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Update dependencies, add cache config from env #8

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Feb 16, 2024
Merged

Update dependencies, add cache config from env #8

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4e9cab2
Update dependencies, add cache config from env
dmpotter44 Feb 8, 2024
16bbcbe
Update service library
dmpotter44 Feb 16, 2024
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5 changes: 4 additions & 1 deletion .env
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Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,7 @@

MATCHING_SERVICE_ENDPOINT=https://trialsapi.compositeapps.net/v1/trials/search
MATCHING_SERVICE_AUTH_TOKEN=""
MATCHING_SERVICE_PORT=3003
MATCHING_SERVICE_PORT=3003

# The cache file to use for clinical trial data cached from clinicaltrials.gov
CTGOV_CACHE_FILE=ctgov-cache.db
3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -16,3 +16,6 @@
# System Files
.DS_Store
Thumbs.db

# Cache file
/ctgov-cache.db
2,636 changes: 2,005 additions & 631 deletions package-lock.json
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6 changes: 3 additions & 3 deletions package.json
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Expand Up @@ -22,16 +22,16 @@
"author": "",
"license": "Apache-2.0",
"dependencies": {
"clinical-trial-matching-service": "^0.0.12",
"clinical-trial-matching-service": "^0.1.1",
"dotenv-flow": "^4.0.0"
},
"devDependencies": {
"@istanbuljs/nyc-config-typescript": "^1.0.1",
"@types/express": "^4.17.17",
"@types/fhir": "^0.0.37",
"@types/fhir": "^0.0.40",
"@types/jasmine": "^5.1.0",
"@types/node": "^20.8.6",
"@types/supertest": "^2.0.9",
"@types/supertest": "^6.0.2",
"@typescript-eslint/eslint-plugin": "^6.2.0",
"@typescript-eslint/parser": "^6.2.0",
"eslint": "^8.30.0",
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4 changes: 4 additions & 0 deletions spec/server.spec.ts
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Expand Up @@ -3,6 +3,10 @@ import { Server } from "http";
import ClinicalTrialMatchingService from "clinical-trial-matching-service";

describe("startServer()", () => {
beforeAll(() => {
// Set the CTGov backup service to use a memory DB, overriding the .env config
process.env.CTGOV_CACHE_FILE = ':memory:';
});
beforeEach(() => {
// Don't actually want to start the server listening, so spy on the
// prototype to prevent that from happening
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9 changes: 3 additions & 6 deletions src/query.ts
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Expand Up @@ -321,7 +321,7 @@ export class APIQuery {
* update the returned trials with additional information pulled from
* ClinicalTrials.gov
*/
export function convertResponseToSearchSet(
export async function convertResponseToSearchSet(
response: QueryResponse,
ctgService?: ClinicalTrialsGovService
): Promise<SearchSet> {
Expand All @@ -340,12 +340,9 @@ export function convertResponseToSearchSet(
}
if (ctgService) {
// If given a backup service, use it
return ctgService.updateResearchStudies(studies).then(() => {
return new SearchSet(studies);
});
return new SearchSet(await ctgService.updateResearchStudies(studies));
} else {
// Otherwise, resolve immediately
return Promise.resolve(new SearchSet(studies));
return new SearchSet(studies);
}
}

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8 changes: 3 additions & 5 deletions src/server.ts
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Expand Up @@ -37,11 +37,9 @@ export default async function startServer(
configuration = configFromEnv("MATCHING_SERVICE_");
}

// Create a ClinicalTrialGovService. It takes a path to a temporary directory
// that is used to store its cache.
const ctgService = await createClinicalTrialsGovService(
path.resolve(__dirname, "../ctgov-cache")
);
// Create a ClinicalTrialsGovService. It takes a path to a SQLite database to
// store its cache.
const ctgService = await createClinicalTrialsGovService(process.env.CTGOV_CACHE_FILE);
const getMatchingClinicalTrials = createClinicalTrialLookup(
configuration,
ctgService
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