[ALS-5056] Create sumtype for QueryRequest

- Interface, implementations for general use, GIC

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRS.java

@@ -87,7 +87,7 @@ public Map<UUID,String> resources(@Context HttpHeaders headers){
 	@Consumes("*/*")
 	public PaginatedSearchResult<?> searchGenomicConceptValues(
 			@PathParam("resourceId") UUID resourceId,
-			QueryRequest searchQueryRequest,
+			GeneralQueryRequest searchQueryRequest,
 			@QueryParam("genomicConceptPath") String genomicConceptPath,
 			@QueryParam("query") String query,
 			@QueryParam("page") Integer page,
@@ -155,10 +155,11 @@ public QueryStatus query(
 
 		@Context SecurityContext context
 	) {
-		if (isInstitutionQuery == null || !isInstitutionQuery) {
+		if (dataQueryRequest instanceof GeneralQueryRequest) {
 			return queryService.query(dataQueryRequest, headers);
 		} else {
-			return queryService.institutionalQuery(dataQueryRequest, headers, context.getUserPrincipal().getName());
+			String email = context.getUserPrincipal().getName();
+			return queryService.institutionalQuery((GICQueryRequest) dataQueryRequest, headers, email);
 		}
 	}
 
@@ -187,7 +188,7 @@ public QueryStatus queryStatus(
 		UUID queryId,
 
 		@Parameter
-		QueryRequest credentialsQueryRequest,
+		GeneralQueryRequest credentialsQueryRequest,
 
 		@Context
 		HttpHeaders headers,

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/JWTFilter.java

@@ -8,7 +8,7 @@
 import edu.harvard.dbmi.avillach.data.entity.AuthUser;
 import edu.harvard.dbmi.avillach.data.repository.QueryRepository;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
-import edu.harvard.dbmi.avillach.domain.QueryRequest;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.service.ResourceWebClient;
 import edu.harvard.dbmi.avillach.util.exception.ApplicationException;
 import edu.harvard.dbmi.avillach.util.response.PICSUREResponse;
@@ -204,7 +204,7 @@ private AuthUser callTokenIntroEndpoint(ContainerRequestContext requestContext,
 						edu.harvard.dbmi.avillach.data.entity.Resource resource = resourceRepo.getById(resourceUUID);
 						//logger.info("resource obj: " + resource + "    path: " + resource.getResourceRSPath());
 						if (resource != null && resource.getResourceRSPath() != null){
-							QueryRequest queryRequest = new QueryRequest();
+							GeneralQueryRequest queryRequest = new GeneralQueryRequest();
 							queryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken());
 							queryRequest.setResourceUUID(resourceUUID);
 							queryRequest.setQuery(((Map)queryObject).get("query"));

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureInfoService.java

@@ -3,6 +3,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import edu.harvard.dbmi.avillach.data.entity.Resource;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.domain.QueryRequest;
 import edu.harvard.dbmi.avillach.domain.ResourceInfo;
 import edu.harvard.dbmi.avillach.util.Utilities;
@@ -46,7 +47,7 @@ public ResourceInfo info(UUID resourceId, QueryRequest credentialsQueryRequest,
 			throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH);
 		}
 		if (credentialsQueryRequest == null){
-			credentialsQueryRequest = new QueryRequest();
+			credentialsQueryRequest = new GeneralQueryRequest();
 		}
 		if (credentialsQueryRequest.getResourceCredentials() == null){
 			credentialsQueryRequest.setResourceCredentials(new HashMap<String, String>());

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryService.java

@@ -7,13 +7,14 @@
 import edu.harvard.dbmi.avillach.data.entity.Resource;
 import edu.harvard.dbmi.avillach.data.repository.QueryRepository;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
+import edu.harvard.dbmi.avillach.domain.GICQueryRequest;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.domain.QueryRequest;
 import edu.harvard.dbmi.avillach.domain.QueryStatus;
 import edu.harvard.dbmi.avillach.security.JWTFilter;
 import edu.harvard.dbmi.avillach.util.Utilities;
 import edu.harvard.dbmi.avillach.util.exception.ApplicationException;
 import edu.harvard.dbmi.avillach.util.exception.ProtocolException;
-import org.apache.commons.lang3.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -93,7 +94,7 @@ public QueryStatus query(QueryRequest dataQueryRequest, HttpHeaders headers) {
 	 * @return {@link QueryStatus}
 	 */
 	@Transactional
-	public QueryStatus queryStatus(UUID queryId, QueryRequest credentialsQueryRequest, HttpHeaders headers) {
+	public QueryStatus queryStatus(UUID queryId, GeneralQueryRequest credentialsQueryRequest, HttpHeaders headers) {
 		if (queryId == null){
 			throw new ProtocolException(ProtocolException.MISSING_QUERY_ID);
 		}
@@ -282,7 +283,7 @@ public QueryStatus queryMetadata(UUID queryId, HttpHeaders headers){
 	 *                         and resource specific query (could be a string or a json object)
 	 * @return {@link QueryStatus}
 	 */
-	public QueryStatus institutionalQuery(QueryRequest dataQueryRequest, HttpHeaders headers, String email) {
+	public QueryStatus institutionalQuery(GICQueryRequest dataQueryRequest, HttpHeaders headers, String email) {
 		String siteCode = siteParsingService.parseSiteOfOrigin(email).orElseThrow(() -> new RuntimeException("Bad email"));
 		dataQueryRequest.setInstitutionOfOrigin(siteCode);
 		Resource resource = verifyQueryRequest(dataQueryRequest, headers);
@@ -314,19 +315,16 @@ private Query copyQuery(QueryRequest dataQueryRequest, Resource resource, QueryS
 				throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST);
 			}
 		}
-
 		Map<String, Object> metaData = response.getResultMetadata();
 		metaData = metaData == null ? new HashMap<>() : metaData;
-		if (dataQueryRequest.getCommonAreaUUID() != null) {
-			metaData.put("commonAreaUUID", dataQueryRequest.getCommonAreaUUID());
-		}
 
-		if (!StringUtils.isEmpty(dataQueryRequest.getInstitutionOfOrigin())) {
-			metaData.put("site", dataQueryRequest.getInstitutionOfOrigin());
+		if (dataQueryRequest instanceof GICQueryRequest) {
+			GICQueryRequest gicRequest = (GICQueryRequest) dataQueryRequest;
+			metaData.put("commonAreaUUID", gicRequest.getCommonAreaUUID());
+			metaData.put("site", gicRequest.getInstitutionOfOrigin());
+			metaData.put("sharingStatus", DataSharingStatus.Unknown);
 		}
 
-		metaData.put("sharingStatus", DataSharingStatus.Unknown);
-
 		queryEntity.setQuery(queryJson);
 
 		if (!metaData.isEmpty()) {

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureSearchService.java

@@ -4,6 +4,7 @@
 import edu.harvard.dbmi.avillach.data.entity.Resource;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
 import edu.harvard.dbmi.avillach.domain.PaginatedSearchResult;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.domain.QueryRequest;
 import edu.harvard.dbmi.avillach.domain.SearchResults;
 import edu.harvard.dbmi.avillach.util.Utilities;
@@ -33,7 +34,7 @@ public class PicsureSearchService {
 	 * Executes a concept search against a target resource
 	 *
 	 * @param resourceId         - UUID of target resource
-	 * @param searchQueryRequest - {@link QueryRequest} containing resource specific credentials object
+	 * @param searchQueryRequest - {@link GeneralQueryRequest} containing resource specific credentials object
 	 *                           and resource specific query (could be a string or a json object)
 	 * @param headers
 	 * @return {@link SearchResults}
@@ -65,7 +66,7 @@ public SearchResults search(UUID resourceId, QueryRequest searchQueryRequest, Ht
 		return resourceWebClient.search(resource.getResourceRSPath(), searchQueryRequest);
 	}
 
-	public PaginatedSearchResult<?> searchGenomicConceptValues(UUID resourceId, QueryRequest queryRequest, String conceptPath, String query, Integer page, Integer size
+	public PaginatedSearchResult<?> searchGenomicConceptValues(UUID resourceId, GeneralQueryRequest queryRequest, String conceptPath, String query, Integer page, Integer size
 			, HttpHeaders headers) {
 		Resource resource = resourceRepo.getById(resourceId);
 		if (resource == null){

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SystemService.java

@@ -24,7 +24,7 @@
 import edu.harvard.dbmi.avillach.PicSureWarInit;
 import edu.harvard.dbmi.avillach.data.entity.Resource;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
-import edu.harvard.dbmi.avillach.domain.QueryRequest;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.domain.ResourceInfo;
 import edu.harvard.dbmi.avillach.util.exception.ApplicationException;
 
@@ -126,7 +126,7 @@ private boolean testPSAMAResponds() throws UnsupportedOperationException, IOExce
 
 	private boolean testResourcesRespond(List<Resource> resourcesToTest) {
 		for(Resource resource : resourcesToTest) {
-			ResourceInfo info = new ResourceWebClient().info(resource.getResourceRSPath(), new QueryRequest());
+			ResourceInfo info = new ResourceWebClient().info(resource.getResourceRSPath(), new GeneralQueryRequest());
 			if(info==null) {
 				return false;
 			}

pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureInfoServiceTest.java

@@ -2,7 +2,7 @@
 
 import edu.harvard.dbmi.avillach.data.entity.Resource;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
-import edu.harvard.dbmi.avillach.domain.QueryRequest;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.domain.ResourceInfo;
 import edu.harvard.dbmi.avillach.service.PicsureInfoService;
 import edu.harvard.dbmi.avillach.service.ResourceWebClient;
@@ -60,7 +60,7 @@ public void setUp() {
 
     @Test
     public void testInfoEndpoints() {
-        QueryRequest infoRequest = new QueryRequest();
+        GeneralQueryRequest infoRequest = new GeneralQueryRequest();
         Map<String, String> clientCredentials = new HashMap<String, String>();
         infoRequest.setResourceCredentials(clientCredentials);
 

pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureQueryServiceTest.java

@@ -12,7 +12,6 @@
 import java.nio.charset.StandardCharsets;
 import java.util.*;
 
-import javax.ws.rs.core.HttpHeaders;
 import javax.ws.rs.core.MultivaluedHashMap;
 import javax.ws.rs.core.MultivaluedMap;
 import javax.ws.rs.core.Response;
@@ -32,7 +31,7 @@
 import edu.harvard.dbmi.avillach.data.entity.Resource;
 import edu.harvard.dbmi.avillach.data.repository.QueryRepository;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
-import edu.harvard.dbmi.avillach.domain.QueryRequest;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.domain.QueryStatus;
 import edu.harvard.dbmi.avillach.service.PicsureQueryService;
 import edu.harvard.dbmi.avillach.service.ResourceWebClient;
@@ -111,7 +110,7 @@ public void testQueryEmptyRequest() {
 	@Test
 	public void testQueryMissingResourceId() {
 
-		QueryRequest dataQueryRequest = new QueryRequest();
+		GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest();
 		// At this level we don't check the credentials themselves, just that the map
 		// exists
 		Map<String, String> clientCredentials = new HashMap<String, String>();
@@ -134,7 +133,7 @@ public void testQueryMissingResourceId() {
 	@Test
 	public void testQueryInvalidResourceId() {
 
-		QueryRequest dataQueryRequest = new QueryRequest();
+		GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest();
 		// At this level we don't check the credentials themselves, just that the map
 		// exists
 		Map<String, String> clientCredentials = new HashMap<String, String>();
@@ -155,7 +154,7 @@ public void testQueryInvalidResourceId() {
 
 	@Test
 	public void testQueryValidRequest() {
-		QueryRequest dataQueryRequest = new QueryRequest();
+		GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest();
 		// At this level we don't check the credentials themselves, just that the map exists
 		Map<String, String> clientCredentials = new HashMap<String, String>();
 		dataQueryRequest.setResourceCredentials(clientCredentials);
@@ -184,7 +183,7 @@ public void testQueryValidRequest() {
 	@Test
 	public void testQueryStatusNoId() {
 
-		QueryRequest statusRequest = new QueryRequest();
+		GeneralQueryRequest statusRequest = new GeneralQueryRequest();
 		Map<String, String> clientCredentials = new HashMap<String, String>();
 		statusRequest.setResourceCredentials(clientCredentials);
 		try {
@@ -201,7 +200,7 @@ public void testQueryStatusNoId() {
 	@Test
 	public void testQueryStatusInvalidId() {
 
-		QueryRequest statusRequest = new QueryRequest();
+		GeneralQueryRequest statusRequest = new GeneralQueryRequest();
 		Map<String, String> clientCredentials = new HashMap<String, String>();
 		statusRequest.setResourceCredentials(clientCredentials);
 
@@ -220,7 +219,7 @@ public void testQueryStatusInvalidId() {
 	@Test
 	public void testQueryStatusValid() {
 
-		QueryRequest statusRequest = new QueryRequest();
+		GeneralQueryRequest statusRequest = new GeneralQueryRequest();
 		Map<String, String> clientCredentials = new HashMap<String, String>();
 		statusRequest.setResourceCredentials(clientCredentials);
 		// Setup a pre-existing query Entity
@@ -253,7 +252,7 @@ public void testQueryStatusValid() {
 	public void testQueryResultNoId() {
 
 
-		QueryRequest resultRequest = new QueryRequest();
+		GeneralQueryRequest resultRequest = new GeneralQueryRequest();
 		Map<String, String> clientCredentials = new HashMap<String, String>();
 		resultRequest.setResourceCredentials(clientCredentials);
 		try {
@@ -271,7 +270,7 @@ public void testQueryResultNoId() {
 	public void testQueryResultInvalidId() {
 
 
-		QueryRequest resultRequest = new QueryRequest();
+		GeneralQueryRequest resultRequest = new GeneralQueryRequest();
 		Map<String, String> clientCredentials = new HashMap<String, String>();
 		resultRequest.setResourceCredentials(clientCredentials);
 		try {
@@ -290,7 +289,7 @@ public void testQueryResultInvalidId() {
 	public void testQueryResultValid() {
 
 
-		QueryRequest resultRequest = new QueryRequest();
+		GeneralQueryRequest resultRequest = new GeneralQueryRequest();
 		Map<String, String> clientCredentials = new HashMap<String, String>();
 		resultRequest.setResourceCredentials(clientCredentials);	
 
@@ -331,7 +330,7 @@ public void testQuerySyncNoQuery() {
 	@Test
 	public void testQuerySyncNoResourceId() {
 
-		QueryRequest dataQueryRequest = new QueryRequest();
+		GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest();
 		// At this level we don't check the credentials themselves, just that the map
 		// exists
 		Map<String, String> clientCredentials = new HashMap<String, String>();
@@ -353,7 +352,7 @@ public void testQuerySyncNoResourceId() {
 	@Test
 	public void testQuerySyncInvalidResourceId() {
 
-		QueryRequest dataQueryRequest = new QueryRequest();
+		GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest();
 		// At this level we don't check the credentials themselves, just that the map
 		// exists
 		Map<String, String> clientCredentials = new HashMap<String, String>();
@@ -374,7 +373,7 @@ public void testQuerySyncInvalidResourceId() {
 	@Test
 	public void testQuerySyncValidNoResponseId() {
 
-		QueryRequest dataQueryRequest = new QueryRequest();
+		GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest();
 		// At this level we don't check the credentials themselves, just that the map
 		// exists
 		Map<String, String> clientCredentials = new HashMap<String, String>();
@@ -446,7 +445,7 @@ public void testShouldQueryMetadata() {
 	@Test
 	public void testQuerySyncValidWithResponseId() {
 
-		QueryRequest dataQueryRequest = new QueryRequest();
+		GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest();
 		// At this level we don't check the credentials themselves, just that the map
 		// exists
 		Map<String, String> clientCredentials = new HashMap<String, String>();

pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureSearchServiceTest.java

@@ -12,7 +12,7 @@
 import java.util.UUID;
 
 import edu.harvard.dbmi.avillach.data.entity.Resource;
-import edu.harvard.dbmi.avillach.domain.QueryRequest;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import org.junit.runner.RunWith;
 import org.mockito.ArgumentMatchers;
 import org.mockito.InjectMocks;
@@ -58,7 +58,7 @@ public void setUp() {
 
     @Test
     public void testSearch() {
-        QueryRequest searchQueryRequest = new QueryRequest();
+        GeneralQueryRequest searchQueryRequest = new GeneralQueryRequest();
         Map<String, String> clientCredentials = new HashMap<String, String>();
         clientCredentials.put("bearer key", "bearer token");
         searchQueryRequest.setResourceCredentials(clientCredentials);

pic-sure-api-wildfly/src/test/java/edu/harvard/dbmi/avillach/AggregateResourceIT.java

@@ -123,8 +123,8 @@ public void testQuery() throws IOException {
 
 
         //Create multiple queries and add them to a main query as a list
-        QueryRequest queryRequest1 = new QueryRequest();
-        QueryRequest queryRequest2 = new QueryRequest();
+        QueryRequest queryRequest1 = new GeneralQueryRequest();
+        QueryRequest queryRequest2 = new GeneralQueryRequest();
         Map<String, String> credentials = new HashMap<String, String>();
         queryRequest1.setResourceCredentials(credentials);
         queryRequest1.setQuery(queryString);
@@ -136,7 +136,7 @@ public void testQuery() throws IOException {
         queryList.add(queryRequest1);
         queryList.add(queryRequest2);
 
-        QueryRequest topQuery = new QueryRequest();
+        QueryRequest topQuery = new GeneralQueryRequest();
         topQuery.setQuery(queryList);
         topQuery.setResourceUUID(aggregateUUID);
 
@@ -234,7 +234,7 @@ public void testQueryStatus() throws IOException {
                         .withStatus(200)
                         .withBody(objectMapper.writeValueAsString(resourceResponse))));
 
-        QueryRequest request = new QueryRequest();
+        QueryRequest request = new GeneralQueryRequest();
         Map<String, String> credentials = new HashMap<String, String>();
         request.setResourceCredentials(credentials);
         String body = objectMapper.writeValueAsString(request);
@@ -309,12 +309,12 @@ public void testResult() throws IOException, InterruptedException {
                         .withStatus(200)
                         .withBody(objectMapper.writeValueAsString(resultResponse))));
 
-        QueryRequest resultRequest = new QueryRequest();
+        QueryRequest resultRequest = new GeneralQueryRequest();
 
         Map<String, String> credentials = new HashMap<String, String>();
         credentials.put(IRCTResourceRS.IRCT_BEARER_TOKEN_KEY, token);
 
-        QueryRequest request = new QueryRequest();
+        QueryRequest request = new GeneralQueryRequest();
         request.setResourceCredentials(credentials);
         String body = objectMapper.writeValueAsString(request);