Merge pull request #20 in LFOR/fhirpath.js from feature/LF-1598/evalu…

…ating-for-part-of-resource to master

* commit 'c8fbd132c80efdd387c81d23fbd3ed33b6e20b1a':
  npm audit fix
  refactor: evaluating expression for a part of a resource
  Evaluating expression for a part of a resource

CHANGELOG.md

@@ -3,6 +3,10 @@
 This log documents significant changes for each release.  This project follows
 [Semantic Versioning](http://semver.org/).
 
+## [2.7.0] - 2020-10-21
+### Added
+- Evaluating expression for a part of a resource
+
 ## [2.6.2] - 2020-10-09
 ### Fixed
 - Comparison of dates indicated with different level of precision

README.md

@@ -108,6 +108,17 @@ lower case, e.g., 'dstu2', 'stu3' or 'r4').
 fhirpath --expression 'Observation.value' --resourceJSON '{"resourceType": "Observation", "valueString": "Green"}' --model r4
 ```
 
+Also, you can pass in a filename or a string of JSON representing a part of the resource.
+In that case, you should pass in the base path from which this part of the resource was extracted.
+```sh
+fhirpath --basePath QuestionnaireResponse.item --expression 'answer.value' --model r4 --resourceFile questionnaire-part-example.json
+
+> fhirpath(answer.value) =>
+> [
+>  "2 year"
+> ]
+```
+
 If given just the FHIRPath expression, the utility will print the parsed tree:
 
 ```sh

bin/fhirpath

@@ -5,9 +5,10 @@ const fs = require('fs');
 const yaml = require('js-yaml');
 const options = require('commander');
 options.description('Parses and/or runs a FHIRPath expression.  If neither --resourceFile nor --resourceJSON is provided, the parse tree of the FHIRPath expression will be output.');
-options.option('-e, --expression <expr>', 'FHIRPath expression');
-options.option('-f, --resourceFile <path name>', 'A file containing the JSON resource.');
-options.option('-r, --resourceJSON <JSON>', 'JSON resource.');
+options.option('-b, --basePath <path>', 'base path in the resource from which the JSON data was extracted.');
+options.option('-e, --expression <expr>', 'FHIRPath expression.');
+options.option('-f, --resourceFile <path name>', 'A file containing the JSON resource or part of it, if basePath is passed.');
+options.option('-r, --resourceJSON <JSON>', 'JSON resource or part of it, if basePath is passed.');
 options.option('-v, --variables <JSON>', 'JSON hash of variables.');
 options.option('-m, --model <dstu2 | stu3 | r4>', 'Include FHIR model data.');
 options.parse(process.argv);
@@ -16,8 +17,10 @@ options.parse(process.argv);
 // it can be extended with understading urls and files
 // TODO: introduce subcommands to inspect, eval fhirpath etc
 
-let expr =  options.expression;
-if (!expr)
+const expression =  options.expression;
+const base =  options.basePath;
+
+if (!expression)
   options.help();
 else {
   let resourceJSON = options.resourceJSON;
@@ -28,8 +31,8 @@ else {
   }
   if (!resourceJSON) {
     // Just display the parse tree
-    let res = fp.parse(expr);
-    console.log('Parse tree for fhirpath(' + expr + ') =>');
+    let res = fp.parse(expression);
+    console.log('Parse tree for fhirpath(' + expression + ') =>');
     console.log(yaml.dump(res));
   }
   else {
@@ -44,8 +47,8 @@ else {
         throw new Error('FHIR model must be one of '+supportedVersions);
       model = require('../fhir-context/'+options.model);
     }
-    let res = fp.evaluate(resource, expr, context, model);
-    console.log('fhirpath(' + expr + ') =>');
+    let res = fp.evaluate(resource, base ? {base, expression} : expression, context, model);
+    console.log('fhirpath(' + expression + ') =>');
     console.log(JSON.stringify(res, null, " "));
   }
 }

package.json

@@ -1,6 +1,6 @@
 {
   "name": "fhirpath",
-  "version": "2.6.2",
+  "version": "2.7.0",
   "description": "A FHIRPath engine",
   "main": "src/fhirpath.js",
   "dependencies": {

src/fhirpath.js

@@ -670,17 +670,23 @@ function applyParsedPath(resource, parsedPath, context, model) {
 }
 
 /**
- *  Evaluates the "path" FHIRPath expression on the given resource, using data
- *  from "context" for variables mentioned in the "path" expression.
- * @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} path - fhirpath expression, sample 'Patient.name.given'
+ *  Evaluates the "path" FHIRPath expression on the given resource or part of the resource,
+ *  using data from "context" for variables mentioned in the "path" expression.
+ * @param {(object|object[])} fhirData -  FHIR resource, part of a resource (in this case
+ *  path.base should be provided), bundle as js object or array of resources.
+ *  This object/array will be modified by this function to add type information.
+ * @param {string|object} path - string with fhirpath expression, sample 'Patient.name.given',
+ *  or object, if fhirData represents the part of the FHIR resource:
+ * @param {string} path.base - base path in resource from which fhirData was extracted
+ * @param {string} path.expression - fhirpath expression relative to path.base
  * @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");
  */
-var evaluate = function(resource, path, context, model) {
-  const node = parser.parse(path);
+var evaluate = function(fhirData, path, context, model) {
+  const pathIsObject = typeof path === 'object';
+  const resource = pathIsObject ? makeResNode(fhirData, path.base) : fhirData;
+  const node = parser.parse(pathIsObject ? path.expression : path);
   return applyParsedPath(resource, node, context, model);
 };
 

test/bin_fhirpath.test.js

@@ -37,6 +37,12 @@ describe ('bin/fhirpath', function () {
     tempFileObj.removeCallback();
   });
 
+  it ('should evaluate when given a file with a part of a resource', function() {
+    checkOutput("bin/fhirpath -b QuestionnaireResponse.item "
+      +"-e 'answer.value = 2 year' -m r4 -f '"
+      +__dirname+"/resources/questionnaire-part-example.json'", /true/g);
+  });
+
   it ('should accept a hash of variables', function() {
     checkOutput("bin/fhirpath -e '%v1 + 2' -r '{}' -v '{\"v1\": 5}'", /7/g);
   });

test/cases/simple.yaml

@@ -107,6 +107,13 @@ tests:
     desc: 'Parenthesized expression'
     result: [2,3]
 
+  - desc: Evaluating expression for a part of a resource
+    inputfile: questionnaire-part-example.json
+    model: 'r4'
+    expression: {base: 'QuestionnaireResponse.item', expression: 'answer.value = 2 year'}
+    result:
+      - true
+
 
 
 subject:

test/fhirpath.test.js

@@ -59,13 +59,14 @@ const generateTest = (test, testResource) => {
   };
 
   expressions.forEach(expression => {
+    const expressionText = expression instanceof Object ? JSON.stringify(expression) : expression;
     switch(test.type) {
     case 'skipped':
       return it.skip(`Disabled test ${test.desc}`, () => {});
     case 'focused':
-      return it.only(((test.desc || '') + ': ' + (expression || '')), () => getTestData(expression));
+      return it.only(((test.desc || '') + ': ' + (expressionText|| '')), () => getTestData(expression));
     default:
-      return it(((test.desc || '') + ': ' + (expression || '')), () => getTestData(expression));
+      return it(((test.desc || '') + ': ' + (expressionText || '')), () => getTestData(expression));
     }
   });
 };

test/resources/questionnaire-part-example.json

@@ -0,0 +1,10 @@
+{
+  "answer": {
+    "valueQuantity": {
+      "value": 2,
+      "unit": "year(real UCUM code in field 'code')",
+      "system": "http://unitsofmeasure.org",
+      "code": "a"
+    }
+  }
+}