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LIMS-59: Never write null to DewarTransportHistory.storageLocation #597

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merged 7 commits into from
Oct 12, 2023
Merged

LIMS-59: Never write null to DewarTransportHistory.storageLocation #597

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05514ca
LIMS-59: Never write null to DewarTransportHistory.storageLocation
Jun 19, 2023
f53b4ff
LIMS-59: Write a location to DTH when marking a dewar as unprocessing
Jun 26, 2023
9bd23f5
LIMS-59: Check for nulls before doing inserts
Sep 4, 2023
b3a8193
LIMS-59: Ensure tests pass
Oct 12, 2023
fbb38cb
Update test
Oct 12, 2023
131e512
Merge branch 'fix/LIMS-59/never-write-null-to-DTH-storageLocation' of…
Oct 12, 2023
a282d0b
tidy
Oct 12, 2023
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12 changes: 8 additions & 4 deletions api/src/Model/Services/AssignData.php
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@

namespace SynchWeb\Model\Services;

use SynchWeb\Utils;

class AssignData
{
private $db;
Expand Down Expand Up @@ -85,9 +87,10 @@ function updateDewar($dewarId, $status)

function deactivateDewar($dewarId)
{
$this->updateDewarHistory($dewarId, 'unprocessing');
$location = $this->db->pq("SELECT storagelocation FROM dewar WHERE dewarid=:1", array($dewarId));
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$this->updateDewarHistory($dewarId, 'unprocessing', $location[0]['STORAGELOCATION']);

$conts = $this->db->pq("SELECT containerid as id FROM container WHERE dewarid=:1", array($dewarId));
$conts = $this->db->pq("SELECT containerid FROM container WHERE dewarid=:1", array($dewarId));
foreach ($conts as $container)
{
$this->updateContainerAndHistory($container['CONTAINERID'], 'at facility', '', '');
Expand All @@ -99,9 +102,10 @@ function updateDewarHistory($did, $status, $beamline = null, $additionalStatusDe
$st = $status;
if ($additionalStatusDetail)
$st .= ' (' . $additionalStatusDetail . ')';
$loc = Utils::getValueOrDefault($beamline, '');
$this->db->pq("INSERT INTO dewartransporthistory
(dewarid, dewarstatus, storagelocation, arrivaldate)
VALUES (:1, :2, :3, CURRENT_TIMESTAMP)", array($did, $st, $beamline));
VALUES (:1, :2, :3, CURRENT_TIMESTAMP)", array($did, $st, $loc));

$this->updateDewar($did, $status);
}
Expand All @@ -113,4 +117,4 @@ function getContainerBarcodesForProposal($proposalId)
INNER JOIN containerregistry_has_proposal crhp ON crhp.containerregistryid = cr.containerregistryid
WHERE crhp.proposalid = :1", array($proposalId));
}
}
}
31 changes: 17 additions & 14 deletions api/src/Page/Shipment.php
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Original file line number Diff line number Diff line change
Expand Up @@ -864,6 +864,8 @@ function _transfer_dewar()
global $transfer_email;
if (!$this->has_arg('DEWARID'))
$this->_error('No dewar specified');
if (!$this->has_arg('LOCATION'))
$this->_error('No location specified');

$dew = $this->db->pq("SELECT d.dewarid,s.shippingid
FROM dewar d
Expand Down Expand Up @@ -1049,7 +1051,7 @@ function _dispatch_dewar()
$dewar_location = $last_history['STORAGELOCATION'];
} else {
// Use the current location of the dewar instead if no history
$dewar_location = $dew['STORAGELOCATION'];
$dewar_location = Utils::getValueOrDefault($dew['STORAGELOCATION'], '');
}
}
// Check if the last history storage location is an EBIC prefix or not
Expand Down Expand Up @@ -1562,16 +1564,16 @@ function _send_shipment()
}

$this->db->pq("UPDATE shipping SET shippingstatus='sent to facility' where shippingid=:1", array($ship['SHIPPINGID']));
$this->db->pq("UPDATE dewar SET dewarstatus='sent to facility' where shippingid=:1", array($ship['SHIPPINGID']));
$this->db->pq("UPDATE dewar SET dewarstatus='sent to facility', storagelocation='off-site' where shippingid=:1", array($ship['SHIPPINGID']));
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$dewars = $this->db->pq("SELECT d.dewarid, s.visit_number as vn, s.beamlinename as bl, TO_CHAR(s.startdate, 'DD-MM-YYYY HH24:MI') as startdate
FROM dewar d
LEFT OUTER JOIN blsession s ON s.sessionid = d.firstexperimentid
WHERE d.shippingid=:1", array($ship['SHIPPINGID']));
foreach ($dewars as $d) {
$this->db->pq(
"INSERT INTO dewartransporthistory (dewartransporthistoryid,dewarid,dewarstatus,arrivaldate)
VALUES (s_dewartransporthistory.nextval,:1,'sent to facility',CURRENT_TIMESTAMP) RETURNING dewartransporthistoryid INTO :id",
"INSERT INTO dewartransporthistory (dewartransporthistoryid,dewarid,dewarstatus,storagelocation,arrivaldate)
VALUES (s_dewartransporthistory.nextval,:1,'sent to facility','off-site',CURRENT_TIMESTAMP) RETURNING dewartransporthistoryid INTO :id",
array($d['DEWARID'])
);
}
Expand Down Expand Up @@ -2798,11 +2800,11 @@ function _create_awb()
continue;

$p = $awb['pieces'][$i];
$this->db->pq("UPDATE dewar SET $tno=:1, deliveryAgent_barcode=:2, dewarstatus='awb created' WHERE dewarid=:3", array($awb['awb'], $p['licenseplate'], $d['DEWARID']));
$this->db->pq("UPDATE dewar SET $tno=:1, deliveryAgent_barcode=:2, dewarstatus='awb created', storagelocation='off-site' WHERE dewarid=:3", array($awb['awb'], $p['licenseplate'], $d['DEWARID']));

$this->db->pq(
"INSERT INTO dewartransporthistory (dewartransporthistoryid,dewarid,dewarstatus,arrivaldate)
VALUES (s_dewartransporthistory.nextval,:1,'awb created',CURRENT_TIMESTAMP) RETURNING dewartransporthistoryid INTO :id",
"INSERT INTO dewartransporthistory (dewartransporthistoryid,dewarid,dewarstatus,storagelocation,arrivaldate)
VALUES (s_dewartransporthistory.nextval,:1,'awb created','off-site',CURRENT_TIMESTAMP) RETURNING dewartransporthistoryid INTO :id",
array($d['DEWARID'])
);
}
Expand Down Expand Up @@ -2955,10 +2957,10 @@ function _do_request_pickup($options)
WHERE shippingid=:4", array($pickup['confirmationnumber'], $pickup['readybytime'], $pickup['callintime'], $options['shippingid']));

foreach ($options['dewars'] as $i => $d) {
$this->db->pq("UPDATE dewar SET dewarstatus='pickup booked' WHERE dewarid=:1", array($d['DEWARID']));
$this->db->pq("UPDATE dewar SET dewarstatus='pickup booked', storagelocation='off-site' WHERE dewarid=:1", array($d['DEWARID']));
$this->db->pq(
"INSERT INTO dewartransporthistory (dewartransporthistoryid,dewarid,dewarstatus,arrivaldate)
VALUES (s_dewartransporthistory.nextval,:1,'pickup booked',CURRENT_TIMESTAMP) RETURNING dewartransporthistoryid INTO :id",
"INSERT INTO dewartransporthistory (dewartransporthistoryid,dewarid,dewarstatus,storagelocation,arrivaldate)
VALUES (s_dewartransporthistory.nextval,:1,'pickup booked','off-site',CURRENT_TIMESTAMP) RETURNING dewartransporthistoryid INTO :id",
array($d['DEWARID'])
);
}
Expand Down Expand Up @@ -3090,7 +3092,7 @@ function _cancel_pickup()
$this->_error('No such lab contact');
$cont = $cont[0];

$dewars = $this->db->pq("SELECT d.dewarid
$dewars = $this->db->pq("SELECT d.dewarid, d.storagelocation
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could the dewar storage location not be null?

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I've added a check for null on line 3116

FROM dewar d
WHERE d.shippingid=:1 AND d.deliveryagent_barcode IS NOT NULL", array($this->arg('sid')));

Expand All @@ -3111,10 +3113,11 @@ function _cancel_pickup()

foreach ($dewars as $i => $d) {
$this->db->pq("UPDATE dewar SET dewarstatus='pickup cancelled' WHERE dewarid=:1", array($d['DEWARID']));
$loc = Utils::getValueOrDefault($d['STORAGELOCATION'], '');
$this->db->pq(
"INSERT INTO dewartransporthistory (dewarid,dewarstatus,arrivaldate)
VALUES (:1,'pickup cancelled',CURRENT_TIMESTAMP)",
array($d['DEWARID'])
"INSERT INTO dewartransporthistory (dewarid,dewarstatus,storagelocation,arrivaldate)
VALUES (:1,'pickup cancelled',:2,CURRENT_TIMESTAMP)",
array($d['DEWARID'], $loc)
);
}
} catch (\Exception $e) {
Expand Down
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