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Merge pull request #165 from bcgsc/Bugfix/KBDEV-993-handle-MOA-loader…
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…-errors

Bugfix/kbdev 993 handle moa loader errors
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@sshugsc
sshugsc authored Oct 23, 2024
2 parents 9d48950 + 51c3868 commit 9465023
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Showing 3 changed files with 88 additions and 92 deletions.
156 changes: 82 additions & 74 deletions src/moa/index.js
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Original file line number Diff line number Diff line change
Expand Up @@ -256,28 +256,46 @@ const loadVariant = async (conn, moaVariant) => {
});
}
} else if (moaVariant.feature_type === 'mutational_signature') {
const signature = await conn.getUniqueRecordBy({
filters: {
AND: [
{ source: { filters: { name: 'cosmic' }, target: 'Source' } },
{ sourceId: `SBS${Number.parseInt(moaVariant.cosmic_signature_number, 10)}` },
{ sourceIdVersion: `${Number.parseInt(moaVariant.cosmic_signature_version, 10)}` },
],
},
target: 'Signature',
});
const variantType = await conn.getVocabularyTerm('signature present');
return conn.addVariant({
content: {
// KBDEV-994 adding displayName
// TODO: test displayName in KBDEV-993 and remove both comments.
displayName: `${signature.name.toUpperCase()} signature present`,
reference1: rid(signature),
type: rid(variantType),
},
existsOk: true,
target: 'CategoryVariant',
});
// Cosmic signature
let signature = {};

try {
signature = await conn.getUniqueRecordBy({
target: 'Signature',
filters: {
AND: [
{
source: {
target: 'Source',
filters: { name: 'cosmic' },
},
},
{ sourceId: moaVariant.cosmic_signature },
{ sourceIdVersion: '3' },
],
},
});
} catch (err) {
// Enforcing usage of v3 Cosmic signatures
throw Error(`Missing Cosmic signature ${moaVariant.cosmic_signature}`);
}

// 'high signature' variant type (prefered over 'signature present')
const variantType = await conn.getVocabularyTerm('high signature');

// Corresponding 'high signature' CategoryVariant
try {
return await conn.addVariant({
content: {
reference1: rid(signature),
type: rid(variantType),
},
existsOk: true,
target: 'CategoryVariant',
});
} catch (err) {
throw Error(`Unable to add variant for Cosmic signature ${moaVariant.cosmic_signature}`);
}
// } else if (moaVariant.feature_type === 'mutational_burden') {
} else if (moaVariant.feature_type === 'copy_number') {
const variantType = await conn.getVocabularyTerm(moaVariant.direction);
Expand Down Expand Up @@ -309,14 +327,13 @@ const loadRecord = async (conn, moaRecord, moaSource, relevanceTerms) => {
disease = await conn.getUniqueRecordBy({
filters: {
AND: [
{ name: moaRecord.oncotree_term },
{ sourceId: moaRecord.oncotree_code },
{ source: { filters: { name: 'oncotree' }, target: 'Source' } },
],
},
target: 'Disease',
});
} else if (moaRecord.oncotree_term) {
} else if (moaRecord.oncotree_term & moaRecord.oncotree_term !== 'Any solid tumor') {
disease = await conn.getUniqueRecordBy({
filters: {
AND: [
Expand All @@ -327,6 +344,9 @@ const loadRecord = async (conn, moaRecord, moaSource, relevanceTerms) => {
target: 'Disease',
});
} else if (moaRecord.disease) {
if (moaRecord.disease === 'Any solid tumor') {
moaRecord.disease = 'all solid tumors';
}
disease = await conn.getUniqueRecordBy({
filters: {
AND: [
Expand Down Expand Up @@ -362,18 +382,30 @@ const loadRecord = async (conn, moaRecord, moaSource, relevanceTerms) => {
if (sourceRecord.nct && sourceRecord.source_type !== 'Abstract') {
articles.push(await _trials.fetchAndLoadById(conn, sourceRecord.nct));
} else if (['FDA', 'Guideline'].includes(sourceRecord.source_type)) {
articles.push(await conn.addRecord({
content: {
try {
const record = await conn.getUniqueRecordBy({
filters: { AND: [{ source: rid(moaSource) }, { sourceId: sourceRecord.source_id }, { name: `${sourceRecord.source_type}-${sourceRecord.source_id}` }] },
target: 'CuratedContent',
});
articles.push(await conn.updateRecord('CuratedContent', record['@rid'], {
citation: sourceRecord.citation,
displayName: `${SOURCE_DEFN.displayName} ${sourceRecord.source_type}-${sourceRecord.source_id}`,
name: `${sourceRecord.source_type}-${sourceRecord.source_id}`,
source: rid(moaSource),
sourceId: sourceRecord.source_id,
url: sourceRecord.url,
},
existsOk: true,
target: 'CuratedContent',
}));
}));
} catch (err) {
articles.push(await conn.addRecord({
content: {
citation: sourceRecord.citation,
displayName: `${SOURCE_DEFN.displayName} ${sourceRecord.source_type}-${sourceRecord.source_id}`,
name: `${sourceRecord.source_type}-${sourceRecord.source_id}`,
source: rid(moaSource),
sourceId: sourceRecord.source_id,
url: sourceRecord.url,
},
existsOk: true,
target: 'CuratedContent',
}));
}
} else {
throw Error(`Unable to process evidence (${sourceRecord.source_type})`);
}
Expand Down Expand Up @@ -503,9 +535,9 @@ const parseRelevance = (moaRecord) => {
relevance.push('no sensitivity');
}
}
if (moaRecord.favorable_prognosis === true) {
if (moaRecord.favorable_prognosis === 1) {
relevance.push('favourable prognosis');
} else if (moaRecord.favorable_prognosis === false) {
} else if (moaRecord.favorable_prognosis === 0) {
relevance.push('unfavourable prognosis');
}

Expand All @@ -525,61 +557,37 @@ const parseRelevance = (moaRecord) => {
return relevance;
};


const upload = async ({ conn, url = 'https://moalmanac.org/api/assertions' }) => {
const source = await conn.addSource(SOURCE_DEFN);
const records = await requestWithRetry({ json: true, method: 'GET', uri: url });
logger.info(`loaded ${records.length} assertions from MOA API`);

const counts = { error: 0, skipped: 0, success: 0 };
const existingRecords = await conn.getRecords({
filters: { source: rid(source) },
returnProperties: ['@rid', 'sourceId', 'updatedAt'],
target: 'Statement',
});

const existing = {};

for (const record of existingRecords) {
const key = record.sourceId;

if (existing[key] === undefined) {
existing[key] = [];
}
existing[key].push(record);
}

for (const rawRecord of records) {
try {
logger.info(`loading: ${rawRecord.assertion_id} / ${records.length}`);
const record = fixStringNulls(rawRecord);
checkSpec(validateMoaRecord, record);
const key = `${record.assertion_id}`;
const lastUpdate = new Date(record.last_updated).getTime();
const relevance = parseRelevance(record);

// do we have the expected number of GraphKB records for this MOA assertion
if (existing[key] && existing[key].length === relevance.length) {
// check the last update date of the assertion against the timestamp in GraphKB
if (existing[key].every(r => lastUpdate <= r.updatedAt)) {
logger.debug('Skip. Current record exists and does not need updating');
counts.skipped++;
continue;
// handle empty space in url
if (record.sources[0].url && record.sources[0].url.includes(' ')) {
record.sources[0].url = record.sources[0].url.replace(/\s/g, '');
}
// work around to match with gkb records
if (record.therapy_name) {
if (record.therapy_name.includes('Amivantamab-vmjw')) {
record.therapy_name = record.therapy_name.replace('Amivantamab-vmjw', 'amivantamab');
} else if (record.therapy_name === 'KU0058684') {
record.therapy_name = 'olaparib';
} else if (record.therapy_name === 'Tovorafenib') {
record.therapy_name = 'pan-raf kinase inhibitor tak-580';
}
}
const updatedRecords = (await loadRecord(conn, record, source, relevance)).map(r => r['@rid']);

if (existing[key]) {
const toRemove = existing[key].map(r => r['@rid']).filter(r => !updatedRecords.includes(r));
checkSpec(validateMoaRecord, record);
const relevance = parseRelevance(record);

if (toRemove.length) {
logger.warn(`Removing ${toRemove.length} records that are out of date`);
await loadRecord(conn, record, source, relevance);

for (const recordId of toRemove) {
await conn.deleteRecord('Statement', recordId);
}
}
}
counts.success++;
} catch (err) {
logger.warn(`${err}`);
Expand Down
20 changes: 4 additions & 16 deletions src/moa/spec.json
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Original file line number Diff line number Diff line change
Expand Up @@ -36,10 +36,6 @@
]
},
"rearrangement_type": {
"enum": [
"Translocation",
"Fusion"
],
"type": [
"string",
"null"
Expand All @@ -56,7 +52,7 @@
{
"properties": {
"alternate_allele": {
"pattern": "^[ATCG]*$",
"pattern": "^[ATCG-]*$",
"type": [
"string",
"null"
Expand Down Expand Up @@ -173,7 +169,7 @@
},
"pathogenic": {
"enum": [
"1.0",
"1",
null
]
},
Expand Down Expand Up @@ -285,24 +281,16 @@
},
{
"properties": {
"cosmic_signature_number": {
"pattern": "^\\d+$",
"cosmic_signature": {
"type": "string"
},
"cosmic_signature_version": {
"enum": [
"2.0",
"2"
]
},
"feature_type": {
"const": "mutational_signature"
}
},
"required": [
"feature_type",
"cosmic_signature_number",
"cosmic_signature_version"
"cosmic_signature"
],
"type": "object"
},
Expand Down
4 changes: 2 additions & 2 deletions test/moa.test.js
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Original file line number Diff line number Diff line change
Expand Up @@ -77,14 +77,14 @@ describe('parseRelevance', () => {

test('favorable prognosis', () => {
expect(parseRelevance({
favorable_prognosis: true,
favorable_prognosis: 1,
features: [],
})).toEqual(['favourable prognosis']);
});

test('unfavorable prognosis', () => {
expect(parseRelevance({
favorable_prognosis: false,
favorable_prognosis: 0,
features: [],
})).toEqual(['unfavourable prognosis']);
});
Expand Down

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