diff --git a/lib/download-vsac.js b/lib/download-vsac.js index aea689e..d5b1cfe 100644 --- a/lib/download-vsac.js +++ b/lib/download-vsac.js @@ -25,32 +25,32 @@ function downloadFromVSAC(username, password, input, output, vsDB={}) { mkdirp.sync(output); } return getTicketGrantingTicket(username, password) - .then((ticketGrantingTicket) => { - const promises = oids.map(oid => { + .then((ticketGrantingTicket) => { + const promises = oids.map(oid => { // Catch errors and convert to resolutions returning an error. This ensures Promise.all waits for all promises. // See: http://stackoverflow.com/questions/31424561/wait-until-all-es6-promises-complete-even-rejected-promises - return downloadValueSet(ticketGrantingTicket, oid, output, vsDB) - .catch((err) => { - debug(`Error downloading valueset ${oid}`, err); - return new Error(`Error downloading valueset: ${oid}`); + return downloadValueSet(ticketGrantingTicket, oid, output, vsDB) + .catch((err) => { + debug(`Error downloading valueset ${oid}`, err); + return new Error(`Error downloading valueset: ${oid}`); + }); }); - }); - return Promise.all(promises); - }) - .then((results) => { - const errors = results.filter(r => r instanceof Error); - if (results.length - errors.length > 0) { + return Promise.all(promises); + }) + .then((results) => { + const errors = results.filter(r => r instanceof Error); + if (results.length - errors.length > 0) { // There were results, so write the file first before resolving/rejecting - return writeFile(path.join(output, 'valueset-db.json'), JSON.stringify(vsDB, null, 2)) - .then( - (result) => errors.length == 0 ? result : Promise.reject(errors), - (err) => { errors.push(err); return Promise.reject(errors); } - ); - } - if (errors.length > 0) { - return Promise.reject(errors); - } - }); + return writeFile(path.join(output, 'valueset-db.json'), JSON.stringify(vsDB, null, 2)) + .then( + (result) => errors.length == 0 ? result : Promise.reject(errors), + (err) => { errors.push(err); return Promise.reject(errors); } + ); + } + if (errors.length > 0) { + return Promise.reject(errors); + } + }); } else { return Promise.resolve(); } @@ -68,13 +68,13 @@ function getTicketGrantingTicket(username, password) { function downloadValueSet(ticketGrantingTicket, oid, output, vsDB={}) { return getServiceTicket(ticketGrantingTicket) - .then((serviceTicket) => { - return getValueSet(serviceTicket, oid); - }) - .then((data) => { - parseVSACXML(data, vsDB); - return writeFile(path.join(output, `${oid}.xml`), data); - }); + .then((serviceTicket) => { + return getValueSet(serviceTicket, oid); + }) + .then((data) => { + parseVSACXML(data, vsDB); + return writeFile(path.join(output, `${oid}.xml`), data); + }); } function getServiceTicket(ticketGrantingTicket) { diff --git a/lib/vsac-code-systems.json b/lib/vsac-code-systems.json index b6bc728..db0bfa1 100644 --- a/lib/vsac-code-systems.json +++ b/lib/vsac-code-systems.json @@ -1,9 +1,12 @@ { - "2.16.840.1.113883.12.112": { "name": "DischargeDisposition" }, + "1.3.6.1.4.1.12009.10.3.1": { "name": "UCUM", "uri": "http://unitsofmeasure.org" }, + "2.16.840.1.113883.12.112": { "name": "DischargeDisposition", "uri": "http://hl7.org/fhir/v2/0112" }, "2.16.840.1.113883.12.292": { "name": "CVX", "uri": "http://hl7.org/fhir/sid/cvx" }, "2.16.840.1.113883.18.2": { "name": "AdministrativeSex" , "uri": "http://hl7.org/fhir/v2/0001" }, "2.16.840.1.113883.3.221.5": { "name": "SOP" , "uri": "http://www.nlm.nih.gov/research/umls/sop" }, "2.16.840.1.113883.3.26.1.1": { "name": "NCI" , "uri": "http://ncimeta.nci.nih.gov" }, + "2.16.840.1.113883.3.26.1.5": { "name": "NDFRT", "uri": "http://hl7.org/fhir/ndfrt" }, + "2.16.840.1.113883.4.9": { "name": "UNII" , "uri": "http://fdasis.nlm.nih.gov" }, "2.16.840.1.113883.5.1": { "name": "AdministrativeGender" , "uri": "http://hl7.org/fhir/v3/AdministrativeGender" }, "2.16.840.1.113883.5.1001": { "name": "ActMood" , "uri": "http://hl7.org/fhir/v3/ActMood"}, "2.16.840.1.113883.5.1002": { "name": "ActRelationshipType" , "uri": "http://hl7.org/fhir/v3/ActRelationshipType" }, @@ -24,23 +27,26 @@ "2.16.840.1.113883.5.61": { "name": "LanguageAbilityProficiency", "uri": "http://hl7.org/fhir/v3/LanguageAbilityProficiency" }, "2.16.840.1.113883.5.63": { "name": "LivingArrangement" , "uri": "http://hl7.org/fhir/v3/LivingArrangement" }, "2.16.840.1.113883.5.7": { "name": "ActPriority" , "uri": "http://hl7.org/fhir/v3/ActPriority" }, + "2.16.840.1.113883.5.79": { "name": "mediaType", "uri": "http://hl7.org/fhir/v3/MediaType" }, "2.16.840.1.113883.5.8": { "name": "ActReason" , "uri": "http://hl7.org/fhir/v3/ActReason" }, "2.16.840.1.113883.5.83": { "name": "ObservationInterpretation" , "uri": "http://hl7.org/fhir/v3/ObservationInterpretation" }, "2.16.840.1.113883.5.88": { "name": "ParticipationFunction" , "uri": "http://hl7.org/fhir/v3/ParticipationFunction" }, "2.16.840.1.113883.5.90": { "name": "ParticipationType" , "uri": "http://hl7.org/fhir/v3/ParticipationType" }, "2.16.840.1.113883.6.1": { "name": "LOINC", "uri": "http://loinc.org" }, - "2.16.840.1.113883.6.101": { "name": "NUCCPT" , "uri": "http://nucc.org/provider-taxonomy" }, - "2.16.840.1.113883.6.103": { "name": "ICD9CM", "uri": "http://hl7.org/fhir/sid/icd-9-cm/diagnosis" }, - "2.16.840.1.113883.6.104": { "name": "ICD9CM", "uri": "http://hl7.org/fhir/sid/icd-9-cm/procedure" }, + "2.16.840.1.113883.6.101": { "name": "NUCCPT" , "uri": "http://nucc.org/provider-taxonomy" }, + "2.16.840.1.113883.6.103": { "name": "ICD9CM", "uri": "http://hl7.org/fhir/sid/icd-9-cm" }, + "2.16.840.1.113883.6.104": { "name": "ICD9CM", "uri": "http://hl7.org/fhir/sid/icd-9-cm" }, "2.16.840.1.113883.6.12": { "name": "CPT", "uri": "http://www.ama-assn.org/go/cpt" }, "2.16.840.1.113883.6.13": { "name": "CDT" , "uri": "http://www.nlm.nih.gov/research/umls/cdt" }, "2.16.840.1.113883.6.14": { "name": "HCPCS" }, "2.16.840.1.113883.6.238": { "name": "CDCREC" }, "2.16.840.1.113883.6.259": { "name": "HSLOC" }, "2.16.840.1.113883.6.285": { "name": "HCPCS" }, + "2.16.840.1.113883.6.345": { "name": "MED-RT", "uri": "http://www.nlm.nih.gov/research/umls/MED-RT" }, "2.16.840.1.113883.6.4": { "name": "ICD10PCS", "uri": "http://www.icd10data.com/icd10pcs" }, "2.16.840.1.113883.6.86": { "name": "UMLS" , "uri": "http://www.nlm.nih.gov/research/umls" }, "2.16.840.1.113883.6.88": { "name": "RXNORM", "uri": "http://www.nlm.nih.gov/research/umls/rxnorm" }, "2.16.840.1.113883.6.90": { "name": "ICD10CM", "uri": "http://hl7.org/fhir/sid/icd-10-cm" }, - "2.16.840.1.113883.6.96": { "name": "SNOMEDCT", "uri": "http://snomed.info/sct" } + "2.16.840.1.113883.6.96": { "name": "SNOMEDCT", "uri": "http://snomed.info/sct" }, + "2.16.840.1.113883.5.4": { "name": "ActCode", "uri": "http://hl7.org/fhir/v3/ActCode" } } \ No newline at end of file diff --git a/package.json b/package.json index e3ee4d7..7903ec4 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cql-exec-vsac", - "version": "1.0.3", + "version": "1.0.4", "license": "Apache-2.0", "repository": { "type": "git", @@ -15,20 +15,23 @@ "lint:fix": "./node_modules/.bin/eslint . --fix" }, "dependencies": { - "debug": "^2.6.4", - "mkdirp": "^0.5.1", - "request": "^2.81.0", - "request-promise-native": "^1.0.3", - "xml2js": "^0.4.17" + "debug": "^4.1.1", + "mkdirp": "^1.0.3", + "request": "^2.88.2", + "request-promise-native": "^1.0.8", + "xml2js": "^0.4.23" }, "devDependencies": { - "chai": "^3.5.0", - "chai-as-promised": "^6.0.0", - "cql-execution": "^1.2.0", - "eslint": "^3.19.0", - "fs-extra": "^2.1.2", - "mocha": "^3.2.0", - "nock": "^9.0.13" + "chai": "^4.2.0", + "chai-as-promised": "^7.1.1", + "cql-execution": "^1.3.7", + "eslint": "^6.8.0", + "fs-extra": "^8.1.0", + "mocha": "^7.0.1", + "nock": "^11.8.2" + }, + "resolutions": { + "sshpk": "^1.13.2" }, "peerDependencies": { "cql-execution": "^1.2.0" diff --git a/test/test.js b/test/test.js index ac97306..8613469 100644 --- a/test/test.js +++ b/test/test.js @@ -229,25 +229,25 @@ describe('CodeService', function() { ]; return service.ensureValueSets(vsList, username, password) - .then(function() { - should.fail(0, 1, 'This code should never be executed since there were errors'); - }) - .catch(function(error) { + .then(function() { + should.fail(0, 1, 'This code should never be executed since there were errors'); + }) + .catch(function(error) { // Test that the value sets were properly loaded into memory - service.valueSets.should.not.be.empty; - Object.keys(service.valueSets).should.have.length(3); - const vs1 = service.findValueSet('1.2.3.4.5.6.7.8.9.10'); - should.not.exist(vs1); - const vs2 = service.findValueSet('2.16.840.1.113883.3.600.2390', '20170418'); - vs2.codes.should.have.length(24); - // Test that the value sets were properly written to the cache - const cached = require(path.join(tmpCache, 'valueset-db.json')); - JSON.parse(JSON.stringify(service.valueSets)).should.eql(cached); - // Test that the error was thrown - error.should.have.length(1); - error[0].should.be.an('error'); - error[0].message.should.contain('1.2.3.4.5.6.7.8.9.10'); - }); + service.valueSets.should.not.be.empty; + Object.keys(service.valueSets).should.have.length(3); + const vs1 = service.findValueSet('1.2.3.4.5.6.7.8.9.10'); + should.not.exist(vs1); + const vs2 = service.findValueSet('2.16.840.1.113883.3.600.2390', '20170418'); + vs2.codes.should.have.length(24); + // Test that the value sets were properly written to the cache + const cached = require(path.join(tmpCache, 'valueset-db.json')); + JSON.parse(JSON.stringify(service.valueSets)).should.eql(cached); + // Test that the error was thrown + error.should.have.length(1); + error[0].should.be.an('error'); + error[0].message.should.contain('1.2.3.4.5.6.7.8.9.10'); + }); }); it('should error if no username/password is supplied', function() { @@ -263,12 +263,12 @@ describe('CodeService', function() { {name: 'Systolic Blood Pressure', id: '2.16.840.1.113883.3.526.3.1032', version: '20170320'} ]; return service.ensureValueSets(vsList, null, null) - .then(function() { - should.fail(0, 1, 'This code should never be executed'); - }) - .catch(function(error) { - error.should.eql('Failed to download value sets since UMLS_USER_NAME and/or UMLS_PASSWORD is not set.'); - }); + .then(function() { + should.fail(0, 1, 'This code should never be executed'); + }) + .catch(function(error) { + error.should.eql('Failed to download value sets since UMLS_USER_NAME and/or UMLS_PASSWORD is not set.'); + }); } finally { [process.env['UMLS_USER_NAME'], process.env['UMLS_PASSWORD']] = [oldU, oldP]; } @@ -286,12 +286,12 @@ describe('CodeService', function() { ]; return service.ensureValueSets(vsList, wrongU, wrongP) - .then(function() { - should.fail(0, 1, 'This code should never be executed'); - }) - .catch(function(error) { - error.statusCode.should.equal(401); - }); + .then(function() { + should.fail(0, 1, 'This code should never be executed'); + }) + .catch(function(error) { + error.statusCode.should.equal(401); + }); }); it('should error if invalid ticket granting ticket is supplied', function() { @@ -308,14 +308,14 @@ describe('CodeService', function() { {name: 'Systolic Blood Pressure', id: '2.16.840.1.113883.3.526.3.1032', version: '20170320'} ]; return service.ensureValueSets(vsList, username, password) - .then(function() { - should.fail(0, 1, 'This code should never be executed'); - }) - .catch(function(error) { - error.should.have.length(1); - error[0].should.be.an('error'); - error[0].message.should.contain('2.16.840.1.113883.3.526.3.1032'); - }); + .then(function() { + should.fail(0, 1, 'This code should never be executed'); + }) + .catch(function(error) { + error.should.have.length(1); + error[0].should.be.an('error'); + error[0].message.should.contain('2.16.840.1.113883.3.526.3.1032'); + }); }); it('should error if invalid service granting ticket is supplied', function() { @@ -336,14 +336,14 @@ describe('CodeService', function() { {name: 'Systolic Blood Pressure', id: '2.16.840.1.113883.3.526.3.1032', version: '20170320'} ]; return service.ensureValueSets(vsList, username, password) - .then(function() { - should.fail(0, 1, 'This code should never be executed'); - }) - .catch(function(error) { - error.should.have.length(1); - error[0].should.be.an('error'); - error[0].message.should.contain('2.16.840.1.113883.3.526.3.1032'); - }); + .then(function() { + should.fail(0, 1, 'This code should never be executed'); + }) + .catch(function(error) { + error.should.have.length(1); + error[0].should.be.an('error'); + error[0].message.should.contain('2.16.840.1.113883.3.526.3.1032'); + }); }); it('should error if value set is not found', function() { @@ -363,14 +363,14 @@ describe('CodeService', function() { {name: 'Fake Value Set', id: '1.2.3.4.5.6.7.8.9.10', version: '20170320'} ]; return service.ensureValueSets(vsList, username, password) - .then(function() { - should.fail(0, 1, 'This code should never be executed'); - }) - .catch(function(error) { - error.should.have.length(1); - error[0].should.be.an('error'); - error[0].message.should.contain('1.2.3.4.5.6.7.8.9.10'); - }); + .then(function() { + should.fail(0, 1, 'This code should never be executed'); + }) + .catch(function(error) { + error.should.have.length(1); + error[0].should.be.an('error'); + error[0].message.should.contain('1.2.3.4.5.6.7.8.9.10'); + }); }); }); }); \ No newline at end of file diff --git a/yarn.lock b/yarn.lock index da2eaa7..4c4be5e 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2,42 +2,83 @@ # yarn lockfile v1 -acorn-jsx@^3.0.0: - version "3.0.1" - resolved "https://registry.yarnpkg.com/acorn-jsx/-/acorn-jsx-3.0.1.tgz#afdf9488fb1ecefc8348f6fb22f464e32a58b36b" +"@babel/code-frame@^7.0.0": + version "7.8.3" + resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.8.3.tgz#33e25903d7481181534e12ec0a25f16b6fcf419e" + integrity sha512-a9gxpmdXtZEInkCSHUJDLHZVBgb1QS0jhss4cPP93EW7s+uC5bikET2twEF3KV+7rDblJcmNvTR7VJejqd2C2g== dependencies: - acorn "^3.0.4" + "@babel/highlight" "^7.8.3" -acorn@^3.0.4: - version "3.3.0" - resolved "https://registry.yarnpkg.com/acorn/-/acorn-3.3.0.tgz#45e37fb39e8da3f25baee3ff5369e2bb5f22017a" +"@babel/highlight@^7.8.3": + version "7.8.3" + resolved "https://registry.yarnpkg.com/@babel/highlight/-/highlight-7.8.3.tgz#28f173d04223eaaa59bc1d439a3836e6d1265797" + integrity sha512-PX4y5xQUvy0fnEVHrYOarRPXVWafSjTW9T0Hab8gVIawpl2Sj0ORyrygANq+KjcNlSSTw0YCLSNA8OyZ1I4yEg== + dependencies: + chalk "^2.0.0" + esutils "^2.0.2" + js-tokens "^4.0.0" -acorn@^5.0.1: - version "5.0.3" - resolved "https://registry.yarnpkg.com/acorn/-/acorn-5.0.3.tgz#c460df08491463f028ccb82eab3730bf01087b3d" +acorn-jsx@^5.1.0: + version "5.1.0" + resolved "https://registry.yarnpkg.com/acorn-jsx/-/acorn-jsx-5.1.0.tgz#294adb71b57398b0680015f0a38c563ee1db5384" + integrity sha512-tMUqwBWfLFbJbizRmEcWSLw6HnFzfdJs2sOJEOwwtVPMoH/0Ay+E703oZz78VSXZiiDcZrQ5XKjPIUQixhmgVw== -ajv-keywords@^1.0.0: - 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