TEST DO NOT MERGE

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Query.java

@@ -1,7 +1,10 @@
 package edu.harvard.dbmi.avillach.data.entity;
 
 import java.io.*;
+import java.nio.charset.StandardCharsets;
 import java.sql.Date;
+import java.util.Optional;
+import java.util.UUID;
 import java.util.zip.GZIPInputStream;
 import java.util.zip.GZIPOutputStream;
 
@@ -12,7 +15,6 @@
 @Entity(name = "query")
 public class Query extends BaseEntity {
 
-	//TODO may not need these two things
 	private Date startTime;
 
 	private Date readyTime;
@@ -80,18 +82,19 @@ public String getQuery() {
             return "";
         }
 
-		String outStr = "";
-		try (GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(this.query));
-	        BufferedReader bf = new BufferedReader(new InputStreamReader(gis, "UTF-8"));){
-
+		StringBuilder outStr = new StringBuilder();
+		try (
+			GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(this.query));
+	        BufferedReader bf = new BufferedReader(new InputStreamReader(gis, StandardCharsets.UTF_8))
+		){
 	        String line;
-	        while ((line=bf.readLine())!=null) {
-	          outStr += line;
+	        while ((line = bf.readLine()) != null) {
+	          outStr.append(line);
 	        }
 		} catch (IOException e) {
 			e.printStackTrace();
 		}
-        return outStr;
+        return outStr.toString();
 	}
 
 	public void setQuery(String queryStr) {
@@ -102,7 +105,7 @@ public void setQuery(String queryStr) {
 
 		try (ByteArrayOutputStream obj=new ByteArrayOutputStream();
 			GZIPOutputStream gzip = new GZIPOutputStream(obj);){
-			gzip.write(queryStr.getBytes("UTF-8"));
+			gzip.write(queryStr.getBytes(StandardCharsets.UTF_8));
 	        gzip.close();
 	        this.query = obj.toByteArray();
 		} catch (IOException e) {

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/BaseRepository.java

@@ -84,8 +84,8 @@ public T getById(K id){
 	 * @return
 	 */
 	public List<T> getByColumn(String columnName, Object value){
-	    CriteriaQuery query = query();
-		Root root = root(query);
+	    CriteriaQuery<T> query = query();
+		Root<T> root = root(query);
 		return getByColumns(query, root, eq(cb(),root,columnName,value));
 	}
 

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

@@ -30,6 +30,9 @@ public class PicsureQueryService {
 	public static final String QUERY_RESULT_METADATA_FIELD = "queryResultMetadata";
 	private static final String QUERY_JSON_FIELD = "queryJson";
 
+	private static final String COMMON_AREA_ID = "commonAreaId";
+
+
 	private final Logger logger = LoggerFactory.getLogger(PicsureQueryService.class);
 
 	private final static ObjectMapper mapper = new ObjectMapper();
@@ -62,7 +65,8 @@ public QueryStatus query(QueryRequest dataQueryRequest, HttpHeaders headers) {
 
 		QueryStatus results = resourceWebClient.query(resource.getResourceRSPath(), dataQueryRequest);
 
-		Query queryEntity = copyQuery(dataQueryRequest, resource, results);
+		String commonAreaId = dataQueryRequest.getResourceCredentials().get(COMMON_AREA_ID);
+		Query queryEntity = copyQuery(dataQueryRequest, resource, results, commonAreaId);
 		queryRepo.persist(queryEntity);
 
 		logger.debug("PicsureQueryService() persisted queryEntity with id: " + queryEntity.getUuid());
@@ -192,19 +196,12 @@ public Response querySync(QueryRequest queryRequest, HttpHeaders headers) {
 		Query queryEntity = new Query();
 		queryEntity.setResource(resource);
 		queryEntity.setStartTime(new Date(Calendar.getInstance().getTime().getTime()));
+		extractQueryJson(queryRequest)
+			.ifPresentOrElse(
+				queryEntity::setQuery,
+				() -> { throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); }
+			);
 
-
-		String queryJson = null;
-		if( queryRequest.getQuery() != null) {
-			try {
-				ObjectMapper mapper = new ObjectMapper();
-				queryJson = mapper.writeValueAsString( queryRequest);
-			} catch (JsonProcessingException e) {
-				throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST);
-			}
-		}
-
-		queryEntity.setQuery(queryJson);
 		queryRepo.persist(queryEntity);
 		queryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken());
 
@@ -233,7 +230,19 @@ public Response querySync(QueryRequest queryRequest, HttpHeaders headers) {
 		return syncResponse;
 	}
 
-    /**
+	private Optional<String> extractQueryJson(QueryRequest queryRequest) {
+		if( queryRequest.getQuery() != null) {
+			try {
+				ObjectMapper mapper = new ObjectMapper();
+				return Optional.of(mapper.writeValueAsString(queryRequest));
+			} catch (JsonProcessingException e) {
+				return Optional.empty();
+			}
+		}
+		return Optional.of("");
+	}
+
+	/**
      * @param queryId      The UUID of the query to get metadata about
      * @return a QueryStatus object containing the metadata stored about the given query
      */
@@ -280,17 +289,32 @@ public QueryStatus institutionalQuery(QueryRequest dataQueryRequest, HttpHeaders
 		Resource resource = verifyQueryRequest(dataQueryRequest, headers);
 		dataQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken());
 
+		// Start by persisting the basic query. We do this to generate the common area ID
+		Query initialQuery = new Query();
+		initialQuery.setResource(resource);
+		initialQuery.setStartTime(new Date(Calendar.getInstance().getTime().getTime()));
+		extractQueryJson(dataQueryRequest)
+			.ifPresentOrElse(
+				initialQuery::setQuery,
+				() -> { throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); }
+			);
+
+		queryRepo.persist(initialQuery);
+		dataQueryRequest.getResourceCredentials().put(COMMON_AREA_ID, initialQuery.getUuid().toString());
+
+
 		QueryStatus response = resourceWebClient.query(resource.getResourceRSPath(), dataQueryRequest);
-		Query queryEntity = copyQuery(dataQueryRequest, resource, response);
+		Query queryEntity = copyQuery(dataQueryRequest, resource, response, null);
+
 		queryRepo.persist(queryEntity);
 		// we don't want the user to see the common area ID for now, but this could be useful later
 		// for editing the query
-		response.getResultMetadata().put("commonAreaId", queryEntity.getUuid().toString());
+		response.getResultMetadata().put(COMMON_AREA_ID, queryEntity.getUuid().toString());
 
 		return response;
 	}
 
-	private Query copyQuery(QueryRequest dataQueryRequest, Resource resource, QueryStatus response) {
+	private Query copyQuery(QueryRequest dataQueryRequest, Resource resource, QueryStatus response, String commonId) {
 		Query queryEntity = new Query();
 		queryEntity.setResourceResultId(response.getResourceResultId());
 		queryEntity.setResource(resource);
@@ -307,6 +331,10 @@ private Query copyQuery(QueryRequest dataQueryRequest, Resource resource, QueryS
 			}
 		}
 
+		if (commonId != null && !commonId.isEmpty() && response.getResultMetadata() != null) {
+			response.getResultMetadata().put(COMMON_AREA_ID, commonId);
+		}
+
 		queryEntity.setQuery(queryJson);
 
 		if (response.getResultMetadata() != null) {