Refactor pre-pop package to add pre-processing code

aehrc · May 19, 2024 · 4365a73 · 4365a73
1 parent 6eb151c
commit 4365a73
Show file tree

Hide file tree

Showing 44 changed files with 1,325 additions and 22 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/packages/sdc-populate/package.json b/packages/sdc-populate/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@aehrc/sdc-populate",
-  "version": "1.9.0",
+  "version": "2.0.0",
   "description": "Performs the $populate operation from the HL7 FHIR SDC (Structured Data Capture) specification: http://hl7.org/fhir/uv/sdc",
   "main": "lib/index.js",
   "scripts": {

diff --git a/...es/sdc-populate/src/api/expandValueset.ts → ...stionnaireOperation/api/expandValueset.ts b/...es/sdc-populate/src/api/expandValueset.ts → ...stionnaireOperation/api/expandValueset.ts
diff --git a/...dc-populate/src/api/fetchQuestionnaire.ts → ...nnaireOperation/api/fetchQuestionnaire.ts b/...dc-populate/src/api/fetchQuestionnaire.ts → ...nnaireOperation/api/fetchQuestionnaire.ts
diff --git a/.../sdc-populate/src/api/lookupCodeSystem.ts → ...ionnaireOperation/api/lookupCodeSystem.ts b/.../sdc-populate/src/api/lookupCodeSystem.ts → ...ionnaireOperation/api/lookupCodeSystem.ts
diff --git a/packages/sdc-populate/src/SDCPopulateQuestionnaireOperation/index.ts b/packages/sdc-populate/src/SDCPopulateQuestionnaireOperation/index.ts
@@ -0,0 +1,22 @@
+/*
+ * Copyright 2024 Commonwealth Scientific and Industrial Research
+ * Organisation (CSIRO) ABN 41 687 119 230.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+// Export interfaces
+export * from './interfaces';
+
+// Export utils
+export * from './utils';
diff --git a/...late/src/interfaces/callback.interface.ts → ...peration/interfaces/callback.interface.ts b/...late/src/interfaces/callback.interface.ts → ...peration/interfaces/callback.interface.ts
diff --git a/...e/src/interfaces/expressions.interface.ts → ...ation/interfaces/expressions.interface.ts b/...e/src/interfaces/expressions.interface.ts → ...ation/interfaces/expressions.interface.ts
diff --git a/...ages/sdc-populate/src/interfaces/index.ts → ...uestionnaireOperation/interfaces/index.ts b/...ages/sdc-populate/src/interfaces/index.ts → ...uestionnaireOperation/interfaces/index.ts
diff --git a/...c/interfaces/inputParameters.interface.ts → ...n/interfaces/inputParameters.interface.ts b/...c/interfaces/inputParameters.interface.ts → ...n/interfaces/inputParameters.interface.ts
diff --git a/.../interfaces/outputParameters.interface.ts → .../interfaces/outputParameters.interface.ts b/.../interfaces/outputParameters.interface.ts → .../interfaces/outputParameters.interface.ts
@@ -50,6 +50,7 @@ export interface IssuesParameter extends ParametersParameter {
 }
 
 // This is used for debugging purposes, it does not exist in the FHIR spec
+// It is used to return the context result to the renderer
 export interface CustomContextResultParameter extends ParametersParameter {
   name: 'contextResult-custom';
   valueAttachment: Attachment;

diff --git a/...populate/src/utils/addDisplayToCodings.ts → ...ireOperation/utils/addDisplayToCodings.ts b/...populate/src/utils/addDisplayToCodings.ts → ...ireOperation/utils/addDisplayToCodings.ts
diff --git a/...es/sdc-populate/src/utils/answerOption.ts → ...stionnaireOperation/utils/answerOption.ts b/...es/sdc-populate/src/utils/answerOption.ts → ...stionnaireOperation/utils/answerOption.ts
diff --git a/...c-populate/src/utils/constructResponse.ts → ...naireOperation/utils/constructResponse.ts b/...c-populate/src/utils/constructResponse.ts → ...naireOperation/utils/constructResponse.ts
diff --git a/...pulate/src/utils/createFhirPathContext.ts → ...eOperation/utils/createFhirPathContext.ts b/...pulate/src/utils/createFhirPathContext.ts → ...eOperation/utils/createFhirPathContext.ts
diff --git a/...ulate/src/utils/createOutputParameters.ts → ...Operation/utils/createOutputParameters.ts b/...ulate/src/utils/createOutputParameters.ts → ...Operation/utils/createOutputParameters.ts
diff --git a/...src/utils/createQuestionnaireReference.ts → ...ion/utils/createQuestionnaireReference.ts b/...src/utils/createQuestionnaireReference.ts → ...ion/utils/createQuestionnaireReference.ts
diff --git a/...populate/src/utils/evaluateExpressions.ts → ...ireOperation/utils/evaluateExpressions.ts b/...populate/src/utils/evaluateExpressions.ts → ...ireOperation/utils/evaluateExpressions.ts
diff --git a/packages/sdc-populate/src/utils/index.ts → ...lateQuestionnaireOperation/utils/index.ts b/packages/sdc-populate/src/utils/index.ts → ...lateQuestionnaireOperation/utils/index.ts
diff --git a/...dc-populate/src/utils/operationOutcome.ts → ...nnaireOperation/utils/operationOutcome.ts b/...dc-populate/src/utils/operationOutcome.ts → ...nnaireOperation/utils/operationOutcome.ts
diff --git a/packages/sdc-populate/src/utils/parse.ts → ...lateQuestionnaireOperation/utils/parse.ts b/packages/sdc-populate/src/utils/parse.ts → ...lateQuestionnaireOperation/utils/parse.ts
diff --git a/packages/sdc-populate/src/utils/populate.ts → ...eQuestionnaireOperation/utils/populate.ts b/packages/sdc-populate/src/utils/populate.ts → ...eQuestionnaireOperation/utils/populate.ts
@@ -30,10 +30,10 @@ import { isEncounterContextParameter } from './typePredicates';
 import { addDisplayToInitialExpressionsCodings } from './addDisplayToCodings';
 
 /**
- * Main function of this populate module.
+ * Executes the SDC Populate Questionnaire operation - $populate.
  * Input and output specific parameters conformant to the SDC populate specification.
  * @see {@link https://hl7.org/fhir/uv/sdc/OperationDefinition-Questionnaire-populate.html}
- * Added populationContextResults for visual and debugging purposes.
+ * Added custom output parameters populationContextResults for visual and debugging purposes.
  *
  * @author Sean Fong
  */

diff --git a/...dc-populate/src/utils/processValueSets.ts → ...nnaireOperation/utils/processValueSets.ts b/...dc-populate/src/utils/processValueSets.ts → ...nnaireOperation/utils/processValueSets.ts
diff --git a/...te/src/utils/readPopulationExpressions.ts → ...ration/utils/readPopulationExpressions.ts b/...te/src/utils/readPopulationExpressions.ts → ...ration/utils/readPopulationExpressions.ts
diff --git a/...-populate/src/utils/removeEmptyAnswers.ts → ...aireOperation/utils/removeEmptyAnswers.ts b/...-populate/src/utils/removeEmptyAnswers.ts → ...aireOperation/utils/removeEmptyAnswers.ts
diff --git a/...-populate/src/utils/sortResourceArrays.ts → ...aireOperation/utils/sortResourceArrays.ts b/...-populate/src/utils/sortResourceArrays.ts → ...aireOperation/utils/sortResourceArrays.ts
diff --git a/.../sdc-populate/src/utils/typePredicates.ts → ...ionnaireOperation/utils/typePredicates.ts b/.../sdc-populate/src/utils/typePredicates.ts → ...ionnaireOperation/utils/typePredicates.ts
diff --git a/...-populate/src/utils/variableProcessing.ts → ...aireOperation/utils/variableProcessing.ts b/...-populate/src/utils/variableProcessing.ts → ...aireOperation/utils/variableProcessing.ts
diff --git a/packages/sdc-populate/src/inAppPopulation/index.ts b/packages/sdc-populate/src/inAppPopulation/index.ts
@@ -0,0 +1,18 @@
+/*
+ * Copyright 2024 Commonwealth Scientific and Industrial Research
+ * Organisation (CSIRO) ABN 41 687 119 230.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+export * from './utils';
diff --git a/packages/sdc-populate/src/inAppPopulation/interfaces/inAppPopulation.interface.ts b/packages/sdc-populate/src/inAppPopulation/interfaces/inAppPopulation.interface.ts
@@ -0,0 +1,71 @@
+/*
+ * Copyright 2024 Commonwealth Scientific and Industrial Research
+ * Organisation (CSIRO) ABN 41 687 119 230.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+// interfaces
+import type { Coding, Expression, Extension, Reference } from 'fhir/r4';
+
+export interface LaunchContext extends Extension {
+  url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-launchContext';
+  extension: LaunchContextExtensions;
+}
+
+type LaunchContextExtensions =
+  | [LaunchContextName, LaunchContextType]
+  | [LaunchContextName, LaunchContextType, LaunchContextDescription];
+
+type LaunchContextName = LaunchContextNameId | LaunchContextNameCoding;
+
+// for backwards compatibility with old questionnaires (though it is not conformant)
+interface LaunchContextNameId extends Extension {
+  url: 'name';
+  valueId: string;
+}
+
+interface LaunchContextNameCoding extends Extension {
+  url: 'name';
+  valueCoding: LaunchContextNameCodingValueCoding;
+}
+
+interface LaunchContextNameCodingValueCoding extends Coding {
+  code: 'patient' | 'encounter' | 'location' | 'user' | 'study';
+}
+
+interface LaunchContextType extends Extension {
+  url: 'type';
+  valueCode: string;
+}
+
+interface LaunchContextDescription extends Extension {
+  url: 'description';
+  valueString: string;
+}
+
+export interface SourceQuery extends Extension {
+  url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-sourceQueries';
+  valueReference: Reference;
+}
+
+export interface QuestionnaireLevelXFhirQueryVariable extends Extension {
+  url: 'http://hl7.org/fhir/StructureDefinition/variable';
+  valueExpression: XFhirQueryVariableExpression;
+}
+
+interface XFhirQueryVariableExpression extends Expression {
+  name: string;
+  language: 'application/x-fhir-query';
+  expression: string;
+}