FM2-183: Add support for DSTU3 (#158)

api/pom.xml

@@ -17,10 +17,18 @@
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-base</artifactId>
  </dependency>
+ <dependency>
+ <groupId>ca.uhn.hapi.fhir</groupId>
+ <artifactId>hapi-fhir-structures-dstu3</artifactId>
+ </dependency>
  <dependency>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-structures-r4</artifactId>
  </dependency>
+ <dependency>
+ <groupId>ca.uhn.hapi.fhir</groupId>
+ <artifactId>hapi-fhir-converter</artifactId>
+ </dependency>
  <dependency>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-server</artifactId>

api/src/main/java/org/openmrs/module/fhir2/providers/r3/AllergyIntoleranceFhirResourceProvider.java

@@ -0,0 +1,94 @@
+/*
+ * This Source Code Form is subject to the terms of the Mozilla Public License,
+ * v. 2.0. If a copy of the MPL was not distributed with this file, You can
+ * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
+ *
+ * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
+ * graphic logo is a trademark of OpenMRS Inc.
+ */
+package org.openmrs.module.fhir2.providers.r3;
+
+import javax.validation.constraints.NotNull;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+import ca.uhn.fhir.rest.annotation.History;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.OptionalParam;
+import ca.uhn.fhir.rest.annotation.Read;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.param.ReferenceAndListParam;
+import ca.uhn.fhir.rest.param.TokenAndListParam;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import lombok.AccessLevel;
+import lombok.Setter;
+import org.hl7.fhir.convertors.conv30_40.AllergyIntolerance30_40;
+import org.hl7.fhir.convertors.conv30_40.Bundle30_40;
+import org.hl7.fhir.convertors.conv30_40.Provenance30_40;
+import org.hl7.fhir.dstu3.model.AllergyIntolerance;
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.Resource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Provenance;
+import org.openmrs.module.fhir2.api.FhirAllergyIntoleranceService;
+import org.openmrs.module.fhir2.providers.util.FhirProviderUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.stereotype.Component;
+
+@Component("allergyIntoleranceFhirR3ResourceProvider")
+@Qualifier("fhirR3Resources")
+@Setter(AccessLevel.PACKAGE)
+public class AllergyIntoleranceFhirResourceProvider implements IResourceProvider {
+
+ @Override
+ public Class<? extends IBaseResource> getResourceType() {
+ return AllergyIntolerance.class;
+ }
+
+ @Autowired
+ private FhirAllergyIntoleranceService allergyIntoleranceService;
+
+ @Read
+ @SuppressWarnings("unused")
+ public AllergyIntolerance getAllergyIntoleranceById(@IdParam @NotNull IdType id) {
+ org.hl7.fhir.r4.model.AllergyIntolerance allergyIntolerance = allergyIntoleranceService.get(id.getIdPart());
+ if (allergyIntolerance == null) {
+ throw new ResourceNotFoundException("Could not find allergyIntolerance with Id " + id.getIdPart());
+ }
+
+ return AllergyIntolerance30_40.convertAllergyIntolerance(allergyIntolerance);
+ }
+
+ @History
+ @SuppressWarnings("unused")
+ public List<Resource> getAllergyIntoleranceHistoryById(@IdParam @NotNull IdType id) {
+ org.hl7.fhir.r4.model.AllergyIntolerance allergyIntolerance = allergyIntoleranceService.get(id.getIdPart());
+ if (allergyIntolerance == null) {
+ throw new ResourceNotFoundException("Could not find allergy with Id " + id.getIdPart());
+ }
+
+ return allergyIntolerance.getContained().stream().filter(r -> r instanceof Provenance).map(r -> (Provenance) r)
+ .map(Provenance30_40::convertProvenance).collect(Collectors.toList());
+ }
+
+ @Search
+ @SuppressWarnings("unused")
+ public Bundle searchForAllergies(
+ @OptionalParam(name = AllergyIntolerance.SP_PATIENT, chainWhitelist = { "", Patient.SP_IDENTIFIER,
+ Patient.SP_GIVEN, Patient.SP_FAMILY,
+ Patient.SP_NAME }, targetTypes = Patient.class) ReferenceAndListParam patientReference,
+ @OptionalParam(name = AllergyIntolerance.SP_CATEGORY) TokenAndListParam category,
+ @OptionalParam(name = AllergyIntolerance.SP_CODE) TokenAndListParam allergen,
+ @OptionalParam(name = AllergyIntolerance.SP_SEVERITY) TokenAndListParam severity,
+ @OptionalParam(name = AllergyIntolerance.SP_MANIFESTATION) TokenAndListParam manifestationCode,
+ @OptionalParam(name = AllergyIntolerance.SP_CLINICAL_STATUS) TokenAndListParam clinicalStatus) {
+ return Bundle30_40.convertBundle(FhirProviderUtils.convertSearchResultsToBundle(allergyIntoleranceService
+ .searchForAllergies(patientReference, category, allergen, severity, manifestationCode, clinicalStatus)));
+ }
+}

api/src/main/java/org/openmrs/module/fhir2/providers/r3/ConditionFhirResourceProvider.java

@@ -0,0 +1,93 @@
+/*
+ * This Source Code Form is subject to the terms of the Mozilla Public License,
+ * v. 2.0. If a copy of the MPL was not distributed with this file, You can
+ * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
+ *
+ * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
+ * graphic logo is a trademark of OpenMRS Inc.
+ */
+package org.openmrs.module.fhir2.providers.r3;
+
+import javax.validation.constraints.NotNull;
+
+import java.util.List;
+
+import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.SortSpec;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.param.QuantityAndListParam;
+import ca.uhn.fhir.rest.param.ReferenceAndListParam;
+import ca.uhn.fhir.rest.param.TokenAndListParam;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import lombok.AccessLevel;
+import lombok.Setter;
+import org.hl7.fhir.convertors.conv30_40.Bundle30_40;
+import org.hl7.fhir.convertors.conv30_40.Condition30_40;
+import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.openmrs.module.fhir2.api.FhirConditionService;
+import org.openmrs.module.fhir2.providers.util.FhirProviderUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.stereotype.Component;
+
+@Component("conditionFhirR3ResourceProvider")
+@Qualifier("fhirR3Resources")
+@Setter(AccessLevel.PACKAGE)
+public class ConditionFhirResourceProvider implements IResourceProvider {
+
+ @Autowired
+ private FhirConditionService conditionService;
+
+ @Override
+ public Class<? extends IBaseResource> getResourceType() {
+ return Condition.class;
+ }
+
+ @Read
+ @SuppressWarnings("unused")
+ public Condition getConditionById(@IdParam @NotNull IdType id) {
+ org.hl7.fhir.r4.model.Condition condition = conditionService.getConditionByUuid(id.getIdPart());
+ if (condition == null) {
+ throw new ResourceNotFoundException("Could not find condition with Id " + id.getIdPart());
+ }
+
+ return Condition30_40.convertCondition(condition);
+ }
+
+ @History
+ @SuppressWarnings("unused")
+ public List<Resource> getConditionHistoryById(@IdParam @NotNull IdType id) {
+ org.hl7.fhir.r4.model.Condition condition = conditionService.getConditionByUuid(id.getIdPart());
+ if (condition == null) {
+ throw new ResourceNotFoundException("Could not find condition with Id " + id.getIdPart());
+ }
+ return Condition30_40.convertCondition(condition).getContained();
+ }
+
+ @Create
+ @SuppressWarnings("unused")
+ public MethodOutcome createCondition(@ResourceParam Condition newCondition) {
+ return FhirProviderUtils.buildCreate(conditionService.saveCondition(Condition30_40.convertCondition(newCondition)));
+ }
+
+ @Search
+ @SuppressWarnings("unused")
+ public Bundle searchConditions(
+ @OptionalParam(name = Condition.SP_PATIENT, chainWhitelist = { "", Patient.SP_IDENTIFIER, Patient.SP_NAME,
+ Patient.SP_GIVEN, Patient.SP_FAMILY }) ReferenceAndListParam patientParam,
+ @OptionalParam(name = Condition.SP_SUBJECT, chainWhitelist = { "", Patient.SP_IDENTIFIER, Patient.SP_NAME,
+ Patient.SP_GIVEN, Patient.SP_FAMILY }) ReferenceAndListParam subjectParam,
+ @OptionalParam(name = Condition.SP_CODE) TokenAndListParam code,
+ @OptionalParam(name = Condition.SP_CLINICAL_STATUS) TokenAndListParam clinicalStatus,
+ @OptionalParam(name = Condition.SP_ONSET_DATE) DateRangeParam onsetDate,
+ @OptionalParam(name = Condition.SP_ONSET_AGE) QuantityAndListParam onsetAge,
+ @OptionalParam(name = Condition.SP_ASSERTED_DATE) DateRangeParam recordedDate, @Sort SortSpec sort) {
+ return Bundle30_40
+ .convertBundle(FhirProviderUtils.convertSearchResultsToBundle(conditionService.searchConditions(patientParam,
+ subjectParam, code, clinicalStatus, onsetDate, onsetAge, recordedDate, sort)));
+ }
+}

api/src/main/java/org/openmrs/module/fhir2/providers/r3/DiagnosticReportFhirResourceProvider.java

@@ -0,0 +1,71 @@
+/*
+ * This Source Code Form is subject to the terms of the Mozilla Public License,
+ * v. 2.0. If a copy of the MPL was not distributed with this file, You can
+ * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
+ *
+ * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
+ * graphic logo is a trademark of OpenMRS Inc.
+ */
+package org.openmrs.module.fhir2.providers.r3;
+
+import javax.validation.constraints.NotNull;
+
+import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import lombok.AccessLevel;
+import lombok.Setter;
+import org.hl7.fhir.convertors.conv30_40.DiagnosticReport30_40;
+import org.hl7.fhir.dstu3.model.DiagnosticReport;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.openmrs.module.fhir2.api.FhirDiagnosticReportService;
+import org.openmrs.module.fhir2.providers.util.FhirProviderUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.stereotype.Component;
+
+@Component("diagnosticReportFhirR3ResourceProvider")
+@Qualifier("fhirR3Resources")
+@Setter(AccessLevel.PACKAGE)
+public class DiagnosticReportFhirResourceProvider implements IResourceProvider {
+
+ @Autowired
+ private FhirDiagnosticReportService diagnosticReportService;
+
+ @Override
+ public Class<? extends IBaseResource> getResourceType() {
+ return DiagnosticReport.class;
+ }
+
+ @Read
+ @SuppressWarnings("unused")
+ public DiagnosticReport getDiagnosticReportById(@IdParam @NotNull IdType id) {
+ org.hl7.fhir.r4.model.DiagnosticReport diagnosticReport = diagnosticReportService.get(id.getIdPart());
+ if (diagnosticReport == null) {
+ throw new ResourceNotFoundException("Could not find diagnosticReport with Id " + id.getIdPart());
+ }
+
+ return DiagnosticReport30_40.convertDiagnosticReport(diagnosticReport);
+ }
+
+ @Create
+ public MethodOutcome createDiagnosticReport(@ResourceParam DiagnosticReport diagnosticReport) {
+ return FhirProviderUtils.buildCreate(
+ diagnosticReportService.create(DiagnosticReport30_40.convertDiagnosticReport(diagnosticReport)));
+ }
+
+ @Update
+ public MethodOutcome updateDiagnosticReport(@IdParam IdType id, @ResourceParam DiagnosticReport diagnosticReport) {
+ String idPart = null;
+
+ if (id != null) {
+ idPart = id.getIdPart();
+ }
+
+ return FhirProviderUtils.buildUpdate(
+ diagnosticReportService.update(idPart, DiagnosticReport30_40.convertDiagnosticReport(diagnosticReport)));
+ }
+}

api/src/main/java/org/openmrs/module/fhir2/providers/r3/EncounterFhirResourceProvider.java

@@ -0,0 +1,83 @@
+/*
+ * This Source Code Form is subject to the terms of the Mozilla Public License,
+ * v. 2.0. If a copy of the MPL was not distributed with this file, You can
+ * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
+ *
+ * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
+ * graphic logo is a trademark of OpenMRS Inc.
+ */
+package org.openmrs.module.fhir2.providers.r3;
+
+import javax.validation.constraints.NotNull;
+
+import java.util.List;
+
+import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.param.ReferenceAndListParam;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import lombok.AccessLevel;
+import lombok.Setter;
+import org.hl7.fhir.convertors.conv30_40.Bundle30_40;
+import org.hl7.fhir.convertors.conv30_40.Encounter30_40;
+import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.openmrs.module.fhir2.api.FhirEncounterService;
+import org.openmrs.module.fhir2.providers.util.FhirProviderUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.stereotype.Component;
+
+@Component("encounterFhirR3ResourceProvider")
+@Qualifier("fhirR3Resources")
+@Setter(AccessLevel.PACKAGE)
+public class EncounterFhirResourceProvider implements IResourceProvider {
+
+ @Autowired
+ private FhirEncounterService encounterService;
+
+ @Override
+ public Class<? extends IBaseResource> getResourceType() {
+ return Encounter.class;
+ }
+
+ @Read
+ @SuppressWarnings("unused")
+ public Encounter getEncounterById(@IdParam @NotNull IdType id) {
+ org.hl7.fhir.r4.model.Encounter encounter = encounterService.get(id.getIdPart());
+ if (encounter == null) {
+ throw new ResourceNotFoundException("Could not find encounter with Id " + id.getIdPart());
+ }
+
+ return Encounter30_40.convertEncounter(encounter);
+ }
+
+ @History
+ @SuppressWarnings("unused")
+ public List<Resource> getEncounterHistoryById(@IdParam @NotNull IdType id) {
+ org.hl7.fhir.r4.model.Encounter encounter = encounterService.get(id.getIdPart());
+ if (encounter == null) {
+ throw new ResourceNotFoundException("Could not find encounter with Id " + id.getIdPart());
+ }
+ return Encounter30_40.convertEncounter(encounter).getContained();
+ }
+
+ @Search
+ public Bundle searchEncounter(@OptionalParam(name = Encounter.SP_DATE) DateRangeParam date,
+ @OptionalParam(name = Encounter.SP_LOCATION, chainWhitelist = { "", Location.SP_ADDRESS_CITY,
+ Location.SP_ADDRESS_STATE, Location.SP_ADDRESS_COUNTRY,
+ Location.SP_ADDRESS_POSTALCODE }, targetTypes = Location.class) ReferenceAndListParam location,
+ @OptionalParam(name = Encounter.SP_PARTICIPANT, chainWhitelist = { "", Practitioner.SP_IDENTIFIER,
+ Practitioner.SP_GIVEN, Practitioner.SP_FAMILY,
+ Practitioner.SP_NAME }, targetTypes = Practitioner.class) ReferenceAndListParam participantReference,
+ @OptionalParam(name = Encounter.SP_SUBJECT, chainWhitelist = { "", Patient.SP_IDENTIFIER, Patient.SP_GIVEN,
+ Patient.SP_FAMILY,
+ Patient.SP_NAME }, targetTypes = Patient.class) ReferenceAndListParam subjectReference) {
+ return Bundle30_40.convertBundle(FhirProviderUtils.convertSearchResultsToBundle(
+ encounterService.searchForEncounters(date, location, participantReference, subjectReference)));
+
+ }
+
+}