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🔧 Change ven api to support query builder sqons input #244

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merged 1 commit into from
Feb 6, 2025
Merged

🔧 Change ven api to support query builder sqons input #244

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35 changes: 14 additions & 21 deletions src/app.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -205,36 +205,29 @@ export default (keycloak: Keycloak, getProject: (projectId: string) => ArrangerP
app.post('/venn', keycloak.protect(), async (req, res, next) => {
const lengthOk = (l: Sqon[]) => [2, 3].includes(l.length);
try {
const rawSqons = req.body?.sqons;
const qbSqons = req.body?.qbSqons;
const rawEntitySqons = req.body?.entitySqons;

if (!lengthOk(rawSqons) || !lengthOk(rawEntitySqons)) {
if (!lengthOk(qbSqons) || !lengthOk(rawEntitySqons)) {
res.status(StatusCodes.UNPROCESSABLE_ENTITY).send('Bad Inputs');
return;
}

const data: VennOutput[][] = [];
for (const [inputSqons, rawIndex, noOpCounts] of [
[rawSqons, 'participant', true],
[rawEntitySqons, req.body?.index, false],
]) {
// Convert sqon(s) with set_id if exists to intelligible sqon for ES query translation.
const { resolvedSqons: sqons, m: mSetItToIds } = await resolveSetsInAllSqonsWithMapper(
inputSqons,
null,
req.headers.authorization,
);
const { resolvedSqons: sqons, m: mSetItToIds } = await resolveSetsInAllSqonsWithMapper(
rawEntitySqons,
null,
req.headers.authorization,
);

const index = ['participant', 'file', 'biospecimen'].includes(rawIndex) ? rawIndex : 'participant';
const index = ['participant', 'file', 'biospecimen'].includes(req.body?.index)
? req.body?.index
: 'participant';

const datum1 = await venn(sqons, index);
const datum2 = datum1.map(x => ({ ...x, sqon: replaceIdsWithSetId(x.sqon, mSetItToIds) }));

const datum1 = await venn(sqons, index, noOpCounts);
const datum2 = datum1.map(x => ({ ...x, sqon: replaceIdsWithSetId(x.sqon, mSetItToIds) }));
data.push(datum2);
}
const indexOfParticipantEntity = 0;
const indexOfEntity = 1;
res.send({
data: reformatVenn(data[indexOfParticipantEntity], data[indexOfEntity]),
data: reformatVenn(datum2, qbSqons),
});
} catch (e) {
next(e);
Expand Down
47 changes: 13 additions & 34 deletions src/endpoints/venn/venn.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -17,18 +17,12 @@ type VennEntityOutput = {
entitySqon: Sqon;
};

type VennParticipantOutput = {
operation: string;
sqon: Sqon;
type VennOutputReformattedElement = VennEntityOutput & {
setId?: string;
};

type VennOutputReformattedElement = VennEntityOutput &
VennParticipantOutput & {
setId?: string;
};

export type VennOutputReformatted = {
summary: VennOutputReformattedElement[];
summary: (VennOutputReformattedElement & { qbSqon: Sqon })[];
operations: VennOutputReformattedElement[];
};

Expand Down Expand Up @@ -100,18 +94,10 @@ const setFormulasTrio = (s1: Sqon, s2: Sqon, s3: Sqon) => [

const mNestedFields = new Map();

export const venn = async (sqons: Sqon[], index: string, noOpCounts = false): Promise<VennOutput[]> => {
export const venn = async (sqons: Sqon[], index: string): Promise<VennOutput[]> => {
const setFormulas =
sqons.length === 2 ? setFormulasDuo(sqons[0], sqons[1]) : setFormulasTrio(sqons[0], sqons[1], sqons[2]);

// Only Venn formulas in Sqon speak is needed. Counts are not.
if (noOpCounts) {
return setFormulas.map(x => ({
...x,
count: undefined,
}));
}

const client = EsInstance.getInstance();
const indexName = `${index}_centric`;
if (!mNestedFields.has(index)) {
Expand Down Expand Up @@ -153,21 +139,16 @@ export const reformatWhenSpecifiedEntity = (os: VennOutput[]): VennEntityOutput[
entityCount: o.count,
}));

const reformatWhenUnspecifiedSqon = (os: VennOutput[]): VennParticipantOutput[] =>
os.map(o => ({
operation: o.operation,
sqon: o.sqon,
}));

const mergeOutputs = (xs: VennEntityOutput[], ys: VennParticipantOutput[]) =>
// Assumes that lists are of same length as well as "operation" value for same index loop
xs.map((x, i) => ({ ...x, ...ys[i] }));

const reformatToTables = (data: VennOutputReformattedElement[]): VennOutputReformatted => {
const reformatToTables = (data: VennOutputReformattedElement[], qbSqons: Sqon[]): VennOutputReformatted => {
const opToQbSqon = {
['Q₁']: qbSqons[0],
['Q₂']: qbSqons[1],
['Q₃']: qbSqons[2],
};
const tables = data.reduce(
(xs: VennOutputReformatted, x: VennOutputReformattedElement) => {
if (['Q₁', 'Q₂', 'Q₃'].some(y => y === x.operation)) {
return { ...xs, summary: [...xs.summary, x] };
return { ...xs, summary: [...xs.summary, { ...x, qbSqon: opToQbSqon[x.operation] }] };
}
return { ...xs, operations: [...xs.operations, x] };
},
Expand All @@ -183,7 +164,5 @@ const reformatToTables = (data: VennOutputReformattedElement[]): VennOutputRefor
};
};

export const reformatVenn = (participantOutputs: VennOutput[], entityOutputs: VennOutput[]): VennOutputReformatted =>
reformatToTables(
mergeOutputs(reformatWhenSpecifiedEntity(entityOutputs), reformatWhenUnspecifiedSqon(participantOutputs)),
);
export const reformatVenn = (outputs: VennOutput[], qbSqons: Sqon[]): VennOutputReformatted =>
reformatToTables(reformatWhenSpecifiedEntity(outputs), qbSqons);
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