode, l.country";
+        $extc = "p.personid, p.givenname, p.familyname, CONCAT(p.givenname, ' ', p.familyname) as fullname, p.login, p.emailaddress, p.phonenumber, l.name as labname, l.address, l.city, l.postcode, l.country";
         $rows = $this->db->paginate("(SELECT $extc
                                FROM person p
                                LEFT OUTER JOIN ProposalHasPerson prhp ON prhp.personid = p.personid

diff --git a/api/src/Page/Contact.php b/api/src/Page/Contact.php
@@ -149,19 +149,62 @@ function _add_contact() {
                 WHERE c.cardname=:1 and c.proposalid=:2", array($this->arg('CARDNAME'), $this->proposalid));
             if (sizeof($cont)) $this->_error('The specified card name already exists');
 
-            $this->db->pq("INSERT INTO laboratory (laboratoryid,name,address,city,postcode,country) 
-                VALUES (s_laboratory.nextval, :1, :2, :3, :4, :5) RETURNING laboratoryid INTO :id", 
-                array($this->arg('LABNAME'), $this->arg('ADDRESS'), $this->arg('CITY'), $this->arg('POSTCODE'), $this->arg('COUNTRY')));
-            $lid = $this->db->id();
-
-            $email = $this->has_arg('EMAILADDRESS') ? $this->arg('EMAILADDRESS') : '';
-            $phone = $this->has_arg('PHONENUMBER') ? $this->arg('PHONENUMBER') : '';
-
-            $this->db->pq("INSERT INTO person (personid, givenname, familyname, emailaddress, phonenumber, laboratoryid) 
-                VALUES (s_person.nextval, :1, :2, :3, :4, :5) RETURNING personid INTO :id", 
-                array($this->arg('GIVENNAME'), $this->arg('FAMILYNAME'), $email, $phone, $lid));
+            if ($this->has_arg('PERSONID')) {
+                $pid = $this->arg('PERSONID');
+
+                $check = $this->db->pq("SELECT c.labcontactid
+                    FROM labcontact c
+                    WHERE c.personid=:1 and c.proposalid=:2", array($pid, $this->proposalid));
+                if (sizeof($check)) $this->_error('The specified login already has a lab contact for this proposal');
+
+                $lab = $this->db->pq("SELECT l.laboratoryid FROM laboratory l
+                    INNER JOIN person p ON l.laboratoryid = p.laboratoryid
+                    WHERE p.personid=:1", array($pid));
+
+                if (sizeof($lab)) {
+                    # Update laboratory
+                    $lfields = array('LABNAME', 'ADDRESS', 'CITY', 'COUNTRY', 'POSTCODE');
+                    foreach ($lfields as $i => $f) {
+                        if ($this->has_arg($f)) {
+                            $c = $f == 'LABNAME' ? 'NAME' : $f;
+                            $this->db->pq('UPDATE laboratory SET '.$c.'=:1 WHERE laboratoryid=:2', array($this->arg($f), $lab['LABORATORYID']));
+                        }
+                    }
+                }
+                else {
+                    # Create laboratory
+                    $this->db->pq("INSERT INTO laboratory (laboratoryid,name,address,city,postcode,country)
+                        VALUES (s_laboratory.nextval, :1, :2, :3, :4, :5) RETURNING laboratoryid INTO :id",
+                        array($this->arg('LABNAME'), $this->arg('ADDRESS'), $this->arg('CITY'), $this->arg('POSTCODE'), $this->arg('COUNTRY')));
+                    $lid = $this->db->id();
+                    $this->db->pq('UPDATE person SET laboratoryid=:1 WHERE personid=:2', array($lid, $pid));
+                }
+
+                # Update person
+                $pfields = array('FAMILYNAME', 'GIVENNAME', 'PHONENUMBER', 'EMAILADDRESS');
+                foreach ($pfields as $i => $f) {
+                    if ($this->has_arg($f)) {
+                        $this->db->pq('UPDATE person SET '.$f.'=:1 WHERE personid=:2', array($this->arg($f), $pid));
+                    }
+                }
+
+            }
+            else {
 
-            $pid = $this->db->id();
+                $this->db->pq("INSERT INTO laboratory (laboratoryid,name,address,city,postcode,country)
+                    VALUES (s_laboratory.nextval, :1, :2, :3, :4, :5) RETURNING laboratoryid INTO :id",
+                    array($this->arg('LABNAME'), $this->arg('ADDRESS'), $this->arg('CITY'), $this->arg('POSTCODE'), $this->arg('COUNTRY')));
+                $lid = $this->db->id();
+
+                $email = $this->has_arg('EMAILADDRESS') ? $this->arg('EMAILADDRESS') : '';
+                $phone = $this->has_arg('PHONENUMBER') ? $this->arg('PHONENUMBER') : '';
+
+                $this->db->pq("INSERT INTO person (personid, givenname, familyname, emailaddress, phonenumber, laboratoryid)
+                    VALUES (s_person.nextval, :1, :2, :3, :4, :5) RETURNING personid INTO :id",
+                    array($this->arg('GIVENNAME'), $this->arg('FAMILYNAME'), $email, $phone, $lid));
+
+                $pid = $this->db->id();
+            }
 
             $c = $this->def_arg('DEFAULTCOURRIERCOMPANY', '');
             $ca = $this->has_arg('COURIERACCOUNT') ? $this->arg('COURIERACCOUNT') : '';

diff --git a/api/src/Page/DC.php b/api/src/Page/DC.php
@@ -47,6 +47,7 @@ class DC extends Page
         array('/chi', 'post', '_chk_image'),
         array('/imq/:id', 'get', '_image_qi'),
         array('/grid/:id', 'get', '_grid_info'),
+        array('/grid/xrc/:id', 'get', '_grid_xrc'),
         array('/grid/map', 'get', '_grid_map'),
         array('/ed/:id', 'get', '_edge', array('id' => '\d+'), 'edge'),
         array('/mca/:id', 'get', '_mca', array('id' => '\d+'), 'mca'),
@@ -394,6 +395,7 @@ function _data_collections($single = null)
         # Data collection group
         if ($this->has_arg('dcg') || $this->has_arg('PROCESSINGJOBID')) {
             $fields = "count(distinct dca.datacollectionfileattachmentid) as dcac,
+                    if(dca.fileType='recip',1,0) as recip,
                     count(distinct dcc.datacollectioncommentid) as dccc,
                     1 as dcc,
                     smp.name as sample,
@@ -527,6 +529,7 @@ function _data_collections($single = null)
             }
         } else {
             $fields = "count(distinct dca.datacollectionfileattachmentid) as dcac,
+                    if(dca.fileType='recip',1,0) as recip,
                     count(distinct dcc.datacollectioncommentid) as dccc,
                     count(distinct dc.datacollectionid) as dcc,
                     min(smp.name) as sample,
@@ -677,6 +680,7 @@ function _data_collections($single = null)
                 SELECT
                     $extc
                     1 as dcac,
+                    0 as recip,
                     1 as dccc,
                     1 as dcc,
                     smp.name as sample,
@@ -769,6 +773,7 @@ function _data_collections($single = null)
             SELECT
                 $extc
                 1 as dcac,
+                0 as recip,
                 1 as dccc,
                 1 as dcc,
                 smp.name as sample,
@@ -861,6 +866,7 @@ function _data_collections($single = null)
             SELECT
                 $extc
                 1 as dcac,
+                0 as recip,
                 1 as dccc,
                 1 as dcc,
                 smp.name as sample,
@@ -1443,17 +1449,19 @@ function _null_or($field, $conversion)
     # Grid Scan Info
     function _grid_info()
     {
-        $info = $this->db->pq("SELECT dc.datacollectiongroupid, dc.datacollectionid, dc.axisstart, p.posx as x, p.posy as y, p.posz as z, g.dx_mm, g.dy_mm, g.steps_x, g.steps_y, IFNULL(g.micronsperpixelx,g.pixelspermicronx) as micronsperpixelx, IFNULL(g.micronsperpixely,g.pixelspermicrony) as micronsperpixely, g.snapshot_offsetxpixel, g.snapshot_offsetypixel, g.orientation, g.snaked, DATE_FORMAT(dc.starttime, '%Y%m%d') as startdate
+        $info = $this->db->pq("SELECT dc.datacollectiongroupid, dc.datacollectionid, dc.axisstart, p.posx as x, p.posy as y, p.posz as z, g.dx_mm, g.dy_mm, g.steps_x, g.steps_y, IFNULL(g.micronsperpixelx,g.pixelspermicronx) as micronsperpixelx, IFNULL(g.micronsperpixely,g.pixelspermicrony) as micronsperpixely, g.snapshot_offsetxpixel, g.snapshot_offsetypixel, g.orientation, g.snaked, DATE_FORMAT(dc.starttime, '%Y%m%d') as startdate, xrc.status as xrcstatus, xrcr.xraycentringresultid
                 FROM gridinfo g
                 INNER JOIN datacollection dc on (dc.datacollectionid = g.datacollectionid) or (dc.datacollectiongroupid = g.datacollectiongroupid)
                 LEFT OUTER JOIN position p ON dc.positionid = p.positionid
+                LEFT OUTER JOIN xraycentring xrc ON dc.datacollectiongroupid = xrc.datacollectiongroupid
+                LEFT OUTER JOIN xraycentringresult xrcr ON xrc.xraycentringid = xrcr.xraycentringid
                 WHERE dc.datacollectionid = :1 ", array($this->arg('id')));
 
         if (!sizeof($info))
             $this->_output(array());
         else {
             foreach ($info[0] as $k => &$v) {
-                if ($k == 'ORIENTATION')
+                if ($k == 'ORIENTATION' || $k == 'XRCSTATUS')
                     continue;
                 $v = floatval($v);
             }
@@ -1475,6 +1483,32 @@ function _grid_map()
     }
 
 
+    # XRC
+    function _grid_xrc()
+    {
+        $info = $this->db->pq("SELECT dc.datacollectiongroupid, dc.datacollectionid,
+                xrc.xraycentringtype as method, xrcr.xraycentringresultid,
+                xrcr.centreofmassx as x, xrcr.centreofmassy as y, xrcr.centreofmassz as z
+                FROM datacollection dc
+                INNER JOIN xraycentring xrc ON xrc.datacollectiongroupid = dc.datacollectiongroupid
+                INNER JOIN xraycentringresult xrcr ON xrcr.xraycentringid = xrc.xraycentringid
+                WHERE dc.datacollectionid = :1 ", array($this->arg('id')));
+
+        if (!sizeof($info))
+            $this->_output(array('total' => 0, 'data' => array()));
+        else {
+            foreach ($info as &$i) {
+                foreach ($i as $k => &$v) {
+                    if ($k == 'METHOD')
+                        continue;
+                    $v = round(floatval($v), 2);
+                }
+            }
+            $this->_output(array('total' => sizeof($info), 'data' => $info));
+        }
+    }
+
+
     # ------------------------------------------------------------------------
     # Fluorescence Map Info
     function _fluo_map()

diff --git a/api/src/Page/Processing.php b/api/src/Page/Processing.php
@@ -87,10 +87,11 @@ function _screening_status($where, $ids) {
 
     function _xrc_status($where, $ids) {
         $dcs = $this->db->pq(
-            "SELECT xrc.status as xrcstatus, dc.datacollectionid
+            "SELECT xrc.status as xrcstatus, dc.datacollectionid, xrc.xrayCentringType as method, xrcr.xraycentringresultid as xrcresults
             FROM datacollection dc 
             INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid
             LEFT OUTER JOIN xraycentring xrc ON xrc.datacollectiongroupid = dc.datacollectiongroupid
+            LEFT OUTER JOIN XrayCentringResult xrcr ON xrc.xrayCentringId = xrcr.xrayCentringId
             INNER JOIN blsession s ON s.sessionid = dcg.sessionid 
             INNER JOIN proposal p ON p.proposalid = s.proposalid
             WHERE $where",
@@ -104,13 +105,15 @@ function _xrc_status($where, $ids) {
             }
 
             $statuses[$dc['DATACOLLECTIONID']]['XrayCentring'] =
-                $dc['XRCSTATUS'] === null
-                    ? 0
-                    : ($dc['XRCSTATUS'] === 'pending'
-                        ? 1
-                        : ($dc['XRCSTATUS'] === 'success'
-                            ? 2
-                            : 3));
+                $dc['METHOD'] !== '3d'
+                    ? -1
+                    : ($dc['XRCSTATUS'] === null
+                        ? 0
+                        : ($dc['XRCSTATUS'] === 'pending'
+                            ? 1
+                            : ($dc['XRCSTATUS'] === 'success' && $dc['XRCRESULTS'] !== null
+                                ? 2
+                                : 3)));
         }
 
         return $statuses;