WIP_FM2-428: Add support for Batch Bundles

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

@@ -93,9 +93,11 @@ private FhirConstants() {
 	public static final String OPENMRS_FHIR_EXT_NON_CODED_CONDITION = OPENMRS_FHIR_EXT_PREFIX + "/non-coded-condition";
 
 	public static final String OPENMRS_FHIR_EXT_MEDICINE = OPENMRS_FHIR_EXT_PREFIX + "/medicine";
-	
+
 	public static final String OPENMRS_FHIR_EXT_TASK_IDENTIFIER = OPENMRS_FHIR_EXT_PREFIX + "/task/identifier";
-
+
+	public static final String OPENMRS_FHIR_EXT_BATCH_IDENTIFIER = OPENMRS_FHIR_EXT_PREFIX + "/bundle/identifier";
+
 	public static final String OPENMRS_FHIR_EXT_USER_IDENTIFIER = OPENMRS_FHIR_EXT_PREFIX + "/user/identifier";
 
 	public static final String OPENMRS_FHIR_EXT_PROVIDER_IDENTIFIER = OPENMRS_FHIR_EXT_PREFIX + "/provider/identifier";

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

@@ -0,0 +1,27 @@
+/*
+ * 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 ca.uhn.fhir.model.api.Include;
+import ca.uhn.fhir.rest.annotation.Sort;
+import ca.uhn.fhir.rest.api.SortSpec;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+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 org.hl7.fhir.r4.model.Bundle;
+
+import java.util.HashSet;
+
+public interface FhirBatchService extends FhirService<Bundle> {
+
+	IBundleProvider searchBatches(TokenAndListParam identifier, TokenAndListParam batchType);
+}

api/src/main/java/org/openmrs/module/fhir2/api/dao/FhirBatchDao.java

@@ -0,0 +1,25 @@
+/*
+ * 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;
+
+import org.openmrs.BaseOpenmrsData;
+import org.openmrs.annotation.Authorized;
+import org.openmrs.module.fhir2.api.search.param.SearchParameterMap;
+import org.openmrs.module.fhir2.model.FhirBatch;
+import org.openmrs.module.fhir2.model.FhirDiagnosticReport;
+import org.openmrs.util.PrivilegeConstants;
+
+import javax.annotation.Nonnull;
+import java.util.Collection;
+import java.util.List;
+
+public interface FhirBatchDao extends FhirDao<FhirBatch> {
+
+}

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

@@ -0,0 +1,43 @@
+/*
+ * 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 ca.uhn.fhir.rest.param.TokenAndListParam;
+import org.hibernate.Criteria;
+import org.openmrs.module.fhir2.FhirConstants;
+import org.openmrs.module.fhir2.api.dao.FhirBatchDao;
+import org.openmrs.module.fhir2.api.search.param.SearchParameterMap;
+import org.openmrs.module.fhir2.model.FhirBatch;
+
+import java.util.Optional;
+
+import static org.hibernate.criterion.Restrictions.eq;
+
+public class FhirBatchDaoImpl extends BaseFhirDao<FhirBatch> implements FhirBatchDao {
+
+
+	@Override
+	protected void setupSearchParams(Criteria criteria, SearchParameterMap theParams) {
+		theParams.getParameters().forEach(entry -> {
+			switch (entry.getKey()) {
+				case FhirConstants.OPENMRS_FHIR_EXT_BATCH_IDENTIFIER:
+					handleCommonSearchParameters(entry.getValue()).ifPresent(criteria::add);
+					break;
+				case FhirConstants.ENCOUNTER_TYPE_REFERENCE_SEARCH_HANDLER:
+					entry.getValue()
+							.forEach(param -> handleAndListParam((TokenAndListParam) param.getParam(),
+									t -> Optional.of(eq("bh.uuid", t.getValue()))));
+
+					break;
+			}
+		});
+	}
+
+}

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

@@ -0,0 +1,57 @@
+/*
+ * 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 ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.TokenAndListParam;
+import lombok.AccessLevel;
+import lombok.Getter;
+import lombok.Setter;
+import org.hl7.fhir.r4.model.Bundle;
+import org.openmrs.module.fhir2.FhirConstants;
+import org.openmrs.module.fhir2.api.FhirBatchService;
+import org.openmrs.module.fhir2.api.dao.FhirBatchDao;
+import org.openmrs.module.fhir2.api.search.SearchQuery;
+import org.openmrs.module.fhir2.api.search.SearchQueryInclude;
+import org.openmrs.module.fhir2.api.search.param.SearchParameterMap;
+import org.openmrs.module.fhir2.api.translators.BatchTranslator;
+import org.openmrs.module.fhir2.model.FhirBatch;
+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 FhirBatchServiceImpl extends BaseFhirService<Bundle, FhirBatch> implements FhirBatchService {
+
+	@Autowired
+	private FhirBatchDao dao;
+
+	@Autowired
+	private SearchQueryInclude<Bundle> searchQueryInclude;
+
+	@Autowired
+	private BatchTranslator translator;
+
+	@Autowired
+	private SearchQuery<FhirBatch, Bundle, FhirBatchDao, BatchTranslator, SearchQueryInclude<Bundle>> searchQuery;
+
+
+	@Override
+	public IBundleProvider searchBatches(TokenAndListParam identifier, TokenAndListParam batchType) {
+		SearchParameterMap theParams = new SearchParameterMap()
+				.addParameter(FhirConstants.OPENMRS_FHIR_EXT_BATCH_IDENTIFIER, identifier)
+				.addParameter(FhirConstants.ENCOUNTER_TYPE_REFERENCE_SEARCH_HANDLER, batchType);
+
+		return searchQuery.getQueryResults(theParams, dao, translator, searchQueryInclude);
+	}
+}

api/src/main/java/org/openmrs/module/fhir2/api/translators/BatchTranslator.java

@@ -0,0 +1,31 @@
+package org.openmrs.module.fhir2.api.translators;
+
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.DiagnosticReport;
+import org.openmrs.Order;
+import org.openmrs.module.fhir2.api.translators.ToFhirTranslator;
+import org.openmrs.module.fhir2.model.FhirBatch;
+import org.openmrs.module.fhir2.model.FhirDiagnosticReport;
+
+import javax.annotation.Nonnull;
+
+public interface BatchTranslator extends OpenmrsFhirUpdatableTranslator<FhirBatch, Bundle> {
+
+	/**
+	 * Maps a {@link Order} to a {@link Bundle}
+	 *
+	 * @param fhirBatch the FhirBatch object to translate
+	 * @return the corresponding FHIR Bundle
+	 */
+	@Override
+	Bundle toFhirResource(@Nonnull FhirBatch fhirBatch);
+
+	/**
+	 * Maps {@link Bundle} to {@link FhirBatch}
+	 *
+	 * @param bundle the FHIR batch to translate
+	 * @return the corresponding OpenMRS FhirBatch
+	 */
+	@Override
+	FhirBatch toOpenmrsType(@Nonnull Bundle bundle);
+}

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/BatchTranslatorImpl.java

@@ -0,0 +1,44 @@
+package org.openmrs.module.fhir2.api.translators.impl;
+
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.DiagnosticReport;
+import org.openmrs.Concept;
+import org.openmrs.Obs;
+import org.openmrs.module.fhir2.FhirConstants;
+import org.openmrs.module.fhir2.api.translators.BatchTranslator;
+import org.openmrs.module.fhir2.model.FhirBatch;
+import org.openmrs.module.fhir2.model.FhirDiagnosticReport;
+
+import javax.annotation.Nonnull;
+
+import static org.apache.commons.lang3.Validate.notNull;
+
+public class BatchTranslatorImpl implements BatchTranslator {
+
+	@Override
+	public Bundle toFhirResource(@Nonnull FhirBatch fhirBatch) {
+		notNull(fhirBatch, "The batch operation should not be null");
+
+		Bundle bundle = new Bundle();
+
+		bundle.setId(fhirBatch.getUuid());
+
+		if (fhirBatch.getDateChanged() != null) {
+			bundle.getMeta().setLastUpdated(fhirBatch.getDateChanged());
+		} else {
+			bundle.getMeta().setLastUpdated(fhirBatch.getDateCreated());
+		}
+
+		return bundle;
+	}
+
+	@Override
+	public FhirBatch toOpenmrsType(@Nonnull Bundle bundle) {
+		return toOpenmrsType(new FhirBatch(), bundle);
+	}
+
+	@Override
+	public FhirBatch toOpenmrsType(@Nonnull FhirBatch existingObject, @Nonnull Bundle resource) {
+		return null;
+	}
+}

api/src/main/java/org/openmrs/module/fhir2/model/FhirBatch.java

@@ -0,0 +1,40 @@
+/*
+ * 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.model;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import lombok.NoArgsConstructor;
+import org.openmrs.BaseOpenmrsData;
+import org.openmrs.BaseOpenmrsMetadata;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Table;
+
+@Data
+@NoArgsConstructor
+@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = false)
+@Entity
+@Table(name = "fhir_batch")
+public class FhirBatch extends BaseOpenmrsMetadata {
+
+	private static final long serialVersionUID = 1L;
+
+	@EqualsAndHashCode.Include
+	@Id
+	@GeneratedValue(strategy = GenerationType.AUTO)
+	@Column(name = "diagnostic_report_id")
+	private Integer id;
+
+}

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

@@ -0,0 +1,104 @@
+/*
+ * 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 static lombok.AccessLevel.PACKAGE;
+
+import ca.uhn.fhir.rest.annotation.Create;
+import ca.uhn.fhir.rest.annotation.Delete;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.annotation.OptionalParam;
+import ca.uhn.fhir.rest.annotation.Read;
+import ca.uhn.fhir.rest.annotation.ResourceParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.annotation.Update;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.TokenAndListParam;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import lombok.Setter;
+import org.hl7.fhir.convertors.conv30_40.Bundle30_40;
+import org.hl7.fhir.convertors.conv30_40.DiagnosticReport30_40;
+import org.hl7.fhir.convertors.conv30_40.Observation30_40;
+import org.hl7.fhir.dstu3.model.DiagnosticReport;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.Observation;
+import org.hl7.fhir.dstu3.model.OperationOutcome;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.openmrs.module.fhir2.api.FhirBatchService;
+import org.openmrs.module.fhir2.api.annotations.R3Provider;
+import org.openmrs.module.fhir2.api.search.SearchQueryBundleProviderR3Wrapper;
+import org.openmrs.module.fhir2.providers.util.FhirProviderUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import javax.annotation.Nonnull;
+
+@Component("batchFhirResourceProvider")
+@R3Provider
+@Setter(PACKAGE)
+public class BatchFhirResourceProvider implements IResourceProvider {
+
+	@Autowired
+	FhirBatchService batchService;
+
+	@Override
+	public Class<? extends IBaseResource> getResourceType() {return Bundle.class;}
+
+	@Read
+	@SuppressWarnings("unused")
+	public Bundle getBatchById(@IdParam @Nonnull IdType id) {
+		org.hl7.fhir.r4.model.Bundle batch = batchService.get(id.getIdPart());
+		if (batch == null) {
+			throw new ResourceNotFoundException("Could not find observation with Id " + id.getIdPart());
+		}
+
+		return Bundle30_40.convertBundle(batch);
+	}
+
+	@Create
+	@SuppressWarnings("unused")
+	public MethodOutcome createBatch(@ResourceParam Bundle bundle) {
+		return FhirProviderUtils.buildCreate(Bundle30_40.convertBundle(batchService.create(Bundle30_40.convertBundle(bundle))));
+	}
+
+	@Update
+	@SuppressWarnings("unused")
+	public MethodOutcome updateBatch(@IdParam IdType id, @ResourceParam Bundle bundle) {
+		String idPart = null;
+
+		if (id != null) {
+			idPart = id.getIdPart();
+		}
+
+		return FhirProviderUtils.buildUpdate(Bundle30_40.convertBundle(batchService.update(idPart, Bundle30_40.convertBundle(bundle))));
+	}
+
+	@Delete
+	@SuppressWarnings("unused")
+	public OperationOutcome deleteBatch(@IdParam @Nonnull IdType id) {
+		org.hl7.fhir.r4.model.Bundle batch = batchService.delete(id.getIdPart());
+		if (batch == null) {
+			throw new ResourceNotFoundException("Could not find medication to delete with id " + id.getIdPart());
+		}
+
+		return FhirProviderUtils.buildDelete(Bundle30_40.convertBundle(batch));
+	}
+
+	@Search
+	public IBundleProvider searchForBatch(
+			@OptionalParam(name = Bundle.SP_IDENTIFIER) TokenAndListParam identifier,
+			@OptionalParam(name = Bundle.SP_TYPE) TokenAndListParam batchType) {
+		return new SearchQueryBundleProviderR3Wrapper(batchService.searchBatches(identifier, batchType));
+	}
+}