Issue #2027 support prefer result=minimal for search requests

fhir-bulkdata-webapp/src/main/java/com/ibm/fhir/bulkdata/dto/ReadResultDTO.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2021
+ * (C) Copyright IBM Corp. 2021, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -8,6 +8,7 @@
 
 import java.io.Serializable;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 import com.ibm.fhir.model.resource.Resource;
@@ -26,23 +27,26 @@ public ReadResultDTO() {
         // No Operation
     }
 
-    public ReadResultDTO(List<Resource> resources) {
+    public ReadResultDTO(List<? extends Resource> resources) {
         this.resources.addAll(resources);
     }
 
     /**
      * @return the resources
      */
-    public List<Resource> getResources() {
-        return resources;
+    public List<? extends Resource> getResources() {
+        return Collections.unmodifiableList(this.resources);
     }
 
     /**
+     * Replace the contents of the internal resources list with the contents
+     * of the given resources list
      * @param resources
      *            the resources to set
      */
-    public void setResources(List<Resource> resources) {
-        this.resources = resources;
+    public void setResources(List<? extends Resource> resources) {
+        this.resources.clear();
+        this.resources.addAll(resources);
     }
 
     public void addResource(Resource resource) {

fhir-bulkdata-webapp/src/main/java/com/ibm/fhir/bulkdata/export/patient/resource/PatientResourceHandler.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2021
+ * (C) Copyright IBM Corp. 2021, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -26,6 +26,7 @@
 import com.ibm.fhir.model.resource.Resource;
 import com.ibm.fhir.operation.bulkdata.model.type.BulkDataContext;
 import com.ibm.fhir.persistence.FHIRPersistence;
+import com.ibm.fhir.persistence.ResourceResult;
 import com.ibm.fhir.persistence.context.FHIRPersistenceContext;
 import com.ibm.fhir.persistence.context.FHIRPersistenceContextFactory;
 import com.ibm.fhir.search.SearchConstants;
@@ -128,8 +129,8 @@ public List<Resource> executeSearch(Set<String> patientIds) throws Exception {
                 FHIRPersistenceContext persistenceContext = FHIRPersistenceContextFactory.createPersistenceContext(null, searchContext);
 
                 Date startTime = new Date(System.currentTimeMillis());
-                List<Resource> resources = fhirPersistence.search(persistenceContext, resourceType).getResource();
-
+                List<ResourceResult<? extends Resource>> resourceResults = fhirPersistence.search(persistenceContext, resourceType).getResourceResults();
+                List<? extends Resource> resources = ResourceResult.toResourceList(resourceResults);
                 if (isDoDuplicationCheck) {
                     resources = resources.stream()
                             // the add returns false if the id already exists, which filters it out of the collection

fhir-bulkdata-webapp/src/main/java/com/ibm/fhir/bulkdata/export/system/resource/SystemExportResourceHandler.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2021
+ * (C) Copyright IBM Corp. 2021, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -35,7 +35,7 @@ public SystemExportResourceHandler() {
         // No Operation
     }
 
-    public void fillChunkData(String exportFormat, ExportTransientUserData chunkData, List<Resource> resources) throws Exception {
+    public void fillChunkData(String exportFormat, ExportTransientUserData chunkData, List<? extends Resource> resources) throws Exception {
         int resSubTotal = 0;
         if (chunkData == null) {
             String msg = "fillChunkDataBuffer: chunkData is null, this should never happen!";

fhir-bulkdata-webapp/src/main/java/com/ibm/fhir/bulkdata/export/writer/SparkParquetWriter.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2019, 2021
+ * (C) Copyright IBM Corp. 2019, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -82,7 +82,7 @@ public SparkParquetWriter(boolean useIAM, String cosEndpoint, String apiKeyOrAcc
      * @throws FHIRGeneratorException
      * @implnote If a cos URI is passed, the file will be created if needed. For a file URI
      */
-    public void writeParquet(List<Resource> resources, String outDirName)
+    public void writeParquet(List<? extends Resource> resources, String outDirName)
             throws FHIRGeneratorException {
         List<String> jsonResources = new ArrayList<>();
 

fhir-bulkdata-webapp/src/main/java/com/ibm/fhir/bulkdata/jbatch/export/patient/ChunkReader.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2019, 2021
+ * (C) Copyright IBM Corp. 2019, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -50,6 +50,7 @@
 import com.ibm.fhir.operation.bulkdata.model.type.BulkDataContext;
 import com.ibm.fhir.operation.bulkdata.model.type.OperationFields;
 import com.ibm.fhir.persistence.FHIRPersistence;
+import com.ibm.fhir.persistence.ResourceResult;
 import com.ibm.fhir.persistence.context.FHIRPersistenceContext;
 import com.ibm.fhir.persistence.context.FHIRPersistenceContextFactory;
 import com.ibm.fhir.persistence.helper.FHIRPersistenceHelper;
@@ -203,7 +204,8 @@ public Object readItem() throws Exception {
         try {
             FHIRPersistenceContext persistenceContext = FHIRPersistenceContextFactory.createPersistenceContext(null, searchContext);
             Date startTime = new Date(System.currentTimeMillis());
-            List<Resource> patientResources = fhirPersistence.search(persistenceContext, Patient.class).getResource();
+            List<ResourceResult<? extends Resource>> resourceResults = fhirPersistence.search(persistenceContext, Patient.class).getResourceResults();
+            List<? extends Resource> patientResources = ResourceResult.toResourceList(resourceResults);
             if (isDoDuplicationCheck) {
                 patientResources = patientResources.stream()
                         .filter(r -> loadedPatientIds.add(r.getId()))
@@ -248,7 +250,7 @@ public Object readItem() throws Exception {
                 if (!patientIds.isEmpty()) {
                     handler.register(chunkData, ctx, fhirPersistence, pageSize, resourceType, searchParametersForResoureTypes, ctx.getSource());
 
-                    List<Resource> resources = Patient.class.isAssignableFrom(resourceType) ?
+                    List<? extends Resource> resources = Patient.class.isAssignableFrom(resourceType) ?
                             patientResources : handler.executeSearch(patientIds);
                     if (FHIRMediaType.APPLICATION_PARQUET.equals(ctx.getFhirExportFormat())) {
                         dto.setResources(resources);

fhir-bulkdata-webapp/src/main/java/com/ibm/fhir/bulkdata/jbatch/export/system/ChunkReader.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2019, 2021
+ * (C) Copyright IBM Corp. 2019, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -48,6 +48,7 @@
 import com.ibm.fhir.operation.bulkdata.model.type.BulkDataContext;
 import com.ibm.fhir.operation.bulkdata.model.type.OperationFields;
 import com.ibm.fhir.persistence.FHIRPersistence;
+import com.ibm.fhir.persistence.ResourceResult;
 import com.ibm.fhir.persistence.context.FHIRPersistenceContext;
 import com.ibm.fhir.persistence.context.FHIRPersistenceContextFactory;
 import com.ibm.fhir.persistence.helper.FHIRPersistenceHelper;
@@ -211,7 +212,7 @@ public Object readItem() throws Exception {
         FHIRSearchContext searchContext = SearchUtil.parseQueryParameters(resourceType, queryParameters);
         searchContext.setPageSize(pageSize);
         searchContext.setPageNumber(pageNum);
-        List<Resource> resources = null;
+        List<? extends Resource> resources = null;
 
         ReadResultDTO dto = new ReadResultDTO();
 
@@ -223,7 +224,9 @@ public Object readItem() throws Exception {
         try {
             // Execute the search query to obtain the page of resources
             persistenceContext = FHIRPersistenceContextFactory.createPersistenceContext(null, searchContext);
-            resources = fhirPersistence.search(persistenceContext, resourceType).getResource();
+            List<ResourceResult<? extends Resource>> resourceResults = fhirPersistence.search(persistenceContext, resourceType).getResourceResults();
+            resources = ResourceResult.toResourceList(resourceResults);
+
             if (isDoDuplicationCheck) {
                 resources = resources.stream()
                         // the add returns false if the id already exists, which filters it out of the collection

fhir-bulkdata-webapp/src/main/java/com/ibm/fhir/bulkdata/provider/impl/S3Provider.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2021
+ * (C) Copyright IBM Corp. 2021, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -442,7 +442,7 @@ private void pushFhirJsonsToCos(InputStream in, int dataLength) throws Exception
         }
     }
 
-    private void pushFhirParquetToCos(List<Resource> resources) throws Exception {
+    private void pushFhirParquetToCos(List<? extends Resource> resources) throws Exception {
         if (chunkData == null) {
             logger.warning("pushFhirParquetToCos: chunkData is null, this should never happen!");
             throw new Exception("pushFhirParquetToCos: chunkData is null, this should never happen!");

fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/api/ResourceDAO.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2017, 2021
+ * (C) Copyright IBM Corp. 2017, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -111,11 +111,12 @@ List<Resource> search(String sqlSelect)
      * Searches for Resources that contain one of the passed ids.
      * @param resourceType - The type of the FHIR Resource
      * @param resourceIds - A List of resource ids.
+     * @param includeResourceData - fetch the resource DATA column
      * @return List<Resource> - A List of resources matching the the passed list of ids.
      * @throws FHIRPersistenceDataAccessException
      * @throws FHIRPersistenceDBConnectException
      */
-    List<Resource> searchByIds(String resourceType, List<Long> resourceIds) throws FHIRPersistenceDataAccessException, FHIRPersistenceDBConnectException;
+    List<Resource> searchByIds(String resourceType, List<Long> resourceIds, boolean includeResourceData) throws FHIRPersistenceDataAccessException, FHIRPersistenceDBConnectException;
 
     /**
      * Executes a count query based on the data contained in the passed {@link Select} statement, using its encapsulated search string and bind variables.

fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/ResourceDAOImpl.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2017, 2021
+ * (C) Copyright IBM Corp. 2017, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -127,6 +127,10 @@ public class ResourceDAOImpl extends FHIRDbDAOImpl implements ResourceDAO {
             "SELECT R.RESOURCE_ID, R.LOGICAL_RESOURCE_ID, R.VERSION_ID, R.LAST_UPDATED, R.IS_DELETED, R.DATA, LR.LOGICAL_ID, R.RESOURCE_PAYLOAD_KEY " +
                     "FROM %s_RESOURCES R, %s_LOGICAL_RESOURCES LR WHERE R.LOGICAL_RESOURCE_ID = LR.LOGICAL_RESOURCE_ID AND " +
                     "R.RESOURCE_ID IN ";
+    private static final String SQL_SEARCH_BY_IDS_NO_DATA =
+            "SELECT R.RESOURCE_ID, R.LOGICAL_RESOURCE_ID, R.VERSION_ID, R.LAST_UPDATED, R.IS_DELETED, CAST(NULL AS BLOB) AS DATA, LR.LOGICAL_ID, R.RESOURCE_PAYLOAD_KEY " +
+                    "FROM %s_RESOURCES R, %s_LOGICAL_RESOURCES LR WHERE R.LOGICAL_RESOURCE_ID = LR.LOGICAL_RESOURCE_ID AND " +
+                    "R.RESOURCE_ID IN ";
 
     private static final String SQL_ORDER_BY_IDS = "ORDER BY CASE R.RESOURCE_ID ";
 
@@ -658,7 +662,7 @@ public List<Resource> search(String sqlSelect) throws FHIRPersistenceDataAccessE
     }
 
     @Override
-    public List<Resource> searchByIds(String resourceType, List<Long> resourceIds)
+    public List<Resource> searchByIds(String resourceType, List<Long> resourceIds, boolean includeResourceData)
             throws FHIRPersistenceDataAccessException, FHIRPersistenceDBConnectException {
         final String METHODNAME = "searchByIds";
         log.entering(CLASSNAME, METHODNAME);
@@ -678,7 +682,11 @@ public List<Resource> searchByIds(String resourceType, List<Long> resourceIds)
         double dbCallDuration;
 
         try {
-            stmtString = getSearchByIdsSql(resourceType);
+            if (includeResourceData) {
+                stmtString = getSearchByIdsSql(resourceType);
+            } else {
+                stmtString = getSearchByIdsNoDataSql(resourceType);
+            }
             idQuery.append(stmtString);
             idQuery.append("(");
             // resourceIds should have a max length of 1000 (the max page size)
@@ -719,6 +727,10 @@ protected String getSearchByIdsSql(String resourceType) {
         return String.format(SQL_SEARCH_BY_IDS, resourceType, resourceType);
     }
 
+    protected String getSearchByIdsNoDataSql(String resourceType) {
+        return String.format(SQL_SEARCH_BY_IDS_NO_DATA, resourceType, resourceType);
+    }
+
     @Override
     public int searchCount(String sqlSelectCount) throws FHIRPersistenceDataAccessException, FHIRPersistenceDBConnectException {
         final String METHODNAME = "searchCount";

fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/domain/SearchQueryRenderer.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2021
+ * (C) Copyright IBM Corp. 2021, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -131,17 +131,21 @@ public class SearchQueryRenderer implements SearchQueryVisitor<QueryData> {
     // Enable use of legacy whole-system search parameters for the search request
     private final boolean legacyWholeSystemSearchParamsEnabled;
 
+    // Include DATA in the data fetch queries
+    private final boolean includeResourceData;
     /**
      * Public constructor
      * @param identityCache
      * @param rowOffset
      * @param rowsPerPage
+     * @param includeResourceData
      */
     public SearchQueryRenderer(JDBCIdentityCache identityCache,
-        int rowOffset, int rowsPerPage) {
+            int rowOffset, int rowsPerPage, boolean includeResourceData) {
         this.identityCache = identityCache;
         this.rowOffset = rowOffset;
         this.rowsPerPage = rowsPerPage;
+        this.includeResourceData = includeResourceData;
         this.legacyWholeSystemSearchParamsEnabled =
                 FHIRConfigHelper.getBooleanProperty(PROPERTY_SEARCH_ENABLE_LEGACY_WHOLE_SYSTEM_SEARCH_PARAMS, false);
     }
@@ -352,7 +356,7 @@ public QueryData joinResources(QueryData queryData, boolean includeResourceTypeI
         final String xxResources = resourceResources(queryData.getResourceType());
         final String lrAliasName = "LR";
         SelectAdapter select = Select.select("R.RESOURCE_ID", "R.LOGICAL_RESOURCE_ID", "R.VERSION_ID", "R.LAST_UPDATED",
-                "R.IS_DELETED", "R.DATA", "LR.LOGICAL_ID", "R.RESOURCE_PAYLOAD_KEY");
+                "R.IS_DELETED", getDataCol(), "LR.LOGICAL_ID", "R.RESOURCE_PAYLOAD_KEY");
 
         // Resource type id is used for whole-system-search cases where the query
         // can return resources of different types (e.g. both Patient and Observation)
@@ -401,7 +405,7 @@ public QueryData wrapInclude(QueryData query) {
         final String rAlias = "R";
         final String rTable = query.getResourceType() + "_RESOURCES";
         SelectAdapter select = Select.select("LR.RESOURCE_ID", "LR.LOGICAL_RESOURCE_ID", "LR.VERSION_ID",
-                "LR.LAST_UPDATED", "LR.IS_DELETED", "R.DATA", "LR.LOGICAL_ID", "R.RESOURCE_PAYLOAD_KEY");
+                "LR.LAST_UPDATED", "LR.IS_DELETED", getDataCol(), "LR.LOGICAL_ID", "R.RESOURCE_PAYLOAD_KEY");
         select.from(query.getQuery().build(), alias(lrAlias))
             .innerJoin(rTable, alias(rAlias), on(lrAlias, "RESOURCE_ID").eq(rAlias, "RESOURCE_ID"));
         return new QueryData(select, lrAlias, null, query.getResourceType(), 0);
@@ -2727,4 +2731,14 @@ private List<String> getValueAttributeNames(Type type) throws FHIRPersistenceExc
     private boolean isWholeSystemSearch(String resourceType) {
         return Resource.class.getSimpleName().equals(resourceType);
     }
+
+    /**
+     * Get the select column entry for the resource data column. If
+     * the includeResourceData flag is false, the column is replaced
+     * with a literal NULL.
+     * @return
+     */
+    private String getDataCol() {
+        return this.includeResourceData ? "R.DATA" : "CAST(NULL AS BLOB) AS DATA";
+    }
 }