From 306d6c5e5acccdd97c086f4868a1a9bb4cef26df Mon Sep 17 00:00:00 2001
From: Julie Sullivan <julie.sullivan@gmail.com>
Date: Mon, 24 Feb 2020 10:03:00 +0000
Subject: [PATCH] string map instead of object map #528

---
 .../core/api/queries/AbstractQuery.java       | 37 -------------------
 .../opencb/cellbase/core/GeneQueryTest.java   |  5 +--
 .../server/rest/GenericRestWSServer.java      |  6 +--
 .../server/rest/feature/GeneWSServer.java     |  3 +-
 4 files changed, 6 insertions(+), 45 deletions(-)

diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/api/queries/AbstractQuery.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/api/queries/AbstractQuery.java
index 6af5bef9a9..8b30c9457a 100644
--- a/cellbase-core/src/main/java/org/opencb/cellbase/core/api/queries/AbstractQuery.java
+++ b/cellbase-core/src/main/java/org/opencb/cellbase/core/api/queries/AbstractQuery.java
@@ -104,43 +104,6 @@ private Map<String, Class<?>> loadPropertiesMap() {
         return internalPropertiesMap;
     }
 
-//    @Deprecated
-//    public static <T> T of(Map<String, String> map, Class<T> clazz)
-//            throws NoSuchFieldException, IllegalAccessException, InstantiationException, InvocationTargetException {
-//        T query = clazz.newInstance();
-//        for (Map.Entry<String, String> entry : map.entrySet()) {
-//            String fieldName = entry.getKey();
-//            String value = entry.getValue();
-//            Field field = clazz.getField(fieldName);
-////            Method method = clazz.getMethod("set" + fieldName);
-//            if (fieldName.equals("region")) {
-////                method.invoke(Region.parseRegions()); ....
-//                List<Region> regions = Region.parseRegions(value);
-//                BeanUtils.setProperty(query, fieldName, regions);
-//            } else {
-//                switch (field.getType().toString()) {
-//                    case "Boolean":
-//                        Boolean bool = Boolean.parseBoolean(value);
-////                    method.invoke(bool);
-//                        BeanUtils.setProperty(query, fieldName, bool);
-//                        break;
-//                    case "Integer":
-//                        Integer intValue = Integer.parseInt(value);
-//                        BeanUtils.setProperty(query, fieldName, intValue);
-//                        break;
-//                    case "List":
-//                        List<String> valuesArray = Arrays.asList(value);
-//                        BeanUtils.setProperty(query, fieldName, valuesArray);
-//                        break;
-//                    default:
-//                        BeanUtils.setProperty(query, fieldName, value);
-//                        break;
-//                }
-//            }
-//        }
-//        return query;
-//    }
-
     /**
      * Checks if values for query are legal, e.g. >= 0 and <= MAX Checks the following parameters:
      *
diff --git a/cellbase-core/src/test/java/org/opencb/cellbase/core/GeneQueryTest.java b/cellbase-core/src/test/java/org/opencb/cellbase/core/GeneQueryTest.java
index ffb6a1918d..1a72001a9e 100644
--- a/cellbase-core/src/test/java/org/opencb/cellbase/core/GeneQueryTest.java
+++ b/cellbase-core/src/test/java/org/opencb/cellbase/core/GeneQueryTest.java
@@ -21,8 +21,7 @@
 import org.opencb.biodata.models.core.Region;
 import org.opencb.cellbase.core.api.queries.GeneQuery;
 
-import java.util.HashMap;
-import java.util.Map;
+import java.util.*;
 
 import static org.junit.Assert.*;
 
@@ -44,7 +43,6 @@ public void testQuery() {
         paramMap.put("annotationDrugsGene", "x,y");
         paramMap.put("xxx", "");
 
-//        geneQuery.updateParams(paramMap);
         geneQuery = new GeneQuery(paramMap);
         assertEquals("1", geneQuery.getIds().get(0));
 
@@ -114,4 +112,5 @@ public void testCount() {
         geneQuery.updateParams(paramMap);
         assertFalse(geneQuery.getCount());
     }
+
 }
\ No newline at end of file
diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java
index e7fbd9f0d6..56b76ce7cc 100755
--- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java
+++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java
@@ -70,7 +70,7 @@ public class GenericRestWSServer implements IWSServer {
     protected Query query;
     protected QueryOptions queryOptions;
     protected ObjectMap params;
-    protected Map<String, Object> uriParams;
+    protected Map<String, String> uriParams;
     protected UriInfo uriInfo;
     protected HttpServletRequest httpServletRequest;
     protected ObjectMapper jsonObjectMapper;
@@ -173,8 +173,8 @@ private void checkVersion() throws VersionException {
         }
     }
 
-    public Map<String, Object> convertMultiToMap(MultivaluedMap<String, String> m) {
-        Map<String, Object> map = new HashMap<String, Object>();
+    public Map<String, String> convertMultiToMap(MultivaluedMap<String, String> m) {
+        Map<String, String> map = new HashMap<String, String>();
         if (m == null) {
             return map;
         }
diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java
index cf6b2d2e9a..40b4833fce 100755
--- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java
+++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java
@@ -307,8 +307,7 @@ public Response getAggregationStats(@DefaultValue("") @QueryParam("fields")
                     required = false, defaultValue = "0", dataType = "java.util.List", paramType = "query")
     })
     public Response getAll() throws CellbaseException {
-        GeneQuery geneQuery = new GeneQuery();
-        geneQuery.updateParams(uriParams);
+        GeneQuery geneQuery = new GeneQuery(uriParams);
         CellBaseDataResult<Gene> queryResults = geneManager.search(geneQuery);
         return createOkResponse(queryResults);
     }