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fixed issue
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@ridz1208
ridz1208 committed Dec 16, 2024
1 parent 0292427 commit 897680a
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Showing 4 changed files with 104 additions and 84 deletions.
72 changes: 38 additions & 34 deletions modules/biobank/jsx/customFields.js
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Original file line number Diff line number Diff line change
@@ -1,85 +1,89 @@
import React from 'react';
import PropTypes from 'prop-types';
import {
TextboxElement,
DateElement,
TimeElement,
CheckboxElement,
FileElement
} from 'jsx/Form';

/**
* Biobank Custom Attribute Fields
*
* @param {object} props The component's props.
*/
function CustomFields(props) {
const {options, errors, fields, object} = props;
const {options, errors, attributes, object} = props;

return Object.keys(fields).map(
return attributes.map(
(attribute, key) => {
const datatype = options.specimen.attributeDatatypes[
fields[attribute]['datatypeId']
].datatype;
const datatype = options.specimen.attributeDatatypes[attribute.datatypeId]
.datatype;
if (datatype === 'text' || datatype === 'number') {
return (
<TextboxElement
key={key}
name={attribute}
label={fields[attribute].label}
name={attribute.id}
label={attribute.label}
onUserInput={props.setData}
required={fields[attribute].required}
value={object[attribute]}
errorMessage={errors[attribute]}
required={attribute.required}
value={object[attribute.id]}
errorMessage={errors[attribute.id]}
/>
);
}
if (datatype === 'date') {
return (
<DateElement
key={key}
name={attribute}
label={fields[attribute].label}
name={attribute.id}
label={attribute.label}
onUserInput={props.setData}
required={fields[attribute].required}
value={object[attribute]}
errorMessage={errors[attribute]}
required={attribute.required}
value={object[attribute.id]}
errorMessage={errors[attribute.id]}
/>
);
}
if (datatype === 'time') {
return (
<TimeElement
key={key}
name={attribute}
label={fields[attribute].label}
name={attribute.id}
label={attribute.label}
onUserInput={props.setData}
required={fields[attribute].required}
value={object[attribute]}
errorMessage={errors[attribute]}
required={attribute.required}
value={object[attribute.id]}
errorMessage={errors[attribute.id]}
/>
);
}
if (datatype === 'boolean') {
// TODO: delete the following line.
// object[attribute] == null && props.setData(attribute, false);
return (
<CheckboxElement
key={key}
name={attribute}
label={fields[attribute].label}
name={attribute.id}
label={attribute.label}
onUserInput={props.setData}
required={fields[attribute].required}
value={object[attribute]}
errorMessage={errors[attribute]}
required={attribute.required}
value={object[attribute.id]}
errorMessage={errors[attribute.id]}
/>
);
}
// Do not present the possibility of uploading if file is already set
// File must instead be deleted or overwritten.
if (datatype === 'file' && !(props.data||{})[attribute]) {
if (datatype === 'file' && !(props.data||{})[attribute.id]) {
return (
<FileElement
key={key}
name={attribute}
label={fields[attribute].label}
name={attribute.id}
label={attribute.label}
onUserInput={props.setData}
required={fields[attribute].required}
value={props.current.files[object[attribute]]}
errorMessage={errors[attribute]}
required={attribute.required}
value={props.current.files[object[attribute.id]]}
errorMessage={errors[attribute.id]}
/>
);
}
Expand All @@ -88,7 +92,7 @@ function CustomFields(props) {
}

CustomFields.propTypes = {
fields: PropTypes.object.isRequired,
attributes: PropTypes.array.isRequired,
options: PropTypes.object.isRequired,
object: PropTypes.object.isRequired,
setData: PropTypes.func.isRequired,
Expand Down
50 changes: 23 additions & 27 deletions modules/biobank/jsx/processForm.js
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,6 @@ const SpecimenProcessForm = (props) => {
);

let specimenProtocols = {};
let specimenProtocolAttributes = {};
Object.entries(options.specimen.protocols).forEach(
([id, protocol]) => {
// FIXME: I really don't like 'toLowerCase()' function, but it's the
Expand All @@ -73,19 +72,17 @@ const SpecimenProcessForm = (props) => {
if (typeId == protocol.typeId && process == processStage
) {
specimenProtocols[id] = protocol.label;
const attribute = options.specimen.protocolAttributes[id];
specimenProtocolAttributes[id] = attribute;
}
}
);

const renderProtocolFields = () => {
if (specimenProtocolAttributes[process.protocolId]) {
if (options.specimen.protocolAttributes[process.protocolId]) {
if (process.data) {
return <CustomFields
options={options}
errors={errors.data || {}}
fields={specimenProtocolAttributes[process.protocolId]}
attributes={options.specimen.protocolAttributes[process.protocolId]}
object={process.data}
setData={setData} />;
} else {
Expand Down Expand Up @@ -178,29 +175,28 @@ const SpecimenProcessForm = (props) => {
updateButton,
];
} else if (edit === false) {
const protocolStaticFields = process.data &&
Object.keys(process.data).map(
(key) => {
let value = process.data[key];
if (process.data[key] === true) {
value = 'Yes';
} else if (process.data[key] === false) {
value = 'No';
}
// FIXME: The label used to be produced in the following way:
// label={options.specimen.protocolAttributes[process.protocolId][key].label}
// However, causes issues when there is data in the data
// object, but the protocolId is not associated with any attributes.
// This is a configuration/importing issue that should be fixed.
return (
<StaticElement
key={key}
label={options.specimen.attributes[key].label}
text={value}
/>
);
const protocolAttributes = options.specimen.protocolAttributes[
process.protocolId
] || [];

const protocolStaticFields = protocolAttributes.map((attribute) => {
let value = process.data[attribute.id]; // Fetch the corresponding value from process.data

// Convert boolean values to "Yes" or "No"
if (value === true) {
value = 'Yes';
} else if (value === false) {
value = 'No';
}
);

return (
<StaticElement
key={attribute.id}
label={attribute.label} // Use the attribute label from the ordered list
text={value || '—'} // Use an empty string if value is undefined
/>
);
});

const collectionStaticFields = (processStage === 'collection') && (
<StaticElement
Expand Down
7 changes: 7 additions & 0 deletions modules/biobank/jsx/specimenForm.js
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Original file line number Diff line number Diff line change
Expand Up @@ -551,6 +551,13 @@ class SpecimenBarcodeForm extends React.Component {
this.setSpecimen = this.setSpecimen.bind(this);
}

componentDidUpdate(prevProps, prevState) {
// Check if typeId has changed
if (prevProps.item.typeId !== this.props.item.typeId) {
this.props.setListItem('collection', {}, this.props.itemKey);
}
}

/**
* Set the current container.
*
Expand Down
59 changes: 36 additions & 23 deletions modules/biobank/php/specimendao.class.inc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -393,33 +393,46 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
*/
public function getProtocolAttributes() : array
{
$query = "SELECT bsp.SpecimenProtocolID as protocolId,
bsa.SpecimenAttributeID as attributeId,
bsa.Label as label,
bsa.DatatypeID as datatypeId,
bspa.Required as required,
bspa.ShowInDataTable as showInDataTable
FROM biobank_specimen_protocol_attribute_rel bspa
LEFT JOIN biobank_specimen_protocol bsp
USING (SpecimenProtocolID)
LEFT JOIN biobank_specimen_attribute bsa
USING (SpecimenAttributeID)";
$query = "
SELECT
bsp.SpecimenProtocolID as protocolId,
bsa.SpecimenAttributeID as attributeId,
bsa.Label as label,
bsa.DatatypeID as datatypeId,
bspa.Required as required,
bspa.ShowInDataTable as showInDataTable,
bspa.OrderIndex as orderIndex
FROM biobank_specimen_protocol_attribute_rel bspa
LEFT JOIN biobank_specimen_protocol bsp
USING (SpecimenProtocolID)
LEFT JOIN biobank_specimen_attribute bsa
USING (SpecimenAttributeID)
ORDER BY bsp.SpecimenProtocolID, bspa.OrderIndex
";

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

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

$attrib['label'] = $row['label'];
$attrib['datatypeId'] = $row['datatypeId'];
$attrib['required'] = (int) $row['required'];
$attrib['showInDataTable'] = (int) $row['showInDataTable'];

// Add the attribute data, keeping the order intact
$protocolAttributes[$protocolId][] = [
'id' => $row['attributeId'],
'label' => $row['label'],
'datatypeId' => $row['datatypeId'],
'required' => (int) $row['required'],
'showInDataTable' => (int) $row['showInDataTable'],
'orderIndex' => (int) $row['orderIndex'],
];
}

return $pA;
}
return $protocolAttributes;
}

/**
* Queries all rows from the biobank_specimen_protocol_attribute_rel table
Expand Down

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