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Merged in vsac-cache-updater (pull request #13)
Vsac cache updater Approved-by: David Winters <dwinters@mitre.org> Approved-by: Tom Read <tread@mitre.org> Approved-by: Noranda Brown <noranda@norandabrown.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| 8.11.3 | ||
| 10.13.0 |
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| Original file line number | Diff line number | Diff line change |
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| // This script updates the valueset-db.json file with any changes from the CQL | ||
| // library and/or changes in the value set definitions in VSAC. It should be | ||
| // called with the UMLS Username and Password as arguments. | ||
| const fs = require('fs'); | ||
| const path = require('path'); | ||
| const temp = require('temp'); | ||
| const { Library, Repository } = require('cql-execution'); | ||
| const { CodeService } = require('cql-exec-vsac'); | ||
| const dstu2FactorsELM = require('../cql/dstu2/Factors_to_Consider_in_Managing_Chronic_Pain.json'); | ||
| const dstu2CommonsELM = require('../cql/dstu2/CDS_Connect_Commons_for_FHIRv102.json'); | ||
| const dstu2HelpersELM = require('../cql/dstu2/FHIRHelpers.json'); | ||
| const r4FactorsELM = require('../cql/r4/Factors_to_Consider_in_Managing_Chronic_Pain_FHIRv400.json'); | ||
| const r4CommonsELM = require('../cql/r4/CDS_Connect_Commons_for_FHIRv400.json'); | ||
| const r4HelpersELM = require('../cql/r4/FHIRHelpers.json'); | ||
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| // First ensure a username and password are provided | ||
| const [user, password] = process.argv.slice(2); | ||
| if (user == null || password == null) { | ||
| console.error('The UMLS username and password must be passed in as arguments'); | ||
| process.exit(1); | ||
| } | ||
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| // Then initialize the cql-exec-vsac CodeService, pointing to a temporary | ||
| // folder to dump the valueset cache files. | ||
| temp.track(); // track temporary files and delete them when the process exits | ||
| const tempFolder = temp.mkdirSync('vsac-cache'); | ||
| const codeService = new CodeService(tempFolder); | ||
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| console.log(`Using temp folder: ${tempFolder}`); | ||
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| // Then setup the CQL libraries that we need to analyze to extract the | ||
| // valuesets from. In theory, the DSTU2 and R4 libraries should use the | ||
| // same valuesets, but in case they don't we go ahead and load both of | ||
| // them. | ||
| const dstu2Lib = new Library(dstu2FactorsELM, new Repository({ | ||
| CDS_Connect_Commons_for_FHIRv102: dstu2CommonsELM, | ||
| FHIRHelpers: dstu2HelpersELM | ||
| })); | ||
| const r4Lib = new Library(r4FactorsELM, new Repository({ | ||
| CDS_Connect_Commons_for_FHIRv400: r4CommonsELM, | ||
| FHIRHelpers: r4HelpersELM | ||
| })); | ||
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| // Then use the ensureValueSetsInLibrary function to analyze the Pain | ||
| // Management Summary CQL, request all the value sets from VSAC, and store | ||
| // their data in the temporary folder. The second argument (true) | ||
| // indicates to also look at dependency libraries. This has no affect | ||
| // for the current CQL, but may be helpful for people who extend it. | ||
| console.log(`Loading value sets from VSAC using account: ${user}`); | ||
| codeService.ensureValueSetsInLibrary(dstu2Lib, true, user, password) | ||
| .then(() => codeService.ensureValueSetsInLibrary(r4Lib, true, user, password)) | ||
| .then(() => { | ||
| // The valueset-db.json that the codeService produces isn't exactly the | ||
| // format that the Pain Management Summary wants, so now we must reformat | ||
| // it into the desired format. | ||
| const tempDBFile = path.join(tempFolder, 'valueset-db.json'); | ||
| const original = JSON.parse(fs.readFileSync(tempDBFile, 'utf8')); | ||
| let oidKeys = Object.keys(original).sort(); | ||
| console.log(`Loaded ${oidKeys.length} value sets`); | ||
| console.log('Translating JSON to expected format') | ||
| const fixed = {}; | ||
| for (const oid of oidKeys) { | ||
| fixed[oid] = {}; | ||
| for (const version of Object.keys(original[oid])) { | ||
| fixed[oid][version] = original[oid][version]['codes'].sort((a, b) => { | ||
| if (a.code < b.code) return -1; | ||
| else if (a.code > b.code) return 1; | ||
| return 0; | ||
| }); | ||
| } | ||
| } | ||
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| // And finally write the result to the real locations of the valueset-db.json. | ||
| const dbPath = path.join(__dirname, '..', 'cql', 'valueset-db.json'); | ||
| fs.writeFileSync(dbPath, JSON.stringify(fixed, null, 2), 'utf8'); | ||
| console.log('Updated:', dbPath); | ||
| }) | ||
| .catch((error) => { | ||
| let message = error.message; | ||
| if (error.statusCode === 401) { | ||
| // The default 401 message isn't helpful at all | ||
| message = 'invalid password or unauthorized access' | ||
| } | ||
| console.error('Error updating valueset-db.json:', message); | ||
| process.exit(1); | ||
| }); | ||
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