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KPMP-5566_add-participant-clinical-info #270

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merged 7 commits into from
Oct 28, 2024
Merged

KPMP-5566_add-participant-clinical-info #270

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b93961d
update query
Dert1129 Oct 25, 2024
138036d
use enrollmentCategory
Dert1129 Oct 25, 2024
22e9f29
remove dot
Dert1129 Oct 25, 2024
e0a6ad7
log clincial datasets var
Dert1129 Oct 28, 2024
1ab3347
remove json.parse
Dert1129 Oct 28, 2024
dd2838e
add clinicalKeysToPresentationStyle
Dert1129 Oct 28, 2024
9feef42
fix tests and alc error
Dert1129 Oct 28, 2024
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3 changes: 0 additions & 3 deletions src/actions/Clinical/clinicalDatasetAction.js
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Original file line number Diff line number Diff line change
Expand Up @@ -13,9 +13,6 @@ export const fetchAndSetSummaryDatasets = (participant_id) => {
export const fetchAndSetClinicalDatasets = (participant_id) => {
return async (dispatch) => {
let clinicalDatasets = await fetchParticipantClinicalDataset(participant_id);
if (clinicalDatasets) {
clinicalDatasets = JSON.parse(clinicalDatasets.clinicalData);
}
clinicalDatasets = mapClinicalKeysToPresentationStyle(clinicalDatasets);
dispatch(setClinicalDatasets(clinicalDatasets));
}
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46 changes: 28 additions & 18 deletions src/helpers/Api.js
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ export const fetchParticipantSummaryDataset = async (redcapId) => {
const query = gql`
query participantSummaryDataset($redcapId: String!) {
participantSummaryDataset(redcapId: $redcapId){
tissueType
enrollmentCategory
redcapId
}
}`;
Expand Down Expand Up @@ -66,21 +66,31 @@ export const fetchParticipantExperimentCounts = async (redcapId) => {
};

export const fetchParticipantClinicalDataset = async (redcapId) => {
const query = gql`
query participantSummaryDataset($redcapId: String!) {
participantSummaryDataset(redcapId: $redcapId){
clinicalData
}
}`;
const response = await apolloClient.query({
query: query,
variables: {
redcapId: redcapId
const query = gql`
query {
getParticipantClinicalDataset(redcapId: "${redcapId}"){
kdigoStage
baselineEgfr
proteinuria
a1c
albuminuria
diabetesHistory
diabetesDuration
hypertensionHistory
hypertensionDuration
onRaasBlockade
race
}
});
if (response && response.data && response.data.participantSummaryDataset) {
return response.data.participantSummaryDataset;
} else {
store.dispatch(sendMessageToBackend("Could not retrieve participantSummaryDataset (clinical data): " + response.error));
}
};
}`;
const response = await apolloClient.query({
query: query,
variables: {
redcapId: redcapId
}
});
if (response && response.data && response.data.getParticipantClinicalDataset) {
return response.data.getParticipantClinicalDataset;
} else {
store.dispatch(sendMessageToBackend("Could not retrieve getParticipantClinicalDataset (clinical data): " + response.error));
}
};
66 changes: 33 additions & 33 deletions src/helpers/dataHelper.js
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Original file line number Diff line number Diff line change
Expand Up @@ -76,56 +76,56 @@ export const mapClinicalKeysToPresentationStyle = (data) => {
if (!data || data === {}) {
return result;
}
if (data['A1c (%) (Binned)']) {
result['A1C (%)'] = data['A1c (%) (Binned)'] ? data['A1c (%) (Binned)'] : "";
if (data.a1c) {
result['A1C (%)'] = data.a1c ? data.a1c : "";
}
if (data['Albuminuria (mg) (Binned)']) {
result['Albuminuria (mg)'] = data['Albuminuria (mg) (Binned)'] ? data['Albuminuria (mg) (Binned)'] : "";
if (data.albuminuria) {
result['Albuminuria (mg)'] = data.albuminuria ? data.albuminuria : "";
}
if (data['Baseline eGFR (ml/min/1.73m2) (Binned)']) {
result['Baseline eGFR (ml/min/1.73m2)'] = data['Baseline eGFR (ml/min/1.73m2) (Binned)'] ? data['Baseline eGFR (ml/min/1.73m2) (Binned)'].replace(' ml/min/1.73m2', '') : "";
if (data.baselineEgfr) {
result['Baseline eGFR (ml/min/1.73m2)'] = data.baselineEgfr ? data.baselineEgfr.replace(' ml/min/1.73m2', '') : "";
}
if (data['Diabetes Duration (Years)']) {
result['Diabetes Duration (Years)'] = data['Diabetes Duration (Years)'] ? data['Diabetes Duration (Years)'].replace(' Years', '') : "";
if (data.diabetesDuration) {
result['Diabetes Duration (Years)'] = data.diabetesDuration ? data.diabetesDuration.replace(' Years', '') : "";
}
if (data['Diabetes History']) {
result['Diabetes History'] = data['Diabetes History'] ? data['Diabetes History'] : "";
if (data.diabetesHistory) {
result['Diabetes History'] = data.diabetesHistory ? data.diabetesHistory : "";
}
if (data['Hypertension Duration (Years)']) {
result['Hypertension Duration (years)'] = data['Hypertension Duration (Years)'] ? data['Hypertension Duration (Years)'].replace(' Years', '') : "";
if (data.hypertensionDuration) {
result['Hypertension Duration (years)'] = data.hypertensionDuration ? data.hypertensionDuration.replace(' Years', '') : "";
}
if (data['Hypertension History']) {
result['Hypertension History'] = data['Hypertension History'] ? data['Hypertension History'] : "";
if (data.hypertensionHistory) {
result['Hypertension History'] = data.hypertensionHistory ? data.hypertensionHistory : "";
}
if (data['KDIGO Stage']) {
result['KDIGO Stage'] = data['KDIGO Stage'] ? data['KDIGO Stage'] : "";
if (data.kdigoStage) {
result['KDIGO Stage'] = data.kdigoStage ? data.kdigoStage : "";
}
if (data['On RAAS Blockade']) {
result['On RAAS Blockade'] = data['On RAAS Blockade'] ? data['On RAAS Blockade'] : "";
if (data.onRaasBlockade) {
result['On RAAS Blockade'] = data.onRaasBlockade ? data.onRaasBlockade : "";
}
if (data['Proteinuria (mg) (Binned)']) {
result['Proteinuria (mg)'] = data['Proteinuria (mg) (Binned)'] ? data['Proteinuria (mg) (Binned)'] : "";
if (data.proteinuria) {
result['Proteinuria (mg)'] = data.proteinuria ? data.proteinuria : "";
}
if (data['Race']) {
result['Ethnicity'] = data['Race'] ? data['Race'] : "";
if (data.race) {
result['Ethnicity'] = data.race ? data.race : "";
}
if (data['Age (Years) (Binned)']) {
result['Age (Years)'] = data['Age (Years) (Binned)'] ? data['Age (Years) (Binned)'].replace(' Years', '') : "";
if (data.age) {
result['Age (Years)'] = data.age ? data.age.replace(' Years', '') : "";
}

if (data['Sample Type']) {
result['Sample Type'] = data['Sample Type'] ? data['Sample Type'] : "";
if (data.sampleType) {
result['Sample Type'] = data.sampleType ? data.sampleType : "";
}

if (data['Sex']) {
result['Sex'] = data['Sex'] ? data['Sex'] : "";
if (data.sex) {
result['Sex'] = data.sex ? data.sex : "";
}
if (data['Protocol']) {
result['Protocol'] = data['Protocol'] ? data['Protocol'] : "";
if (data.protocol) {
result['Protocol'] = data.protocol ? data.protocol : "";
}
if (data['Tissue Source']) {
result['Tissue Source'] = data['Tissue Source'] ? data['Tissue Source'] : "";
if (data.tissueSource) {
result['Tissue Source'] = data.tissueSource ? data.tissueSource : "";
}

return result;
};
};
182 changes: 94 additions & 88 deletions src/helpers/dataHelper.test.js
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Original file line number Diff line number Diff line change
Expand Up @@ -68,109 +68,115 @@ describe('dataHelper', () => {

describe('mapClinicalKeysToPresentationStyle', () => {
it('should return remapped values when object params given', () => {
let clinicalUnmapped = {};
clinicalUnmapped['A1c (%) (Binned)']= "test-a1c";
clinicalUnmapped['Albuminuria (mg) (Binned)'] = "test-albuminuria";
clinicalUnmapped['Baseline eGFR (ml/min/1.73m2) (Binned)'] = "test-baseline_egfr";
clinicalUnmapped['Diabetes Duration (Years)'] = "test-diabetes_duration";
clinicalUnmapped['Diabetes History'] = "test-diabetes_history";
clinicalUnmapped['Hypertension Duration (Years)'] = "test-hypertension_duration";
clinicalUnmapped['Hypertension History'] = "test-hypertension_history";
clinicalUnmapped['KDIGO Stage'] = "test-kdigo_stage";
clinicalUnmapped['On RAAS Blockade'] = "test-on_raas_blockade";
clinicalUnmapped['Proteinuria (mg) (Binned)'] = "test-proteinuria";
clinicalUnmapped['Race'] = "test-Ethnicity";
clinicalUnmapped['Age (Years) (Binned)'] = "test-Age";
clinicalUnmapped['Sex'] = "test-sex";
clinicalUnmapped['Protocol'] = "test-Protocol";
clinicalUnmapped['Sample Type'] = "test-Sample Type";
clinicalUnmapped['Tissue Source'] = "test-Tissue Source";
let clinicalUnmapped = {
"a1c": "test-a1c",
"albuminuria": "test-albuminuria",
"baselineEgfr": "test-baseline_egfr",
"diabetesDuration": "test-diabetes_duration",
"diabetesHistory": "test-diabetes_history",
"hypertensionDuration": "test-hypertension_duration",
"hypertensionHistory": "test-hypertension_history",
"kdigoStage": "testdkigo_stage",
"onRaasBlockade": "test-on_raas_blockade",
"proteinuria": "proteinuria",
"race": "test-Ethnicity",
"age": "test-Age",
"sex": "test-sex",
"protocol": "test-protocol",
"sampleType": "test-sample_type",
"tissueSource": "test-tissue_source"
};
const clinicalMappingResult = mapClinicalKeysToPresentationStyle(clinicalUnmapped);
const expectedClinicalMapping = {};
expectedClinicalMapping['A1C (%)']= "test-a1c";
expectedClinicalMapping['Albuminuria (mg)'] = "test-albuminuria";
expectedClinicalMapping['Baseline eGFR (ml/min/1.73m2)'] = "test-baseline_egfr";
expectedClinicalMapping['Diabetes Duration (Years)'] = "test-diabetes_duration";
expectedClinicalMapping['Diabetes History'] = "test-diabetes_history";
expectedClinicalMapping['Hypertension Duration (years)'] = "test-hypertension_duration";
expectedClinicalMapping['Hypertension History'] = "test-hypertension_history";
expectedClinicalMapping['KDIGO Stage'] = "test-kdigo_stage";
expectedClinicalMapping['On RAAS Blockade'] = "test-on_raas_blockade";
expectedClinicalMapping['Proteinuria (mg)'] = "test-proteinuria";
expectedClinicalMapping['Ethnicity'] = "test-Ethnicity";
expectedClinicalMapping['Age (Years)'] = "test-Age";
expectedClinicalMapping['Sex'] = "test-sex";
expectedClinicalMapping['Protocol'] = "test-Protocol";
expectedClinicalMapping['Sample Type'] = "test-Sample Type";
expectedClinicalMapping['Tissue Source'] = "test-Tissue Source";
const expectedClinicalMapping = {
'A1C (%)': "test-a1c",
'Albuminuria (mg)': 'test-albuminuria',
'Baseline eGFR (ml/min/1.73m2)': 'test-baseline_egfr',
'Diabetes Duration (Years)': 'test-diabetes_duration',
'Diabetes History': 'test-diabetes_history',
'Hypertension Duration (years)': 'test-hypertension_duration',
'Hypertension History': 'test-hypertension_history',
'KDIGO Stage': 'testdkigo_stage',
'On RAAS Blockade': 'test-on_raas_blockade',
'Proteinuria (mg)': 'proteinuria',
'Ethnicity': 'test-Ethnicity',
'Age (Years)': 'test-Age',
'Sample Type': 'test-sample_type',
'Sex': 'test-sex',
'Protocol': 'test-protocol',
'Tissue Source': 'test-tissue_source'
}
expect(clinicalMappingResult).toEqual(expectedClinicalMapping);
}),
it('should return remapped values when object params given even when bad data is sent', () => {
let clinicalUnmapped = {};
clinicalUnmapped['A1c (%) (EXAMPLE SHOULD BE BINNED)']= "test-a1c";
clinicalUnmapped['Albuminuria (mg) (Binned)'] = "test-albuminuria";
let clinicalUnmapped = {
"a1c": "test-a1c",
"albuminuria": "test-albuminuria",
};
const clinicalMappingResult = mapClinicalKeysToPresentationStyle(clinicalUnmapped);
const expectedClinicalMapping = {};
expectedClinicalMapping['A1C (%)']= "";
expectedClinicalMapping['Albuminuria (mg)'] = "test-albuminuria";
expectedClinicalMapping['Baseline eGFR (ml/min/1.73m2)'] = "";
expectedClinicalMapping['Diabetes Duration (Years)'] = "";
expectedClinicalMapping['Diabetes History'] = "";
expectedClinicalMapping['Hypertension Duration (years)'] = "";
expectedClinicalMapping['Hypertension History'] = "";
expectedClinicalMapping['KDIGO Stage'] = "";
expectedClinicalMapping['On RAAS Blockade'] = "";
expectedClinicalMapping['Proteinuria (mg)'] = "";
expectedClinicalMapping['Ethnicity'] = "";
expectedClinicalMapping['Age (Years)'] = "";
expectedClinicalMapping['Sex'] = "";
expectedClinicalMapping['Protocol'] = "";
expectedClinicalMapping['Sample Type'] = "";
expectedClinicalMapping['Tissue Source'] = "";
const expectedClinicalMapping = {
'A1C (%)': "test-a1c",
'Albuminuria (mg)': 'test-albuminuria',
'Baseline eGFR (ml/min/1.73m2)': '',
'Diabetes Duration (Years)': '',
'Diabetes History': '',
'Hypertension Duration (years)': '',
'Hypertension History': '',
'KDIGO Stage': '',
'On RAAS Blockade': '',
'Proteinuria (mg)': '',
'Ethnicity': '',
'Age (Years)': '',
'Sample Type': '',
'Sex': '',
'Protocol': '',
'Tissue Source': ''
};
expect(clinicalMappingResult).toEqual(expectedClinicalMapping);
}),
it('should return remapped values when empty object params given', () => {
let clinicalUnmapped = {};
const clinicalMappingResult = mapClinicalKeysToPresentationStyle(clinicalUnmapped);
const expectedClinicalMapping = {};
expectedClinicalMapping['A1C (%)']= "";
expectedClinicalMapping['Albuminuria (mg)'] = "";
expectedClinicalMapping['Baseline eGFR (ml/min/1.73m2)'] = "";
expectedClinicalMapping['Diabetes Duration (Years)'] = "";
expectedClinicalMapping['Diabetes History'] = "";
expectedClinicalMapping['Hypertension Duration (years)'] = "";
expectedClinicalMapping['Hypertension History'] = "";
expectedClinicalMapping['KDIGO Stage'] = "";
expectedClinicalMapping['On RAAS Blockade'] = "";
expectedClinicalMapping['Proteinuria (mg)'] = "";
expectedClinicalMapping['Ethnicity'] = "";
expectedClinicalMapping['Age (Years)'] = "";
expectedClinicalMapping['Sex'] = "";
expectedClinicalMapping['Protocol'] = "";
expectedClinicalMapping['Sample Type'] = "";
expectedClinicalMapping['Tissue Source'] = "";
const expectedClinicalMapping = {
'A1C (%)': "",
'Albuminuria (mg)': '',
'Baseline eGFR (ml/min/1.73m2)': '',
'Diabetes Duration (Years)': '',
'Diabetes History': '',
'Hypertension Duration (years)': '',
'Hypertension History': '',
'KDIGO Stage': '',
'On RAAS Blockade': '',
'Proteinuria (mg)': '',
'Ethnicity': '',
'Age (Years)': '',
'Sample Type': '',
'Sex': '',
'Protocol': '',
'Tissue Source': ''
};
expect(clinicalMappingResult).toEqual(expectedClinicalMapping);
}),
it('should return remapped values when null params given', () => {
let clinicalUnmapped = null;
const clinicalMappingResult = mapClinicalKeysToPresentationStyle(clinicalUnmapped);
const expectedClinicalMapping = {};
expectedClinicalMapping['A1C (%)']= "";
expectedClinicalMapping['Albuminuria (mg)'] = "";
expectedClinicalMapping['Baseline eGFR (ml/min/1.73m2)'] = "";
expectedClinicalMapping['Diabetes Duration (Years)'] = "";
expectedClinicalMapping['Diabetes History'] = "";
expectedClinicalMapping['Hypertension Duration (years)'] = "";
expectedClinicalMapping['Hypertension History'] = "";
expectedClinicalMapping['KDIGO Stage'] = "";
expectedClinicalMapping['On RAAS Blockade'] = "";
expectedClinicalMapping['Proteinuria (mg)'] = "";
expectedClinicalMapping['Ethnicity'] = "";
expectedClinicalMapping['Age (Years)'] = "";
expectedClinicalMapping['Sex'] = "";
expectedClinicalMapping['Protocol'] = "";
expectedClinicalMapping['Sample Type'] = "";
expectedClinicalMapping['Tissue Source'] = "";
const expectedClinicalMapping = {
'A1C (%)': "",
'Albuminuria (mg)': '',
'Baseline eGFR (ml/min/1.73m2)': '',
'Diabetes Duration (Years)': '',
'Diabetes History': '',
'Hypertension Duration (years)': '',
'Hypertension History': '',
'KDIGO Stage': '',
'On RAAS Blockade': '',
'Proteinuria (mg)': '',
'Ethnicity': '',
'Age (Years)': '',
'Sample Type': '',
'Sex': '',
'Protocol': '',
'Tissue Source': ''
};
expect(clinicalMappingResult).toEqual(expectedClinicalMapping);
})
})
Expand Down
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