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bugfix/DEVSU-2492 add minimal scope to kbmatch #411

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merged 3 commits into from
Dec 19, 2024
Merged

bugfix/DEVSU-2492 add minimal scope to kbmatch #411

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43941c3
add minimal scope to kbMatches
sshugsc Dec 16, 2024
2c33756
lint & test
sshugsc Dec 16, 2024
b6de65e
Merge branch 'develop' into bugfix/DEVSU-2492-add-minimal-scope-to-kb…
bnguyen-bcgsc Dec 17, 2024
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3 changes: 3 additions & 0 deletions app/models/reports/kbMatches.js
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,9 @@ module.exports = (sequelize, Sq) => {
return {model: sequelize.models[modelName].scope('public'), as: modelName};
}),
},
minimal: {
attributes: {exclude: ['id', 'reportId', 'variantId', 'deletedAt', 'updatedBy']},
},
extended: {
attributes: {exclude: ['id', 'reportId', 'variantId', 'deletedAt', 'updatedBy']},
include: Object.values(KB_PIVOT_MAPPING).map((modelName) => {
Expand Down
57 changes: 6 additions & 51 deletions app/routes/report/report.js
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Expand Up @@ -105,7 +105,7 @@ router.route('/')
.get(async (req, res) => {
let {
query: {
paginated, limit, offset, sort, project, states, role, searchText, keyVariant, matchingThreshold, category, approvedTherapy, kbVariant, disease, relevance, context, status, reference, sample, evidenceLevel, matchedCancer, pmidRef, variantType,
paginated, limit, offset, sort, project, states, role, searchText, keyVariant, matchingThreshold, kbVariant,
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},
} = req;

Expand All @@ -125,7 +125,7 @@ router.route('/')
try {
// validate request query parameters
validateAgainstSchema(reportGetSchema, {
paginated, limit, offset, sort, project, states, role, searchText, keyVariant, matchingThreshold, category, approvedTherapy, kbVariant, disease, relevance, context, status, reference, sample, evidenceLevel, matchedCancer, pmidRef, variantType,
paginated, limit, offset, sort, project, states, role, searchText, keyVariant, matchingThreshold, kbVariant,
}, false);
} catch (err) {
const message = `Error while validating the query params of the report GET request ${err}`;
Expand Down Expand Up @@ -184,15 +184,12 @@ router.route('/')
...((kbVariant && matchingThreshold) ? {
'$kbMatches.kb_variant$': {
[Op.in]: literal(
`(SELECT "kb_variant"
FROM (SELECT "kb_variant", word_similarity('${kbVariant}', "kb_variant") FROM reports_kb_matches) AS subquery
`(SELECT "kb_variant"
FROM (SELECT "kb_variant", word_similarity('${kbVariant}', "kb_variant") FROM reports_kb_matches) AS subquery
WHERE word_similarity >= ${matchingThreshold})`,
),
},
} : {}),
...((variantType) ? {
'$kbMatches.variant_type$': {[Op.eq]: `${variantType}`},
} : {}),
},
distinct: 'id',
// **searchText with paginated with patientInformation set to required: true
Expand Down Expand Up @@ -262,51 +259,9 @@ router.route('/')
model: db.models.genomicAlterationsIdentified.scope('public'),
as: 'genomicAlterationsIdentified',
}] : []),
...((category || approvedTherapy || kbVariant || disease || relevance || context || status || reference || sample || evidenceLevel || matchedCancer || pmidRef || variantType) ? [{
model: db.models.kbMatches.scope('public'),
...((kbVariant && matchingThreshold) ? [{
model: db.models.kbMatches.scope('minimal'),
as: 'kbMatches',
include: [
{
model: db.models.kbMatchedStatements.scope('kbMatchesInclude'),
as: 'kbMatchedStatements',
through: {attributes: []},
where: {
...((category) ? {
category: {[Op.eq]: `${category}`},
} : {}),
...((approvedTherapy) ? {
approvedTherapy: {[Op.eq]: `${approvedTherapy}`},
} : {}),
...((disease) ? {
disease: {[Op.eq]: `${disease}`},
} : {}),
...((relevance) ? {
relevance: {[Op.eq]: `${relevance}`},
} : {}),
...((context) ? {
context: {[Op.eq]: `${context}`},
} : {}),
...((status) ? {
status: {[Op.eq]: `${status}`},
} : {}),
...((reference) ? {
reference: {[Op.eq]: `${reference}`},
} : {}),
...((sample) ? {
sample: {[Op.eq]: `${sample}`},
} : {}),
...((evidenceLevel) ? {
evidence_level: {[Op.eq]: `${evidenceLevel}`},
} : {}),
...((matchedCancer) ? {
matched_cancer: {[Op.eq]: `${matchedCancer}`},
} : {}),
...((pmidRef) ? {
pmid_ref: {[Op.eq]: `${pmidRef}`},
} : {}),
},
},
],
}] : []),
],
};
Expand Down
5 changes: 3 additions & 2 deletions test/routes/report/report.test.js
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,7 @@ describe('/reports/{REPORTID}', () => {
const UNREVIEWED_ACCESS = 'unreviewed Access';

const KEYVARIANT = 'uniqueKeyVariant';
const KBVARIANT = 'uniqueKbVariant';

let project;
let project2;
Expand Down Expand Up @@ -503,7 +504,7 @@ describe('/reports/{REPORTID}', () => {

test('/ - kb match - 200 Success', async () => {
const res = await request
.get('/api/reports?category=unknown&variantType=cnv')
.get(`/api/reports?kbVariant=${KBVARIANT}&&matchingThreshold=1`)
.auth(username, password)
.type('json')
.expect(HTTP_STATUS.OK);
Expand All @@ -512,7 +513,7 @@ describe('/reports/{REPORTID}', () => {

for (const resReport of res.body.reports) {
for (const gAI of resReport.kbMatches) {
expect(gAI.variantType).toEqual('cnv');
expect(gAI.kbVariant).toEqual(KBVARIANT);
}
}
}, LONGER_TIMEOUT);
Expand Down
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