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DSERV-632 Adding rsid to /variants/phenotypes response #330

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DSERV-632 Adding rsid to /variants/phenotypes response #330

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25 changes: 13 additions & 12 deletions src/routers/datatypeRouters/edges/variants_phenotypes.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ const variantsPhenotypesQueryFormat = z.object({
})

const variantPhenotypeFormat = z.object({
rsid: z.array(z.string()).nullable(),
phenotype_term: z.string().nullable(),
study: z.string().or(studyFormat).optional(),
log10pvalue: z.number().nullable(),
Expand Down Expand Up @@ -192,20 +193,19 @@ async function findPhenotypesFromVariantSearch (input: paramsFormatType): Promis
}

query = `
LET primaryEdges = (
FOR record IN ${variantToPhenotypeSchema.db_collection_name as string}
FILTER record._from IN ['${variantIDs.join('\', \'')}'] ${phenotypeFilter}
RETURN record._id
)

FOR edgeRecord IN ${variantPhenotypeToStudy.db_collection_name as string}
FILTER edgeRecord._from IN primaryEdges ${hyperEdgeFilter.replaceAll('record', 'edgeRecord')}
SORT '_key'
LIMIT ${input.page as number * limit}, ${limit}
RETURN {
'study': ${input.verbose === 'true' ? `(${verboseQuery})[0]` : 'edgeRecord._to'},
${getDBReturnStatements(variantPhenotypeToStudy).replaceAll('record', 'edgeRecord')}
}
RETURN (
FOR edgeRecord IN ${variantPhenotypeToStudy.db_collection_name as string}
FILTER edgeRecord._from == record._id ${hyperEdgeFilter.replaceAll('record', 'edgeRecord')}
SORT '_key'
LIMIT ${input.page as number * limit}, ${limit}
RETURN {
'rsid': DOCUMENT(record._from).rsid,
'study': ${input.verbose === 'true' ? `(${verboseQuery})[0]` : 'edgeRecord._to'},
${getDBReturnStatements(variantPhenotypeToStudy).replaceAll('record', 'edgeRecord')}
}
)[0]
`
} else {
query = `
Expand All @@ -214,6 +214,7 @@ async function findPhenotypesFromVariantSearch (input: paramsFormatType): Promis
SORT record._key
LIMIT ${input.page as number * limit}, ${limit}
RETURN {
'rsid': DOCUMENT((FOR vp in ${variantToPhenotypeSchema.db_collection_name as string} FILTER vp._id == record._from RETURN vp._from)[0]).rsid,
'study': ${input.verbose === 'true' ? `(${verboseQuery.replaceAll('edgeRecord', 'record')})[0]` : 'record._to'},
${getDBReturnStatements(variantPhenotypeToStudy)}
}
Expand Down