Migrate to new JSONObject/JSONArray (#208)

Author: bbimber

OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncController.java

@@ -22,8 +22,8 @@
 import org.apache.directory.api.ldap.model.exception.LdapOperationException;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
-import org.json.old.JSONArray;
-import org.json.old.JSONObject;
+import org.json.JSONArray;
+import org.json.JSONObject;
 import org.labkey.api.action.ApiResponse;
 import org.labkey.api.action.ApiSimpleResponse;
 import org.labkey.api.action.Marshal;
@@ -665,7 +665,7 @@ public ApiResponse execute(LdapForm form, BindException errors)
 
             if (form.getAllowedDn() != null && form.getAllowedDn().length() > 0)
             {
-                String allowed = StringUtils.join(form.getAllowedDn().toArray(), LdapSettings.DELIM);
+                String allowed = StringUtils.join(form.getAllowedDn().toList(), LdapSettings.DELIM);
                 props.put(LdapSettings.ALLOWED_DN_PROP, allowed);
             }
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceOutputFile.java

@@ -16,7 +16,7 @@
 package org.labkey.api.sequenceanalysis;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
-import org.json.old.JSONObject;
+import org.json.JSONObject;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/model/AnalysisModel.java

@@ -15,7 +15,7 @@
  */
 package org.labkey.api.sequenceanalysis.model;
 
-import org.json.old.JSONObject;
+import org.json.JSONObject;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.security.User;

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractAlignmentStepProvider.java

@@ -16,7 +16,7 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 import org.jetbrains.annotations.Nullable;
-import org.json.old.JSONObject;
+import org.json.JSONObject;
 
 import java.util.ArrayList;
 import java.util.Collection;

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractParameterizedOutputHandler.java

@@ -16,7 +16,7 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 import org.apache.commons.lang3.StringUtils;
-import org.json.old.JSONObject;
+import org.json.JSONObject;
 import org.labkey.api.data.Container;
 import org.labkey.api.module.Module;
 import org.labkey.api.pipeline.PipelineJobException;

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractPipelineStepProvider.java

@@ -16,12 +16,11 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 import org.jetbrains.annotations.Nullable;
-import org.json.old.JSONArray;
-import org.json.old.JSONObject;
+import org.json.JSONArray;
+import org.json.JSONObject;
 import org.labkey.api.view.template.ClientDependency;
 
 import java.lang.reflect.ParameterizedType;
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.LinkedHashSet;
@@ -40,8 +39,7 @@ abstract public class AbstractPipelineStepProvider<StepType extends PipelineStep
     private String _websiteURL;
     private String _description;
     private LinkedHashSet<String> _clientDependencyPaths;
-    private List<ToolParameterDescriptor> _parameters;
-    List<PipelineStepProvider> _prerequisites = new ArrayList<>();
+    private final List<ToolParameterDescriptor> _parameters;
 
     public AbstractPipelineStepProvider(String name, String label, @Nullable String toolName, String description, @Nullable List<ToolParameterDescriptor> parameters, @Nullable Collection<String> clientDependencyPaths, @Nullable String websiteURL)
     {
@@ -78,20 +76,6 @@ public String getDescription()
         return _description;
     }
 
-    @Override
-    public List<PipelineStepProvider> getPrerequisites()
-    {
-        return _prerequisites;
-    }
-
-    protected void addPrerequisites(PipelineStepProvider... providers)
-    {
-        for (PipelineStepProvider p : providers)
-        {
-            _prerequisites.add(p);
-        }
-    }
-
     @Override
     public Collection<ClientDependency> getClientDependencies()
     {
@@ -149,12 +133,7 @@ public JSONObject toJSON()
             parameters.put(td.toJSON());
         }
         json.put("parameters", parameters);
-        JSONArray prerequisites = new JSONArray();
-        for (PipelineStepProvider p : getPrerequisites())
-        {
-            //prerequisites.put(td.toJSON());
-        }
-        json.put("prerequisites", prerequisites);
+
         return json;
     }
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractVariantProcessingStepProvider.java

@@ -16,7 +16,7 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 import org.jetbrains.annotations.Nullable;
-import org.json.old.JSONObject;
+import org.json.JSONObject;
 
 import java.util.Collection;
 import java.util.List;

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/HasJobParams.java

@@ -1,6 +1,6 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
-import org.json.old.JSONObject;
+import org.json.JSONObject;
 
 import java.util.Map;
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineStepProvider.java

@@ -16,7 +16,7 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 
-import org.json.old.JSONObject;
+import org.json.JSONObject;
 import org.labkey.api.view.template.ClientDependency;
 
 import java.util.Collection;
@@ -62,11 +62,6 @@ public interface PipelineStepProvider<StepType extends PipelineStep>
      */
     public String getDescription();
 
-    /**
-     * @return A list of any steps that must run prior to this step
-     */
-    public List<PipelineStepProvider> getPrerequisites();
-
     /**
      * @return A list of any addition JS or CSS files required to display this UI on the client.
      */

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceOutputHandler.java

@@ -16,7 +16,7 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 import org.jetbrains.annotations.Nullable;
-import org.json.old.JSONObject;
+import org.json.JSONObject;
 import org.labkey.api.data.Container;
 import org.labkey.api.module.Module;
 import org.labkey.api.pipeline.PipeRoot;