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Fix: make sure hare concept id is part of histogram and overlap queries #1228

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merged 2 commits into from
Feb 8, 2023
Merged

Fix: make sure hare concept id is part of histogram and overlap queries #1228

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f801333
fix: make sure hare concept id is part of histogram and overlap queries
pieterlukasse Feb 7, 2023
7067ae7
fix: filter out undefined/null items from variables list
pieterlukasse Feb 8, 2023
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77 changes: 12 additions & 65 deletions src/Analysis/GWASV2/Utils/cohortMiddlewareApi.js
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Original file line number Diff line number Diff line change
Expand Up @@ -5,69 +5,6 @@ import { headers } from '../../../configs';

const hareConceptId = 2000007027;

export const fetchConceptStatsByHare = async (
cohortDefinitionId,
selectedCovariates,
selectedDichotomousCovariates,
sourceId,
) => {
const variablesPayload = {
variables: [
...selectedDichotomousCovariates.map(({ uuid, ...withNoId }) => withNoId),
...selectedCovariates.map((c) => ({
variable_type: 'concept',
concept_id: c.concept_id,
})),
],
};
const conceptStatsEndPoint = `${cohortMiddlewarePath}concept-stats/by-source-id/${sourceId}/by-cohort-definition-id/${cohortDefinitionId}/breakdown-by-concept-id/${hareConceptId}`;
const reqBody = {
method: 'POST',
credentials: 'include',
headers,
body: JSON.stringify(variablesPayload),
};
const response = await fetch(conceptStatsEndPoint, reqBody);
if (!response.ok) {
const message = `An error has occured: ${response.status}`;
throw new Error(message);
}
return response.json();
};

export const fetchOverlapInfo = async (
sourceId,
caseCohortDefinitionId,
controlCohortDefinitionId,
selectedHare,
selectedCovariates,
selectedDichotomousCovariates,
) => {
const variablesPayload = {
variables: [
...selectedDichotomousCovariates.map(({ uuid, ...withNoId }) => withNoId),
...selectedCovariates.map((c) => ({
variable_type: 'concept',
concept_id: c.concept_id,
})),
],
};
const statsEndPoint = `${cohortMiddlewarePath}cohort-stats/check-overlap/by-source-id/${sourceId}/by-case-control-cohort-definition-ids/${caseCohortDefinitionId}/${controlCohortDefinitionId}/filter-by-concept-id-and-value/${hareConceptId}/${selectedHare.concept_value_as_concept_id}`;
const reqBody = {
method: 'POST',
credentials: 'include',
headers,
body: JSON.stringify(variablesPayload),
};
const response = await fetch(statsEndPoint, reqBody);
if (!response.ok) {
const message = `An error has occured: ${response.status}`;
throw new Error(message);
}
return response.json();
};

// Basically a copy of fetchOverlapInfo above, but without the HARE arguments:
export const fetchSimpleOverlapInfo = async (
sourceId,
cohortAId,
Expand All @@ -76,7 +13,12 @@ export const fetchSimpleOverlapInfo = async (
outcome,
) => {
const variablesPayload = {
variables: [...selectedCovariates, outcome],
variables: [...selectedCovariates, outcome,
// add extra filter to make sure we only count persons that have a HARE group as well:
{
variable_type: 'concept',
concept_id: hareConceptId,
}],
};
const statsEndPoint = `${cohortMiddlewarePath}cohort-stats/check-overlap/by-source-id/${sourceId}/by-cohort-definition-ids/${cohortAId}/${cohortBId}`;
const reqBody = {
Expand All @@ -101,7 +43,12 @@ export const fetchHistogramInfo = async (
selectedConceptId,
) => {
const variablesPayload = {
variables: [...selectedCovariates, outcome],
variables: [...selectedCovariates, outcome,
// add extra filter to make sure we only count persons that have a HARE group as well:
{
variable_type: 'concept',
concept_id: hareConceptId,
}],
};
const endPoint = `${cohortMiddlewarePath}histogram/by-source-id/${sourceId}/by-cohort-definition-id/${cohortId}/by-histogram-concept-id/${selectedConceptId}`;
const reqBody = {
Expand Down