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Merge pre-release/2025-R1.2 into master #904

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Merged
ndg63276 merged 6 commits into from
Feb 9, 2025
Merged

Merge pre-release/2025-R1.2 into master #904

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5fc0e78
LIMS-1590: Dont allow name editing for lab contacts when login is set…
ndg63276 Jan 28, 2025
3366ee9
LIMS-1558: Add functionality for SMILES code for any sample (#880)
ndg63276 Jan 28, 2025
acb33c9
LIMS-1490: Use callback URL for incoming dewars via shipping service …
ndg63276 Jan 28, 2025
f4393fb
LIMS-1570: Remove unused app file (#874)
gfrn Jan 28, 2025
ad1b919
LIMS-1537: Add more options to reprocessing (#876)
ndg63276 Jan 28, 2025
f996391
LIMS-1466: Disable dispatch form validation when using the shipping s…
ndg63276 Jan 28, 2025
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2 changes: 1 addition & 1 deletion api/src/Controllers/AuthenticationController.php
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Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,7 @@ private function checkAuthRequiredForSpecificSituations($parts): bool
($parts[0] == 'shipment' && $parts[1] == 'containers' && $parts[2] == 'history' && in_array($_SERVER["REMOTE_ADDR"], $bcr)) ||

# Allow shipping service to update dewar status
($parts[0] == 'shipment' && $parts[1] == 'dewars' && $parts[2] == 'confirmdispatch')
($parts[0] == 'shipment' && $parts[1] == 'dewars' && ($parts[2] == 'confirmdispatch' || $parts[2] == 'confirmpickup'))
)
{
$need_auth = false;
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1 change: 0 additions & 1 deletion api/src/Page.php
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Original file line number Diff line number Diff line change
Expand Up @@ -221,7 +221,6 @@ function auth($require_staff)
if ($require_staff)
{
$auth = $this->staff;

}
// Barcode Scanners
else if ($this->bcr() && !$this->user->loginId)
Expand Down
27 changes: 13 additions & 14 deletions api/src/Page/Contact.php
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Original file line number Diff line number Diff line change
Expand Up @@ -39,10 +39,10 @@ class Contact extends Page
# Get List of Lab Contacts
function _get_contacts() {
if (!$this->has_arg('prop')) $this->_error('No proposal specified');

$args = array($this->proposalid);
$where = 'WHERE c.proposalid = :1';

if ($this->has_arg('cid')) {
$where .= ' AND c.labcontactid=:'.(sizeof($args)+1);
array_push($args, $this->arg('cid'));
Expand All @@ -63,37 +63,36 @@ function _get_contacts() {
$pp = $this->has_arg('per_page') ? $this->arg('per_page') : 15;
$start = 0;
$end = $pp;

if ($this->has_arg('page')) {
$pg = $this->arg('page') - 1;
$start = $pg*$pp;
$end = $pg*$pp+$pp;
}

$st = sizeof($args)+1;
$en = $st + 1;
array_push($args, $start);
array_push($args, $end);

$order = 'c.labcontactid DESC';
$rows = $this->db->paginate("SELECT c.labcontactid, c.cardname, pe.givenname, pe.familyname, pe.phonenumber, l.name as labname, l.address, l.city, l.country, c.courieraccount, c.billingreference, c.defaultcourriercompany, c.dewaravgcustomsvalue, c.dewaravgtransportvalue, pe.emailaddress, l.postcode, l.country

$rows = $this->db->paginate("SELECT c.labcontactid, c.cardname, pe.givenname, pe.familyname, pe.phonenumber, IF(pe.login IS NOT NULL, pe.login, IF(pe.externalid IS NOT NULL, 'External', NULL)) AS login, l.name as labname, l.address, l.city, l.country, c.courieraccount, c.billingreference, c.defaultcourriercompany, c.dewaravgcustomsvalue, c.dewaravgtransportvalue, pe.emailaddress, l.postcode, l.country
FROM labcontact c
INNER JOIN person pe ON c.personid = pe.personid
INNER JOIN laboratory l ON l.laboratoryid = pe.laboratoryid
INNER JOIN proposal p ON p.proposalid = c.proposalid
$where ORDER BY $order", $args);

if ($this->has_arg('cid')) {
if (sizeof($rows))$this->_output($rows[0]);
else $this->_error('No such contact');

} else $this->_output(array('total' => $tot,
'data' => $rows,
));
} else {
$this->_output(array('total' => $tot, 'data' => $rows));
}
}


# ------------------------------------------------------------------------
# Update field for lab contact
function _update_contact() {
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84 changes: 78 additions & 6 deletions api/src/Page/Shipment.php
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Expand Up @@ -146,6 +146,7 @@ class Shipment extends Page
'TOKEN' => '\w+',
'tracking_number' => '\w+',
'AWBURL' => '[\w\:\/\.\-]+',
'pickup_confirmation_code' => '\w+',

'manifest' => '\d',
'currentuser' => '\d',
Expand Down Expand Up @@ -200,6 +201,7 @@ class Shipment extends Page
array('/dewars/transfer', 'post', '_transfer_dewar'),
array('/dewars/dispatch', 'post', '_dispatch_dewar'),
array('/dewars/confirmdispatch/did/:did/token/:TOKEN', 'post', '_dispatch_dewar_confirmation'),
array('/dewars/confirmpickup/sid/:sid/token/:TOKEN', 'post', '_pickup_dewar_confirmation'),

array('/dewars/tracking(/:DEWARID)', 'get', '_get_dewar_tracking'),

Expand Down Expand Up @@ -1444,7 +1446,70 @@ function _dispatch_dewar_confirmation()
$this->_output(1);
}

function _pickup_dewar_confirmation()
{
if (!$this->has_arg('sid'))
$this->_error('No shipment specified');
if (!$this->has_arg('TOKEN'))
$this->_error('No token specified');
if (!$this->has_arg('tracking_number'))
$this->_error('No tracking number specified');

// Check token against each dewar
$dewars = $this->db->pq(
"SELECT d.dewarid,
json_unquote(json_extract(d.extra, '$.token')) as token
FROM dewar d
WHERE d.shippingid=:1",
array($this->arg('sid'))
);

foreach ($dewars as $dew) {
if ($this->arg('TOKEN') !== $dew['TOKEN']) {
$this->_error('Incorrect token');
}
}

$this->db->pq("UPDATE shipping set shippingstatus='awb created' WHERE shippingid=:1", array($this->arg('sid')));

foreach ($dewars as $dew) {
// Update the dewar status and storage location
$this->db->pq(
"UPDATE dewar
set dewarstatus='awb created', storagelocation='off-site', trackingnumbertosynchrotron=:2
WHERE dewarid=:1",
array($dew['DEWARID'], $this->arg('tracking_number'))
);

// Update dewar transport history
$this->db->pq(
"INSERT INTO dewartransporthistory (dewartransporthistoryid,dewarid,dewarstatus,storagelocation,arrivaldate)
VALUES (s_dewartransporthistory.nextval,:1,'awb created','off-site',CURRENT_TIMESTAMP)
RETURNING dewartransporthistoryid INTO :id",
array($dew['DEWARID'])
);
}

if ($this->has_arg('pickup_confirmation_code')) {

$this->db->pq("UPDATE shipping set shippingstatus='pickup booked' WHERE shippingid=:1", array($this->arg('sid')));

foreach ($dewars as $dew) {
// Update the dewar status
$this->db->pq("UPDATE dewar set dewarstatus='pickup booked' WHERE dewarid=:1", array($dew['DEWARID']));

// Update dewar transport history (plus 1s so history appears in order)
$this->db->pq(
"INSERT INTO dewartransporthistory (dewartransporthistoryid,dewarid,dewarstatus,storagelocation,arrivaldate)
VALUES (s_dewartransporthistory.nextval,:1,'pickup booked','off-site',CURRENT_TIMESTAMP+1)
RETURNING dewartransporthistoryid INTO :id",
array($dew['DEWARID'])
);
}
}

$this->_output(1);
}

function _get_dewar_tracking()
{
Expand Down Expand Up @@ -3086,20 +3151,27 @@ function($package, $index) {return array("piecenumber" => $index+1, "licenseplat
function _create_shipment_shipment_request($shipment, array $dewars): int
{

// if (!is_null($shipment['EXTERNALSHIPPINGIDTOSYNCHROTRON'])) {
// return $shipment['EXTERNALSHIPPINGIDTOSYNCHROTRON'];
// }
$shipping_id = (int) $shipment['SHIPPINGID'];

$token = md5(openssl_random_pseudo_bytes(7));
$this->db->pq(
"UPDATE dewar SET extra = JSON_SET(IFNULL(extra, '{}'), '$.token', :1 ) WHERE shippingid=:2",
array($token, $shipping_id)
);

$callback_url = "/api/shipment/dewars/confirmpickup/sid/{$shipping_id}/token/{$token}";

$external_shipping_id = $this->_create_dewars_shipment_request(
$dewars,
$shipment['PROP'],
(int) $shipment['SHIPPINGID'],
(int) $shipment['SHIPPINGID']
$shipping_id,
$shipping_id,
$callback_url
);

$this->db->pq(
"UPDATE shipping SET externalShippingIdToSynchrotron=:1 WHERE shippingId=:2",
array($external_shipping_id, $shipment['SHIPPINGID'])
array($external_shipping_id, $shipping_id)
);
return $external_shipping_id;
}
Expand Down
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