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LIMS-849: Improve view of DC groups #1024

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LIMS-849: Improve view of DC groups #1024

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c4e806a
LIMS-849: Improve view of data collection groups
Jan 12, 2026
8b49fda
LIMS-849: Add 'stacking' effect for data collection groups
Jan 14, 2026
ecbef69
LIMS-849: Make link to group bold
Jan 16, 2026
328cc25
LIMS-849: Change cursor to spinner while processing results load
Jan 16, 2026
4bcfa85
Merge branch 'master' into improvement/LIMS-849/improve-view-of-dc-gr…
ndg63276 Jan 22, 2026
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94 changes: 43 additions & 51 deletions api/src/Page/DC.php
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Original file line number Diff line number Diff line change
Expand Up @@ -458,8 +458,7 @@ function _data_collections($single = null)
dc.c2lens,
dc.objaperture,
dc.magnification,
dose.total as totaldose,
CAST(dc.totalabsorbeddose AS DECIMAL(5, 2)) as totalabsdose,
dc.totalabsorbeddose as totaldose,
d.detectorpixelsizehorizontal,
d.detectorpixelsizevertical,
d.detectormanufacturer,
Expand Down Expand Up @@ -539,6 +538,12 @@ function _data_collections($single = null)
array_push($args, $this->arg('dcg'));
}
} else {
$groupby = 'GROUP BY dc.datacollectiongroupid';
$numimgs = 'totals.numimg';
if ($this->has_arg('expandgroups')) {
$groupby = 'GROUP BY dc.datacollectionid';
$numimgs = 'dc.numberofimages as numimg';
}
$fields = "count(distinct dca.datacollectionfileattachmentid) as dcac,
if(dca.fileType='recip',1,0) as recip,
count(distinct dcc.datacollectioncommentid) as dccc,
Expand Down Expand Up @@ -569,7 +574,7 @@ function _data_collections($single = null)
min(dc.resolution) as resolution,
min(dc.exposuretime) as exposuretime,
min(dc.axisstart) as axisstart,
min(dc.numberofimages) as numimg,
$numimgs,
TO_CHAR(min(dc.starttime), 'DD-MM-YYYY HH24:MI:SS') as st,
min(dc.transmission) as transmission,
min(dc.axisrange) as axisrange,
Expand All @@ -596,12 +601,11 @@ function _data_collections($single = null)
max(dc.c2lens) as c2lens,
max(dc.objaperture) as objaperture,
max(dc.magnification) as magnification,
dose.total as totaldose,
CAST(dc.totalabsorbeddose AS DECIMAL(5, 2)) as totalabsdose,
max(d.detectormanufacturer) as detectormanufacturer,
max(d.detectormodel) as detectormodel,
totals.totaldose as totaldose,
max(d.detectorpixelsizehorizontal) as detectorpixelsizehorizontal,
max(d.detectorpixelsizevertical) as detectorpixelsizevertical,
max(d.detectormanufacturer) as detectormanufacturer,
max(d.detectormodel) as detectormodel,
max(TIMESTAMPDIFF('MINUTE', dc.starttime, CURRENT_TIMESTAMP)) as age,
max(dc.numberofpasses) as numberofpasses,
max(dc.c1aperture) as c1aperture,
Expand All @@ -626,11 +630,7 @@ function _data_collections($single = null)
max(ses.archived) as archived,
max(ses.purgedProcessedData) as purgedProcessedData,
IFNULL(max(dc.rotationaxis), 'Omega') as rotationaxis,
dc.detector2theta";
$groupby = "GROUP BY dc.datacollectiongroupid";
if ($this->has_arg('expandgroups')) {
$groupby = "GROUP BY dc.datacollectionid";
}
min(dc.detector2theta) as detector2theta";
}

// We don't want to remove duplicates, since if two counts are equal, one might go uncounted
Expand Down Expand Up @@ -687,8 +687,8 @@ function _data_collections($single = null)
FROM datacollection dc
INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid
INNER JOIN (
select datacollectiongroupid, sum(totalabsorbeddose) as total from datacollection group by datacollectiongroupid) dose
ON dc.datacollectiongroupid = dose.datacollectiongroupid
select datacollectiongroupid, sum(totalabsorbeddose) as totaldose, sum(numberofimages) as numimg from datacollection group by datacollectiongroupid) totals
ON dc.datacollectiongroupid = totals.datacollectiongroupid
INNER JOIN blsession ses ON ses.sessionid = dcg.sessionid
LEFT OUTER JOIN experimenttype et on dcg.experimenttypeid = et.experimenttypeid
$sample_joins[0]
Expand Down Expand Up @@ -782,7 +782,6 @@ function _data_collections($single = null)
0,
0,
0,
0,
ses.beamlinename as bl,
es.blsubsampleid,
'',
Expand Down Expand Up @@ -879,7 +878,6 @@ function _data_collections($single = null)
0,
0,
0,
0,
ses.beamlinename as bl,
xrf.blsubsampleid,
'',
Expand Down Expand Up @@ -976,7 +974,6 @@ function _data_collections($single = null)
0,
0,
0,
0,
ses.beamlinename as bl,
1 as blsubsampleid,
'',
Expand Down Expand Up @@ -1441,45 +1438,40 @@ function _get_ap($com)
function _image_qi($id)
{
session_write_close();
$iqs = array(array(), array(), array(), array(), array());
$iqs = array(array(), array(), array(), array());
$args = array($id);
$offset = 0;
$offsets = array($id => 0);
if ($this->has_arg('dcg') && $this->arg('dcg') == 1) {
$dcs = $this->db->pq("SELECT datacollectionid, numberofimages
FROM datacollection dc
WHERE datacollectiongroupid = (
SELECT dataCollectionGroupId
FROM DataCollection
WHERE dataCollectionId = :1
)
ORDER BY datacollectionid ASC", $args);
$args = array();
foreach ($dcs as $i => $id) {
array_push($args, $id['DATACOLLECTIONID']);
$offsets[$id['DATACOLLECTIONID']] = $offset;
$offset += $id['NUMBEROFIMAGES'];
}
}

#$this->db->set_debug(True);
$dcids = implode(', ', $args);

$where = $id;
$args = array();
/*
$dcg = $this->db->pq("SELECT datacollectiongroupid as dcg FROM datacollection WHERE datacollectionid=:1", array($id));
if (!sizeof($dcg)) $this->error('No such data collection');
$dcids = $this->db->pq("SELECT datacollectionid as id FROM datacollection WHERE datacollectiongroupid=:1", array($dcg[0]['DCG']));
$where = array();
$args = array();
foreach ($dcids as $i => $id) {
//array_push($where, ':'.($i+1));
array_push($where, $id['ID']);
//array_push($args, $id['ID']);
}
$where = implode($where, ', ');
*/

/*$tot = $this->db->pq("SELECT count(im.imagenumber) as tot
FROM image im
INNER JOIN imagequalityindicators imq ON imq.imageid = im.imageid AND (im.datacollectionid IN ($where))
ORDER BY imagenumber", $args);
$int = intval($tot[0]['TOT'] / 250);
array_push($args, $int);*/

#im.datacollectionid=:1
$imqs = $this->db->pq("SELECT imq.imagenumber as nim, imq.method2res as res, imq.spottotal as s, imq.totalintegratedsignal, imq.goodbraggcandidates as b, imq.dozor_score as d
$imqs = $this->db->pq("SELECT imq.datacollectionid, imq.imagenumber, imq.method2res, imq.spottotal, imq.totalintegratedsignal, imq.goodbraggcandidates
FROM imagequalityindicators imq
WHERE imq.datacollectionid IN ($where)
ORDER BY imq.imagenumber", $args);
WHERE imq.datacollectionid IN ($dcids)
ORDER BY imq.datacollectionid asc, imq.imagenumber asc", array());

foreach ($imqs as $imq) {
array_push($iqs[0], array(intval($imq['NIM']), $this->_null_or($imq['S'], 'int')));
array_push($iqs[1], array(intval($imq['NIM']), $this->_null_or($imq['B'], 'int')));
array_push($iqs[2], array(intval($imq['NIM']), $this->_null_or($imq['RES'], 'float')));
array_push($iqs[3], array(intval($imq['NIM']), $this->_null_or($imq['TOTALINTEGRATEDSIGNAL'], 'float')));
array_push($iqs[4], array(intval($imq['NIM']), $this->_null_or($imq['D'], 'float')));
$globalImageNumber = $imq['IMAGENUMBER'] + $offsets[$imq['DATACOLLECTIONID']];
array_push($iqs[0], array($globalImageNumber, $this->_null_or($imq['SPOTTOTAL'], 'int')));
array_push($iqs[1], array($globalImageNumber, $this->_null_or($imq['GOODBRAGGCANDIDATES'], 'int')));
array_push($iqs[2], array($globalImageNumber, $this->_null_or($imq['METHOD2RES'], 'float')));
array_push($iqs[3], array($globalImageNumber, $this->_null_or($imq['TOTALINTEGRATEDSIGNAL'], 'float')));
}

$this->_output($iqs);
Expand Down
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