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feat(anni): split up activity scores again
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@tamslo
tamslo committed Aug 5, 2024
1 parent f5d0940 commit 3126ce7
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Showing 3 changed files with 116 additions and 95 deletions.
104 changes: 104 additions & 0 deletions anni/src/database/helpers/contraction-utils.ts
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Original file line number Diff line number Diff line change
@@ -0,0 +1,104 @@
import { DrugWithGuidelines } from './cpic-constructors';
import { IGuideline_Any, IExternalData } from '../models/Guideline';

function externalDataInformationKey(externalData: IExternalData): string {
return [
externalData.comments ?? '',
externalData.recommendation,
...Object.entries(externalData.implications).map(
([gene, implication]) => `${gene}${implication}`,
),
].join('');
}

// used to merge guidelines with equal information (e.g. when the same
// guideline is used for multiple phenotypes)
function phenotypeInformationKey(guideline: IGuideline_Any): string {
return [
...Object.keys(guideline.phenotypes).map(
(gene) => `${gene}${guideline.phenotypes[gene]}`,
),
...guideline.externalData
.map((externalData) => externalDataInformationKey(externalData))
.sort((a, b) => (a > b ? 1 : -1)),
].join('');
}

// merge same-information guidelines per phenotype if information matches (e.g.,
// different activity scores with same guideline)
// never merge FDA guidelines
function contractByPhenotypeAndInformation(
drugsWithGuidelines: Array<DrugWithGuidelines>,
source: string,
): Array<DrugWithGuidelines> {
return drugsWithGuidelines.map(({ drug, guidelines }) => {
// Do not concat FDA guidelines
if (source == 'FDA') return { drug, guidelines };
const phenotypeInformationMap = new Map<string, IGuideline_Any>();
guidelines.forEach((guideline) => {
const key = phenotypeInformationKey(guideline);
if (phenotypeInformationMap.has(key)) {
const existingGuideline = phenotypeInformationMap.get(key)!;
// ensure that we don't miss information when
// getting only first index from externalData
const oneLookupPresent = Object.values(
guideline.lookupkey,
).every((value) => value.length == 1);
if (!oneLookupPresent) {
throw Error('Expected only one lookup entry (per gene)');
}
Object.keys(existingGuideline.lookupkey).forEach((gene) => {
existingGuideline.lookupkey[gene].push(
guideline.lookupkey[gene][0],
);
});
} else {
phenotypeInformationMap.set(key, guideline);
}
});
return {
drug,
guidelines: Array.from(phenotypeInformationMap.values()),
};
});
}

// merge same-lookupkey guidelines (per activity score, if present; e.g. when a
// drug-lookupkey-pair has multiple different guidelines because the drug is
// used for different applications such as clopidogrel or has a pediatric
// guideline)
function contractByLookupkey(
drugsWithGuidelines: Array<DrugWithGuidelines>,
): Array<DrugWithGuidelines> {
return drugsWithGuidelines.map(({ drug, guidelines }) => {
const lookupMap = new Map<string, IGuideline_Any>();
guidelines.forEach((guideline) => {
const key = Object.keys(guideline.lookupkey)
.map((gene) => `${gene}${guideline.lookupkey[gene]}`)
.join('');
if (lookupMap.has(key)) {
const existingGuideline = lookupMap.get(key)!;
// ensure that we don't miss information when
// getting only first index from externalData
const oneGuidelinePresent = guideline.externalData.length == 1;
if (!oneGuidelinePresent) {
throw Error('Expected only one externalData entry');
}
existingGuideline.externalData.push(guideline.externalData[0]);
} else {
lookupMap.set(key, guideline);
}
});
return { drug, guidelines: Array.from(lookupMap.values()) };
});
}

export function contractGuidelines(
drugsWithGuidelines: Array<DrugWithGuidelines>,
source: string,
): Array<DrugWithGuidelines> {
return contractByPhenotypeAndInformation(
contractByLookupkey(drugsWithGuidelines),
source,
);
}
101 changes: 9 additions & 92 deletions anni/src/database/helpers/cpic-constructors.ts
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Original file line number Diff line number Diff line change
@@ -1,6 +1,12 @@
import { contractGuidelines } from './contraction-utils';
import { CpicRecommendation } from '../../common/cpic-api';
import { IDrug_Any } from '../models/Drug';
import { IGuideline_Any, IExternalData } from '../models/Guideline';
import { IGuideline_Any } from '../models/Guideline';

export interface DrugWithGuidelines {
drug: IDrug_Any;
guidelines: Array<IGuideline_Any>;
}

function guidelineFromRecommendation(
recommendation: CpicRecommendation,
Expand Down Expand Up @@ -41,29 +47,6 @@ function guidelineFromRecommendation(
};
}

// used to merge guidelines with equal information (e.g. when the same
// guideline is used for multiple phenotypes)
function informationKey(externalData: IExternalData): string {
return [
externalData.comments ?? '',
externalData.recommendation,
...Object.entries(externalData.implications).map(
([gene, implication]) => `${gene}${implication}`,
),
].join('');
}

// used to merge guidelines with same lookupkeys/phenotypes (e.g. when a
// drug-phenotype-pair has multiple different guideline because the drug is
// used for different applications such as clopidogrel or when multiple
// lookupkeys match to the same phenotye, as it often is the case for
// activity scores)
function phenotypeKey(guideline: IGuideline_Any): string {
return Object.keys(guideline.phenotypes)
.map((gene) => `${gene}${guideline.phenotypes[gene]}`)
.join('');
}

function drugFromRecommendation(recommendation: CpicRecommendation): IDrug_Any {
return {
name: recommendation.drug.name,
Expand All @@ -77,71 +60,7 @@ function drugFromRecommendation(recommendation: CpicRecommendation): IDrug_Any {
};
}

// initially (before contracting) guideline.externalData and values
// (phenotype descriptions) of guideline.lookupkey should be of length
// 1, as we set it this way ourselves in guidelineFromRecommendation
function ensureInitialGuidelineStructure(guideline: IGuideline_Any) {
if (
guideline.externalData.length != 1 ||
!Object.values(guideline.lookupkey).every((value) => value.length == 1)
) {
throw Error('Expected different initial guideline data structure');
}
}

// merge same-phenotype guidelines
function contractByPhenotype(
drugsWithGuidelines: Array<DrugWithGuidelines>,
): Array<DrugWithGuidelines> {
return drugsWithGuidelines.map(({ drug, guidelines }) => {
const phenotypeMap = new Map<string, IGuideline_Any>();
guidelines.forEach((guideline) => {
const key = phenotypeKey(guideline);
const existingGuideline = phenotypeMap.get(key);
if (existingGuideline) {
// ensure that we don't miss information when
// getting only first index from externalData
// and lookupkey[gene]
ensureInitialGuidelineStructure(guideline);
existingGuideline.externalData.push(guideline.externalData[0]);
Object.keys(existingGuideline.lookupkey).forEach((gene) => {
existingGuideline.lookupkey[gene].push(
guideline.lookupkey[gene][0],
);
});
} else {
phenotypeMap.set(key, guideline);
}
});
return { drug, guidelines: Array.from(phenotypeMap.values()) };
});
}

// merge same-information guidelines
function contractByInformation(
drugsWithGuidelines: Array<DrugWithGuidelines>,
): Array<DrugWithGuidelines> {
return drugsWithGuidelines.map(({ drug, guidelines }) => {
guidelines.forEach((guideline) => {
const informationMap = new Map<string, IExternalData>();
guideline.externalData.forEach((externalData) => {
const key = informationKey(externalData);
if (!informationMap.has(key)) {
informationMap.set(key, externalData);
}
});
guideline.externalData = Array.from(informationMap.values());
});
return { drug, guidelines };
});
}

export interface DrugWithGuidelines {
drug: IDrug_Any;
guidelines: Array<IGuideline_Any>;
}

export function getDrugsWithContractedGuidelines(
export function getDrugsWithGuidelines(
recommendations: Array<CpicRecommendation>,
source: string,
): Array<DrugWithGuidelines> {
Expand All @@ -159,9 +78,7 @@ export function getDrugsWithContractedGuidelines(
}
});

return contractByInformation(
contractByPhenotype(Array.from(drugIdMap.values())),
);
return contractGuidelines(Array.from(drugIdMap.values()), source);
}

export function getAdditionalDrugs(
Expand Down
6 changes: 3 additions & 3 deletions anni/src/pages/api/init-external.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ import dbConnect from '../../database/helpers/connect';
import {
DrugWithGuidelines,
getAdditionalDrugs,
getDrugsWithContractedGuidelines,
getDrugsWithGuidelines,
} from '../../database/helpers/cpic-constructors';
import Drug from '../../database/models/Drug';
import Guideline from '../../database/models/Guideline';
Expand All @@ -25,7 +25,7 @@ const getCpicData = async (): Promise<DrugWithGuidelines[]> => {
},
);
const recommendations = response.data;
return getDrugsWithContractedGuidelines(recommendations, 'CPIC');
return getDrugsWithGuidelines(recommendations, 'CPIC');
};

type GHContentResponse = {
Expand Down Expand Up @@ -57,7 +57,7 @@ const getAdditionalData = async (): Promise<DrugWithGuidelines[][]> => {
if (source == 'additional_drugs') {
return getAdditionalDrugs(response.data);
}
return getDrugsWithContractedGuidelines(response.data, source);
return getDrugsWithGuidelines(response.data, source);
}),
);
};
Expand Down

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