@aehrc/smart-forms-renderer 0.2.0 → 0.4.0

package/src/utils/populate.js

@@ -0,0 +1,78 @@
+/*
+ * Copyright 2023 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.
+ */
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+import { getLaunchContexts, getQuestionnaireLevelXFhirQueryVariables, getSourceQueries } from './populateContexts';
+import { isInputParameters } from 'sdc-populate';
+import { createPopulateInputParameters } from './populateInputParams';
+import { requestPopulate } from '../api/populate';
+/**
+ * Pre-populate questionnaire from CMS patient data to form a populated questionnaireResponse
+ *
+ * @author Sean Fong
+ */
+export function populateQuestionnaire(questionnaire, fhirClient, patient, user, encounter, populateForm, exitSpinner) {
+    var _a;
+    return __awaiter(this, void 0, void 0, function* () {
+        // Get launch contexts, source queries and questionnaire-level variables
+        const launchContexts = getLaunchContexts(questionnaire);
+        const sourceQueries = getSourceQueries(questionnaire);
+        const questionnaireLevelVariables = getQuestionnaireLevelXFhirQueryVariables(questionnaire);
+        if (launchContexts.length === 0 &&
+            sourceQueries.length === 0 &&
+            questionnaireLevelVariables.length === 0) {
+            exitSpinner();
+            return;
+        }
+        // Define population input parameters from launch contexts, source queries and questionnaire-level variables
+        const inputParameters = createPopulateInputParameters(questionnaire, patient, user, encounter, launchContexts, sourceQueries, questionnaireLevelVariables);
+        if (!inputParameters) {
+            exitSpinner();
+            return;
+        }
+        if (!isInputParameters(inputParameters)) {
+            exitSpinner();
+            return;
+        }
+        // Perform population if parameters satisfies input parameters
+        const outputParameters = yield requestPopulate(fhirClient, inputParameters);
+        if (outputParameters.resourceType === 'OperationOutcome') {
+            exitSpinner();
+            return;
+        }
+        const responseParameter = outputParameters.parameter.find((param) => param.name === 'response');
+        const issuesParameter = outputParameters.parameter.find((param) => param.name === 'issues');
+        if (issuesParameter) {
+            for (const issue of issuesParameter.resource.issue) {
+                if ((_a = issue.details) === null || _a === void 0 ? void 0 : _a.text) {
+                    console.warn(issue.details.text);
+                }
+            }
+            populateForm({ populated: responseParameter.resource, hasWarnings: true });
+            return;
+        }
+        populateForm({ populated: responseParameter.resource, hasWarnings: false });
+    });
+}
+//# sourceMappingURL=populate.js.map

package/src/utils/populate.js.map

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package/src/utils/populate.ts

@@ -0,0 +1,117 @@
+/*
+ * Copyright 2023 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.
+ */
+
+import type {
+  Encounter,
+  Patient,
+  Practitioner,
+  Questionnaire,
+  QuestionnaireResponse
+} from 'fhir/r4';
+import {
+  getLaunchContexts,
+  getQuestionnaireLevelXFhirQueryVariables,
+  getSourceQueries
+} from './populateContexts';
+import type { IssuesParameter, ResponseParameter } from 'sdc-populate';
+import { isInputParameters } from 'sdc-populate';
+import type Client from 'fhirclient/lib/Client';
+import { createPopulateInputParameters } from './populateInputParams';
+import { requestPopulate } from '../api/populate';
+
+export interface PopulateFormParams {
+  populated: QuestionnaireResponse;
+  hasWarnings: boolean;
+}
+/**
+ * Pre-populate questionnaire from CMS patient data to form a populated questionnaireResponse
+ *
+ * @author Sean Fong
+ */
+export async function populateQuestionnaire(
+  questionnaire: Questionnaire,
+  fhirClient: Client,
+  patient: Patient,
+  user: Practitioner,
+  encounter: Encounter | null,
+  populateForm: {
+    (params: PopulateFormParams): void;
+  },
+  exitSpinner: { (): void }
+) {
+  // Get launch contexts, source queries and questionnaire-level variables
+  const launchContexts = getLaunchContexts(questionnaire);
+  const sourceQueries = getSourceQueries(questionnaire);
+  const questionnaireLevelVariables = getQuestionnaireLevelXFhirQueryVariables(questionnaire);
+
+  if (
+    launchContexts.length === 0 &&
+    sourceQueries.length === 0 &&
+    questionnaireLevelVariables.length === 0
+  ) {
+    exitSpinner();
+    return;
+  }
+
+  // Define population input parameters from launch contexts, source queries and questionnaire-level variables
+  const inputParameters = createPopulateInputParameters(
+    questionnaire,
+    patient,
+    user,
+    encounter,
+    launchContexts,
+    sourceQueries,
+    questionnaireLevelVariables
+  );
+
+  if (!inputParameters) {
+    exitSpinner();
+    return;
+  }
+
+  if (!isInputParameters(inputParameters)) {
+    exitSpinner();
+    return;
+  }
+
+  // Perform population if parameters satisfies input parameters
+  const outputParameters = await requestPopulate(fhirClient, inputParameters);
+
+  if (outputParameters.resourceType === 'OperationOutcome') {
+    exitSpinner();
+    return;
+  }
+
+  const responseParameter = outputParameters.parameter.find(
+    (param) => param.name === 'response'
+  ) as ResponseParameter;
+  const issuesParameter = outputParameters.parameter.find((param) => param.name === 'issues') as
+    | IssuesParameter
+    | undefined;
+
+  if (issuesParameter) {
+    for (const issue of issuesParameter.resource.issue) {
+      if (issue.details?.text) {
+        console.warn(issue.details.text);
+      }
+    }
+    populateForm({ populated: responseParameter.resource, hasWarnings: true });
+    return;
+  }
+
+  populateForm({ populated: responseParameter.resource, hasWarnings: false });
+}

package/src/utils/populateCallback.js

@@ -0,0 +1,40 @@
+/*
+ * Copyright 2023 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.
+ */
+import axios from 'axios';
+const ABSOLUTE_URL_REGEX = /^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$/;
+export const fetchResourceCallback = (query, requestConfig) => {
+    let { clientEndpoint } = requestConfig;
+    const { authToken } = requestConfig;
+    const headers = {
+        Accept: 'application/json;charset=utf-8',
+        Authorization: `Bearer ${authToken}`
+    };
+    if (!clientEndpoint.endsWith('/')) {
+        clientEndpoint += '/';
+    }
+    if (ABSOLUTE_URL_REGEX.test(query)) {
+        return axios.get(query, {
+            headers: headers
+        });
+    }
+    else {
+        return axios.get(clientEndpoint + query, {
+            headers: headers
+        });
+    }
+};
+//# sourceMappingURL=populateCallback.js.map

package/src/utils/populateCallback.js.map

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package/src/utils/populateCallback.ts

@@ -0,0 +1,53 @@
+/*
+ * Copyright 2023 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.
+ */
+
+import type { FetchResourceCallback } from 'sdc-populate';
+import axios from 'axios';
+
+const ABSOLUTE_URL_REGEX = /^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$/;
+
+export interface RequestConfig {
+  clientEndpoint: string;
+  authToken: string;
+}
+
+export const fetchResourceCallback: FetchResourceCallback = (
+  query: string,
+  requestConfig: RequestConfig
+) => {
+  let { clientEndpoint } = requestConfig;
+  const { authToken } = requestConfig;
+
+  const headers = {
+    Accept: 'application/json;charset=utf-8',
+    Authorization: `Bearer ${authToken}`
+  };
+
+  if (!clientEndpoint.endsWith('/')) {
+    clientEndpoint += '/';
+  }
+
+  if (ABSOLUTE_URL_REGEX.test(query)) {
+    return axios.get(query, {
+      headers: headers
+    });
+  } else {
+    return axios.get(clientEndpoint + query, {
+      headers: headers
+    });
+  }
+};

package/src/utils/populateContexts.js

@@ -0,0 +1,76 @@
+/*
+ * Copyright 2023 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 function getLaunchContexts(questionnaire) {
+    if (questionnaire.extension && questionnaire.extension.length > 0) {
+        return questionnaire.extension.filter((extension) => isLaunchContext(extension));
+    }
+    return [];
+}
+export function isLaunchContext(extension) {
+    var _a, _b;
+    const hasLaunchContextName = extension.url ===
+        'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-launchContext' &&
+        !!((_a = extension.extension) === null || _a === void 0 ? void 0 : _a.find((ext) => ext.url === 'name' &&
+            (ext.valueId ||
+                (ext.valueCoding &&
+                    (ext.valueCoding.code === 'patient' ||
+                        ext.valueCoding.code === 'encounter' ||
+                        ext.valueCoding.code === 'location' ||
+                        ext.valueCoding.code === 'user' ||
+                        ext.valueCoding.code === 'study' ||
+                        ext.valueCoding.code === 'sourceQueries')))));
+    const hasLaunchContextType = !!((_b = extension.extension) === null || _b === void 0 ? void 0 : _b.find((ext) => ext.url === 'type' &&
+        ext.valueCode &&
+        (ext.valueCode === 'Patient' ||
+            ext.valueCode === 'Practitioner' ||
+            ext.valueCode === 'Encounter')));
+    return (extension.url ===
+        'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-launchContext' &&
+        hasLaunchContextName &&
+        hasLaunchContextType);
+}
+// get source query references
+export function getSourceQueries(questionnaire) {
+    if (questionnaire.extension && questionnaire.extension.length > 0) {
+        return questionnaire.extension.filter((extension) => isSourceQuery(extension));
+    }
+    return [];
+}
+export function isSourceQuery(extension) {
+    return (extension.url ===
+        'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-sourceQueries' &&
+        !!extension.valueReference);
+}
+/**
+ * Filter x-fhir-query variables from questionnaire's extensions needed for population
+ *
+ * @author Sean Fong
+ */
+export function getQuestionnaireLevelXFhirQueryVariables(questionnaire) {
+    if (questionnaire.extension && questionnaire.extension.length > 0) {
+        return questionnaire.extension.filter((extension) => isXFhirQueryVariable(extension));
+    }
+    return [];
+}
+export function isXFhirQueryVariable(extension) {
+    var _a, _b, _c;
+    return (extension.url === 'http://hl7.org/fhir/StructureDefinition/variable' &&
+        !!((_a = extension.valueExpression) === null || _a === void 0 ? void 0 : _a.name) &&
+        ((_b = extension.valueExpression) === null || _b === void 0 ? void 0 : _b.language) === 'application/x-fhir-query' &&
+        !!((_c = extension.valueExpression) === null || _c === void 0 ? void 0 : _c.expression));
+}
+//# sourceMappingURL=populateContexts.js.map

package/src/utils/populateContexts.js.map

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package/src/utils/populateContexts.ts

@@ -0,0 +1,112 @@
+/*
+ * Copyright 2023 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.
+ */
+
+import type { Extension, Questionnaire } from 'fhir/r4';
+import type {
+  LaunchContext,
+  QuestionnaireLevelXFhirQueryVariable,
+  SourceQuery
+} from '../interfaces/populate.interface';
+
+export function getLaunchContexts(questionnaire: Questionnaire): LaunchContext[] {
+  if (questionnaire.extension && questionnaire.extension.length > 0) {
+    return questionnaire.extension.filter((extension) =>
+      isLaunchContext(extension)
+    ) as LaunchContext[];
+  }
+
+  return [];
+}
+
+export function isLaunchContext(extension: Extension): extension is LaunchContext {
+  const hasLaunchContextName =
+    extension.url ===
+      'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-launchContext' &&
+    !!extension.extension?.find(
+      (ext) =>
+        ext.url === 'name' &&
+        (ext.valueId ||
+          (ext.valueCoding &&
+            (ext.valueCoding.code === 'patient' ||
+              ext.valueCoding.code === 'encounter' ||
+              ext.valueCoding.code === 'location' ||
+              ext.valueCoding.code === 'user' ||
+              ext.valueCoding.code === 'study' ||
+              ext.valueCoding.code === 'sourceQueries')))
+    );
+
+  const hasLaunchContextType = !!extension.extension?.find(
+    (ext) =>
+      ext.url === 'type' &&
+      ext.valueCode &&
+      (ext.valueCode === 'Patient' ||
+        ext.valueCode === 'Practitioner' ||
+        ext.valueCode === 'Encounter')
+  );
+
+  return (
+    extension.url ===
+      'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-launchContext' &&
+    hasLaunchContextName &&
+    hasLaunchContextType
+  );
+}
+
+// get source query references
+export function getSourceQueries(questionnaire: Questionnaire): SourceQuery[] {
+  if (questionnaire.extension && questionnaire.extension.length > 0) {
+    return questionnaire.extension.filter((extension) => isSourceQuery(extension)) as SourceQuery[];
+  }
+
+  return [];
+}
+
+export function isSourceQuery(extension: Extension): extension is SourceQuery {
+  return (
+    extension.url ===
+      'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-sourceQueries' &&
+    !!extension.valueReference
+  );
+}
+
+/**
+ * Filter x-fhir-query variables from questionnaire's extensions needed for population
+ *
+ * @author Sean Fong
+ */
+export function getQuestionnaireLevelXFhirQueryVariables(
+  questionnaire: Questionnaire
+): QuestionnaireLevelXFhirQueryVariable[] {
+  if (questionnaire.extension && questionnaire.extension.length > 0) {
+    return questionnaire.extension.filter((extension) =>
+      isXFhirQueryVariable(extension)
+    ) as QuestionnaireLevelXFhirQueryVariable[];
+  }
+
+  return [];
+}
+
+export function isXFhirQueryVariable(
+  extension: Extension
+): extension is QuestionnaireLevelXFhirQueryVariable {
+  return (
+    extension.url === 'http://hl7.org/fhir/StructureDefinition/variable' &&
+    !!extension.valueExpression?.name &&
+    extension.valueExpression?.language === 'application/x-fhir-query' &&
+    !!extension.valueExpression?.expression
+  );
+}

package/src/utils/populateInputParams.js

@@ -0,0 +1,193 @@
+/*
+ * Copyright 2023 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.
+ */
+function createPatientSubject(questionnaire, patient) {
+    const subjectTypes = questionnaire.subjectType;
+    // If subjectTypes array is not empty AND "Patient" is not in the array, we cannot create a Patient subject reference.
+    if (subjectTypes && subjectTypes.length > 0) {
+        const patientSubject = subjectTypes.find((subject) => subject === 'Patient');
+        if (!patientSubject) {
+            return null;
+        }
+    }
+    return {
+        type: 'Patient',
+        reference: 'Patient/' + patient.id
+    };
+}
+function createCanonicalParam(canonicalUrl) {
+    return {
+        name: 'canonical',
+        valueString: canonicalUrl
+    };
+}
+// setting local parameter as false as we are calling $populate with an NPM package, not a server
+// package doesn't contain any fhir resources to "know" the context from
+function createLocalParam() {
+    return {
+        name: 'local',
+        valueBoolean: false
+    };
+}
+function createLaunchContextParam(launchContext, patient, user, encounter) {
+    var _a, _b;
+    const name = (_a = launchContext.extension[0].valueId) !== null && _a !== void 0 ? _a : (_b = launchContext.extension[0].valueCoding) === null || _b === void 0 ? void 0 : _b.code;
+    if (!name) {
+        return null;
+    }
+    // let resource :string
+    const resourceType = launchContext.extension[1].valueCode;
+    let resource;
+    switch (resourceType) {
+        case 'Patient':
+            resource = patient;
+            break;
+        case 'Practitioner':
+            resource = user;
+            break;
+        case 'Encounter':
+            resource = encounter;
+            break;
+        default:
+            return null;
+    }
+    if (!resource) {
+        return null;
+    }
+    return {
+        name: 'context',
+        part: [
+            {
+                name: 'name',
+                valueString: name
+            },
+            {
+                name: 'content',
+                resource: resource
+            }
+        ]
+    };
+}
+function createSourceQueryParams(sourceQuery, index) {
+    const reference = sourceQuery.valueReference.reference;
+    if (reference && reference.startsWith('#')) {
+        const containedReference = reference.slice(1);
+        return {
+            name: 'context',
+            part: [
+                {
+                    name: 'name',
+                    valueString: containedReference
+                },
+                {
+                    name: 'content',
+                    valueReference: sourceQuery.valueReference
+                }
+            ]
+        };
+    }
+    // if sourceQuery cannot be referenced to a contained bundle, return itself as a context
+    // this most likely shouldn't happen
+    return {
+        name: 'context',
+        part: [
+            {
+                name: 'name',
+                valueString: `sourceQuery${index}`
+            },
+            {
+                name: 'content',
+                valueReference: sourceQuery.valueReference
+            }
+        ]
+    };
+}
+function createVariableParam(variable) {
+    const query = variable.valueExpression.expression;
+    const resourceType = query.split('?')[0];
+    return {
+        name: 'context',
+        part: [
+            {
+                name: 'name',
+                valueString: variable.valueExpression.name
+            },
+            {
+                name: 'content',
+                valueReference: { reference: query, type: resourceType }
+            }
+        ]
+    };
+}
+/**
+ * Define population input parameters without any batch response contexts
+ *
+ * @author Sean Fong
+ */
+export function createPopulateInputParameters(questionnaire, patient, user, encounter, launchContexts, sourceQueries, questionnaireLevelVariables) {
+    var _a, _b, _c;
+    const patientSubject = createPatientSubject(questionnaire, patient);
+    if (!patientSubject) {
+        return null;
+    }
+    const inputParameters = {
+        resourceType: 'Parameters',
+        parameter: [
+            {
+                name: 'questionnaire',
+                resource: questionnaire
+            },
+            {
+                name: 'subject',
+                valueReference: patientSubject
+            }
+        ]
+    };
+    // canonical
+    if (questionnaire.url) {
+        (_a = inputParameters.parameter) === null || _a === void 0 ? void 0 : _a.push(createCanonicalParam(questionnaire.url));
+    }
+    // contexts
+    const contexts = [];
+    // add launch contexts
+    if (launchContexts.length > 0) {
+        for (const launchContext of launchContexts) {
+            const launchContextParam = createLaunchContextParam(launchContext, patient, user, encounter);
+            if (launchContextParam) {
+                contexts.push(launchContextParam);
+            }
+        }
+    }
+    // add source queries
+    if (sourceQueries.length > 0) {
+        for (const [index, sourceQuery] of sourceQueries.entries()) {
+            contexts.push(createSourceQueryParams(sourceQuery, index));
+        }
+    }
+    // add questionnaire-level variables
+    if (questionnaireLevelVariables.length > 0) {
+        for (const variable of questionnaireLevelVariables) {
+            contexts.push(createVariableParam(variable));
+        }
+    }
+    if (contexts.length > 0) {
+        (_b = inputParameters.parameter) === null || _b === void 0 ? void 0 : _b.push(...contexts);
+    }
+    // local
+    (_c = inputParameters.parameter) === null || _c === void 0 ? void 0 : _c.push(createLocalParam());
+    return inputParameters;
+}
+//# sourceMappingURL=populateInputParams.js.map