From d5c0f1b3df2b33a5530d80fe26aad137c04cf650 Mon Sep 17 00:00:00 2001 From: sedinkinya Date: Tue, 16 Aug 2022 17:15:37 -0400 Subject: [PATCH 1/5] Convert context variable values when MemberInvocation is not used --- CHANGELOG.md | 5 +++++ package-lock.json | 4 ++-- package.json | 2 +- src/fhirpath.js | 18 ++++++++++++++++++ test/api.test.js | 20 ++++++++++++++++++-- 5 files changed, 44 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b1fd74b..df2ecb6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,11 @@ This log documents significant changes for each release. This project follows [Semantic Versioning](http://semver.org/). +## [2.14.7] - 2022-08-15 +### Fixed +- FHIR Quantities passed as context variables are now converted to System + Quantities when necessary. + ## [2.14.6] - 2022-06-29 ### Fixed - FHIR Quantities are now only converted to System Quantities when necessary, so diff --git a/package-lock.json b/package-lock.json index 66a5572..a02291f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "fhirpath", - "version": "2.14.6", + "version": "2.14.7", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "fhirpath", - "version": "2.14.6", + "version": "2.14.7", "license": "MIT", "dependencies": { "@lhncbc/ucum-lhc": "^4.1.3", diff --git a/package.json b/package.json index 370e35c..06f2a0a 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "fhirpath", - "version": "2.14.6", + "version": "2.14.7", "description": "A FHIRPath engine", "main": "src/fhirpath.js", "dependencies": { diff --git a/src/fhirpath.js b/src/fhirpath.js index 49636c5..29d7054 100644 --- a/src/fhirpath.js +++ b/src/fhirpath.js @@ -636,6 +636,24 @@ function applyParsedPath(resource, parsedPath, context, model) { // Set up default standard variables, and allow override from the variables. // However, we'll keep our own copy of dataRoot for internal processing. let vars = {context: resource, ucum: 'http://unitsofmeasure.org'}; + // Restore the ResourceNodes for the top-level objects of the context + // variables. The nested objects will be converted to ResourceNodes + // in the MemberInvocation method. + if (context) { + context = Object.keys(context).reduce((restoredContext, key) => { + const path = context[key]?.__path__; + if (path) { + if (Array.isArray(context[key])) { + restoredContext[key] = context[key].map(i => makeResNode(i, path)); + } else { + restoredContext[key] = makeResNode(context[key], path); + } + } else { + restoredContext[key] = context[key]; + } + return restoredContext; + }, {}); + } let ctx = {dataRoot, vars: Object.assign(vars, context), model}; let rtn = engine.doEval(ctx, dataRoot, parsedPath.children[0]); let firstRtn = Array.isArray(rtn) ? rtn[0] : rtn; diff --git a/test/api.test.js b/test/api.test.js index 2f7f6a6..e3c7b7b 100644 --- a/test/api.test.js +++ b/test/api.test.js @@ -22,7 +22,7 @@ describe('compile', () => { expect(f({}, {a: 1})).toStrictEqual([3]); }); - it('should apply the FHIR model for a part of the resource placed in the environment variable', () => { + it('should apply the FHIR model for a part of the resource placed in the context variable', () => { const getPartOfResource = fhirpath.compile( "QuestionnaireResponse.item.where(linkId = \'2\')", r4_model @@ -40,7 +40,7 @@ describe('compile', () => { }); describe('evaluate', () => { - it('should apply the FHIR model for a part of the resource placed in the environment variable', () => { + it('should apply the FHIR model for a part of the resource placed in the context variable (with MemberInvocation)', () => { const partOfResource = fhirpath.evaluate( require('../test/resources/quantity-example.json'), 'QuestionnaireResponse.item.where(linkId = \'2\')' @@ -54,6 +54,22 @@ describe('evaluate', () => { expect(result).toStrictEqual([true]); }); + it('should apply the FHIR model for a part of the resource placed in the context variable (without MemberInvocation)', () => { + const partOfResource = fhirpath.evaluate( + require('../test/resources/quantity-example.json'), + "QuestionnaireResponse.item.where(linkId = '2').answer.value", + null, + r4_model + ); + let result = fhirpath.evaluate( + {}, + "%partOfResource.toQuantity('s').value", + {partOfResource}, + r4_model + ); + expect(result).toStrictEqual([180]); + }); + it('should not change the context variable during expression evaluation', () => { const someVar = fhirpath.evaluate( require('../test/resources/quantity-example.json'), From bdd0aa07847a15feeab268bedaaab3032e7b85ad Mon Sep 17 00:00:00 2001 From: sedinkinya Date: Mon, 22 Aug 2022 18:34:45 -0400 Subject: [PATCH 2/5] npm audit fix --- demo/package-lock.json | 180 +++++++++++++++++++++++++-------- package-lock.json | 220 +++++++++++++++++++++-------------------- 2 files changed, 252 insertions(+), 148 deletions(-) diff --git a/demo/package-lock.json b/demo/package-lock.json index ae1403e..7ea9599 100644 --- a/demo/package-lock.json +++ b/demo/package-lock.json @@ -34,6 +34,64 @@ "node": ">=10.0.0" } }, + "node_modules/@jridgewell/gen-mapping": { + "version": "0.3.2", + "resolved": "https://registry.npmjs.org/@jridgewell/gen-mapping/-/gen-mapping-0.3.2.tgz", + "integrity": "sha512-mh65xKQAzI6iBcFzwv28KVWSmCkdRBWoOh+bYQGW3+6OZvbbN3TqMGo5hqYxQniRcH9F2VZIoJCm4pa3BPDK/A==", + "dev": true, + "dependencies": { + "@jridgewell/set-array": "^1.0.1", + "@jridgewell/sourcemap-codec": "^1.4.10", + "@jridgewell/trace-mapping": "^0.3.9" + }, + "engines": { + "node": ">=6.0.0" + } + }, + "node_modules/@jridgewell/resolve-uri": { + "version": "3.1.0", + "resolved": "https://registry.npmjs.org/@jridgewell/resolve-uri/-/resolve-uri-3.1.0.tgz", + "integrity": "sha512-F2msla3tad+Mfht5cJq7LSXcdudKTWCVYUgw6pLFOOHSTtZlj6SWNYAp+AhuqLmWdBO2X5hPrLcu8cVP8fy28w==", + "dev": true, + "engines": { + "node": ">=6.0.0" + } + }, + "node_modules/@jridgewell/set-array": { + "version": "1.1.2", + "resolved": "https://registry.npmjs.org/@jridgewell/set-array/-/set-array-1.1.2.tgz", + "integrity": "sha512-xnkseuNADM0gt2bs+BvhO0p78Mk762YnZdsuzFV018NoG1Sj1SCQvpSqa7XUaTam5vAGasABV9qXASMKnFMwMw==", + "dev": true, + "engines": { + "node": ">=6.0.0" + } + }, + "node_modules/@jridgewell/source-map": { + "version": "0.3.2", + "resolved": "https://registry.npmjs.org/@jridgewell/source-map/-/source-map-0.3.2.tgz", + "integrity": "sha512-m7O9o2uR8k2ObDysZYzdfhb08VuEml5oWGiosa1VdaPZ/A6QyPkAJuwN0Q1lhULOf6B7MtQmHENS743hWtCrgw==", + "dev": true, + "dependencies": { + "@jridgewell/gen-mapping": "^0.3.0", + "@jridgewell/trace-mapping": "^0.3.9" + } + }, + "node_modules/@jridgewell/sourcemap-codec": { + "version": "1.4.14", + "resolved": "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.14.tgz", + "integrity": "sha512-XPSJHWmi394fuUuzDnGz1wiKqWfo1yXecHQMRf2l6hztTO+nPru658AyDngaBe7isIxEkRsPR3FZh+s7iVa4Uw==", + "dev": true + }, + "node_modules/@jridgewell/trace-mapping": { + "version": "0.3.15", + "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.15.tgz", + "integrity": "sha512-oWZNOULl+UbhsgB51uuZzglikfIKSUBO/M9W2OfEjn7cmqoAiCgmv9lyACTUacZwBz0ITnJ2NqjU8Tx0DHL88g==", + "dev": true, + "dependencies": { + "@jridgewell/resolve-uri": "^3.0.3", + "@jridgewell/sourcemap-codec": "^1.4.10" + } + }, "node_modules/@nodelib/fs.scandir": { "version": "2.1.5", "resolved": "https://registry.npmjs.org/@nodelib/fs.scandir/-/fs.scandir-2.1.5.tgz", @@ -475,9 +533,9 @@ } }, "node_modules/acorn": { - 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"integrity": "sha512-Wonm7zOCIJzBGQdB+thsPar0kYuCIzYvxZwlBa87yi/Mdjv7Tip2cyVbLj5o0cFPN4EVkuTwb3GDDyUx2DGnGw==", - "dev": true, - "requires": { - "buffer-from": "^1.0.0", - "source-map": "^0.6.0" - }, - "dependencies": { - "source-map": { - "version": "0.6.1", - "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.6.1.tgz", - "integrity": "sha512-UjgapumWlbMhkBgzT7Ykc5YXUT46F0iKu8SGXq0bcwP5dz/h0Plj6enJqjz1Zbq2l5WaqYnrVbwWOWMyF3F47g==", - "dev": true - } - } - } + "source-map-support": "~0.5.20" } }, "terser-webpack-plugin": { From f9c7aacc92579300c651227cceed8d3bc7afadf8 Mon Sep 17 00:00:00 2001 From: sedinkinya Date: Mon, 22 Aug 2022 19:16:54 -0400 Subject: [PATCH 3/5] Fixed a comment --- src/fhirpath.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fhirpath.js b/src/fhirpath.js index 29d7054..0c1017e 100644 --- a/src/fhirpath.js +++ b/src/fhirpath.js @@ -623,7 +623,7 @@ function parse(path) { * returning the result of doEval. * @param {(object|object[])} resource - FHIR resource, bundle as js object or array of resources * This resource will be modified by this function to add type information. - * @param {string} parsedPath - fhirpath expression, sample 'Patient.name.given' + * @param {object} parsedPath - a special object created by the parser that describe the structure of a fhirpath expression. * @param {object} context - a hash of variable name/value pairs. * @param {object} model - The "model" data object specific to a domain, e.g. R4. * For example, you could pass in the result of require("fhirpath/fhir-context/r4"); From 48a517b6f833f9896ac09f5e70ce74eb6c93f2bc Mon Sep 17 00:00:00 2001 From: sedinkinya Date: Mon, 22 Aug 2022 19:19:58 -0400 Subject: [PATCH 4/5] Updated CHANGELOG.md --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index df2ecb6..a6c975b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,8 +5,8 @@ This log documents significant changes for each release. This project follows ## [2.14.7] - 2022-08-15 ### Fixed -- FHIR Quantities passed as context variables are now converted to System - Quantities when necessary. +- Fixed directly (without member invocation) accessing the value of a variable in the context if this value was fetched + from a resource using fhirpath.js. ## [2.14.6] - 2022-06-29 ### Fixed From c95e68e1d67aa5d55f92b352e0e167bf905e5861 Mon Sep 17 00:00:00 2001 From: sedinkinya Date: Tue, 23 Aug 2022 09:39:27 -0400 Subject: [PATCH 5/5] Fixed a comment --- src/fhirpath.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fhirpath.js b/src/fhirpath.js index 0c1017e..71b7566 100644 --- a/src/fhirpath.js +++ b/src/fhirpath.js @@ -623,7 +623,7 @@ function parse(path) { * returning the result of doEval. * @param {(object|object[])} resource - FHIR resource, bundle as js object or array of resources * This resource will be modified by this function to add type information. - * @param {object} parsedPath - a special object created by the parser that describe the structure of a fhirpath expression. + * @param {object} parsedPath - a special object created by the parser that describes the structure of a fhirpath expression. * @param {object} context - a hash of variable name/value pairs. * @param {object} model - The "model" data object specific to a domain, e.g. R4. * For example, you could pass in the result of require("fhirpath/fhir-context/r4");