Merge pull request #34 from HL7/bugfix/LF-1338-fix-choice-type-suppor…

…t-for-resursive

Bugfix/lf 1338 fix choice type support for resursive

CHANGELOG.md

@@ -3,6 +3,11 @@
 This log documents significant changes for each release.  This project follows
 [Semantic Versioning](http://semver.org/).
 
+## [1.0.1] - 2020-01-17
+### Fixed
+- Issues with the new choice type support raised in
+  https://github.com/HL7/fhirpath.js/pull/34.
+
 ## [1.0.0] - 2019-12-19
 ### Added
 - Support for FHIR "choice types" (e.g. Observation.value).  The support is

fhir-context/extract-model-info.js

@@ -0,0 +1,86 @@
+// Takes a directory of JSON FHIR definitions (STU3 or R4) and extracts the information
+// about "choice types" (polymorphic fields).
+
+const process = require('process');
+const childProcess = require('child_process');
+const path = require('path');
+const fs = require('fs');
+
+const args = require('yargs')
+  .nargs('fhirDefDir', 1)
+  .describe('fhirDefDir', 'the directory pathname for the JSON FHIR '+
+    'definitions to be processed')
+  .nargs('outputDir', 1)
+  .describe('outputDir', 'the directory into which the output files should be written')
+  .demandOption(['fhirDefDir', 'outputDir'])
+  .help('h')
+  .alias('h', 'help')
+  .argv;
+
+const fhirDefDir = args.fhirDefDir;
+const outputDir = args.outputDir;
+
+// Files defining choice type fields
+const choiceTypeFiles = ['profiles-types.json', 'profiles-resources.json',
+  'profiles-others.json'];
+
+let choiceTypePaths = {};
+let pathsDefinedElsewhere = {};
+for (let f of choiceTypeFiles) {
+  // File all of the "path" information from the file.  There will be
+  // duplicates, but we will use a hash to get a unique list.
+  let fData = JSON.parse(fs.readFileSync(path.join(fhirDefDir, f)));
+  // Walk the tree, looking for "path", and then finding the associated "type"
+  // field, if any.
+  let currentResource;
+  function visitNode(n) {
+    if (n.kind === "resource") {
+      currentResource = n;
+      // Only process definitions that are not constraints on resources defined
+      // elsewhere.
+      if (currentResource.derivation !== "constraint") {
+        // Only process snapshot definitions (not differentials)
+        visitNode(currentResource.snapshot);
+      }
+    }
+    else {
+      if (n.id && n.path && n.contentReference) {
+        if (n.contentReference[0] !== '#')
+          throw new Error('Unhandled new type of contentReference');
+        let refID = n.contentReference.slice(1);
+        // The content references point to IDs, and we want the path, which is
+        // the same except for slice labels.  Remove those.
+        refID = refID.replace(/:[^\.]+/g, '');
+        pathsDefinedElsewhere[n.path] = refID;
+      }
+      if (n.id && n.path && n.type && n.path.match(/\[x\]$/)) {
+        // Uppercase the first letter of the type codes so they can be appended to
+        // the choice field name.
+        let types = n.type.map(t=>t.code[0].toUpperCase() + t.code.slice(1));
+        // Remove the [x] from end of the path
+        choiceTypePaths[n.path.slice(0, -3)] = types;
+      }
+      else {
+        // Check sub-nodes that are objects or arrays
+        if (Array.isArray(n)) {
+          for (let e of n)
+           visitNode(e);
+        }
+        else if (typeof n === "object") {
+          for (let k of Object.keys(n))
+            visitNode(n[k]);
+        }
+      }
+    }
+  }
+  visitNode(fData);
+}
+
+// Output the results as JSON hash for ease of import and ease of checking
+// whether a path is a choice type path.
+// Since there are no nested objects, we can easily sort the output keys.
+fs.writeFileSync(path.join(outputDir, 'choiceTypePaths.json'),
+  JSON.stringify(choiceTypePaths, Object.keys(choiceTypePaths).sort(), 2));
+fs.writeFileSync(path.join(outputDir, 'pathsDefinedElsewhere.json'),
+  JSON.stringify(pathsDefinedElsewhere, Object.keys(pathsDefinedElsewhere).sort(), 2));
+

fhir-context/r4/choiceTypePaths.json

@@ -1362,4 +1362,4 @@
     "Code",
     "DateTime"
   ]
-}
+}

fhir-context/r4/index.js

@@ -7,5 +7,11 @@ module.exports = {
    *  A hash of resource element paths (e.g. Observation.value) that are known
    *  to point to fiels that are choice types.
    */
-  choiceTypePaths: require('./choiceTypePaths')
+  choiceTypePaths: require('./choiceTypePaths'),
+
+  /**
+   *  A hash from paths to the path for which their content is defined, e.g.
+   *  Questionnaire.item.item -> Questionnaire.item.
+   */
+  pathsDefinedElsewhere: require('./pathsDefinedElsewhere')
 }

fhir-context/r4/pathsDefinedElsewhere.json

@@ -0,0 +1,57 @@
+{
+  "Bundle.entry.link": "Bundle.link",
+  "CapabilityStatement.rest.operation": "CapabilityStatement.rest.resource.operation",
+  "CapabilityStatement.rest.searchParam": "CapabilityStatement.rest.resource.searchParam",
+  "ChargeItemDefinition.propertyGroup.applicability": "ChargeItemDefinition.applicability",
+  "ClaimResponse.addItem.adjudication": "ClaimResponse.item.adjudication",
+  "ClaimResponse.addItem.detail.adjudication": "ClaimResponse.item.adjudication",
+  "ClaimResponse.addItem.detail.subDetail.adjudication": "ClaimResponse.item.adjudication",
+  "ClaimResponse.adjudication": "ClaimResponse.item.adjudication",
+  "ClaimResponse.item.detail.adjudication": "ClaimResponse.item.adjudication",
+  "ClaimResponse.item.detail.subDetail.adjudication": "ClaimResponse.item.adjudication",
+  "CodeSystem.concept.concept": "CodeSystem.concept",
+  "Composition.section.section": "Composition.section",
+  "ConceptMap.group.element.target.product": "ConceptMap.group.element.target.dependsOn",
+  "Consent.provision.provision": "Consent.provision",
+  "Contract.term.asset.answer": "Contract.term.offer.answer",
+  "Contract.term.group": "Contract.term",
+  "ExampleScenario.process.step.alternative.step": "ExampleScenario.process.step",
+  "ExampleScenario.process.step.operation.request": "ExampleScenario.instance.containedInstance",
+  "ExampleScenario.process.step.operation.response": "ExampleScenario.instance.containedInstance",
+  "ExampleScenario.process.step.process": "ExampleScenario.process",
+  "ExplanationOfBenefit.addItem.adjudication": "ExplanationOfBenefit.item.adjudication",
+  "ExplanationOfBenefit.addItem.detail.adjudication": "ExplanationOfBenefit.item.adjudication",
+  "ExplanationOfBenefit.addItem.detail.subDetail.adjudication": "ExplanationOfBenefit.item.adjudication",
+  "ExplanationOfBenefit.adjudication": "ExplanationOfBenefit.item.adjudication",
+  "ExplanationOfBenefit.item.detail.adjudication": "ExplanationOfBenefit.item.adjudication",
+  "ExplanationOfBenefit.item.detail.subDetail.adjudication": "ExplanationOfBenefit.item.adjudication",
+  "GraphDefinition.link.target.link": "GraphDefinition.link",
+  "ImplementationGuide.definition.page.page": "ImplementationGuide.definition.page",
+  "Invoice.totalPriceComponent": "Invoice.lineItem.priceComponent",
+  "MedicinalProductAuthorization.procedure.application": "MedicinalProductAuthorization.procedure",
+  "MedicinalProductIngredient.substance.strength": "MedicinalProductIngredient.specifiedSubstance.strength",
+  "MedicinalProductPackaged.packageItem.packageItem": "MedicinalProductPackaged.packageItem",
+  "Observation.component.referenceRange": "Observation.referenceRange",
+  "OperationDefinition.parameter.part": "OperationDefinition.parameter",
+  "Parameters.parameter.part": "Parameters.parameter",
+  "PlanDefinition.action.action": "PlanDefinition.action",
+  "Provenance.entity.agent": "Provenance.agent",
+  "Questionnaire.item.item": "Questionnaire.item",
+  "QuestionnaireResponse.item.answer.item": "QuestionnaireResponse.item",
+  "QuestionnaireResponse.item.item": "QuestionnaireResponse.item",
+  "RequestGroup.action.action": "RequestGroup.action",
+  "StructureMap.group.rule.rule": "StructureMap.group.rule",
+  "SubstanceSpecification.molecularWeight": "SubstanceSpecification.structure.isotope.molecularWeight",
+  "SubstanceSpecification.name.synonym": "SubstanceSpecification.name",
+  "SubstanceSpecification.name.translation": "SubstanceSpecification.name",
+  "SubstanceSpecification.structure.molecularWeight": "SubstanceSpecification.structure.isotope.molecularWeight",
+  "TestReport.teardown.action.operation": "TestReport.setup.action.operation",
+  "TestReport.test.action.assert": "TestReport.setup.action.assert",
+  "TestReport.test.action.operation": "TestReport.setup.action.operation",
+  "TestScript.teardown.action.operation": "TestScript.setup.action.operation",
+  "TestScript.test.action.assert": "TestScript.setup.action.assert",
+  "TestScript.test.action.operation": "TestScript.setup.action.operation",
+  "ValueSet.compose.exclude": "ValueSet.compose.include",
+  "ValueSet.expansion.contains.contains": "ValueSet.expansion.contains",
+  "ValueSet.expansion.contains.designation": "ValueSet.compose.include.concept.designation"
+}

fhir-context/stu3/choiceTypePaths.json

@@ -1023,4 +1023,4 @@
     "CodeableConcept",
     "Reference"
   ]
-}
+}

fhir-context/stu3/index.js

@@ -7,5 +7,11 @@ module.exports = {
    *  A hash of resource element paths (e.g. Observation.value) that are known
    *  to point to fiels that are choice types.
    */
-  choiceTypePaths: require('./choiceTypePaths')
+  choiceTypePaths: require('./choiceTypePaths'),
+
+  /**
+   *  A hash from paths to the path for which their content is defined, e.g.
+   *  Questionnaire.item.item -> Questionnaire.item.
+   */
+  pathsDefinedElsewhere: require('./pathsDefinedElsewhere')
 }

fhir-context/stu3/pathsDefinedElsewhere.json

@@ -0,0 +1,37 @@
+{
+  "Bundle.entry.link": "Bundle.link",
+  "CapabilityStatement.rest.searchParam": "CapabilityStatement.rest.resource.searchParam",
+  "ClaimResponse.addItem.adjudication": "ClaimResponse.item.adjudication",
+  "ClaimResponse.addItem.detail.adjudication": "ClaimResponse.item.adjudication",
+  "ClaimResponse.item.detail.adjudication": "ClaimResponse.item.adjudication",
+  "ClaimResponse.item.detail.subDetail.adjudication": "ClaimResponse.item.adjudication",
+  "CodeSystem.concept.concept": "CodeSystem.concept",
+  "Composition.section.section": "Composition.section",
+  "ConceptMap.group.element.target.product": "ConceptMap.group.element.target.dependsOn",
+  "Contract.term.group": "Contract.term",
+  "ExplanationOfBenefit.addItem.adjudication": "ExplanationOfBenefit.item.adjudication",
+  "ExplanationOfBenefit.addItem.detail.adjudication": "ExplanationOfBenefit.item.adjudication",
+  "ExplanationOfBenefit.item.detail.adjudication": "ExplanationOfBenefit.item.adjudication",
+  "ExplanationOfBenefit.item.detail.subDetail.adjudication": "ExplanationOfBenefit.item.adjudication",
+  "GraphDefinition.link.target.link": "GraphDefinition.link",
+  "ImplementationGuide.page.page": "ImplementationGuide.page",
+  "Observation.component.referenceRange": "Observation.referenceRange",
+  "OperationDefinition.parameter.part": "OperationDefinition.parameter",
+  "Parameters.parameter.part": "Parameters.parameter",
+  "PlanDefinition.action.action": "PlanDefinition.action",
+  "Provenance.entity.agent": "Provenance.agent",
+  "Questionnaire.item.item": "Questionnaire.item",
+  "QuestionnaireResponse.item.answer.item": "QuestionnaireResponse.item",
+  "QuestionnaireResponse.item.item": "QuestionnaireResponse.item",
+  "RequestGroup.action.action": "RequestGroup.action",
+  "StructureMap.group.rule.rule": "StructureMap.group.rule",
+  "TestReport.teardown.action.operation": "TestReport.setup.action.operation",
+  "TestReport.test.action.assert": "TestReport.setup.action.assert",
+  "TestReport.test.action.operation": "TestReport.setup.action.operation",
+  "TestScript.teardown.action.operation": "TestScript.setup.action.operation",
+  "TestScript.test.action.assert": "TestScript.setup.action.assert",
+  "TestScript.test.action.operation": "TestScript.setup.action.operation",
+  "ValueSet.compose.exclude": "ValueSet.compose.include",
+  "ValueSet.expansion.contains.contains": "ValueSet.expansion.contains",
+  "ValueSet.expansion.contains.designation": "ValueSet.compose.include.concept.designation"
+}