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[Biobank] Load visit label into specimen entity #285

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[Biobank] Load visit label into specimen entity #285

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18 changes: 10 additions & 8 deletions jsx/globals.js
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Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,15 @@ import PropTypes from 'prop-types';
import {Link} from 'react-router-dom';
import {mapFormOptions} from './helpers.js';

import Modal from '../../../jsx/Modal'; // Temporary CBIGR Override for 26.0
import Loader from '../../../jsx/Loader'; // Temporary CBIGR Override for 26.0
import Modal from '../../../jsx/Modal'; // Temporary CBIGR Override for 26.0
import Loader from '../../../jsx/Loader'; // Temporary CBIGR Override for 26.0
import {
SelectElement,
TextboxElement,
NumericElement,
TextareaElement,
CTA,
} from '../../../jsx/Form'; // Temporary CBIGR Override for 26.0
} from '../../../jsx/Form'; // Temporary CBIGR Override for 26.0
import ContainerParentForm from './containerParentForm';

/**
Expand Down Expand Up @@ -356,11 +356,13 @@ function Globals(props) {
/>
<InlineField
label='Visit Label'
value={options.sessions[specimen.sessionId].label}
value={specimen.sessionLabel}
link={
loris.BaseURL+'/instrument_list/?candID='+
specimen.candidateId+'&sessionID='+
specimen.sessionId
options.sessions[specimen.sessionId]
? loris.BaseURL+'/instrument_list/?candID='+
specimen.candidateId+'&sessionID='+
specimen.sessionId
: null
}
/>
</div>
Expand Down Expand Up @@ -673,7 +675,7 @@ InlineField.propTypes = {
pencil: PropTypes.node.isRequired,
editValue: PropTypes.func.isRequired,
loading: PropTypes.bool.isRequired,
link: PropTypes.string.isRequired,
link: PropTypes.string,
value: PropTypes.string.isRequired,
};

Expand Down
9 changes: 5 additions & 4 deletions jsx/specimenForm.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ import PropTypes from 'prop-types';
import SpecimenProcessForm from './processForm';
import ContainerParentForm from './containerParentForm';
import {ListForm, ListItem} from './listForm';
import Modal from '../../../jsx/Modal'; // Temporary CBIGR Override for 26.0
import Modal from '../../../jsx/Modal'; // Temporary CBIGR Override for 26.0
import {mapFormOptions, clone} from './helpers.js';
import {
SearchableDropdown,
Expand All @@ -12,7 +12,7 @@ import {
CheckboxElement,
DateElement,
ButtonElement,
} from '../../../jsx/Form'; // Temporary CBIGR Override for 26.0
} from '../../../jsx/Form'; // Temporary CBIGR Override for 26.0

const initialState = {
list: {},
Expand Down Expand Up @@ -58,6 +58,7 @@ class SpecimenForm extends React.Component {
.map((item) => item.specimen.id);
current.candidateId = specimen.candidateId;
current.sessionId = specimen.sessionId;
current.sessionLabel = specimen.sessionLabel;
current.typeId = specimen.typeId;
current.originId = container.originId;
current.centerId = container.centerId;
Expand Down Expand Up @@ -224,7 +225,7 @@ class SpecimenForm extends React.Component {
/>
<StaticElement
label="Visit Label"
text={options.sessions[sessionId].label}
text={current.sessionLabel}
/>
</>
);
Expand All @@ -237,7 +238,7 @@ class SpecimenForm extends React.Component {
}
return acc;
}, {})
: {};
: {};
const mappedSessions = mapFormOptions(sessionsObject, 'label');
const candidates = mapFormOptions(
this.props.options.candidates, 'pscid'
Expand Down
28 changes: 28 additions & 0 deletions php/specimen.class.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,7 @@ class Specimen implements
* @var string $candidatePSCID
* @var int $candidateAge
* @var int $sessionId
* @var string $sessionLabel
* @var \CenterID $sessionCenterId
* @var int $poolId
* @var Collection $collection
Expand All @@ -78,6 +79,7 @@ class Specimen implements
private $candidatePSCID;
private $candidateAge;
private $sessionId;
private $sessionLabel;
private $sessionCenterId;
private $poolId;
private $collection;
Expand Down Expand Up @@ -410,6 +412,31 @@ class Specimen implements
return $this->sessionId;
}

/**
* Sets the visit label of the candidate's session/timepoint in which the
* specimen was collected.
*
* @param string $sessionLabel the visit label of the specimen's session
* of collection
*
* @return void
*/
public function setSessionLabel(string $sessionLabel) : void
{
$this->sessionLabel = $sessionLabel;
}

/**
* Gets the visit label of the candidate's session/timepoint in which the
* specimen was collected.
*
* @return ?string
*/
public function getSessionLabel() : ?string
{
return $this->sessionLabel;
}

/**
* Sets the Centeer of the candidate's session/timepoint in which the specimen
* was collected.
Expand Down Expand Up @@ -691,6 +718,7 @@ class Specimen implements
'candidatePSCID' => $this->candidatePSCID,
'candidateAge' => $this->candidateAge,
'sessionId' => $this->sessionId,
'sessionLabel' => $this->sessionLabel,
'sessionCenterId' => $this->sessionCenterId,
'poolId' => $this->poolId,
'collection' => $this->collection->jsonSerialize(),
Expand Down
16 changes: 10 additions & 6 deletions php/specimendao.class.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -119,6 +119,7 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
c.PSCID as CandidatePSCID,
bs.SessionID,
s.CenterID as SessionCenterID,
s.Visit_Label as SessionLabel,
(
SELECT FLOOR(DATEDIFF(s.Date_visit, c.DoB)/365.25)
) as CandidateAge,
Expand Down Expand Up @@ -374,7 +375,7 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
public function getProtocolAttributes() : array
{
$query = "
SELECT
SELECT
bsp.SpecimenProtocolID as protocolId,
bsa.SpecimenAttributeID as attributeId,
bsa.Label as label,
Expand All @@ -389,17 +390,17 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
USING (SpecimenAttributeID)
ORDER BY bsp.SpecimenProtocolID, bspa.OrderIndex
";

$result = $this->db->pselect($query, []);
$protocolAttributes = [];

foreach ($result as $row) {
$protocolId = $row['protocolId'];
// Ensure the protocol exists in the array
if (!isset($protocolAttributes[$protocolId])) {
$protocolAttributes[$protocolId] = [];
}

// Add the attribute data, keeping the order intact
$protocolAttributes[$protocolId][] = [
'id' => $row['attributeId'],
Expand All @@ -410,9 +411,9 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
'orderIndex' => (int) $row['orderIndex'],
];
}

return $protocolAttributes;
}
}

/**
* Queries all rows from the biobank_specimen_protocol_attribute_rel table
Expand Down Expand Up @@ -733,6 +734,9 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
if (isset($data['SessionID'])) {
$specimen->setSessionId((int) $data['SessionID']);
}
if (isset($data['SessionLabel'])) {
$specimen->setSessionLabel((string) $data['SessionLabel']);
}
if (isset($data['SessionID'])) {
$specimen->setSessionCenterId(
new \CenterID(
Expand Down