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Convert group dosing data and group observations to a single CSV file for all subject groups. CSV headers are taken from a standardised list used by the Django app. Remove the previous download button, on the last step of the data stepper, and replace it with a download button in the Data tab.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
| import Papa from 'papaparse'; | ||
| import { | ||
| DatasetRead, | ||
| ProtocolRead, | ||
| SubjectGroupListApiResponse, | ||
| UnitListApiResponse, | ||
| UnitRead | ||
| } from '../../app/backendApi'; | ||
|
|
||
| type Row = { [key: string]: any }; | ||
| type Data = Row[]; | ||
| type SubjectBiomarker = { | ||
| subjectId: any; | ||
| subjectDatasetId: number | undefined; | ||
| time: any; | ||
| timeUnit: UnitRead | undefined; | ||
| value: any; | ||
| unit: UnitRead | undefined; | ||
| qname: string | undefined; | ||
| label: string; | ||
| id: number; | ||
| }; | ||
|
|
||
| const HEADERS: string[] = [ | ||
| 'ID', 'Group', 'Time', 'Time_unit', | ||
| 'Observation', 'Observation_unit', 'Observation_id', 'Observation Variable', | ||
| 'Administration ID', 'Amount', 'Amt_unit', 'Amount Variable', 'Infusion_time', | ||
| 'II', 'ADDL' | ||
| ]; | ||
|
|
||
| function parseDosingRow( | ||
| protocol: ProtocolRead, | ||
| units: UnitListApiResponse | undefined, | ||
| groupId: string | undefined, | ||
| adminId: number | ||
| ) { | ||
| const amountUnit = units?.find(unit => unit.id === protocol.amount_unit)?.symbol || ''; | ||
| const timeUnit = units?.find(unit => unit.id === protocol.time_unit)?.symbol || ''; | ||
| const qname = protocol.mapped_qname; | ||
| const doseType = protocol.dose_type; | ||
| return protocol.doses.map(dose => ({ | ||
| 'Administration ID': adminId, | ||
| Group: groupId, | ||
| Amount: dose.amount.toString(), | ||
| 'Amt_unit': amountUnit, | ||
| Time: dose.start_time.toString(), | ||
| 'Time_unit': timeUnit, | ||
| 'Infusion_time': dose.duration, | ||
| 'ADDL': (dose?.repeats || 1) - 1, | ||
| 'II': dose.repeat_interval, | ||
| 'Amount Variable': qname, | ||
| Observation: '.' | ||
| })) | ||
| } | ||
|
|
||
| function parseBiomarkerRow(row: SubjectBiomarker, groupId: string | undefined): Row { | ||
| return ({ | ||
| 'ID': row.subjectDatasetId, | ||
| 'Time': row.time.toString(), | ||
| 'Time_unit': row.timeUnit?.symbol, | ||
| 'Observation': row.value.toString(), | ||
| 'Observation_unit': row.unit?.symbol, | ||
| 'Observation_id': row.label, | ||
| 'Observation Variable': row.qname, | ||
| Group: groupId, | ||
| Amount: '.' | ||
| }); | ||
| } | ||
|
|
||
| export default function generateCSV( | ||
| dataset: DatasetRead | undefined, | ||
| groups: SubjectGroupListApiResponse, | ||
| subjectBiomarkers: SubjectBiomarker[][] | undefined, | ||
| units: UnitListApiResponse | undefined | ||
| ) { | ||
| const rows: Data = []; | ||
| groups.forEach((group, groupIndex) => { | ||
| const groupId = group?.id_in_dataset || group?.name; | ||
|
|
||
| const dosingRows: Row[] = group.protocols.flatMap((protocol, protocolIndex) => { | ||
| const adminId = groupIndex + 1 + protocolIndex; | ||
| return parseDosingRow(protocol, units, groupId, adminId); | ||
| }); | ||
|
|
||
| const observationRows: Row[] = (subjectBiomarkers || []).flatMap(biomarkerRows => biomarkerRows.map(row => { | ||
| const group = dataset?.groups?.find(group => group.subjects.includes(row.subjectId)); | ||
| const groupId = group?.id_in_dataset || group?.name; | ||
| return parseBiomarkerRow(row, groupId); | ||
| })) | ||
| .filter((row: Row) => row.Group === groupId); | ||
|
|
||
| const subjects = new Set(observationRows?.map((row: Row) => row['ID'])); | ||
| subjects.forEach(subjectId => { | ||
| const subjectObservations = observationRows ? | ||
| observationRows.filter((row: Row) => row['ID'] === subjectId) : | ||
| []; | ||
| const subjectDosing: Row[] = dosingRows | ||
| .filter(row => row.Group === groupId) | ||
| .map(row => ({ ...row, 'ID': subjectId })); | ||
| subjectDosing.concat(subjectObservations) | ||
| .forEach((observation: Row) => { | ||
| const dataRow: Row = {}; | ||
| HEADERS.forEach(header => { | ||
| dataRow[header] = observation[header]; | ||
| }); | ||
| rows.push(dataRow); | ||
| }); | ||
| }); | ||
| }); | ||
| return Papa.unparse(rows); | ||
| } |
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