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LIMS-452: Speed up _get_all_containers #559

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merged 4 commits into from
Aug 16, 2023
Merged

LIMS-452: Speed up _get_all_containers #559

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241d842
LIMS-452: Speed up _get_all_containers
May 17, 2023
d3fd07a
Update api/src/Page/Shipment.php
ndg63276 Aug 16, 2023
d3349a0
Fix bug with 'Has subsamples' filter
Aug 16, 2023
b76bc6c
Merge branch 'prerelease' into improvement/LIMS-452/speed-up-get-all-…
ndg63276 Aug 16, 2023
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27 changes: 11 additions & 16 deletions api/src/Page/Shipment.php
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Original file line number Diff line number Diff line change
Expand Up @@ -1680,7 +1680,7 @@ function _get_all_containers()
} else if ($this->arg('ty') == 'processing') {
$where .= " AND c.containerstatus = 'processing'";
} else if ($this->arg('ty') == 'subsamples') {
$having .= " HAVING COUNT(distinct ss.blsubsampleid) > 0";
$having .= " HAVING subsamples > 0";
}
}

Expand All @@ -1705,6 +1705,7 @@ function _get_all_containers()

if ($this->has_arg('pid')) {
// $this->db->set_debug(True);
$join .= ' LEFT OUTER JOIN crystal cr ON cr.crystalid = s.crystalid LEFT OUTER JOIN protein pr ON pr.proteinid = cr.proteinid';
$where .= ' AND pr.proteinid=:' . (sizeof($args) + 1);
array_push($args, $this->arg('pid'));
}
Expand Down Expand Up @@ -1799,42 +1800,36 @@ function _get_all_containers()
if ($this->has_arg('sort_by')) {
$cols = array(
'NAME' => 'c.code', 'DEWAR' => 'd.code', 'SHIPMENT' => 'sh.shippingname', 'SAMPLES' => 'count(s.blsampleid)', 'SHIPPINGID' => 'sh.shippingid', 'LASTINSPECTION' => 'max(ci.bltimestamp)', 'INSPECTIONS' => 'count(ci.containerinspectionid)',
'DCCOUNT' => 'COUNT(distinct dc.datacollectionid)', 'SUBSAMPLES' => 'count(distinct ss.blsubsampleid)',
'DCCOUNT' => 'COUNT(distinct dc.datacollectionid)', 'SUBSAMPLES' => 'subsamples',
'LASTQUEUECOMPLETED' => 'max(cq2.completedtimestamp)', 'QUEUEDTIMESTAMP' => 'max(cq.createdtimestamp)'
);
$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;
}
// $this->db->set_debug(True);
$rows = $this->db->paginate("SELECT round(TIMESTAMPDIFF('HOUR', min(ci.bltimestamp), CURRENT_TIMESTAMP)/24,1) as age, case when count(ci2.containerinspectionid) > 1 then 0 else 1 end as allow_adhoc, sch.name as schedule, c.scheduleid, c.screenid, sc.name as screen, c.imagerid, i.temperature as temperature, i.name as imager, TO_CHAR(max(ci.bltimestamp), 'HH24:MI DD-MM-YYYY') as lastinspection, round(TIMESTAMPDIFF('HOUR', max(ci.bltimestamp), CURRENT_TIMESTAMP)/24,1) as lastinspectiondays, count(distinct ci.containerinspectionid) as inspections, CONCAT(p.proposalcode, p.proposalnumber) as prop, c.bltimestamp, c.samplechangerlocation, c.beamlinelocation, d.dewarstatus, c.containertype, c.capacity, c.containerstatus, c.containerid, c.code as name, d.code as dewar, sh.shippingname as shipment, d.dewarid, sh.shippingid, count(distinct s.blsampleid) as samples, cq.containerqueueid, TO_CHAR(cq.createdtimestamp, 'DD-MM-YYYY HH24:MI') as queuedtimestamp, CONCAT(CONCAT(CONCAT(p.proposalcode, p.proposalnumber), '-'), ses.visit_number) as visit, ses.beamlinename, c.requestedreturn, c.requestedimagerid, i2.name as requestedimager, c.comments, c.experimenttype, c.storagetemperature, c.barcode, reg.barcode as registry, reg.containerregistryid,
count(distinct ss.blsubsampleid) as subsamples,
ses3.beamlinename as firstexperimentbeamline,
pp.name as pipeline,
$rows = $this->db->paginate("SELECT round(TIMESTAMPDIFF('HOUR', min(ci.bltimestamp), CURRENT_TIMESTAMP)/24,1) as age, case when count(ci2.containerinspectionid) > 1 then 0 else 1 end as allow_adhoc, c.scheduleid, c.screenid, sc.name as screen, c.imagerid, i.temperature as temperature, i.name as imager, TO_CHAR(max(ci.bltimestamp), 'HH24:MI DD-MM-YYYY') as lastinspection, round(TIMESTAMPDIFF('HOUR', max(ci.bltimestamp), CURRENT_TIMESTAMP)/24,1) as lastinspectiondays, count(distinct ci.containerinspectionid) as inspections, CONCAT(p.proposalcode, p.proposalnumber) as prop, c.bltimestamp, c.samplechangerlocation, c.beamlinelocation, d.dewarstatus, c.containertype, c.capacity, c.containerstatus, c.containerid, c.code as name, d.code as dewar, sh.shippingname as shipment, d.dewarid, sh.shippingid, count(distinct s.blsampleid) as samples, cq.containerqueueid, TO_CHAR(cq.createdtimestamp, 'DD-MM-YYYY HH24:MI') as queuedtimestamp, CONCAT(CONCAT(CONCAT(p.proposalcode, p.proposalnumber), '-'), ses.visit_number) as visit, ses.beamlinename, c.requestedreturn, c.requestedimagerid, c.comments, c.experimenttype, c.storagetemperature, c.barcode, reg.barcode as registry, reg.containerregistryid,
(SELECT sch.name FROM schedule sch WHERE sch.scheduleid = c.scheduleid) as schedule,
(SELECT i2.name FROM imager i2 WHERE i2.imagerid = c.requestedimagerid) as requestedimager,
(SELECT count(distinct ss.blsubsampleid) FROM blsubsample ss RIGHT OUTER JOIN blsample s2 ON s2.blsampleid = ss.blsampleid WHERE s2.containerid = c.containerid AND ss.source='manual') as subsamples,
(SELECT ses3.beamlinename FROM blsession ses3 WHERE d.firstexperimentid = ses3.sessionid) as firstexperimentbeamline,
(SELECT pp.name FROM processingpipeline pp WHERE c.prioritypipelineid = pp.processingpipelineid) as pipeline,
TO_CHAR(max(cq2.completedtimestamp), 'HH24:MI DD-MM-YYYY') as lastqueuecompleted, TIMESTAMPDIFF('MINUTE', max(cq2.completedtimestamp), max(cq2.createdtimestamp)) as lastqueuedwell,
c.ownerid, CONCAT(pe.givenname, ' ', pe.familyname) as owner
c.ownerid,
(SELECT CONCAT(pe.givenname, ' ', pe.familyname) FROM person pe WHERE c.ownerid = pe.personid)
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FROM container c
INNER JOIN dewar d ON d.dewarid = c.dewarid
LEFT OUTER JOIN blsession ses3 ON d.firstexperimentid = ses3.sessionid
INNER JOIN shipping sh ON sh.shippingid = d.shippingid
INNER JOIN proposal p ON p.proposalid = sh.proposalid
LEFT OUTER JOIN blsample s ON s.containerid = c.containerid
LEFT OUTER JOIN blsubsample ss ON s.blsampleid = ss.blsampleid AND ss.source='manual'
LEFT OUTER JOIN crystal cr ON cr.crystalid = s.crystalid
LEFT OUTER JOIN protein pr ON pr.proteinid = cr.proteinid
LEFT OUTER JOIN containerinspection ci ON ci.containerid = c.containerid AND ci.state = 'Completed'
LEFT OUTER JOIN imager i ON i.imagerid = c.imagerid
LEFT OUTER JOIN imager i2 ON i2.imagerid = c.requestedimagerid
LEFT OUTER JOIN screen sc ON sc.screenid = c.screenid
LEFT OUTER JOIN schedule sch ON sch.scheduleid = c.scheduleid
LEFT OUTER JOIN containerinspection ci2 ON ci2.containerid = c.containerid AND ci2.state != 'Completed' AND ci2.manual!=1 AND ci2.schedulecomponentid IS NULL
LEFT OUTER JOIN containerqueue cq ON cq.containerid = c.containerid AND cq.completedtimestamp IS NULL
LEFT OUTER JOIN containerqueue cq2 ON cq2.containerid = c.containerid AND cq2.completedtimestamp IS NOT NULL
LEFT OUTER JOIN containerregistry reg ON reg.containerregistryid = c.containerregistryid

LEFT OUTER JOIN blsession ses ON c.sessionid = ses.sessionid
LEFT OUTER JOIN processingpipeline pp ON c.prioritypipelineid = pp.processingpipelineid
LEFT OUTER JOIN person pe ON c.ownerid = pe.personid

$join
WHERE $where
Expand Down