Merge remote-tracking branch 'origin/master' into FM2-626

.github/workflows/main.yml

@@ -20,36 +20,36 @@ jobs:
  JAVA_VERSION: ${{ matrix.java-version }}
 
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  - name: Set up JDK
- uses: actions/setup-java@v3
+ uses: actions/setup-java@v4
  with:
  distribution: 'temurin'
  java-version: ${{ matrix.java-version }}
  - name: Build with Maven
  id: build_with_maven
  run: |
- mvn verify --batch-mode -P integration-test --file pom.xml
- - uses: actions/upload-artifact@v3
+ mvn clean verify --batch-mode -P integration-test --file pom.xml
+ - uses: actions/upload-artifact@v4
  with:
  name: build_artifact
- path: ${{ github.workspace }}/omod/target
+ path: ${{ github.workspace }}/omod/target/*.omod
  - name: Send data to Codecov
- uses: codecov/codecov-action@v1
+ uses: codecov/codecov-action@v4
  with:
  env_vars: PLATFORM, JAVA_VERSION
  test:
  name: Run e2e tests
  needs: build
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  - name: Set up JDK
- uses: actions/setup-java@v3
+ uses: actions/setup-java@v4
  with:
  distribution: 'temurin'
  java-version: 8
- - uses: actions/download-artifact@v3
+ - uses: actions/download-artifact@v4
  with:
  name: build_artifact
  path: ${{ github.workspace }}/omod/target

api-2.5/pom.xml

@@ -3,7 +3,7 @@
  <parent>
  <artifactId>fhir2</artifactId>
  <groupId>org.openmrs.module</groupId>
- <version>2.1.0-SNAPSHOT</version>
+ <version>2.3.0-SNAPSHOT</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
 

api-2.6/pom.xml

@@ -3,7 +3,7 @@
  <parent>
  <artifactId>fhir2</artifactId>
  <groupId>org.openmrs.module</groupId>
- <version>2.1.0-SNAPSHOT</version>
+ <version>2.3.0-SNAPSHOT</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
 

api/pom.xml

@@ -3,7 +3,7 @@
  <parent>
  <groupId>org.openmrs.module</groupId>
  <artifactId>fhir2</artifactId>
- <version>2.1.0-SNAPSHOT</version>
+ <version>2.3.0-SNAPSHOT</version>
  </parent>
 
  <artifactId>fhir2-api</artifactId>

api/src/main/java/org/openmrs/module/fhir2/FhirActivator.java

@@ -27,6 +27,7 @@
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import lombok.Getter;
 import lombok.extern.slf4j.Slf4j;
+import org.openmrs.api.context.Context;
 import org.openmrs.module.BaseModuleActivator;
 import org.openmrs.module.Module;
 import org.openmrs.module.ModuleException;
@@ -36,6 +37,7 @@
 import org.openmrs.module.fhir2.api.spi.ModuleLifecycleListener;
 import org.openmrs.module.fhir2.api.spi.ServiceClassLoader;
 import org.openmrs.module.fhir2.api.translators.FhirTranslator;
+import org.openmrs.module.fhir2.api.util.FhirGlobalPropertyHolder;
 import org.openmrs.module.fhir2.model.GroupMember;
 import org.springframework.beans.BeansException;
 import org.springframework.context.ApplicationContext;
@@ -53,6 +55,8 @@ public class FhirActivator extends BaseModuleActivator implements ApplicationCon
  @Getter
  private static ConfigurableApplicationContext applicationContext;
 
+ private static FhirGlobalPropertyHolder globalPropertyHolder = null;
+
  private final Map<String, Set<Class<?>>> services = new HashMap<>();
 
  private final List<ModuleLifecycleListener> lifecycleListeners = new ArrayList<>();
@@ -65,8 +69,6 @@ public void started() {
  throw new ModuleException("Cannot load FHIR2 module as the main application context is not available");
  }
 
- applicationContext.getBean("fhirR4", FhirContext.class).registerCustomType(GroupMember.class);
-
  loadModules();
  started = true;
  log.info("Started FHIR");
@@ -86,6 +88,13 @@ public void contextRefreshed() {
  return;
  }
 
+ if (globalPropertyHolder == null) {
+ globalPropertyHolder = new FhirGlobalPropertyHolder();
+ Context.getAdministrationService().addGlobalPropertyListener(globalPropertyHolder);
+ }
+
+ FhirGlobalPropertyHolder.reset();
+
  applicationContext.getBean("fhirR4", FhirContext.class).registerCustomType(GroupMember.class);
  loadModules();
 
@@ -95,13 +104,18 @@ public void contextRefreshed() {
  @Override
  public void willStop() {
  lifecycleListeners.forEach(ModuleLifecycleListener::willStop);
- unloadModules();
+
+ if (globalPropertyHolder != null) {
+ Context.getAdministrationService().removeGlobalPropertyListener(globalPropertyHolder);
+ }
  }
 
  @Override
  public void stopped() {
  lifecycleListeners.forEach(ModuleLifecycleListener::stopped);
+ unloadModules();
 
+ globalPropertyHolder = null;
  started = false;
  log.info("Shutdown FHIR");
  }
@@ -117,7 +131,7 @@ public void removeModuleLifecycleLister(@Nonnull ModuleLifecycleListener lifecyc
  }
 
  @Override
- public void setApplicationContext(ApplicationContext applicationContext) throws BeansException {
+ public void setApplicationContext(@Nonnull ApplicationContext applicationContext) throws BeansException {
  if (applicationContext instanceof ConfigurableApplicationContext) {
  FhirActivator.applicationContext = (ConfigurableApplicationContext) applicationContext;
  }

api/src/main/java/org/openmrs/module/fhir2/FhirConstants.java

@@ -269,12 +269,16 @@ private FhirConstants() {
 
  public static final String STATUS_SEARCH_HANDLER = "status.search.handler";
 
+ public static final String TASK_CODE_SEARCH_HANDLER = "task.code.search.handler";
+
  public static final String FULFILLER_STATUS_SEARCH_HANDLER = "fullfillerStatus.search.handler";
 
  public static final String BASED_ON_REFERENCE_SEARCH_HANDLER = "based.on.reference.search.handler";
 
  public static final String OWNER_REFERENCE_SEARCH_HANDLER = "owner.reference.search.handler";
 
+ public static final String FOR_REFERENCE_SEARCH_HANDLER = "for.reference.search.handler";
+
  public static final String RESULT_SEARCH_HANDLER = "result.search.handler";
 
  public static final String COMMON_SEARCH_HANDLER = "common.search.handler";

api/src/main/java/org/openmrs/module/fhir2/api/FhirEpisodeOfCareService.java

@@ -0,0 +1,20 @@
+/*
+ * 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.api;
+
+import javax.annotation.Nonnull;
+
+import org.hl7.fhir.r4.model.EpisodeOfCare;
+
+public interface FhirEpisodeOfCareService extends FhirService<EpisodeOfCare> {
+
+ @Override
+ EpisodeOfCare get(@Nonnull String uuid);
+}

api/src/main/java/org/openmrs/module/fhir2/api/FhirGlobalPropertyService.java

@@ -17,7 +17,7 @@ public interface FhirGlobalPropertyService {
 
  String getGlobalProperty(String property) throws APIException;
 
- Integer getGlobalProperty(String property, Integer defaultValue);
+ int getGlobalPropertyAsInteger(String property, int defaultValue);
 
  String getGlobalProperty(String property, String defaultValue);
 

api/src/main/java/org/openmrs/module/fhir2/api/dao/FhirGlobalPropertyDao.java → api/src/main/java/org/openmrs/module/fhir2/api/dao/FhirEpisodeOfCareDao.java

@@ -9,21 +9,15 @@
  */
 package org.openmrs.module.fhir2.api.dao;
 
-import java.util.Map;
+import javax.annotation.Nonnull;
 
-import org.openmrs.GlobalProperty;
+import org.openmrs.PatientProgram;
 import org.openmrs.annotation.Authorized;
-import org.openmrs.api.APIException;
 import org.openmrs.util.PrivilegeConstants;
 
-public interface FhirGlobalPropertyDao {
+public interface FhirEpisodeOfCareDao extends FhirDao<PatientProgram> {
 
- @Authorized(PrivilegeConstants.GET_GLOBAL_PROPERTIES)
- String getGlobalProperty(String property) throws APIException;
-
- @Authorized(PrivilegeConstants.GET_GLOBAL_PROPERTIES)
- GlobalProperty getGlobalPropertyObject(String property);
-
- @Authorized(PrivilegeConstants.GET_GLOBAL_PROPERTIES)
- Map<String, String> getGlobalProperties(String... properties);
+ @Override
+ @Authorized(PrivilegeConstants.GET_PATIENT_PROGRAMS)
+ PatientProgram get(@Nonnull String uuid);
 }

api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/FhirEpisodeOfCareDaoImpl.java

@@ -0,0 +1,22 @@
+/*
+ * 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.api.dao.impl;
+
+import lombok.AccessLevel;
+import lombok.Setter;
+import org.openmrs.PatientProgram;
+import org.openmrs.module.fhir2.api.dao.FhirEpisodeOfCareDao;
+import org.springframework.stereotype.Component;
+
+@Component
+@Setter(AccessLevel.PACKAGE)
+public class FhirEpisodeOfCareDaoImpl extends BaseFhirDao<PatientProgram> implements FhirEpisodeOfCareDao {
+
+}

api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/FhirTaskDaoImpl.java

@@ -48,6 +48,13 @@ protected <U> void setupSearchParams(OpenmrsFhirCriteriaContext<FhirTask, U> cri
  entry.getValue().forEach(param -> handleReference(criteriaContext,
  (ReferenceAndListParam) param.getParam(), "ownerReference", "o"));
  break;
+ case FhirConstants.FOR_REFERENCE_SEARCH_HANDLER:
+ entry.getValue().forEach(
+ param -> handleReference(criteria, (ReferenceAndListParam) param.getParam(), "forReference", "f"));
+ break;
+ case FhirConstants.TASK_CODE_SEARCH_HANDLER:
+ entry.getValue().forEach(code -> handleTaskCodeConcept(criteria, (TokenAndListParam) code.getParam()));
+ break;
  case FhirConstants.STATUS_SEARCH_HANDLER:
  entry.getValue().forEach(param -> handleStatus(criteriaContext, (TokenAndListParam) param.getParam())
  .ifPresent(handler -> criteriaContext.addPredicate(handler).finalizeQuery()));
@@ -111,4 +118,14 @@ private <U> void handleReference(OpenmrsFhirCriteriaContext<FhirTask, U> criteri
  return Optional.empty();
  }).ifPresent(c -> criteriaContext.addPredicate(c).finalizeQuery());
  }
+
+ private void handleTaskCodeConcept(Criteria criteria, TokenAndListParam code) {
+ if (code != null) {
+ if (lacksAlias(criteria, "tc")) {
+ criteria.createAlias("taskCode", "tc");
+ }
+
+ handleCodeableConcept(criteria, code, "tc", "tcm", "tcrt").ifPresent(criteria::add);
+ }
+ }
 }

api/src/main/java/org/openmrs/module/fhir2/api/impl/FhirEpisodeOfCareServiceImpl.java

@@ -0,0 +1,35 @@
+/*
+ * 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.api.impl;
+
+import lombok.AccessLevel;
+import lombok.Getter;
+import lombok.Setter;
+import org.hl7.fhir.r4.model.EpisodeOfCare;
+import org.openmrs.PatientProgram;
+import org.openmrs.module.fhir2.api.FhirEpisodeOfCareService;
+import org.openmrs.module.fhir2.api.dao.FhirEpisodeOfCareDao;
+import org.openmrs.module.fhir2.api.translators.EpisodeOfCareTranslator;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+import org.springframework.transaction.annotation.Transactional;
+
+@Component
+@Transactional
+@Setter(AccessLevel.PACKAGE)
+@Getter(AccessLevel.PROTECTED)
+public class FhirEpisodeOfCareServiceImpl extends BaseFhirService<EpisodeOfCare, PatientProgram> implements FhirEpisodeOfCareService {
+
+ @Autowired
+ private FhirEpisodeOfCareDao dao;
+
+ @Autowired
+ private EpisodeOfCareTranslator translator;
+}