Migrate to new JSONObject/JSONArray (#162)

Author: bbimber

GenotypeAssays/resources/assay/GenotypeAssay/queries/Batches.query.xml

@@ -11,7 +11,7 @@
                     <column columnName="Hypothesis">
                         <shownInInsertView>false</shownInInsertView>
                     </column>
-                    <column columnName="Comments">
+                    <column columnName="comments">
                         <shownInInsertView>false</shownInInsertView>
                     </column>
                     <column columnName="importMethod">

GenotypeAssays/resources/assay/GenotypeAssay/queries/Runs.query.xml

@@ -7,7 +7,7 @@
                     <column columnName="Name">
                         <columnTitle>Run Name</columnTitle>
                     </column>
-                    <column columnName="Comments">
+                    <column columnName="comments">
                         <columnTitle>Run Description</columnTitle>
                         <nullable>true</nullable>
                     </column>

GenotypeAssays/resources/assay/SnpAssay/queries/Batches.query.xml

@@ -11,7 +11,7 @@
                     <column columnName="Hypothesis">
                         <shownInInsertView>false</shownInInsertView>
                     </column>
-                    <column columnName="Comments">
+                    <column columnName="comments">
                         <shownInInsertView>false</shownInInsertView>
                     </column>
                     <column columnName="importMethod">

GenotypeAssays/resources/assay/SnpAssay/queries/Runs.query.xml

@@ -7,7 +7,7 @@
                     <column columnName="Name">
                         <columnTitle>Run Name</columnTitle>
                     </column>
-                    <column columnName="Comments">
+                    <column columnName="comments">
                         <columnTitle>Run Description</columnTitle>
                         <nullable>true</nullable>
                     </column>

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java

@@ -16,7 +16,7 @@
 
 package org.labkey.genotypeassays;
 
-import org.json.old.JSONArray;
+import org.json.JSONArray;
 import org.labkey.api.action.ApiResponse;
 import org.labkey.api.action.ApiSimpleResponse;
 import org.labkey.api.action.ConfirmAction;

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java

@@ -18,8 +18,8 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.json.old.JSONArray;
-import org.json.old.JSONObject;
+import org.json.JSONArray;
+import org.json.JSONObject;
 import org.labkey.api.assay.AssayProtocolSchema;
 import org.labkey.api.assay.AssayProvider;
 import org.labkey.api.assay.AssayService;
@@ -45,6 +45,7 @@
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
 import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.JsonUtil;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Pair;
 import org.labkey.api.view.ViewContext;
@@ -197,7 +198,7 @@ public Pair<List<Integer>, List<Integer>> cacheHaplotypes(final ViewContext ctx,
 
         Set<Integer> analysisIds = new HashSet<>();
         final Map<Integer, List<JSONObject>> haploMap = new HashMap<>();
-        for (JSONObject row : data.toJSONObjectArray())
+        for (JSONObject row : JsonUtil.toJSONObjectList(data))
         {
             Integer analysisId = row.getInt("analysisId");
             analysisIds.add(analysisId);

GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultGenotypeAssaysImportMethod.java

@@ -1,7 +1,7 @@
 package org.labkey.genotypeassays.assay;
 
+import org.apache.commons.lang3.StringUtils;
 import org.labkey.api.data.Container;
-import org.labkey.api.gwt.client.util.StringUtils;
 import org.labkey.api.laboratory.assay.AssayImportMethod;
 import org.labkey.api.laboratory.assay.AssayParser;
 import org.labkey.api.laboratory.assay.DefaultAssayImportMethod;
@@ -33,7 +33,7 @@ public AssayParser getFileParser(Container c, User u, int assayId)
         return new DefaultGenotypeAssayParser(this, c, u, assayId);
     }
 
-    public class DefaultGenotypeAssayParser extends DefaultAssayParser
+    public static class DefaultGenotypeAssayParser extends DefaultAssayParser
     {
         public DefaultGenotypeAssayParser(AssayImportMethod method, Container c, User u, int assayId)
         {

GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultSnpAssayImportMethod.java

@@ -1,6 +1,6 @@
 package org.labkey.genotypeassays.assay;
 
-import org.json.old.JSONObject;
+import org.json.JSONObject;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.laboratory.assay.DefaultAssayImportMethod;
 import org.labkey.api.view.ViewContext;

GenotypeAssays/src/org/labkey/genotypeassays/assay/GenotypeAssayDataProvider.java

@@ -1,6 +1,6 @@
 package org.labkey.genotypeassays.assay;
 
-import org.json.old.JSONObject;
+import org.json.JSONObject;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.laboratory.NavItem;

GenotypeAssays/src/org/labkey/genotypeassays/assay/SNPAssayDataProvider.java

@@ -1,6 +1,6 @@
 package org.labkey.genotypeassays.assay;
 
-import org.json.old.JSONObject;
+import org.json.JSONObject;
 import org.labkey.api.laboratory.assay.AbstractAssayDataProvider;
 import org.labkey.api.module.Module;
 import org.labkey.api.view.ViewContext;