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LIMS-1257: Allow population of source fields (#769)
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* Restore EM menu in dropdown (#766) (#767)

* LIMS-1257: Allow population of source fields

---------

Co-authored-by: Guilherme Francisco <[email protected]>
Co-authored-by: Mark Williams <[email protected]>
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@ndg63276 @gfrn
3 people authored Jul 9, 2024
1 parent ce82eab commit 0390fd0
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Showing 2 changed files with 21 additions and 15 deletions.
8 changes: 5 additions & 3 deletions api/src/Page/Sample.php
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,7 @@ class Sample extends Page
'MONOCHROMATOR' => '\w+',
'PRESET' => '\d',
'BEAMLINENAME' => '[\w\-]+',
'SOURCE' => '[\w\-]+',

'queued' => '\d',
'UNQUEUE' => '\d',
Expand Down Expand Up @@ -1467,7 +1468,8 @@ function _prepare_sample_args($s = null)
'SAMPLEGROUP',
'STRATEGYOPTION',
'MINIMUMRESOLUTION',
'INITIALSAMPLEGROUP'
'INITIALSAMPLEGROUP',
'SOURCE'
) as $f) {
if ($s)
$a[$f] = array_key_exists($f, $s) ? $s[$f] : null;
Expand Down Expand Up @@ -1518,8 +1520,8 @@ function _do_add_sample($s)
}

$this->db->pq(
"INSERT INTO blsample (blsampleid,crystalid,diffractionplanid,containerid,location,comments,name,code,blsubsampleid,screencomponentgroupid,volume,packingfraction,dimension1,dimension2,dimension3,shape,looptype) VALUES (s_blsample.nextval,:1,:2,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14,:15,:16) RETURNING blsampleid INTO :id",
array($crysid, $did, $a['CONTAINERID'], $a['LOCATION'], $a['COMMENTS'], $a['NAME'], $a['CODE'], $a['BLSUBSAMPLEID'], $a['SCREENCOMPONENTGROUPID'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'])
"INSERT INTO blsample (blsampleid,crystalid,diffractionplanid,containerid,location,comments,name,code,blsubsampleid,screencomponentgroupid,volume,packingfraction,dimension1,dimension2,dimension3,shape,looptype,source) VALUES (s_blsample.nextval,:1,:2,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14,:15,:16,IFNULL(:17,CURRENT_USER)) RETURNING blsampleid INTO :id",
array($crysid, $did, $a['CONTAINERID'], $a['LOCATION'], $a['COMMENTS'], $a['NAME'], $a['CODE'], $a['BLSUBSAMPLEID'], $a['SCREENCOMPONENTGROUPID'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'], $a['SOURCE'])
);
$sid = $this->db->id();

Expand Down
28 changes: 16 additions & 12 deletions api/src/Page/Shipment.php
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,7 @@ class Shipment extends Page
'PUCK' => '\d',
'PROCESSINGPIPELINEID' => '\d+',
'OWNERID' => '\d+',
'SOURCE' => '[\w\-]+',

'CONTAINERREGISTRYID' => '\d+',
'PROPOSALID' => '\d+',
Expand Down Expand Up @@ -1557,16 +1558,17 @@ function _add_dewar()
$fc = $this->has_arg('FACILITYCODE') ? $this->arg('FACILITYCODE') : '';
$wg = $this->has_arg('WEIGHT') ? $this->arg('WEIGHT') : $dewar_weight;
$exp = null;
$source = $this->has_arg('SOURCE') ? $this->arg('SOURCE') : null;

if ($this->has_arg('FIRSTEXPERIMENTID')) {
$experimentId = $this->arg('FIRSTEXPERIMENTID');
$exp = !empty($experimentId) ? $this->arg('FIRSTEXPERIMENTID') : NULL;
}

$this->db->pq(
"INSERT INTO dewar (dewarid,code,trackingnumbertosynchrotron,trackingnumberfromsynchrotron,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,weight)
VALUES (s_dewar.nextval,:1,:2,:3,:4,CURRENT_TIMESTAMP,'opened',:5,:6,:7) RETURNING dewarid INTO :id",
array($this->arg('CODE'), $to, $from, $this->arg('SHIPPINGID'), $exp, $fc, $wg)
"INSERT INTO dewar (dewarid,code,trackingnumbertosynchrotron,trackingnumberfromsynchrotron,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,weight,source)
VALUES (s_dewar.nextval,:1,:2,:3,:4,CURRENT_TIMESTAMP,'opened',:5,:6,:7,IFNULL(:8,CURRENT_USER)) RETURNING dewarid INTO :id",
array($this->arg('CODE'), $to, $from, $this->arg('SHIPPINGID'), $exp, $fc, $wg, $source)
);

$id = $this->db->id();
Expand Down Expand Up @@ -2192,11 +2194,12 @@ function _add_container()
$crid = $this->has_arg('CONTAINERREGISTRYID') ? $this->arg('CONTAINERREGISTRYID') : null;

$pipeline = $this->has_arg('PROCESSINGPIPELINEID') ? $this->arg('PROCESSINGPIPELINEID') : null;
$source = $this->has_arg('SOURCE') ? $this->arg('SOURCE') : null;

$this->db->pq(
"INSERT INTO container (containerid,dewarid,code,bltimestamp,capacity,containertype,scheduleid,screenid,ownerid,requestedimagerid,comments,barcode,experimenttype,storagetemperature,containerregistryid,prioritypipelineid)
VALUES (s_container.nextval,:1,:2,CURRENT_TIMESTAMP,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14) RETURNING containerid INTO :id",
array($this->arg('DEWARID'), $this->arg('NAME'), $cap, $this->arg('CONTAINERTYPE'), $sch, $scr, $own, $rid, $com, $bar, $ext, $tem, $crid, $pipeline)
"INSERT INTO container (containerid,dewarid,code,bltimestamp,capacity,containertype,scheduleid,screenid,ownerid,requestedimagerid,comments,barcode,experimenttype,storagetemperature,containerregistryid,prioritypipelineid,source)
VALUES (s_container.nextval,:1,:2,CURRENT_TIMESTAMP,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14,IFNULL(:15,CURRENT_USER)) RETURNING containerid INTO :id",
array($this->arg('DEWARID'), $this->arg('NAME'), $cap, $this->arg('CONTAINERTYPE'), $sch, $scr, $own, $rid, $com, $bar, $ext, $tem, $crid, $pipeline, $source)
);

$cid = $this->db->id();
Expand Down Expand Up @@ -2672,6 +2675,7 @@ function _add_shipment()
$rt = $this->has_arg('READYBYTIME') ? $this->arg('READYBYTIME') : null;
$ct = $this->has_arg('CLOSETIME') ? $this->arg('CLOSETIME') : null;
$loc = $this->has_arg('PHYSICALLOCATION') ? $this->arg('PHYSICALLOCATION') : null;
$source = $this->has_arg('SOURCE') ? $this->arg('SOURCE') : null;

$hard_drive_enclosed = null;
if ($this->has_arg('ENCLOSEDHARDDRIVE')) {
Expand Down Expand Up @@ -2734,9 +2738,9 @@ function _add_shipment()
$extra = json_encode($extra_array);

$this->db->pq(
"INSERT INTO shipping (shippingid, proposalid, shippingname, deliveryagent_agentname, deliveryagent_agentcode, deliveryagent_shippingdate, deliveryagent_deliverydate, bltimestamp, creationdate, comments, sendinglabcontactid, returnlabcontactid, shippingstatus, safetylevel, readybytime, closetime, physicallocation)
VALUES (s_shipping.nextval,:1,:2,:3,:4,TO_DATE(:5,'DD-MM-YYYY'), TO_DATE(:6,'DD-MM-YYYY'),CURRENT_TIMESTAMP,CURRENT_TIMESTAMP,:7,:8,:9,'opened',:10, :11, :12, :13) RETURNING shippingid INTO :id",
array($this->proposalid, $this->arg('SHIPPINGNAME'), $an, $ac, $sd, $dd, $com, $this->arg('SENDINGLABCONTACTID'), $this->arg('RETURNLABCONTACTID'), $this->arg('SAFETYLEVEL'), $rt, $ct, $loc)
"INSERT INTO shipping (shippingid, proposalid, shippingname, deliveryagent_agentname, deliveryagent_agentcode, deliveryagent_shippingdate, deliveryagent_deliverydate, bltimestamp, creationdate, comments, sendinglabcontactid, returnlabcontactid, shippingstatus, safetylevel, readybytime, closetime, physicallocation, source)
VALUES (s_shipping.nextval,:1,:2,:3,:4,TO_DATE(:5,'DD-MM-YYYY'), TO_DATE(:6,'DD-MM-YYYY'),CURRENT_TIMESTAMP,CURRENT_TIMESTAMP,:7,:8,:9,'opened',:10, :11, :12, :13, IFNULL(:14,CURRENT_USER)) RETURNING shippingid INTO :id",
array($this->proposalid, $this->arg('SHIPPINGNAME'), $an, $ac, $sd, $dd, $com, $this->arg('SENDINGLABCONTACTID'), $this->arg('RETURNLABCONTACTID'), $this->arg('SAFETYLEVEL'), $rt, $ct, $loc, $source)
);

$sid = $this->db->id();
Expand All @@ -2763,9 +2767,9 @@ function _add_shipment()
$n = $fc ? $fc : ('Dewar' . ($i + 1));

$this->db->pq(
"INSERT INTO dewar (dewarid,code,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,weight)
VALUES (s_dewar.nextval,:1,:2,CURRENT_TIMESTAMP,'opened',:3,:4,$dewar_weight) RETURNING dewarid INTO :id",
array($n, $sid, $exp, $fc)
"INSERT INTO dewar (dewarid,code,shippingid,bltimestamp,dewarstatus,firstexperimentid,facilitycode,weight,source)
VALUES (s_dewar.nextval,:1,:2,CURRENT_TIMESTAMP,'opened',:3,:4,:5,IFNULL(:6,CURRENT_USER)) RETURNING dewarid INTO :id",
array($n, $sid, $exp, $fc, $dewar_weight, $source)
);

$id = $this->db->id();
Expand Down

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