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fix: fix workflows query syntax and conditionally fire taxon/accession queries in sample report #314

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merged 2 commits into from
Apr 10, 2024
Merged

fix: fix workflows query syntax and conditionally fire taxon/accession queries in sample report #314

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2adebc8
fix query syntax and conditionally fire taxon/accession queries
Apr 10, 2024
ed1fa66
fix test
Apr 10, 2024
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64 changes: 41 additions & 23 deletions resolver-functions/SampleForReport.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -141,11 +141,11 @@ export const SampleForReportResolver = async (root, args, context)=> {
name
}
}
entityInputs(where: entityType { _in: ["taxon", "accession"] }) {
entityInputs(where: {entityType: {_in: ["taxon", "accession"]}}) {
edges {
node {
inputEntityId
entityType
inputEntityId
}
}
}
Expand All @@ -167,7 +167,7 @@ export const SampleForReportResolver = async (root, args, context)=> {
const workflowsWorkflowRuns: NextGenWorkflowsTypes.WorkflowRun[] = workflowsResp?.data?.workflowRuns || [];

// Fetch taxon info from entities based on workflow run inputs
const taxonEntityIds : { taxon: string[], accession: string [] } = {
const taxonEntityIds : { taxon: string[], accession: string[] } = {
taxon: [],
accession: [],
};
Expand All @@ -181,29 +181,47 @@ export const SampleForReportResolver = async (root, args, context)=> {
);
});

const taxaQuery = `
query TaxaQuery {
taxa(where: {id: {_in: ${taxonEntityIds["taxon"]}}}) {
id
name
upstreamDatabaseIdentifier
let taxonInfo: NextGenEntitiesTypes.Taxon[] = [];
if (taxonEntityIds["taxon"].length > 0) {
const taxaQuery = `
query TaxaQuery {
taxa(where: {id: {_in: ${taxonEntityIds["taxon"]}}}) {
id
name
upstreamDatabaseIdentifier
}
}
accessions(where: {id: {_in: ${taxonEntityIds["accession"]}}}) {
id
accessionId
accessionName
`;

const taxaResp = await get({
args,
context,
serviceType: "entities",
customQuery: taxaQuery,
});
taxonInfo = taxaResp?.data?.taxa || [];
}

let accessionInfo: NextGenEntitiesTypes.Accession[] = [];
if (taxonEntityIds["accession"].length > 0) {
const accessionQuery = `
query AccessionQuery {
accessions(where: {id: {_in: ${taxonEntityIds["accession"]}}}) {
id
accessionId
accessionName
}
}
}
`;
`;

const taxaResp = await get({
args,
context,
serviceType: "entities",
customQuery: taxaQuery,
});
const taxonInfo: NextGenEntitiesTypes.Taxon[] = taxaResp?.data?.taxa || [];
const accessionInfo: NextGenEntitiesTypes.Accession[] = taxaResp?.data?.accessions || [];
const accessionResp = await get({
args,
context,
serviceType: "entities",
customQuery: accessionQuery,
});
accessionInfo = accessionResp?.data?.accessions || [];
}

const nextGenWorkflowRuns: query_SampleForReport_workflow_runs_items[] = workflowsWorkflowRuns.map(workflowRun => {
const consensusGenome = consensusGenomes.find(consensusGenome => {
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