diff --git a/README.md b/README.md
index 40c2dc02..182b921c 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,7 @@
 
 ### Docker
 
-You must install [Docker](https://www.docker.com/) and [docker-compose](https://docs.docker.com/compose/install/).
+You must install [Docker](https://www.docker.com/) and [docker-compose](https://docs.docker.com/compose/install/). 
 
 Clone the repository
 
diff --git a/docs/configuration.md b/docs/configuration.md
index d48b2dbf..99010d6e 100644
--- a/docs/configuration.md
+++ b/docs/configuration.md
@@ -82,3 +82,46 @@ execution =
         }
     }
 ```
+
+## Publisher
+
+The publisher section of the configuration file describes how the Wings system shares data, execution, and provenance. The following properties are available:
+
+```
+    publisher =
+    {
+        file-store=
+        {
+            url = "https://publisher.mint.isi.edu";
+            type = "FILE_SYSTEM";
+        }
+        triple-store = {
+            export-name = "exportTest";
+            export-url = "https://opmw.org/";
+            publish = https://endpoint.mint.isi.edu/provenance/data;
+            query = https://endpoint.mint.isi.edu/provenance/query;
+            domains-directory = /opt/wings/storage/default;
+        }
+    }
+```
+
+### File store
+
+The file store section of the configuration file describes how the Wings system shares data. The following properties are available:
+
+| Name                      | Description                       | Default Value |
+| ------------------------- | --------------------------------- | ------------- |
+| publisher.file-store.url  | URI where the files are published |               |
+| publisher.file-store.type | Type of file store (FILE_SYSTEM)  | FILE_SYSTEM   |
+
+### Triple store
+
+The triple store section of the configuration file describes how the Wings system shares execution and provenance. The following properties are available:
+
+| Name                                     | Description                            | Default Value                                  |
+| ---------------------------------------- | -------------------------------------- | ---------------------------------------------- |
+| publisher.triple-store.export-name       | Name of the export (exportTest)        | exportTest                                     |
+| publisher.triple-store.export-url        | URI where the files are published      | https://opmw.org/                              |
+| publisher.triple-store.publish           | URI where the provenance is published  | https://endpoint.mint.isi.edu/provenance/data  |
+| publisher.triple-store.query             | URI where the provenance is queried    | https://endpoint.mint.isi.edu/provenance/query |
+| publisher.triple-store.domains-directory | Directory where the domains are stored | /opt/wings/storage/default                     |
diff --git a/engines/oodt/adapter/src/main/java/edu/isi/wings/catalog/component/api/impl/oodt/ComponentCreationFM.java b/engines/oodt/adapter/src/main/java/edu/isi/wings/catalog/component/api/impl/oodt/ComponentCreationFM.java
index bcaae829..e8bd7734 100644
--- a/engines/oodt/adapter/src/main/java/edu/isi/wings/catalog/component/api/impl/oodt/ComponentCreationFM.java
+++ b/engines/oodt/adapter/src/main/java/edu/isi/wings/catalog/component/api/impl/oodt/ComponentCreationFM.java
@@ -68,10 +68,14 @@ public class ComponentCreationFM implements ComponentCreationAPI {
 
   OntFactory ontologyFactory;
 
-  private static HashMap<String, String> compHolders =
-    new HashMap<String, String>();
-  private static HashMap<String, Metadata> compMeta =
-    new HashMap<String, Metadata>();
+  private static HashMap<String, String> compHolders = new HashMap<
+    String,
+    String
+  >();
+  private static HashMap<String, Metadata> compMeta = new HashMap<
+    String,
+    Metadata
+  >();
 
   public ComponentCreationFM(Properties props) {
     this.fmurl = props.getProperty("oodt.fmurl");
@@ -102,8 +106,10 @@ public ComponentTree getComponentHierarchy(boolean details) {
     String rootid = this.absurl + "#Component";
     ComponentHolder rootholder = new ComponentHolder(rootid);
     ComponentTreeNode rootnode = new ComponentTreeNode(rootholder);
-    HashMap<String, ComponentTreeNode> tnmap =
-      new HashMap<String, ComponentTreeNode>();
+    HashMap<String, ComponentTreeNode> tnmap = new HashMap<
+      String,
+      ComponentTreeNode
+    >();
     HashMap<String, String> pmap = this.curatorApi.getParentTypeMap();
     try {
       for (ProductType ptype : this.fmclient.getProductTypes()) {
diff --git a/engines/oodt/adapter/src/main/java/edu/isi/wings/catalog/data/api/impl/oodt/DataCreationFM.java b/engines/oodt/adapter/src/main/java/edu/isi/wings/catalog/data/api/impl/oodt/DataCreationFM.java
index 712f3f65..30658317 100644
--- a/engines/oodt/adapter/src/main/java/edu/isi/wings/catalog/data/api/impl/oodt/DataCreationFM.java
+++ b/engines/oodt/adapter/src/main/java/edu/isi/wings/catalog/data/api/impl/oodt/DataCreationFM.java
@@ -59,8 +59,10 @@ public class DataCreationFM implements DataCreationAPI {
   String liburl;
   String onturl;
 
-  private static HashMap<String, String> prodTypes =
-    new HashMap<String, String>();
+  private static HashMap<String, String> prodTypes = new HashMap<
+    String,
+    String
+  >();
 
   public DataCreationFM(Properties props) {
     this.fmurl = props.getProperty("oodt.fmurl");
diff --git a/engines/oodt/adapter/src/main/java/edu/isi/wings/execution/engine/api/impl/oodt/OODTExecutionEngine.java b/engines/oodt/adapter/src/main/java/edu/isi/wings/execution/engine/api/impl/oodt/OODTExecutionEngine.java
index 5d558aee..e59427cf 100644
--- a/engines/oodt/adapter/src/main/java/edu/isi/wings/execution/engine/api/impl/oodt/OODTExecutionEngine.java
+++ b/engines/oodt/adapter/src/main/java/edu/isi/wings/execution/engine/api/impl/oodt/OODTExecutionEngine.java
@@ -242,8 +242,10 @@ public ExecutionMonitoringThread(
     public void run() {
       planexe.onStart(this.logger);
       try {
-        HashMap<String, RuntimeInfo.Status> jobstatus =
-          new HashMap<String, RuntimeInfo.Status>();
+        HashMap<String, RuntimeInfo.Status> jobstatus = new HashMap<
+          String,
+          RuntimeInfo.Status
+        >();
 
         int osleeptime = 1000;
         int maxsleeptime = 4 * osleeptime;
diff --git a/engines/oodt/adapter/src/main/java/edu/isi/wings/execution/engine/api/impl/oodt/OODTWorkflowAdapter.java b/engines/oodt/adapter/src/main/java/edu/isi/wings/execution/engine/api/impl/oodt/OODTWorkflowAdapter.java
index 080b5236..9158270a 100644
--- a/engines/oodt/adapter/src/main/java/edu/isi/wings/execution/engine/api/impl/oodt/OODTWorkflowAdapter.java
+++ b/engines/oodt/adapter/src/main/java/edu/isi/wings/execution/engine/api/impl/oodt/OODTWorkflowAdapter.java
@@ -80,8 +80,10 @@ public OODTWorkflowAdapter(
   public Workflow runWorkflow(RuntimePlan planexe, Metadata meta)
     throws Exception {
     // Get List of all Jobs
-    HashMap<String, WorkflowTask> tasksById =
-      new HashMap<String, WorkflowTask>();
+    HashMap<String, WorkflowTask> tasksById = new HashMap<
+      String,
+      WorkflowTask
+    >();
     HashMap<String, String> opProducers = new HashMap<String, String>();
     HashMap<String, String> taskJobs = new HashMap<String, String>();
     for (RuntimeStep stepexe : planexe.getQueue().getAllSteps()) {
@@ -117,8 +119,10 @@ public Workflow runWorkflow(RuntimePlan planexe, Metadata meta)
     }
 
     // Get Parent Child Relationship between jobs
-    HashMap<String, ArrayList<String>> parents =
-      new HashMap<String, ArrayList<String>>();
+    HashMap<String, ArrayList<String>> parents = new HashMap<
+      String,
+      ArrayList<String>
+    >();
     for (RuntimeStep stepexe : planexe.getQueue().getAllSteps()) {
       ExecutionStep step = stepexe.getStep();
       ArrayList<String> chparents = parents.get(stepexe.getName());
@@ -132,8 +136,10 @@ public Workflow runWorkflow(RuntimePlan planexe, Metadata meta)
     }
 
     // Arrange Jobs into Job Levels
-    TreeMap<Integer, ArrayList<String>> jobLevels =
-      new TreeMap<Integer, ArrayList<String>>();
+    TreeMap<Integer, ArrayList<String>> jobLevels = new TreeMap<
+      Integer,
+      ArrayList<String>
+    >();
     for (String jobid : tasksById.keySet()) {
       Integer lvl = new Integer(getJobLevel(jobid, 0, parents));
       ArrayList<String> lvljobs;
diff --git a/engines/oodt/adapter/src/main/java/edu/isi/wings/util/oodt/CurationServiceAPI.java b/engines/oodt/adapter/src/main/java/edu/isi/wings/util/oodt/CurationServiceAPI.java
index b4e92b0a..8f37d09d 100644
--- a/engines/oodt/adapter/src/main/java/edu/isi/wings/util/oodt/CurationServiceAPI.java
+++ b/engines/oodt/adapter/src/main/java/edu/isi/wings/util/oodt/CurationServiceAPI.java
@@ -49,10 +49,10 @@ private String query(String method, String op, Object... args) {
       String params = "policy=" + URLEncoder.encode(this.policy, "UTF-8");
       for (int i = 0; i < args.length; i += 2) {
         params +=
-          "&" +
-          args[i] +
-          "=" +
-          URLEncoder.encode(args[i + 1].toString(), "UTF-8");
+        "&" +
+        args[i] +
+        "=" +
+        URLEncoder.encode(args[i + 1].toString(), "UTF-8");
       }
 
       URL urlobj = new URL(url);
@@ -117,7 +117,7 @@ public boolean addElementsForProductType(
   ) {
     String elementIds = "";
     for (Element element : elementList) elementIds +=
-      (elementIds != "" ? "," : "") + element.getElementId();
+    (elementIds != "" ? "," : "") + element.getElementId();
     String result =
       this.query(
           "POST",
@@ -169,7 +169,7 @@ public boolean removeElementsForProductType(
   ) {
     String elementIds = "";
     for (Element element : elementList) elementIds +=
-      (elementIds != "" ? "," : "") + element.getElementId();
+    (elementIds != "" ? "," : "") + element.getElementId();
     String result =
       this.query(
           "DELETE",
diff --git a/engines/oodt/wmservices/src/main/java/org/apache/oodt/cas/wmservices/client/WmServicesClient.java b/engines/oodt/wmservices/src/main/java/org/apache/oodt/cas/wmservices/client/WmServicesClient.java
index 4f46b3e2..5a44cfc8 100644
--- a/engines/oodt/wmservices/src/main/java/org/apache/oodt/cas/wmservices/client/WmServicesClient.java
+++ b/engines/oodt/wmservices/src/main/java/org/apache/oodt/cas/wmservices/client/WmServicesClient.java
@@ -116,7 +116,7 @@ private String query(String method, String op, Object... args) {
       for (int i = 0; i < args.length; i += 2) {
         if (i > 0) params += "&";
         params +=
-          args[i] + "=" + URLEncoder.encode(args[i + 1].toString(), "UTF-8");
+        args[i] + "=" + URLEncoder.encode(args[i + 1].toString(), "UTF-8");
       }
       if ("GET".equals(method)) {
         URL urlobj = new URL(url + "?" + params);
diff --git a/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentCreationKB.java b/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentCreationKB.java
index e0d75d34..c9355384 100644
--- a/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentCreationKB.java
+++ b/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentCreationKB.java
@@ -306,9 +306,9 @@ protected boolean incrementComponentVersion(String cid, KBAPI writerkb) {
       KBObject compobj = kb.getIndividual(cid);
       KBObject versionProp = kb.getProperty(this.pcns + "hasVersion");
       KBObject versionVal = kb.getPropertyValue(compobj, versionProp);
-      int currentVersion = (Integer) (
-        versionVal.getValue() != null ? versionVal.getValue() : 0
-      );
+      int currentVersion = (Integer) (versionVal.getValue() != null
+          ? versionVal.getValue()
+          : 0);
 
       int newVersion = currentVersion + 1;
       KBObject cobj = writerkb.getResource(cid);
diff --git a/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentKB.java b/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentKB.java
index b2dfd20b..ee2d9ade 100644
--- a/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentKB.java
+++ b/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentKB.java
@@ -820,11 +820,9 @@ public Component getComponent(String cid, boolean details) {
   protected int getComponentVersion(KBObject compobj) {
     KBObject versionProp = kb.getProperty(this.pcns + "hasVersion");
     KBObject versionVal = kb.getPropertyValue(compobj, versionProp);
-    return (Integer) (
-      (versionVal != null && versionVal.getValue() != null)
+    return (Integer) ((versionVal != null && versionVal.getValue() != null)
         ? versionVal.getValue()
-        : 0
-    );
+        : 0);
   }
 
   protected ArrayList<KBObject> getComponentInputs(KBObject compobj) {
diff --git a/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentReasoningKB.java b/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentReasoningKB.java
index 59b53864..1b1be789 100644
--- a/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentReasoningKB.java
+++ b/planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentReasoningKB.java
@@ -53,14 +53,22 @@ public class ComponentReasoningKB
   private boolean useRules = true;
 
   private HashMap<String, Component> ccache = new HashMap<String, Component>();
-  private HashMap<String, KBRuleList> rulescache =
-    new HashMap<String, KBRuleList>();
-  private HashMap<String, ArrayList<String>> abscache =
-    new HashMap<String, ArrayList<String>>();
-  private HashMap<String, ArrayList<KBObject>> classcache =
-    new HashMap<String, ArrayList<KBObject>>();
-  private HashMap<String, ArrayList<KBTriple>> kbcache =
-    new HashMap<String, ArrayList<KBTriple>>();
+  private HashMap<String, KBRuleList> rulescache = new HashMap<
+    String,
+    KBRuleList
+  >();
+  private HashMap<String, ArrayList<String>> abscache = new HashMap<
+    String,
+    ArrayList<String>
+  >();
+  private HashMap<String, ArrayList<KBObject>> classcache = new HashMap<
+    String,
+    ArrayList<KBObject>
+  >();
+  private HashMap<String, ArrayList<KBTriple>> kbcache = new HashMap<
+    String,
+    ArrayList<KBTriple>
+  >();
 
   private ArrayList<KBTriple> metricTriples;
   private ArrayList<KBObject> metricProps;
@@ -897,8 +905,10 @@ public ArrayList<ComponentPacket> findOutputDataPredictedDescriptions(
           );
 
       // Keep a map of variable object to variable name
-      HashMap<Variable, String> variableNameMap =
-        new HashMap<Variable, String>();
+      HashMap<Variable, String> variableNameMap = new HashMap<
+        Variable,
+        String
+      >();
 
       for (String rolestr : sRoleMap.keySet()) {
         Variable var = sRoleMap.get(rolestr);
@@ -926,8 +936,10 @@ public ArrayList<ComponentPacket> findOutputDataPredictedDescriptions(
 
       // Get a mapping of ArgID's to arg for the Component
       // Also note which roles are inputs
-      HashMap<String, ComponentRole> argMaps =
-        new HashMap<String, ComponentRole>();
+      HashMap<String, ComponentRole> argMaps = new HashMap<
+        String,
+        ComponentRole
+      >();
       HashMap<String, Boolean> sInputRoles = new HashMap<String, Boolean>();
       for (ComponentRole role : comp.getInputs()) {
         argMaps.put(role.getRoleName(), role);
@@ -1199,8 +1211,9 @@ public ArrayList<ComponentPacket> findOutputDataPredictedDescriptions(
 
           // Marking all compatible inputs to be passed through to the output.
           // Note: If not all outputs have a matching input, then component is still run and not skipped
-          ArrayList<ComponentRole> matchingInputs =
-            new ArrayList<ComponentRole>();
+          ArrayList<ComponentRole> matchingInputs = new ArrayList<
+            ComponentRole
+          >();
           for (ComponentRole inrole : comp.getInputs()) {
             if (!inrole.isParam()) {
               if (checkTypeCompatibility(varclasses, inrole.getID())) {
@@ -1261,11 +1274,9 @@ public ArrayList<ComponentPacket> findOutputDataPredictedDescriptions(
       for (Variable var : sRoleMap.values()) {
         if (
           var.isParameterVariable() &&
-          (
-            noParamBindings.containsKey(var.getID()) ||
+          (noParamBindings.containsKey(var.getID()) ||
             var.getBinding() == null ||
-            var.getBinding().getValue() == null
-          )
+            var.getBinding().getValue() == null)
         ) {
           KBObject varobj = tkb.getResource(variableNameMap.get(var));
           KBObject origvarobj = tkb.getResource(var.getID());
diff --git a/planner/src/main/java/edu/isi/wings/catalog/component/classes/requirements/Dependency.java b/planner/src/main/java/edu/isi/wings/catalog/component/classes/requirements/Dependency.java
index 8be90be8..680e97d1 100644
--- a/planner/src/main/java/edu/isi/wings/catalog/component/classes/requirements/Dependency.java
+++ b/planner/src/main/java/edu/isi/wings/catalog/component/classes/requirements/Dependency.java
@@ -70,12 +70,12 @@ public boolean checkDependency(KBAPI api, KBObject obj) {
       if (
         this.operator == Operator.GREATER_THAN &&
         Double.parseDouble(obj.getValueAsString()) >
-        Double.parseDouble(this.desiredValue.toString())
+          Double.parseDouble(this.desiredValue.toString())
       ) return true;
       if (
         this.operator == Operator.LESS_THAN &&
         Double.parseDouble(obj.getValueAsString()) <
-        Double.parseDouble(this.desiredValue.toString())
+          Double.parseDouble(this.desiredValue.toString())
       ) return true;
     }
     return false;
diff --git a/planner/src/main/java/edu/isi/wings/catalog/data/api/impl/kb/DataCreationKB.java b/planner/src/main/java/edu/isi/wings/catalog/data/api/impl/kb/DataCreationKB.java
index c7665dce..f7722c56 100644
--- a/planner/src/main/java/edu/isi/wings/catalog/data/api/impl/kb/DataCreationKB.java
+++ b/planner/src/main/java/edu/isi/wings/catalog/data/api/impl/kb/DataCreationKB.java
@@ -137,8 +137,10 @@ public ArrayList<String> getAllDatatypeIds() {
 
   @Override
   public HashMap<String, ArrayList<String>> getAllDatatypeDatasets() {
-    HashMap<String, ArrayList<String>> typedata =
-      new HashMap<String, ArrayList<String>>();
+    HashMap<String, ArrayList<String>> typedata = new HashMap<
+      String,
+      ArrayList<String>
+    >();
     String query =
       "SELECT ?s ?type\n" +
       "WHERE {\n" +
diff --git a/planner/src/main/java/edu/isi/wings/catalog/data/classes/MetadataProperty.java b/planner/src/main/java/edu/isi/wings/catalog/data/classes/MetadataProperty.java
index 09d0f97e..0c7a216b 100644
--- a/planner/src/main/java/edu/isi/wings/catalog/data/classes/MetadataProperty.java
+++ b/planner/src/main/java/edu/isi/wings/catalog/data/classes/MetadataProperty.java
@@ -74,15 +74,15 @@ public void setRange(String id) {
   public String toString() {
     String str = "";
     str +=
-      "\n" +
-      getName() +
-      "(" +
-      type +
-      ")\nDomains:" +
-      domains +
-      "\nRange:" +
-      range +
-      "\n";
+    "\n" +
+    getName() +
+    "(" +
+    type +
+    ")\nDomains:" +
+    domains +
+    "\nRange:" +
+    range +
+    "\n";
     return str;
   }
 }
diff --git a/planner/src/main/java/edu/isi/wings/catalog/resource/api/impl/kb/ResourceKB.java b/planner/src/main/java/edu/isi/wings/catalog/resource/api/impl/kb/ResourceKB.java
index d1303902..b51802ea 100644
--- a/planner/src/main/java/edu/isi/wings/catalog/resource/api/impl/kb/ResourceKB.java
+++ b/planner/src/main/java/edu/isi/wings/catalog/resource/api/impl/kb/ResourceKB.java
@@ -45,8 +45,10 @@ public class ResourceKB extends TransactionsJena implements ResourceAPI {
   public String onturl, liburl;
   private String tdbRepository;
 
-  private static HashMap<String, Boolean> initializedLibrary =
-    new HashMap<String, Boolean>();
+  private static HashMap<String, Boolean> initializedLibrary = new HashMap<
+    String,
+    Boolean
+  >();
 
   private KBAPI ontkb, libkb;
 
@@ -398,8 +400,9 @@ public ArrayList<SoftwareEnvironment> getAllSoftwareEnvironment() {
     this.start_read();
     boolean batched = this.start_batch_operation();
 
-    ArrayList<SoftwareEnvironment> environment =
-      new ArrayList<SoftwareEnvironment>();
+    ArrayList<SoftwareEnvironment> environment = new ArrayList<
+      SoftwareEnvironment
+    >();
     for (KBObject swobj : this.getInstancesOfClass(
         this.cmap.get("SoftwareGroup"),
         this.libkb
@@ -703,8 +706,10 @@ public void setMachineWhitelist(ArrayList<String> whitelist) {
   }
 
   public void copyFrom(ResourceAPI rc, ComponentCreationAPI cc) {
-    HashMap<String, SoftwareVersion> sws =
-      new HashMap<String, SoftwareVersion>();
+    HashMap<String, SoftwareVersion> sws = new HashMap<
+      String,
+      SoftwareVersion
+    >();
 
     this.start_write();
     boolean batched = this.start_batch_operation();
diff --git a/planner/src/main/java/edu/isi/wings/catalog/resource/classes/Machine.java b/planner/src/main/java/edu/isi/wings/catalog/resource/classes/Machine.java
index ca333f0e..d5b7f953 100644
--- a/planner/src/main/java/edu/isi/wings/catalog/resource/classes/Machine.java
+++ b/planner/src/main/java/edu/isi/wings/catalog/resource/classes/Machine.java
@@ -226,14 +226,10 @@ public MachineDetails call() {
     details.setNumCores(Runtime.getRuntime().availableProcessors());
 
     details.setMaxMemory(
-      (
-        (com.sun.management.OperatingSystemMXBean) ManagementFactory.getOperatingSystemMXBean()
-      ).getTotalPhysicalMemorySize()
+      ((com.sun.management.OperatingSystemMXBean) ManagementFactory.getOperatingSystemMXBean()).getTotalPhysicalMemorySize()
     );
     details.setFreeMemory(
-      (
-        (com.sun.management.OperatingSystemMXBean) ManagementFactory.getOperatingSystemMXBean()
-      ).getFreePhysicalMemorySize()
+      ((com.sun.management.OperatingSystemMXBean) ManagementFactory.getOperatingSystemMXBean()).getFreePhysicalMemorySize()
     );
     File[] roots = File.listRoots();
     for (File root : roots) {
diff --git a/planner/src/main/java/edu/isi/wings/common/CollectionsHelper.java b/planner/src/main/java/edu/isi/wings/common/CollectionsHelper.java
index 72f753c8..f8cff51f 100644
--- a/planner/src/main/java/edu/isi/wings/common/CollectionsHelper.java
+++ b/planner/src/main/java/edu/isi/wings/common/CollectionsHelper.java
@@ -12,16 +12,18 @@ public class CollectionsHelper {
    *
    * @return the combined list of variable object bindings
    */
-  public static ArrayList<VariableBindingsList> combineVariableDataObjectMappings(
-    VariableBindingsListSet listset
-  ) {
-    ArrayList<VariableBindingsList> combinedList =
-      new ArrayList<VariableBindingsList>();
+  public static ArrayList<
+    VariableBindingsList
+  > combineVariableDataObjectMappings(VariableBindingsListSet listset) {
+    ArrayList<VariableBindingsList> combinedList = new ArrayList<
+      VariableBindingsList
+    >();
 
     for (ArrayList<VariableBindingsList> list : listset) {
       if (combinedList.isEmpty()) combinedList = list; else {
-        ArrayList<VariableBindingsList> templist =
-          new ArrayList<VariableBindingsList>();
+        ArrayList<VariableBindingsList> templist = new ArrayList<
+          VariableBindingsList
+        >();
         for (VariableBindingsList map1 : combinedList) {
           for (VariableBindingsList map2 : list) {
             VariableBindingsList cmap = new VariableBindingsList();
diff --git a/planner/src/main/java/edu/isi/wings/common/kb/PropertiesHelper.java b/planner/src/main/java/edu/isi/wings/common/kb/PropertiesHelper.java
index e017e7db..334ed6ea 100644
--- a/planner/src/main/java/edu/isi/wings/common/kb/PropertiesHelper.java
+++ b/planner/src/main/java/edu/isi/wings/common/kb/PropertiesHelper.java
@@ -39,8 +39,10 @@ public class PropertiesHelper {
   private static HashMap<String, String> pcnsmap = null;
   private static HashMap<String, String> dcnsmap = null;
 
-  private static HashMap<String, Logger> classLoggers =
-    new HashMap<String, Logger>();
+  private static HashMap<String, Logger> classLoggers = new HashMap<
+    String,
+    Logger
+  >();
 
   private static String ontdir, logdir, resdir, opdir;
 
diff --git a/planner/src/main/java/edu/isi/wings/execution/engine/classes/ExecutionQueue.java b/planner/src/main/java/edu/isi/wings/execution/engine/classes/ExecutionQueue.java
index cbef7c6d..ce0b1e0e 100644
--- a/planner/src/main/java/edu/isi/wings/execution/engine/classes/ExecutionQueue.java
+++ b/planner/src/main/java/edu/isi/wings/execution/engine/classes/ExecutionQueue.java
@@ -66,7 +66,7 @@ public ArrayList<RuntimeStep> getNextStepsToExecute() {
           if (
             parentStep != null &&
             parentStep.getRuntimeInfo().getStatus() !=
-            RuntimeInfo.Status.SUCCESS
+              RuntimeInfo.Status.SUCCESS
           ) ok = false;
         }
         if (ok) steps.add(step);
diff --git a/planner/src/main/java/edu/isi/wings/execution/tools/api/impl/kb/RunKB.java b/planner/src/main/java/edu/isi/wings/execution/tools/api/impl/kb/RunKB.java
index 4a5ad612..7ab26270 100644
--- a/planner/src/main/java/edu/isi/wings/execution/tools/api/impl/kb/RunKB.java
+++ b/planner/src/main/java/edu/isi/wings/execution/tools/api/impl/kb/RunKB.java
@@ -228,25 +228,19 @@ public int getNumberOfRuns(
       "?run exec:hasExecutionStatus ?status .\n" +
       "?run exec:hasTemplate ?template .\n" +
       "?run exec:hasStartTime ?start .\n" +
-      (
-        status != null
+      (status != null
           ? "?run exec:hasExecutionStatus '" + status + "') .\n"
-          : ""
-      ) +
-      (
-        starttime != null
+          : "") +
+      (starttime != null
           ? "FILTER(?start > '" + starttime + "'^^xsd:dateTime) .\n"
-          : ""
-      ) +
-      (
-        pattern != null
+          : "") +
+      (pattern != null
           ? "FILTER REGEX(str(?template), '" +
           newtplurl +
           ".*" +
           pattern +
           ".*') .\n"
-          : ""
-      ) +
+          : "") +
       "FILTER REGEX(str(?run), '" +
       newrunurl +
       "') .\n" +
@@ -289,25 +283,19 @@ public ArrayList<RuntimePlan> getRunListSimple(
       "?run exec:hasExecutionStatus ?status .\n" +
       "?run exec:hasTemplate ?template .\n" +
       "?run exec:hasStartTime ?start .\n" +
-      (
-        status != null
+      (status != null
           ? "?run exec:hasExecutionStatus '" + status + "') .\n"
-          : ""
-      ) +
-      (
-        starttime != null
+          : "") +
+      (starttime != null
           ? "FILTER(?start > '" + starttime + "'^^xsd:dateTime) .\n"
-          : ""
-      ) +
-      (
-        pattern != null
+          : "") +
+      (pattern != null
           ? "FILTER REGEX(str(?template), '" +
           newtplurl +
           ".*" +
           pattern +
           ".*') .\n"
-          : ""
-      ) +
+          : "") +
       "FILTER REGEX(str(?run), '" +
       newrunurl +
       "') .\n";
@@ -385,41 +373,40 @@ public ArrayList<RuntimePlan> getRunList(
 
     if (status == null || status.equals("SUCCESS")) {
       query +=
-        // Query for Successful runs
-        "{\n" +
-        " ?run exec:hasExecutionStatus 'SUCCESS' .\n" +
-        " ?run exec:hasEndTime ?end .\n" +
-        "}\n";
+      // Query for Successful runs
+      "{\n" +
+      " ?run exec:hasExecutionStatus 'SUCCESS' .\n" +
+      " ?run exec:hasEndTime ?end .\n" +
+      "}\n";
     }
     if (status == null || status.equals("FAILURE")) {
       if (status == null) query += "UNION\n";
       query +=
-        // Query for Failures
-        "{\n" +
-        " ?run exec:hasExecutionStatus 'FAILURE' .\n" +
-        " ?run exec:hasEndTime ?end .\n" +
-        // FIXME: Removing this as we could have failures without any steps
-        /*" ?run exec:hasStep ?step .\n" + 
+      // Query for Failures
+      "{\n" +
+      " ?run exec:hasExecutionStatus 'FAILURE' .\n" +
+      " ?run exec:hasEndTime ?end .\n" +
+      // FIXME: Removing this as we could have failures without any steps
+      /*" ?run exec:hasStep ?step .\n" + 
           (fasterQuery ? " ?step exec:hasExecutionStatus 'FAILURE' .\n": "") + 
           " ?step exec:hasExecutionStatus ?stepstatus .\n" +*/
-        "}\n";
+      "}\n";
     }
     if (status == null || status.equals("RUNNING")) {
       if (status == null) query += "UNION\n";
       query +=
-        // Query for Failures
-        "{\n" +
-        " ?run exec:hasExecutionStatus 'RUNNING' .\n" +
-        " ?run exec:hasStep ?step .\n" +
-        (fasterQuery ? " ?step exec:hasExecutionStatus 'RUNNING' .\n" : "") +
-        " ?step exec:hasExecutionStatus ?stepstatus .\n" +
-        "}\n";
+      // Query for Failures
+      "{\n" +
+      " ?run exec:hasExecutionStatus 'RUNNING' .\n" +
+      " ?run exec:hasStep ?step .\n" +
+      (fasterQuery ? " ?step exec:hasExecutionStatus 'RUNNING' .\n" : "") +
+      " ?step exec:hasExecutionStatus ?stepstatus .\n" +
+      "}\n";
     }
     query += "}\n";
 
     query +=
-      "GROUP BY ?run ?status ?template ?start ?end \n" +
-      "ORDER BY DESC(?start)";
+    "GROUP BY ?run ?status ?template ?start ?end \n" + "ORDER BY DESC(?start)";
 
     if (limit >= 0 && start >= 0) {
       query += " LIMIT " + limit + " OFFSET " + start;
@@ -582,10 +569,8 @@ private RuntimePlan getExecutionRun(String runid, boolean details) {
     RuntimeInfo.Status status = rplan.getRuntimeInfo().getStatus();
     if (
       details ||
-      (
-        status == RuntimeInfo.Status.FAILURE ||
-        status == RuntimeInfo.Status.RUNNING
-      )
+      (status == RuntimeInfo.Status.FAILURE ||
+        status == RuntimeInfo.Status.RUNNING)
     ) {
       try {
         KBAPI tkb = this.ontologyFactory.getKB(rplan.getURL(), OntSpec.PLAIN);
@@ -1042,8 +1027,10 @@ public RuntimePlan rePlan(RuntimePlan oldplanexe) {
         planexe.setPlan(newplan);
 
         // Hash steps from current queue
-        HashMap<String, RuntimeStep> stepMap =
-          new HashMap<String, RuntimeStep>();
+        HashMap<String, RuntimeStep> stepMap = new HashMap<
+          String,
+          RuntimeStep
+        >();
         for (RuntimeStep step : planexe.getQueue().getAllSteps()) stepMap.put(
           step.getID(),
           step
diff --git a/planner/src/main/java/edu/isi/wings/planner/api/impl/kb/WorkflowGenerationKB.java b/planner/src/main/java/edu/isi/wings/planner/api/impl/kb/WorkflowGenerationKB.java
index 840b85e7..2415e29e 100644
--- a/planner/src/main/java/edu/isi/wings/planner/api/impl/kb/WorkflowGenerationKB.java
+++ b/planner/src/main/java/edu/isi/wings/planner/api/impl/kb/WorkflowGenerationKB.java
@@ -208,8 +208,10 @@ public ArrayList<Template> specializeTemplates(Template template) {
     ArrayList<Template> processedTemplates = new ArrayList<Template>();
     // ArrayList<Template> rejectedTemplates = new ArrayList<Template>();
 
-    HashMap<Template, ArrayList<String>> done =
-      new HashMap<Template, ArrayList<String>>();
+    HashMap<Template, ArrayList<String>> done = new HashMap<
+      Template,
+      ArrayList<String>
+    >();
 
     if (template == null) return templates;
 
@@ -329,8 +331,9 @@ public ArrayList<Template> specializeTemplates(Template template) {
           sentMapsComponentDetails
         );
 
-        ArrayList<ComponentPacket> componentDetailsList =
-          new ArrayList<ComponentPacket>();
+        ArrayList<ComponentPacket> componentDetailsList = new ArrayList<
+          ComponentPacket
+        >();
         for (ComponentPacket cmr : allcmrs) {
           this.addExplanations(cmr.getExplanations());
           if (!cmr.getInvalidFlag()) componentDetailsList.add(cmr); else {
@@ -351,8 +354,9 @@ public ArrayList<Template> specializeTemplates(Template template) {
           break;
         } else {
           if (logger.isInfoEnabled()) {
-            ArrayList<ComponentVariable> components =
-              new ArrayList<ComponentVariable>();
+            ArrayList<ComponentVariable> components = new ArrayList<
+              ComponentVariable
+            >();
             for (ComponentPacket componentMapsAndRequirement : componentDetailsList) {
               components.add(componentMapsAndRequirement.getComponent());
             }
@@ -466,12 +470,18 @@ private ArrayList<VariableBindingsList> selectInputDataForVariables(
     ArrayList<String> inputVariableIds = new ArrayList<String>();
     ArrayList<String> nonCollectionIds = new ArrayList<String>();
 
-    HashMap<String, HashSet<String>> varUserBindings =
-      new HashMap<String, HashSet<String>>();
-    HashMap<String, ArrayList<String>> varEquality =
-      new HashMap<String, ArrayList<String>>();
-    HashMap<String, ArrayList<String>> varInequality =
-      new HashMap<String, ArrayList<String>>();
+    HashMap<String, HashSet<String>> varUserBindings = new HashMap<
+      String,
+      HashSet<String>
+    >();
+    HashMap<String, ArrayList<String>> varEquality = new HashMap<
+      String,
+      ArrayList<String>
+    >();
+    HashMap<String, ArrayList<String>> varInequality = new HashMap<
+      String,
+      ArrayList<String>
+    >();
 
     for (Variable inputVariable : inputVariables) {
       if (inputVariable.isDataVariable()) {
@@ -648,12 +658,18 @@ public VariableBindingsListSet selectInputDataObjects(
     );
 
     // Extract dependent variables
-    HashMap<String, HashSet<String>> varGroups =
-      new HashMap<String, HashSet<String>>();
-    HashMap<String, HashSet<String>> varDeps =
-      new HashMap<String, HashSet<String>>();
-    HashMap<String, HashSet<String>> depVars =
-      new HashMap<String, HashSet<String>>();
+    HashMap<String, HashSet<String>> varGroups = new HashMap<
+      String,
+      HashSet<String>
+    >();
+    HashMap<String, HashSet<String>> varDeps = new HashMap<
+      String,
+      HashSet<String>
+    >();
+    HashMap<String, HashSet<String>> depVars = new HashMap<
+      String,
+      HashSet<String>
+    >();
     ArrayList<String> inputVariableIds = new ArrayList<String>();
 
     for (Variable variable : specializedTemplate.getInputVariables()) {
@@ -759,8 +775,10 @@ public Template bindTemplate(
     Template specializedTemplate,
     VariableBindingsList bindings
   ) {
-    HashMap<String, ArrayList<String>> variableBindings =
-      new HashMap<String, ArrayList<String>>();
+    HashMap<String, ArrayList<String>> variableBindings = new HashMap<
+      String,
+      ArrayList<String>
+    >();
 
     Template t = specializedTemplate.createCopy();
     t.setID(UuidGen.generateURIUuid((URIEntity) t));
@@ -853,8 +871,10 @@ public Template bindTemplate(
   public void setDataMetricsForInputDataObjects(
     ArrayList<Template> partialCandidateInstances
   ) {
-    HashMap<String, Metrics> dataObjectNameToDataMetricsMap =
-      new HashMap<String, Metrics>();
+    HashMap<String, Metrics> dataObjectNameToDataMetricsMap = new HashMap<
+      String,
+      Metrics
+    >();
     LogEvent event = curLogEvent;
 
     for (Template partialCandidateInstance : partialCandidateInstances) {
@@ -888,8 +908,10 @@ public ArrayList<Template> configureTemplates(Template template) {
     ArrayList<Template> templates = new ArrayList<Template>();
     ArrayList<Template> processedTemplates = new ArrayList<Template>();
 
-    HashMap<Template, ArrayList<String>> done =
-      new HashMap<Template, ArrayList<String>>();
+    HashMap<Template, ArrayList<String>> done = new HashMap<
+      Template,
+      ArrayList<String>
+    >();
 
     Template t = template.createCopy();
     t.setID(UuidGen.generateURIUuid((URIEntity) t));
@@ -952,12 +974,18 @@ public ArrayList<Template> configureTemplates(Template template) {
               continue;
             }
 
-            HashMap<String, String> prospectiveIds =
-              new HashMap<String, String>();
-            HashMap<String, String> portVariableIds =
-              new HashMap<String, String>();
-            HashMap<String, String> opPortVariableIds =
-              new HashMap<String, String>();
+            HashMap<String, String> prospectiveIds = new HashMap<
+              String,
+              String
+            >();
+            HashMap<String, String> portVariableIds = new HashMap<
+              String,
+              String
+            >();
+            HashMap<String, String> opPortVariableIds = new HashMap<
+              String,
+              String
+            >();
 
             // Add all output links to queue
             // Set temporary output dataset id
@@ -1242,8 +1270,10 @@ public Template getInferredTemplate(Template template) {
         "INFO: --------- Getting an inferred template ---------"
       );
 
-    HashMap<Template, ArrayList<String>> done =
-      new HashMap<Template, ArrayList<String>>();
+    HashMap<Template, ArrayList<String>> done = new HashMap<
+      Template,
+      ArrayList<String>
+    >();
 
     Template currentTemplate = template.createCopy();
     currentTemplate.setID(UuidGen.generateURIUuid((URIEntity) template));
@@ -1532,8 +1562,10 @@ public ExecutionPlan getExecutionPlan(Template template) {
       HashMap<String, String> dparents = dtree.getParents();
 
       HashMap<Node, ExecutionStep> nodeMap = new HashMap<Node, ExecutionStep>();
-      HashMap<ExecutionStep, Node> sensorNodeMap =
-        new HashMap<ExecutionStep, Node>();
+      HashMap<ExecutionStep, Node> sensorNodeMap = new HashMap<
+        ExecutionStep,
+        Node
+      >();
 
       for (Node n : template.getNodes()) {
         // If this is an inactive node
@@ -1590,8 +1622,10 @@ public ExecutionPlan getExecutionPlan(Template template) {
                   bin.getLocation() + ExecutionFile.metaExtension
                 );
 
-                LinkedHashMap<Role, Variable> roleMap =
-                  new LinkedHashMap<Role, Variable>();
+                LinkedHashMap<Role, Variable> roleMap = new LinkedHashMap<
+                  Role,
+                  Variable
+                >();
                 ArrayList<ComponentRole> inroles = c.getInputs();
                 ArrayList<ComponentRole> outroles = c.getOutputs();
                 if (inroles.size() == 1 && outroles.size() == 1) {
@@ -1630,8 +1664,10 @@ public ExecutionPlan getExecutionPlan(Template template) {
           continue;
         }
 
-        LinkedHashMap<Role, Variable> roleMap =
-          new LinkedHashMap<Role, Variable>();
+        LinkedHashMap<Role, Variable> roleMap = new LinkedHashMap<
+          Role,
+          Variable
+        >();
         for (Link outputLink : template.getOutputLinks(n)) {
           Role or = outputLink.getOriginPort().getRole();
           Role r = new Role(or.getID());
@@ -1732,8 +1768,10 @@ private ExecutionStep getExecutionStep(
     code.setCodeDirectory(invocation.getComponentDirectory());
     step.setCodeBinding(code);
 
-    HashMap<String, ArrayList<Object>> argMaps =
-      new HashMap<String, ArrayList<Object>>();
+    HashMap<String, ArrayList<Object>> argMaps = new HashMap<
+      String,
+      ArrayList<Object>
+    >();
     for (ComponentInvocation.Argument arg : invocation.getArguments()) {
       ArrayList<Object> cur = argMaps.get(arg.getName());
       if (cur == null) cur = new ArrayList<Object>();
@@ -2352,12 +2390,16 @@ private ArrayList<VariableBindingsList> groupVariableDataObjectMappings(
     ArrayList<String> groupByVarIds,
     ArrayList<String> variableIds
   ) {
-    HashMap<String, VariableBindingsList> bindingsByGroupByVarIds =
-      new HashMap<String, VariableBindingsList>();
+    HashMap<String, VariableBindingsList> bindingsByGroupByVarIds = new HashMap<
+      String,
+      VariableBindingsList
+    >();
 
     for (VariableBindingsList mapping : listsOfVariableDataObjectMappings) {
-      HashMap<String, ArrayList<KBObject>> varBindings =
-        new HashMap<String, ArrayList<KBObject>>();
+      HashMap<String, ArrayList<KBObject>> varBindings = new HashMap<
+        String,
+        ArrayList<KBObject>
+      >();
       for (VariableBindings dvobinding : mapping) {
         KBObject dv = dvobinding.getDataVariable();
         ArrayList<KBObject> objs = new ArrayList<KBObject>(
@@ -2391,8 +2433,9 @@ private ArrayList<VariableBindingsList> groupVariableDataObjectMappings(
       }
       bindingsByGroupByVarIds.put(groupKey, om);
     }
-    ArrayList<VariableBindingsList> groupedList =
-      new ArrayList<VariableBindingsList>();
+    ArrayList<VariableBindingsList> groupedList = new ArrayList<
+      VariableBindingsList
+    >();
     for (VariableBindingsList vals : bindingsByGroupByVarIds.values()) {
       groupedList.add(vals);
     }
@@ -2414,8 +2457,9 @@ private ArrayList<VariableBindingsList> removeNonVariableMappings(
     ArrayList<VariableBindingsList> listsOfVariableDataObjectMappings,
     ArrayList<String> variableIds
   ) {
-    ArrayList<VariableBindingsList> newlist =
-      new ArrayList<VariableBindingsList>();
+    ArrayList<VariableBindingsList> newlist = new ArrayList<
+      VariableBindingsList
+    >();
 
     for (VariableBindingsList mapping : listsOfVariableDataObjectMappings) {
       VariableBindingsList newmap = new VariableBindingsList();
@@ -2447,8 +2491,9 @@ private ArrayList<VariableBindingsList> filterVariableDataObjectMappings(
     HashMap<String, ArrayList<String>> varEquality,
     HashMap<String, ArrayList<String>> varInequality
   ) {
-    ArrayList<VariableBindingsList> filteredList =
-      new ArrayList<VariableBindingsList>();
+    ArrayList<VariableBindingsList> filteredList = new ArrayList<
+      VariableBindingsList
+    >();
 
     for (VariableBindingsList mapping : fullList) {
       HashMap<String, String> varBindings = new HashMap<String, String>();
diff --git a/planner/src/main/java/edu/isi/wings/planner/cli/Wings.java b/planner/src/main/java/edu/isi/wings/planner/cli/Wings.java
index d901f5f5..bca287c2 100644
--- a/planner/src/main/java/edu/isi/wings/planner/cli/Wings.java
+++ b/planner/src/main/java/edu/isi/wings/planner/cli/Wings.java
@@ -309,8 +309,9 @@ public void writeDataSelections(
     ArrayList<Template> boundWorkflows,
     String file
   ) {
-    ArrayList<HashMap<String, String>> dataBindings =
-      new ArrayList<HashMap<String, String>>();
+    ArrayList<HashMap<String, String>> dataBindings = new ArrayList<
+      HashMap<String, String>
+    >();
     for (Template boundWorkflow : boundWorkflows) {
       HashMap<String, String> dataBinding = new HashMap<String, String>();
       for (Variable iv : boundWorkflow.getInputVariables()) {
@@ -387,10 +388,12 @@ public void writeParameterSelections(
     ArrayList<Template> configuredWorkflows,
     String file
   ) {
-    ArrayList<HashMap<String, String>> paramBindings =
-      new ArrayList<HashMap<String, String>>();
-    ArrayList<HashMap<String, Binding>> paramBindings_b =
-      new ArrayList<HashMap<String, Binding>>();
+    ArrayList<HashMap<String, String>> paramBindings = new ArrayList<
+      HashMap<String, String>
+    >();
+    ArrayList<HashMap<String, Binding>> paramBindings_b = new ArrayList<
+      HashMap<String, Binding>
+    >();
 
     for (Template configuredWorkflow : configuredWorkflows) {
       HashMap<String, Binding> paramBinding_b = new HashMap<String, Binding>();
@@ -410,8 +413,10 @@ public void writeParameterSelections(
         Binding b = paramBinding_b.get(varid);
         if (b.isSet()) {
           for (WingsSet s : b) {
-            HashMap<String, Binding> paramBinding_x =
-              new HashMap<String, Binding>(paramBinding_b);
+            HashMap<String, Binding> paramBinding_x = new HashMap<
+              String,
+              Binding
+            >(paramBinding_b);
             paramBinding_x.put(varid, (Binding) s);
             paramBindings_b.add(paramBinding_x);
           }
diff --git a/planner/src/main/java/edu/isi/wings/workflow/plan/api/impl/pplan/PPlan.java b/planner/src/main/java/edu/isi/wings/workflow/plan/api/impl/pplan/PPlan.java
index 0265560b..666f39b0 100644
--- a/planner/src/main/java/edu/isi/wings/workflow/plan/api/impl/pplan/PPlan.java
+++ b/planner/src/main/java/edu/isi/wings/workflow/plan/api/impl/pplan/PPlan.java
@@ -129,8 +129,10 @@ private void loadFromKB() throws Exception {
     for (KBObject pobj : kb.getInstancesOfClass(plancls, true)) {
       this.setID(pobj.getID());
     }
-    HashMap<String, ExecutionFile> varmaps =
-      new HashMap<String, ExecutionFile>();
+    HashMap<String, ExecutionFile> varmaps = new HashMap<
+      String,
+      ExecutionFile
+    >();
     for (KBObject vobj : kb.getInstancesOfClass(varcls, true)) {
       KBObject pobj = kb.getPropertyValue(vobj, isvarofplanprop);
       if (pobj.getID().equals(this.getID())) {
diff --git a/planner/src/main/java/edu/isi/wings/workflow/plan/api/impl/pplan/PPlanStep.java b/planner/src/main/java/edu/isi/wings/workflow/plan/api/impl/pplan/PPlanStep.java
index 1bc4e7df..e8999c6f 100644
--- a/planner/src/main/java/edu/isi/wings/workflow/plan/api/impl/pplan/PPlanStep.java
+++ b/planner/src/main/java/edu/isi/wings/workflow/plan/api/impl/pplan/PPlanStep.java
@@ -108,7 +108,7 @@ public String getInvocationArgumentString() {
         ) {
           ExecutionFile f = (ExecutionFile) val;
           if (f.getLocation() != null) str += f.getLocation(); else str +=
-            f.getBinding();
+          f.getBinding();
         }
         str += " ";
       }
diff --git a/planner/src/main/java/edu/isi/wings/workflow/template/api/impl/kb/TemplateCreationKB.java b/planner/src/main/java/edu/isi/wings/workflow/template/api/impl/kb/TemplateCreationKB.java
index 845c405f..238376c3 100644
--- a/planner/src/main/java/edu/isi/wings/workflow/template/api/impl/kb/TemplateCreationKB.java
+++ b/planner/src/main/java/edu/isi/wings/workflow/template/api/impl/kb/TemplateCreationKB.java
@@ -203,8 +203,10 @@ public Template createTemplate(String tplid) {
   public HashMap<String, ArrayList<String>> getTemplatesContainingComponents(
     String[] cids
   ) {
-    HashMap<String, ArrayList<String>> componentTemplates =
-      new HashMap<String, ArrayList<String>>();
+    HashMap<String, ArrayList<String>> componentTemplates = new HashMap<
+      String,
+      ArrayList<String>
+    >();
     ArrayList<String> templateIds = this.getTemplateList();
 
     String cidstr = "";
diff --git a/planner/src/main/java/edu/isi/wings/workflow/template/api/impl/kb/TemplateKB.java b/planner/src/main/java/edu/isi/wings/workflow/template/api/impl/kb/TemplateKB.java
index 7b12b3b1..302910b7 100644
--- a/planner/src/main/java/edu/isi/wings/workflow/template/api/impl/kb/TemplateKB.java
+++ b/planner/src/main/java/edu/isi/wings/workflow/template/api/impl/kb/TemplateKB.java
@@ -94,8 +94,10 @@ public class TemplateKB extends URIEntity implements Template, TransactionsAPI {
   private transient HashMap<String, KBObject> conceptObjMap;
   private transient ConstraintEngine constraintEngine;
 
-  private HashMap<String, Template> subtemplates =
-    new HashMap<String, Template>();
+  private HashMap<String, Template> subtemplates = new HashMap<
+    String,
+    Template
+  >();
 
   private transient Template createdFrom;
   private transient Template parent;
@@ -1543,10 +1545,12 @@ public String toString() {
 
     StringBuilder dataVariables = new StringBuilder();
     StringBuilder parameters = new StringBuilder();
-    ArrayList<Variable> parameterVariablesWithBindings =
-      new ArrayList<Variable>();
-    ArrayList<Variable> dataVariablesWithDataBindings =
-      new ArrayList<Variable>();
+    ArrayList<Variable> parameterVariablesWithBindings = new ArrayList<
+      Variable
+    >();
+    ArrayList<Variable> dataVariablesWithDataBindings = new ArrayList<
+      Variable
+    >();
     Variable[] inputVariables = this.getInputVariables();
     for (Variable inputVariable : inputVariables) {
       if (inputVariable.isDataVariable()) {
@@ -2452,8 +2456,8 @@ public void autoLayout() {
       if (n.getMachineIds() != null && n.getMachineIds().size() > 0) {
         ntext += "\\n[Run on ";
         if (n.getMachineIds().size() > 1) ntext +=
-          "1 of " + n.getMachineIds().size() + " machines]"; else ntext +=
-          n.getMachineIds().get(0).replaceAll(".*#", "") + "]";
+        "1 of " + n.getMachineIds().size() + " machines]"; else ntext +=
+        n.getMachineIds().get(0).replaceAll(".*#", "") + "]";
       }
       ArrayList<String> ips = new ArrayList<String>();
       ArrayList<String> ops = new ArrayList<String>();
@@ -2476,24 +2480,24 @@ public void autoLayout() {
       String vtext = v.getName();
       if (v.getBinding() != null) {
         vtext +=
-          " =\\n" +
-          v
-            .getBinding()
-            .toString()
-            .replaceAll("\"", Matcher.quoteReplacement("\\\""))
-            .replaceAll("\\s", "\\\\n");
+        " =\\n" +
+        v
+          .getBinding()
+          .toString()
+          .replaceAll("\"", Matcher.quoteReplacement("\\\""))
+          .replaceAll("\\s", "\\\\n");
       }
       int fsize = 13;
       dotstr +=
-        nl +
-        tab +
-        vid +
-        "[label=\"{{|<ip>|}|{" +
-        vtext +
-        "}|{|<op>|}}\", " +
-        "fontname=\"Tahoma normal\" fontsize=\"" +
-        fsize +
-        "\"];";
+      nl +
+      tab +
+      vid +
+      "[label=\"{{|<ip>|}|{" +
+      vtext +
+      "}|{|<op>|}}\", " +
+      "fontname=\"Tahoma normal\" fontsize=\"" +
+      fsize +
+      "\"];";
 
       varidmap.put(vid, v);
     }
diff --git a/planner/src/main/java/edu/isi/wings/workflow/template/classes/ConstraintProperty.java b/planner/src/main/java/edu/isi/wings/workflow/template/classes/ConstraintProperty.java
index 9347aba9..15b8d315 100644
--- a/planner/src/main/java/edu/isi/wings/workflow/template/classes/ConstraintProperty.java
+++ b/planner/src/main/java/edu/isi/wings/workflow/template/classes/ConstraintProperty.java
@@ -74,15 +74,15 @@ public void setRange(String id) {
   public String toString() {
     String str = "";
     str +=
-      "\n" +
-      getName() +
-      "(" +
-      type +
-      ")\nDomains:" +
-      domains +
-      "\nRange:" +
-      range +
-      "\n";
+    "\n" +
+    getName() +
+    "(" +
+    type +
+    ")\nDomains:" +
+    domains +
+    "\nRange:" +
+    range +
+    "\n";
     return str;
   }
 }
diff --git a/planner/src/main/java/edu/isi/wings/workflow/template/classes/Rules.java b/planner/src/main/java/edu/isi/wings/workflow/template/classes/Rules.java
index 2bcd9993..f57ce3bc 100644
--- a/planner/src/main/java/edu/isi/wings/workflow/template/classes/Rules.java
+++ b/planner/src/main/java/edu/isi/wings/workflow/template/classes/Rules.java
@@ -40,6 +40,6 @@ public String getRulesText() {
 
   public void addRules(Rules ruleset) {
     if (this.rules != null && ruleset.getRulesText() != null) this.rules +=
-      "\n" + ruleset.getRulesText();
+    "\n" + ruleset.getRulesText();
   }
 }
diff --git a/planner/src/main/java/edu/isi/wings/workflow/template/classes/sets/SetExpression.java b/planner/src/main/java/edu/isi/wings/workflow/template/classes/sets/SetExpression.java
index ae33ae27..a9bc76c2 100644
--- a/planner/src/main/java/edu/isi/wings/workflow/template/classes/sets/SetExpression.java
+++ b/planner/src/main/java/edu/isi/wings/workflow/template/classes/sets/SetExpression.java
@@ -91,27 +91,21 @@ public String toString() {
     int i = 0;
     String str = (op == SetOperator.SHIFT ? "Shift" : "");
     str +=
-      (
-        op == SetOperator.INCREASEDIM
-          ? " ["
-          : (op == SetOperator.REDUCEDIM ? "/" : " (")
-      );
+    (op == SetOperator.INCREASEDIM
+        ? " ["
+        : (op == SetOperator.REDUCEDIM ? "/" : " ("));
     for (SetExpression s : this) {
       if (i > 0) str +=
-        (
-          op == SetOperator.XPRODUCT
-            ? " x "
-            : (op == SetOperator.NWISE ? " || " : " ")
-        );
+      (op == SetOperator.XPRODUCT
+          ? " x "
+          : (op == SetOperator.NWISE ? " || " : " "));
       str += s.toString();
       i++;
     }
     str +=
-      (
-        op == SetOperator.INCREASEDIM
-          ? "]"
-          : (op == SetOperator.REDUCEDIM ? "/" : ")")
-      );
+    (op == SetOperator.INCREASEDIM
+        ? "]"
+        : (op == SetOperator.REDUCEDIM ? "/" : ")"));
     return str;
   }
 }
diff --git a/portal.properties b/portal.properties
index dace1762..6f0e3299 100644
--- a/portal.properties
+++ b/portal.properties
@@ -8,7 +8,7 @@
     server = http://localhost:8080;
     graphviz = /usr/bin/dot;
     light-reasoner = false;
-    ontology = 
+    ontology =
     {
         data = http://www.wings-workflows.org/ontology/data.owl;
         component = http://www.wings-workflows.org/ontology/component.owl;
@@ -16,16 +16,16 @@
         execution = http://www.wings-workflows.org/ontology/execution.owl;
     }
 
-    execution = 
+    execution =
     {
-        engine = 
+        engine =
         {
             name = Local;
             implementation = edu.isi.wings.execution.engine.api.impl.local.LocalExecutionEngine;
             type = BOTH;
         }
 
-        engine = 
+        engine =
         {
             name = Distributed;
             implementation = edu.isi.wings.execution.engine.api.impl.distributed.DistributedExecutionEngine;
@@ -35,17 +35,16 @@
 
     publisher =
     {
-        url = "https://publisher.mint.isi.edu";
-        name = "exportTest"
-        upload-server =
+        file-store=
         {
             url = "https://publisher.mint.isi.edu";
-            username = "user";
-            password = "password";
+            type = "FILE_SYSTEM";
         }
         triple-store = {
-            publish = http://ontosoft.isi.edu:3030/provenance/data;
-            query = http://ontosoft.isi.edu:3030/provenance/sparql;
+            export-name = "exportTest";
+            export-url = "https://opmw.org/";
+            publish = https://endpoint.mint.isi.edu/provenance/data;
+            query = https://endpoint.mint.isi.edu/provenance/query;
             domains-directory = /opt/wings/storage/default;
         }
     }
diff --git a/portal/pom.xml b/portal/pom.xml
index 03550b14..d84198a7 100644
--- a/portal/pom.xml
+++ b/portal/pom.xml
@@ -17,7 +17,7 @@
 
 	<properties>
 		<!-- rewrite.version>2.0.12.Final</rewrite.version -->
-		<wings-opmm.version>1.2.4</wings-opmm.version>
+		<wings-opmm.version>2.0.1</wings-opmm.version>
 		<servlet-api.version>2.5</servlet-api.version>
 		<httpclient.version>4.5.2</httpclient.version>
 		<jersey.version>2.27</jersey.version>
diff --git a/portal/src/main/java/edu/isi/wings/portal/classes/config/ExecutionConfig.java b/portal/src/main/java/edu/isi/wings/portal/classes/config/ExecutionConfig.java
index e93af233..839626f1 100644
--- a/portal/src/main/java/edu/isi/wings/portal/classes/config/ExecutionConfig.java
+++ b/portal/src/main/java/edu/isi/wings/portal/classes/config/ExecutionConfig.java
@@ -1,6 +1,5 @@
 package edu.isi.wings.portal.classes.config;
 
-import edu.isi.wings.execution.engine.api.impl.distributed.DistributedExecutionEngine;
 import edu.isi.wings.execution.engine.api.impl.local.LocalExecutionEngine;
 import java.util.HashMap;
 import java.util.Iterator;
@@ -17,18 +16,16 @@ public class ExecutionConfig {
   public ExecutionConfig(PropertyListConfiguration serverConfig) {
     this.engines = new HashMap<String, ExecutionEngineConfig>();
     if (serverConfig.containsKey("execution.engine")) {
-      List<HierarchicalConfiguration> engineNodes =
-        serverConfig.configurationsAt("execution.engine");
+      List<HierarchicalConfiguration> engineNodes = serverConfig.configurationsAt("execution.engine");
       for (HierarchicalConfiguration engineNode : engineNodes) {
         ExecutionEngineConfig engine = this.getExeEngine(engineNode);
         this.engines.put(engine.getName(), engine);
       }
     } else {
       ExecutionEngineConfig defaultLocal = new ExecutionEngineConfig(
-        "Local",
-        LocalExecutionEngine.class.getCanonicalName(),
-        ExecutionEngineConfig.Type.BOTH
-      );
+          "Local",
+          LocalExecutionEngine.class.getCanonicalName(),
+          ExecutionEngineConfig.Type.BOTH);
 
       this.engines.put(defaultLocal.getName(), defaultLocal);
     }
@@ -39,8 +36,7 @@ private ExecutionEngineConfig getExeEngine(HierarchicalConfiguration node) {
     String name = node.getString("name");
     String impl = node.getString("implementation");
     ExecutionEngineConfig.Type type = ExecutionEngineConfig.Type.valueOf(
-      node.getString("type")
-    );
+        node.getString("type"));
     ExecutionEngineConfig engine = new ExecutionEngineConfig(name, impl, type);
     for (Iterator it = node.getKeys("properties"); it.hasNext();) {
       String key = (String) it.next();
@@ -52,21 +48,22 @@ private ExecutionEngineConfig getExeEngine(HierarchicalConfiguration node) {
 
   public void addDefaultEngineConfig(PropertyListConfiguration config) {
     // loop engines and add them to config
-    for (Entry<String, ExecutionEngineConfig> entryEngine : this.engines.entrySet()) {
+    for (Entry<
+      String,
+      ExecutionEngineConfig
+    > entryEngine : this.engines.entrySet()) {
       ExecutionEngineConfig engine = entryEngine.getValue();
       config.addProperty("execution.engine(-1).name", engine.getName());
       config.addProperty(
-        "execution.engine.implementation",
-        engine.getImplementation()
-      );
+          "execution.engine.implementation",
+          engine.getImplementation());
       config.addProperty("execution.engine.type", engine.getType());
       for (Entry<Object, Object> entryProperty : engine
-        .getProperties()
-        .entrySet()) {
+          .getProperties()
+          .entrySet()) {
         config.addProperty(
-          "execution.engine.properties." + entryProperty.getKey(),
-          entryProperty.getValue()
-        );
+            "execution.engine.properties." + entryProperty.getKey(),
+            entryProperty.getValue());
       }
     }
   }
diff --git a/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStore.java b/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStore.java
new file mode 100644
index 00000000..91012a7e
--- /dev/null
+++ b/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStore.java
@@ -0,0 +1,70 @@
+package edu.isi.wings.portal.classes.config;
+
+import edu.isi.wings.portal.classes.config.FileStoreHandler.FileSystem;
+import edu.isi.wings.portal.classes.config.FileStoreHandler.Http;
+import edu.isi.wings.portal.classes.config.FileStoreHandler.SecureShell;
+
+import java.io.File;
+import org.apache.commons.configuration.plist.PropertyListConfiguration;
+
+/**
+ * Created by varun on 13/07/2015.
+ */
+public class FileStore {
+  private static final String PUBLISHER_FILE_STORE_TYPE = "publisher.file-store.type";
+
+  public static enum Type {
+    SSH,
+    HTTP,
+    FILE_SYSTEM,
+  }
+
+  FileStore.Type type;
+  FileSystem fileSystem;
+  SecureShell ssh;
+  Http http;
+
+  public FileStore.Type getType() {
+    return type;
+  }
+
+  public FileSystem getFileSystem() {
+    return fileSystem;
+  }
+
+  public SecureShell getSsh() {
+    return ssh;
+  }
+
+  public Http getHttp() {
+    return http;
+  }
+
+  public FileStore(PropertyListConfiguration serverConfig) {
+    this.type = FileStore.Type.valueOf(serverConfig.getString(PUBLISHER_FILE_STORE_TYPE));
+    switch (this.type) {
+      case FILE_SYSTEM:
+        this.fileSystem = new FileSystem(serverConfig);
+        break;
+      case SSH:
+        this.ssh = new SecureShell(serverConfig);
+        break;
+      case HTTP:
+        this.http = new Http(serverConfig);
+        break;
+    }
+  }
+
+  public String publishFile(File file) throws Exception {
+    switch (this.type) {
+      case FILE_SYSTEM:
+        return this.fileSystem.publishFile(file);
+      case SSH:
+        return this.ssh.publishFile(file);
+      case HTTP:
+        return this.http.publishFile(file);
+      default:
+        throw new Exception("Unknown file store type: " + this.type);
+    }
+  }
+}
diff --git a/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStoreHandler/FileSystem.java b/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStoreHandler/FileSystem.java
new file mode 100644
index 00000000..96d73a4b
--- /dev/null
+++ b/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStoreHandler/FileSystem.java
@@ -0,0 +1,41 @@
+package edu.isi.wings.portal.classes.config.FileStoreHandler;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+import org.apache.commons.configuration.plist.PropertyListConfiguration;
+import org.apache.commons.io.FileUtils;
+
+public class FileSystem {
+  private static final String PUBLISHER_FILE_STORE_FILE_SYSTEM_DIRECTORY = "publisher.file-store.file-system.directory";
+  private String directory;
+
+  public static String getPublisherFileStoreFileSystemDirectory() {
+    return PUBLISHER_FILE_STORE_FILE_SYSTEM_DIRECTORY;
+  }
+
+  public String getDirectory() {
+    return directory;
+  }
+
+  public FileSystem(PropertyListConfiguration serverConfig) {
+    this.directory = serverConfig.getString(PUBLISHER_FILE_STORE_FILE_SYSTEM_DIRECTORY);
+  }
+
+  public String publishFile(File file) throws IOException {
+    String path = this.directory;
+    File directory = new File(path);
+    if (!directory.exists()) {
+      directory.mkdirs();
+    }
+    File newFile = new File(path + "/" + file.getName());
+    FileUtils.copyFile(file, newFile);
+    // return relative path
+    Path path1 = Paths.get(directory.getAbsolutePath());
+    Path path2 = Paths.get(newFile.getAbsolutePath());
+    return path1.relativize(path2).toString();
+  }
+
+}
diff --git a/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStoreHandler/Http.java b/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStoreHandler/Http.java
new file mode 100644
index 00000000..707bb121
--- /dev/null
+++ b/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStoreHandler/Http.java
@@ -0,0 +1,114 @@
+package edu.isi.wings.portal.classes.config.FileStoreHandler;
+
+import java.io.File;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.commons.configuration.plist.PropertyListConfiguration;
+
+public class Http {
+  private static final String PUBLISHER_FILE_STORE_HTTP_URL = "publisher.file-store.http-url";
+  private static final String PUBLISHER_FILE_STORE_HTTP_USERNAME = "publisher.file-store.username";
+  private static final String PUBLISHER_FILE_STORE_HTTP_PASSWORD = "publisher.file-store.password";
+  private static final String PUBLISHER_FILE_STORE_HTTP_MAX_UPLOAD_SIZE = "publisher.file-store.max-upload-size";
+
+  public Http(PropertyListConfiguration serverConfig) {
+  }
+
+  public String publishFile(File file) {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+  private long getSizeFromString(String sizeString) {
+    long kb = 1024;
+    long mb = kb * kb;
+    long gb = kb * mb;
+    long tb = kb * gb;
+
+    Pattern pat = Pattern.compile("(\\d+)\\s*([KkMmGgTt])[Bb]?");
+    Matcher mat = pat.matcher(sizeString);
+    if (mat.find()) {
+      long size = Long.parseLong(mat.group(1));
+      if (mat.groupCount() > 1) {
+        String units = mat.group(2).toLowerCase();
+        if (units.equals("k"))
+          return size * kb;
+        if (units.equals("m"))
+          return size * mb;
+        if (units.equals("g"))
+          return size * gb;
+        if (units.equals("t"))
+          return size * tb;
+      }
+      return size;
+    }
+    return 0;
+  }
+  // private String uploadFile(FileStore server, File datafile) {
+  // String upUrl = server.getUrl();
+  // String username = server.getUsername();
+  // String password = server.getPassword();
+
+  // if (username == null || password == null) {
+  // return ("missing username or password " +
+  // upUrl +
+  // " " +
+  // username +
+  // " " +
+  // password);
+  // }
+  // if (datafile.exists()) {
+  // AsyncHttpClient client = Dsl.asyncHttpClient();
+  // InputStream inputStream;
+
+  // try {
+  // inputStream = new BufferedInputStream(new FileInputStream(datafile));
+  // try {
+  // org.asynchttpclient.Response response = client
+  // .preparePost(upUrl)
+  // .setRealm(
+  // basicAuthRealm(username, password).setUsePreemptiveAuth(true))
+  // .addBodyPart(
+  // new InputStreamPart(
+  // datafile.getName(),
+  // inputStream,
+  // datafile.getName(),
+  // -1,
+  // "application/octet-stream",
+  // UTF_8))
+  // .execute()
+  // .get();
+  // return response.getResponseBody();
+  // } catch (InterruptedException e) {
+  // return null;
+  // } catch (ExecutionException e) {
+  // return null;
+  // }
+  // } catch (FileNotFoundException e) {
+  // return null;
+  // }
+  // }
+  // return null;
+  // }
+
+  // public Response streamData(String dataid, ServletContext context) {
+  // String location = dc.getDataLocation(dataid);
+
+  // if (location != null) {
+  // // Check if this is a file url
+  // File f = null;
+  // try {
+  // URL url = new URL(location);
+  // f = new File(url.getPath());
+  // } catch (MalformedURLException e) {
+  // // Do nothing
+  // }
+  // // Else assume it's a file path
+  // if (f == null)
+  // f = new File(location);
+
+  // return StorageHandler.streamFile(f.getAbsolutePath(), context);
+  // }
+  // return null;
+  // }
+}
diff --git a/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStoreHandler/SecureShell.java b/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStoreHandler/SecureShell.java
new file mode 100644
index 00000000..edac434d
--- /dev/null
+++ b/portal/src/main/java/edu/isi/wings/portal/classes/config/FileStoreHandler/SecureShell.java
@@ -0,0 +1,19 @@
+package edu.isi.wings.portal.classes.config.FileStoreHandler;
+
+import java.io.File;
+
+import org.apache.commons.configuration.plist.PropertyListConfiguration;
+
+public class SecureShell {
+  private static final String PUBLISHER_FILE_STORE_SSH_HOST = "publisher.file-store.host";
+  private static final String PUBLISHER_FILE_STORE_SSH_USERID = "publisher.file-store.userid";
+  private static final String PUBLISHER_FILE_STORE_SSH_PRIVATE_KEY = "publisher.file-store.private-key";
+
+  public SecureShell(PropertyListConfiguration serverConfig) {
+  }
+
+  public String publishFile(File file) {
+    throw new UnsupportedOperationException("Not supported yet.");
+  }
+
+}
diff --git a/portal/src/main/java/edu/isi/wings/portal/classes/config/FileUploadServerConfig.java b/portal/src/main/java/edu/isi/wings/portal/classes/config/FileUploadServerConfig.java
deleted file mode 100644
index 7e82dd78..00000000
--- a/portal/src/main/java/edu/isi/wings/portal/classes/config/FileUploadServerConfig.java
+++ /dev/null
@@ -1,113 +0,0 @@
-package edu.isi.wings.portal.classes.config;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-import org.apache.commons.configuration.plist.PropertyListConfiguration;
-
-/**
- * Created by varun on 13/07/2015.
- */
-public class FileUploadServerConfig {
-
-  private static final String PUBLISHER_UPLOAD_SERVER_MAX_UPLOAD_SIZE =
-    "publisher.upload-server.max-upload-size";
-  private static final String PUBLISHER_UPLOAD_SERVER_PRIVATE_KEY =
-    "publisher.upload-server.private-key";
-  private static final String PUBLISHER_UPLOAD_SERVER_USERID =
-    "publisher.upload-server.userid";
-  private static final String PUBLISHER_UPLOAD_SERVER_HOST =
-    "publisher.upload-server.host";
-  private static final String PUBLISHER_UPLOAD_SERVER_DIRECTORY =
-    "publisher.upload-server.directory";
-  private static final String PUBLISHER_UPLOAD_SERVER_PASSWORD =
-    "publisher.upload-server.password";
-  private static final String PUBLISHER_UPLOAD_SERVER_USERNAME =
-    "publisher.upload-server.username";
-  private static final String PUBLISHER_UPLOAD_SERVER_URL =
-    "publisher.upload-server.url";
-  String url;
-  String directory;
-  String host;
-  String privateKey;
-  String hostUserId;
-  String username;
-  String password;
-  long maxUploadSize = 0; // Defaults to No limit
-
-  public FileUploadServerConfig(PropertyListConfiguration serverConfig) {
-    this.url = serverConfig.getString(PUBLISHER_UPLOAD_SERVER_URL);
-    this.username = serverConfig.getString(PUBLISHER_UPLOAD_SERVER_USERNAME);
-    this.password = serverConfig.getString(PUBLISHER_UPLOAD_SERVER_PASSWORD);
-    this.directory = serverConfig.getString(PUBLISHER_UPLOAD_SERVER_DIRECTORY);
-    this.host = serverConfig.getString(PUBLISHER_UPLOAD_SERVER_HOST);
-    this.hostUserId = serverConfig.getString(PUBLISHER_UPLOAD_SERVER_USERID);
-    this.privateKey =
-      serverConfig.getString(PUBLISHER_UPLOAD_SERVER_PRIVATE_KEY);
-    String maxUploadSizeString = serverConfig.getString(
-      PUBLISHER_UPLOAD_SERVER_MAX_UPLOAD_SIZE
-    );
-    if (maxUploadSizeString != null) {
-      long size = this.getSizeFromString(maxUploadSizeString);
-      this.maxUploadSize = size;
-    }
-  }
-
-  public String getUrl() {
-    return url;
-  }
-
-  public String getDirectory() {
-    return directory;
-  }
-
-  public String getHost() {
-    return host;
-  }
-
-  @JsonIgnore
-  public String getPrivateKey() {
-    return privateKey;
-  }
-
-  @JsonIgnore
-  public String getHostUserId() {
-    return hostUserId;
-  }
-
-  public long getMaxUploadSize() {
-    return maxUploadSize;
-  }
-
-  @JsonIgnore
-  public String getUsername() {
-    return username;
-  }
-
-  @JsonIgnore
-  public String getPassword() {
-    return password;
-  }
-
-  private long getSizeFromString(String sizeString) {
-    long kb = 1024;
-    long mb = kb * kb;
-    long gb = kb * mb;
-    long tb = kb * gb;
-
-    Pattern pat = Pattern.compile("(\\d+)\\s*([KkMmGgTt])[Bb]?");
-    Matcher mat = pat.matcher(sizeString);
-    if (mat.find()) {
-      long size = Long.parseLong(mat.group(1));
-      if (mat.groupCount() > 1) {
-        String units = mat.group(2).toLowerCase();
-        if (units.equals("k")) return size * kb;
-        if (units.equals("m")) return size * mb;
-        if (units.equals("g")) return size * gb;
-        if (units.equals("t")) return size * tb;
-      }
-      return size;
-    }
-    return 0;
-  }
-}
diff --git a/portal/src/main/java/edu/isi/wings/portal/classes/config/MainConfig.java b/portal/src/main/java/edu/isi/wings/portal/classes/config/MainConfig.java
index 5ac2d739..0ea007e2 100644
--- a/portal/src/main/java/edu/isi/wings/portal/classes/config/MainConfig.java
+++ b/portal/src/main/java/edu/isi/wings/portal/classes/config/MainConfig.java
@@ -1,7 +1,5 @@
 package edu.isi.wings.portal.classes.config;
 
-import edu.isi.kcap.wings.opmm_deprecated.Main;
-import java.io.File;
 import javax.servlet.http.HttpServletRequest;
 import org.apache.commons.configuration.plist.PropertyListConfiguration;
 
diff --git a/portal/src/main/java/edu/isi/wings/portal/classes/config/PortalConfig.java b/portal/src/main/java/edu/isi/wings/portal/classes/config/PortalConfig.java
index ca267dac..d0de7125 100644
--- a/portal/src/main/java/edu/isi/wings/portal/classes/config/PortalConfig.java
+++ b/portal/src/main/java/edu/isi/wings/portal/classes/config/PortalConfig.java
@@ -13,7 +13,6 @@ public class PortalConfig {
   public StorageConfig storageConfig;
   public PlannerConfig plannerConfig;
   public ExecutionConfig executionConfig;
-
   public PublisherConfig publisher;
   public boolean sandboxed;
 
@@ -28,24 +27,21 @@ public void initializePortalConfig(HttpServletRequest request) {
   }
 
   public PropertyListConfiguration getPortalConfiguration(
-    HttpServletRequest request
-  ) {
+      HttpServletRequest request) {
     ServletContext app = request.getSession().getServletContext();
     this.portalConfigurationFile = obtainConfigPath(app, request);
     try {
       checkIfFileExists(portalConfigurationFile);
     } catch (Exception e) {
       throw new RuntimeException(
-        "Could not find config file: " + portalConfigurationFile
-      );
+          "Could not find config file: " + portalConfigurationFile);
     }
     return loadConfigurationOnProps();
   }
 
   private String obtainConfigPath(
-    ServletContext app,
-    HttpServletRequest request
-  ) {
+      ServletContext app,
+      HttpServletRequest request) {
     return app.getInitParameter("config.file");
   }
 
@@ -55,28 +51,24 @@ private PropertyListConfiguration loadConfigurationOnProps() {
       props.load(this.portalConfigurationFile);
     } catch (Exception e) {
       throw new RuntimeException(
-        "Could not load config file: " + this.portalConfigurationFile
-      );
+          "Could not load config file: " + this.portalConfigurationFile);
     }
     return props;
   }
 
   private void getPublisherConfiguration(
-    PropertyListConfiguration serverConfig
-  ) {
+      PropertyListConfiguration serverConfig) {
     this.publisher = new PublisherConfig(serverConfig);
   }
 
   private void getOntologyConfiguration(
-    PropertyListConfiguration serverConfig
-  ) {
+      PropertyListConfiguration serverConfig) {
     this.ontologyConfig = new OntologyConfig(serverConfig);
   }
 
   private void getMainConfiguration(
-    PropertyListConfiguration serverConfig,
-    HttpServletRequest request
-  ) {
+      PropertyListConfiguration serverConfig,
+      HttpServletRequest request) {
     this.mainConfig = new MainConfig(serverConfig, request);
   }
 
@@ -89,8 +81,7 @@ private void getPlannerConfiguration(PropertyListConfiguration serverConfig) {
   }
 
   private void getEngineNodeConfiguration(
-    PropertyListConfiguration serverConfig
-  ) {
+      PropertyListConfiguration serverConfig) {
     this.executionConfig = new ExecutionConfig(serverConfig);
   }
 
diff --git a/portal/src/main/java/edu/isi/wings/portal/classes/config/PublisherConfig.java b/portal/src/main/java/edu/isi/wings/portal/classes/config/PublisherConfig.java
index e67f1c77..4eaa16db 100644
--- a/portal/src/main/java/edu/isi/wings/portal/classes/config/PublisherConfig.java
+++ b/portal/src/main/java/edu/isi/wings/portal/classes/config/PublisherConfig.java
@@ -2,63 +2,21 @@
 
 import org.apache.commons.configuration.plist.PropertyListConfiguration;
 
-/**
- * Created by varun on 13/07/2015.
- */
 public class PublisherConfig {
-
-  private static final String PUBLISHER_SPARQL_DOMAINS_DIRECTORY_KEY =
-    "publisher.triple-store.domains-directory";
-  private static final String PUBLISHER_ENDPOINT_QUERY_KEY =
-    "publisher.triple-store.query";
-  private static final String PUBLISHER_ENDPOINT_POST_KEY =
-    "publisher.triple-store.publish";
-  private static final String PUBLISHER_NAME_KEY = "publisher.name";
-  private static final String PUBLISHER_URL_KEY = "publisher.url";
-  String url;
-  String tstorePublishUrl;
-  String tstoreQueryUrl;
-  FileUploadServerConfig uploadServer;
-
-  String domainsDir;
-  String exportName;
+  FileStore fileStore;
+  TripleStoreConfig tripleStore;
 
   public PublisherConfig(PropertyListConfiguration serverConfig) {
-    this.url = serverConfig.getString(PUBLISHER_URL_KEY);
-    this.exportName = serverConfig.getString(PUBLISHER_NAME_KEY);
-    this.tstorePublishUrl = serverConfig.getString(PUBLISHER_ENDPOINT_POST_KEY);
-    this.tstoreQueryUrl = serverConfig.getString(PUBLISHER_ENDPOINT_QUERY_KEY);
-    this.domainsDir =
-      serverConfig.getString(PUBLISHER_SPARQL_DOMAINS_DIRECTORY_KEY);
-    FileUploadServerConfig upserver = new FileUploadServerConfig(serverConfig);
-    this.setUploadServer(upserver);
-  }
-
-  public String getExportName() {
-    return exportName;
-  }
-
-  public String getUrl() {
-    return url;
+    this.tripleStore = new TripleStoreConfig(serverConfig);
+    this.fileStore = new FileStore(serverConfig);
   }
 
-  public String getTstorePublishUrl() {
-    return tstorePublishUrl;
+  public FileStore getFileStore() {
+    return fileStore;
   }
 
-  public String getTstoreQueryUrl() {
-    return tstoreQueryUrl;
+  public TripleStoreConfig getTripleStore() {
+    return tripleStore;
   }
 
-  public FileUploadServerConfig getUploadServer() {
-    return uploadServer;
-  }
-
-  public String getDomainsDir() {
-    return domainsDir;
-  }
-
-  public void setUploadServer(FileUploadServerConfig uploadServer) {
-    this.uploadServer = uploadServer;
-  }
 }
diff --git a/portal/src/main/java/edu/isi/wings/portal/classes/config/TripleStoreConfig.java b/portal/src/main/java/edu/isi/wings/portal/classes/config/TripleStoreConfig.java
new file mode 100644
index 00000000..e6b91fe9
--- /dev/null
+++ b/portal/src/main/java/edu/isi/wings/portal/classes/config/TripleStoreConfig.java
@@ -0,0 +1,56 @@
+package edu.isi.wings.portal.classes.config;
+
+import org.apache.commons.configuration.plist.PropertyListConfiguration;
+
+public class TripleStoreConfig {
+  /**
+   * Handle the following configuration keys:
+   * graph-name = "exportTest"
+   * publish = http://ontosoft.isi.edu:3030/provenance/data;
+   * query = http://ontosoft.isi.edu:3030/provenance/sparql;
+   * domains-directory = /opt/wings/storage/default;
+   *
+   *
+   */
+  private static final String PUBLISHER_SPARQL_DOMAINS_DIRECTORY_KEY = "publisher.triple-store.domains-directory";
+  private static final String PUBLISHER_ENDPOINT_QUERY_KEY = "publisher.triple-store.query";
+  private static final String PUBLISHER_ENDPOINT_POST_KEY = "publisher.triple-store.publish";
+  private static final String PUBLISHER_EXPORT_URL = "publisher.triple-store.export-url";
+  private static final String PUBLISHER_EXPORT_NAME = "publisher.triple-store.export-name";
+
+  String publishUrl;
+  String queryUrl;
+  String exportName;
+  String exportUrl;
+
+  String domainsDir;
+
+  public TripleStoreConfig(PropertyListConfiguration serverConfig) {
+    this.publishUrl = serverConfig.getString(PUBLISHER_ENDPOINT_POST_KEY);
+    this.queryUrl = serverConfig.getString(PUBLISHER_ENDPOINT_QUERY_KEY);
+    this.exportName = serverConfig.getString(PUBLISHER_EXPORT_NAME);
+    this.exportUrl = serverConfig.getString(PUBLISHER_EXPORT_URL);
+    this.domainsDir = serverConfig.getString(PUBLISHER_SPARQL_DOMAINS_DIRECTORY_KEY);
+  }
+
+  public String getPublishUrl() {
+    return publishUrl;
+  }
+
+  public String getQueryUrl() {
+    return queryUrl;
+  }
+
+  public String getExportPath() {
+    return exportName;
+  }
+
+  public String getDomainsDir() {
+    return domainsDir;
+  }
+
+  public String getExportUrl() {
+    return exportUrl;
+  }
+
+}
diff --git a/portal/src/main/java/edu/isi/wings/portal/classes/util/ComponentExecutingThread.java b/portal/src/main/java/edu/isi/wings/portal/classes/util/ComponentExecutingThread.java
index 79388ba6..243d17fa 100644
--- a/portal/src/main/java/edu/isi/wings/portal/classes/util/ComponentExecutingThread.java
+++ b/portal/src/main/java/edu/isi/wings/portal/classes/util/ComponentExecutingThread.java
@@ -98,8 +98,10 @@ private ExecutionPlan getExecutionPlan() {
     code.setCodeDirectory(invocation.getComponentDirectory());
     step.setCodeBinding(code);
 
-    HashMap<String, ArrayList<Object>> argMaps =
-      new HashMap<String, ArrayList<Object>>();
+    HashMap<String, ArrayList<Object>> argMaps = new HashMap<
+      String,
+      ArrayList<Object>
+    >();
     for (ComponentInvocation.Argument arg : invocation.getArguments()) {
       ArrayList<Object> cur = argMaps.get(arg.getName());
       if (cur == null) cur = new ArrayList<Object>();
diff --git a/portal/src/main/java/edu/isi/wings/portal/controllers/ComponentController.java b/portal/src/main/java/edu/isi/wings/portal/controllers/ComponentController.java
index 6330a115..4a9cc3be 100644
--- a/portal/src/main/java/edu/isi/wings/portal/controllers/ComponentController.java
+++ b/portal/src/main/java/edu/isi/wings/portal/controllers/ComponentController.java
@@ -158,9 +158,10 @@ public synchronized boolean incrementWorkflowVersionContainingComponent(
     return true;
   }
 
-  public synchronized HashMap<String, ArrayList<String>> getWorkflowsContainingComponent(
-    String cid
-  ) {
+  public synchronized HashMap<
+    String,
+    ArrayList<String>
+  > getWorkflowsContainingComponent(String cid) {
     if (this.tc == null) return null;
     try {
       ArrayList<String> types = this.cc.getParentComponentTypes(cid);
diff --git a/portal/src/main/java/edu/isi/wings/portal/controllers/DataController.java b/portal/src/main/java/edu/isi/wings/portal/controllers/DataController.java
index 7487d93b..97f455fe 100644
--- a/portal/src/main/java/edu/isi/wings/portal/controllers/DataController.java
+++ b/portal/src/main/java/edu/isi/wings/portal/controllers/DataController.java
@@ -45,7 +45,7 @@
 import edu.isi.wings.portal.classes.JsonHandler;
 import edu.isi.wings.portal.classes.StorageHandler;
 import edu.isi.wings.portal.classes.config.ConfigLoader;
-import edu.isi.wings.portal.classes.config.FileUploadServerConfig;
+import edu.isi.wings.portal.classes.config.FileStore;
 import edu.isi.wings.portal.classes.util.CookieHandler;
 import edu.isi.wings.portal.classes.util.TemplateBindings;
 import edu.isi.wings.workflow.plan.api.ExecutionPlan;
@@ -103,7 +103,8 @@ public DataController(ConfigLoader config, boolean load_external) {
     this.props = config.getProperties();
 
     dc = DataFactory.getCreationAPI(props);
-    if (this.loadExternal) dc = dc.getExternalCatalog();
+    if (this.loadExternal)
+      dc = dc.getExternalCatalog();
 
     cc = ComponentFactory.getCreationAPI(props);
     tc = TemplateFactory.getCreationAPI(props);
@@ -123,16 +124,18 @@ public DataController(ConfigLoader config, boolean load_external) {
    * Querying Methods
    */
   public String getDataJSON(String dataid) {
-    if (this.dc == null) return "{}";
+    if (this.dc == null)
+      return "{}";
 
     String location = this.dc.getDataLocation(dataid);
     DataItem dtype = this.dc.getDatatypeForData(dataid);
-    if (dtype == null) return null;
+    if (dtype == null)
+      return null;
 
-    ArrayList<MetadataProperty> props =
-      this.dc.getMetadataProperties(dtype.getID(), false);
+    ArrayList<MetadataProperty> props = this.dc.getMetadataProperties(dtype.getID(), false);
     ArrayList<String> propids = new ArrayList<String>();
-    for (MetadataProperty prop : props) propids.add(prop.getID());
+    for (MetadataProperty prop : props)
+      propids.add(prop.getID());
     ArrayList<MetadataValue> vals = this.dc.getMetadataValues(dataid, propids);
     String sensor = this.dc.getTypeSensor(dtype.getID());
 
@@ -146,10 +149,10 @@ public String getDataJSON(String dataid) {
   }
 
   public String getDatatypeJSON(String dtype) {
-    if (this.dc == null) return "{}";
+    if (this.dc == null)
+      return "{}";
 
-    ArrayList<MetadataProperty> props =
-      this.dc.getMetadataProperties(dtype, false);
+    ArrayList<MetadataProperty> props = this.dc.getMetadataProperties(dtype, false);
     String format = this.dc.getTypeNameFormat(dtype);
     String sensor = this.dc.getTypeSensor(dtype);
 
@@ -163,7 +166,8 @@ public String getDatatypeJSON(String dtype) {
   public String getDataHierarchyJSON() {
     DataTree tree = dc.getDataHierarchy();
     String dtree = null;
-    if (tree != null) dtree = json.toJson(tree.getRoot());
+    if (tree != null)
+      dtree = json.toJson(tree.getRoot());
     return dtree;
   }
 
@@ -200,7 +204,8 @@ public String getSensorComponentsListJSON() {
   }
 
   private HashMap<String, Object> convertNodeToUINode(DataTreeNode node) {
-    if (node == null) return null;
+    if (node == null)
+      return null;
 
     DataItem item = node.getItem();
     HashMap<String, Object> treeNode = new HashMap<String, Object>();
@@ -209,21 +214,15 @@ private HashMap<String, Object> convertNodeToUINode(DataTreeNode node) {
     treeNode.put("id", item.getID());
     treeNode.put("isClass", (item.getType() == 1 ? true : false));
     treeNode.put(
-      "iconCls",
-      (
-        item.getType() == 1
-          ? "icon-folder fa fa-yellow"
-          : "icon-file-alt fa fa-blue"
-      )
-    );
+        "iconCls",
+        (item.getType() == 1
+            ? "icon-folder fa fa-yellow"
+            : "icon-file-alt fa fa-blue"));
     treeNode.put(
-      "expIconCls",
-      (
-        item.getType() == 1
-          ? "icon-folder-open fa fa-yellow"
-          : "icon-file-alt fa fa-blue"
-      )
-    );
+        "expIconCls",
+        (item.getType() == 1
+            ? "icon-folder-open fa fa-yellow"
+            : "icon-file-alt fa fa-blue"));
     treeNode.put("expanded", false);
     treeNode.put("leaf", (item.getType() == 1 ? false : true));
     treeNode.put("draggable", (item.getType() == 1));
@@ -237,8 +236,7 @@ public String getNodeDataHierarchyJSON(String nodeid) {
       HashMap<String, Object> treeNode = new HashMap<String, Object>();
       ArrayList<DataTreeNode> children = tree.getRoot().getChildren();
       if (children != null && children.size() > 0) {
-        ArrayList<HashMap<String, Object>> uichildren =
-          new ArrayList<HashMap<String, Object>>();
+        ArrayList<HashMap<String, Object>> uichildren = new ArrayList<HashMap<String, Object>>();
         for (DataTreeNode childnode : children) {
           uichildren.add(this.convertNodeToUINode(childnode));
         }
@@ -250,27 +248,25 @@ public String getNodeDataHierarchyJSON(String nodeid) {
   }
 
   public String getDataListJSON() {
-    HashMap<String, ArrayList<String>> typeInstances =
-      dc.getAllDatatypeDatasets();
+    HashMap<String, ArrayList<String>> typeInstances = dc.getAllDatatypeDatasets();
     return json.toJson(typeInstances);
   }
 
   public String getMetricsHierarchyJSON() {
     DataTree tree = dc.getMetricsHierarchy();
     String mtree = null;
-    if (tree != null) mtree = json.toJson(tree.getRoot());
+    if (tree != null)
+      mtree = json.toJson(tree.getRoot());
     return mtree;
   }
 
-  public String publishData(String dataid) {
+  public String publishData(String dataid) throws Exception {
     String location = dc.getDataLocation(dataid);
+    FileStore fileStore = config.portalConfig.getPublisher().getFileStore();
     if (location != null) {
       File datafile = new File(location);
       if (config.portalConfig.getPublisher() != null) {
-        return this.uploadFile(
-            config.portalConfig.getPublisher().getUploadServer(),
-            datafile
-          );
+        return fileStore.publishFile(datafile);
       } else {
         return null;
       }
@@ -278,58 +274,6 @@ public String publishData(String dataid) {
     return null;
   }
 
-  private String uploadFile(FileUploadServerConfig server, File datafile) {
-    String upUrl = server.getUrl();
-    String username = server.getUsername();
-    String password = server.getPassword();
-
-    if (username == null || password == null) {
-      return (
-        "missing username or password " +
-        upUrl +
-        " " +
-        username +
-        " " +
-        password
-      );
-    }
-    if (datafile.exists()) {
-      AsyncHttpClient client = Dsl.asyncHttpClient();
-      InputStream inputStream;
-
-      try {
-        inputStream = new BufferedInputStream(new FileInputStream(datafile));
-        try {
-          org.asynchttpclient.Response response = client
-            .preparePost(upUrl)
-            .setRealm(
-              basicAuthRealm(username, password).setUsePreemptiveAuth(true)
-            )
-            .addBodyPart(
-              new InputStreamPart(
-                datafile.getName(),
-                inputStream,
-                datafile.getName(),
-                -1,
-                "application/octet-stream",
-                UTF_8
-              )
-            )
-            .execute()
-            .get();
-          return response.getResponseBody();
-        } catch (InterruptedException e) {
-          return null;
-        } catch (ExecutionException e) {
-          return null;
-        }
-      } catch (FileNotFoundException e) {
-        return null;
-      }
-    }
-    return null;
-  }
-
   public Response streamData(String dataid, ServletContext context) {
     String location = dc.getDataLocation(dataid);
 
@@ -343,7 +287,8 @@ public Response streamData(String dataid, ServletContext context) {
         // Do nothing
       }
       // Else assume it's a file path
-      if (f == null) f = new File(location);
+      if (f == null)
+        f = new File(location);
 
       return StorageHandler.streamFile(f.getAbsolutePath(), context);
     }
@@ -354,10 +299,10 @@ public Response streamData(String dataid, ServletContext context) {
    * Writing Methods
    */
   public synchronized boolean saveDataJSON(
-    String dataid,
-    String propvals_json
-  ) {
-    if (dc == null) return false;
+      String dataid,
+      String propvals_json) {
+    if (dc == null)
+      return false;
 
     try {
       JsonParser parser = new JsonParser();
@@ -365,13 +310,11 @@ public synchronized boolean saveDataJSON(
 
       DataItem dtype = dc.getDatatypeForData(dataid);
       ArrayList<MetadataProperty> props = dc.getMetadataProperties(
-        dtype.getID(),
-        false
-      );
+          dtype.getID(),
+          false);
 
       ArrayList<String> propids = new ArrayList<String>();
-      HashMap<String, MetadataProperty> pinfos =
-        new HashMap<String, MetadataProperty>();
+      HashMap<String, MetadataProperty> pinfos = new HashMap<String, MetadataProperty>();
       for (MetadataProperty prop : props) {
         propids.add(prop.getID());
         pinfos.put(prop.getID(), prop);
@@ -388,21 +331,18 @@ public synchronized boolean saveDataJSON(
         MetadataProperty pinfo = pinfos.get(propid);
         if (pinfo != null) {
           if (pinfo.isDatatypeProperty()) {
-            if (
-              value.equals("") && !pinfo.getRange().contains("string")
-            ) continue;
+            if (value.equals("") && !pinfo.getRange().contains("string"))
+              continue;
             dc.addDatatypePropertyValue(
-              dataid,
-              propid,
-              value,
-              pinfo.getRange()
-            );
+                dataid,
+                propid,
+                value,
+                pinfo.getRange());
           } else {
             dc.addObjectPropertyValue(
-              dataid,
-              propid,
-              this.domns + value.toString()
-            );
+                dataid,
+                propid,
+                this.domns + value.toString());
           }
         }
       }
@@ -421,54 +361,57 @@ public synchronized boolean saveDataJSON(
   }
 
   public synchronized String registerData(
-    String dataid,
-    String newname,
-    String metadata_json
-  ) {
+      String dataid,
+      String newname,
+      String metadata_json) {
     try {
       JsonParser parser = new JsonParser();
       JsonElement propvals = parser.parse(metadata_json);
       JsonObject pvals = propvals.getAsJsonObject();
-      if (pvals.get("type") == null) return "Datatype not known";
+      if (pvals.get("type") == null)
+        return "Datatype not known";
 
       // Choose the most specific type
       DataTree tree = dc.getDatatypeHierarchy();
       String dtypeid = null;
       for (JsonElement el : pvals.get("type").getAsJsonArray()) {
         String tmpid = el.getAsString();
-        if (dtypeid == null) dtypeid = tmpid; else {
+        if (dtypeid == null)
+          dtypeid = tmpid;
+        else {
           DataTreeNode dnode = tree.findNode(dtypeid);
-          if (dnode.hasChild(tree.findNode(tmpid), false)) dtypeid = tmpid;
+          if (dnode.hasChild(tree.findNode(tmpid), false))
+            dtypeid = tmpid;
         }
       }
 
       String dloc = dc.getDataLocation(dataid);
-      if (dloc == null) return "Existing data not found on server";
+      if (dloc == null)
+        return "Existing data not found on server";
 
       String newid = this.libns + newname;
       String newloc = dc.getDataLocation(newid);
-      if (!dc.addData(newid, dtypeid)) return "Could not add data";
+      if (!dc.addData(newid, dtypeid))
+        return "Could not add data";
 
       if (!dataid.equals(newid)) {
         File origf = new File(dloc);
         File newf = new File(
-          origf.getParentFile().getAbsolutePath() + File.separator + newname
-        );
+            origf.getParentFile().getAbsolutePath() + File.separator + newname);
         newloc = newf.getAbsolutePath();
-        if (origf.exists() && !newf.exists()) FileUtils.copyFile(origf, newf);
+        if (origf.exists() && !newf.exists())
+          FileUtils.copyFile(origf, newf);
       }
-      if (newloc == null) return "Cannot find location for new data";
+      if (newloc == null)
+        return "Cannot find location for new data";
 
-      if (
-        !dc.setDataLocation(newid, newloc)
-      ) return "Could not set data location";
+      if (!dc.setDataLocation(newid, newloc))
+        return "Could not set data location";
 
       ArrayList<MetadataProperty> props = dc.getMetadataProperties(
-        dtypeid,
-        false
-      );
-      HashMap<String, MetadataProperty> pinfos =
-        new HashMap<String, MetadataProperty>();
+          dtypeid,
+          false);
+      HashMap<String, MetadataProperty> pinfos = new HashMap<String, MetadataProperty>();
       for (MetadataProperty prop : props) {
         pinfos.put(prop.getName(), prop);
       }
@@ -480,21 +423,18 @@ public synchronized String registerData(
           MetadataProperty pinfo = pinfos.get(pname);
           if (pinfo != null) {
             if (pinfo.isDatatypeProperty()) {
-              if (
-                value.equals("") && !pinfo.getRange().contains("string")
-              ) continue;
+              if (value.equals("") && !pinfo.getRange().contains("string"))
+                continue;
               dc.addDatatypePropertyValue(
-                newid,
-                pinfo.getID(),
-                value,
-                pinfo.getRange()
-              );
+                  newid,
+                  pinfo.getID(),
+                  value,
+                  pinfo.getRange());
             } else {
               dc.addObjectPropertyValue(
-                newid,
-                pinfo.getID(),
-                this.domns + value.toString()
-              );
+                  newid,
+                  pinfo.getID(),
+                  this.domns + value.toString());
             }
           }
         }
@@ -502,8 +442,7 @@ public synchronized String registerData(
 
       Provenance p = new Provenance(newid);
       p.addActivity(
-        new ProvActivity(ProvActivity.CREATE, "Saving data from a run")
-      );
+          new ProvActivity(ProvActivity.CREATE, "Saving data from a run"));
 
       if (prov.addProvenance(p)) {
         return "OK";
@@ -516,13 +455,13 @@ public synchronized String registerData(
   }
 
   public synchronized String saveDatatypeJSON(
-    String dtypeid,
-    String props_json
-  ) {
+      String dtypeid,
+      String props_json) {
     ArrayList<String> errors = new ArrayList<String>();
     ArrayList<String> warnings = new ArrayList<String>();
 
-    if (dtypeid == null || props_json == null) return "[\"Null inputs\"]";
+    if (dtypeid == null || props_json == null)
+      return "[\"Null inputs\"]";
 
     try {
       JsonParser parser = new JsonParser();
@@ -565,9 +504,9 @@ public synchronized String saveDatatypeJSON(
       }
 
       /*
-      dc.removeMetadataPropertyInLibrary(String propid);
-      dc.renameMetadataPropertyInLibrary(String oldid, String newid);
-      */
+       * dc.removeMetadataPropertyInLibrary(String propid);
+       * dc.renameMetadataPropertyInLibrary(String oldid, String newid);
+       */
 
       // Check all properties being deleted
       JsonObject delops = ops.get("del").getAsJsonObject();
@@ -580,10 +519,9 @@ public synchronized String saveDatatypeJSON(
           this.dc.removeMetadataPropertyDomain(propid, dtypeid);
           eprop.getDomains().remove(dtypeid);
           warnings.add(
-            "Note that the property you deleted currently also " +
-            "exists for other datatypes: " +
-            eprop.getDomains()
-          );
+              "Note that the property you deleted currently also " +
+                  "exists for other datatypes: " +
+                  eprop.getDomains());
         } else {
           this.dc.removeMetadataProperty(propid);
           this.dc.removeMetadataPropertyInLibrary(propid);
@@ -603,17 +541,14 @@ public synchronized String saveDatatypeJSON(
         String npropid = prop.get("pid").getAsString();
         MetadataProperty eprop = this.dc.getMetadataProperty(propid);
         MetadataProperty enprop = this.dc.getMetadataProperty(npropid);
-        if (
-          enprop != null &&
-          !propid.equals(npropid) &&
-          !range.equals(enprop.getRange())
-        ) {
+        if (enprop != null &&
+            !propid.equals(npropid) &&
+            !range.equals(enprop.getRange())) {
           errors.add(
-            "Property " +
-            enprop.getName() +
-            " already exists with a different range: " +
-            enprop.getRange()
-          );
+              "Property " +
+                  enprop.getName() +
+                  " already exists with a different range: " +
+                  enprop.getRange());
           continue;
         }
         if (!eprop.getRange().equals(range)) {
@@ -621,10 +556,10 @@ public synchronized String saveDatatypeJSON(
           this.dc.addMetadataProperty(npropid, dtypeid, range);
           // Re-add any other domains that the property might have had
           for (String domid : eprop.getDomains()) {
-            if (!domid.equals(dtypeid)) this.dc.addMetadataPropertyDomain(
-                npropid,
-                domid
-              );
+            if (!domid.equals(dtypeid))
+              this.dc.addMetadataPropertyDomain(
+                  npropid,
+                  domid);
           }
         } else if (!propid.equals(npropid)) {
           this.dc.renameMetadataProperty(propid, npropid);
@@ -633,10 +568,9 @@ public synchronized String saveDatatypeJSON(
         if (eprop.getDomains().size() > 1) {
           eprop.getDomains().remove(dtypeid);
           warnings.add(
-            "Note that the property you modified also " +
-            "exists for other datatypes, and would have been modified for them as well : " +
-            eprop.getDomains()
-          );
+              "Note that the property you modified also " +
+                  "exists for other datatypes, and would have been modified for them as well : " +
+                  eprop.getDomains());
         }
       }
       this.dc.stop_batch_operation();
@@ -671,10 +605,10 @@ public synchronized String saveDatatypeJSON(
   }
 
   public synchronized boolean addDatatype(String ptype, String dtype) {
-    if (ptype == null || dtype == null) return false;
+    if (ptype == null || dtype == null)
+      return false;
 
-    String provlog =
-      "Creating datatype with parent " + KBUtils.getLocalName(ptype);
+    String provlog = "Creating datatype with parent " + KBUtils.getLocalName(ptype);
     Provenance p = new Provenance(dtype);
     p.addActivity(new ProvActivity(ProvActivity.CREATE, provlog));
 
@@ -682,39 +616,35 @@ public synchronized boolean addDatatype(String ptype, String dtype) {
   }
 
   public synchronized boolean moveDatatypeTo(
-    String dtypeid,
-    String fromtype,
-    String totype
-  ) {
-    if (dtypeid == null || fromtype == null || totype == null) return false;
-
-    String provlog =
-      "Moving Datatype from " +
-      KBUtils.getLocalName(fromtype) +
-      " to " +
-      KBUtils.getLocalName(totype);
+      String dtypeid,
+      String fromtype,
+      String totype) {
+    if (dtypeid == null || fromtype == null || totype == null)
+      return false;
+
+    String provlog = "Moving Datatype from " +
+        KBUtils.getLocalName(fromtype) +
+        " to " +
+        KBUtils.getLocalName(totype);
     Provenance p = new Provenance(dtypeid);
     p.addActivity(new ProvActivity(ProvActivity.UPDATE, provlog));
 
-    return (
-      dc.moveDatatypeParent(dtypeid, fromtype, totype) &&
-      dc.moveDatatypeParentInLibrary(dtypeid, fromtype, totype) &&
-      prov.addProvenance(p)
-    );
+    return (dc.moveDatatypeParent(dtypeid, fromtype, totype) &&
+        dc.moveDatatypeParentInLibrary(dtypeid, fromtype, totype) &&
+        prov.addProvenance(p));
   }
 
   public synchronized boolean moveDataTo(
-    String dataid,
-    String fromtype,
-    String totype
-  ) {
-    if (dataid == null || fromtype == null || totype == null) return false;
-
-    String provlog =
-      "Moving Data from " +
-      KBUtils.getLocalName(fromtype) +
-      " to " +
-      KBUtils.getLocalName(totype);
+      String dataid,
+      String fromtype,
+      String totype) {
+    if (dataid == null || fromtype == null || totype == null)
+      return false;
+
+    String provlog = "Moving Data from " +
+        KBUtils.getLocalName(fromtype) +
+        " to " +
+        KBUtils.getLocalName(totype);
     Provenance p = new Provenance(dataid);
     p.addActivity(new ProvActivity(ProvActivity.UPDATE, provlog));
 
@@ -731,9 +661,8 @@ public synchronized boolean delDatatypes(String[] dtypes) {
   }
 
   public synchronized boolean addDataForDatatype(
-    String dataid,
-    String dtypeid
-  ) {
+      String dataid,
+      String dtypeid) {
     String provlog = "Creating data of type " + KBUtils.getLocalName(dtypeid);
     Provenance p = new Provenance(dataid);
     p.addActivity(new ProvActivity(ProvActivity.CREATE, provlog));
@@ -742,21 +671,19 @@ public synchronized boolean addDataForDatatype(
   }
 
   public synchronized String addRemoteDataForType(
-    String dataLocationUrl,
-    String dtypeid
-  ) {
+      String dataLocationUrl,
+      String dtypeid) {
     try {
-      String provlog =
-        "Downloading from " +
-        dataLocationUrl +
-        " and creating data of type " +
-        KBUtils.getLocalName(dtypeid);
+      String provlog = "Downloading from " +
+          dataLocationUrl +
+          " and creating data of type " +
+          KBUtils.getLocalName(dtypeid);
 
       // Check if it doesn't already exist
       URL url = new URL(dataLocationUrl);
       String filename = KBUtils.sanitizeID(new File(url.getFile()).getName());
       String dataid = this.libns + filename;
-      //System.out.println("Check if data exists");
+      // System.out.println("Check if data exists");
       if (dc.getDataLocation(dataid) != null) {
         // Dataset already exists, so do not overwrite (FIXME : Make it configurable)
         return dataid;
@@ -764,14 +691,14 @@ public synchronized String addRemoteDataForType(
 
       Provenance p = new Provenance(dataid);
       p.addActivity(new ProvActivity(ProvActivity.CREATE, provlog));
-      //System.out.println("Adding new data");
+      // System.out.println("Adding new data");
 
       String location = dc.getDefaultDataLocation(dataid);
-      //System.out.println("Copying "+ url + " to " + location);
+      // System.out.println("Copying "+ url + " to " + location);
       FileUtils.copyURLToFile(url, new File(location));
-      //System.out.println("Add data id: " + dataid);
+      // System.out.println("Add data id: " + dataid);
       dc.addData(dataid, dtypeid);
-      //System.out.println("Set data location of " + dataid);
+      // System.out.println("Set data location of " + dataid);
       if (dc.setDataLocation(dataid, location) && prov.addProvenance(p)) {
         return dataid;
       }
@@ -782,27 +709,26 @@ public synchronized String addRemoteDataForType(
   }
 
   public synchronized boolean addBatchData(
-    String dtypeid,
-    String[] dids,
-    String[] locations,
-    HttpServletRequest request,
-    ServletContext context
-  ) {
+      String dtypeid,
+      String[] dids,
+      String[] locations,
+      HttpServletRequest request,
+      ServletContext context) {
     for (int i = 0; i < dids.length; i++) {
-      if (!dc.addData(dids[i], dtypeid)) return false;
-      if (locations.length > i && locations[i] != null) if (
-        !dc.setDataLocation(dids[i], locations[i])
-      ) return false;
+      if (!dc.addData(dids[i], dtypeid))
+        return false;
+      if (locations.length > i && locations[i] != null)
+        if (!dc.setDataLocation(dids[i], locations[i]))
+          return false;
       this.runSensorWorkflow(dids[i], request, context);
     }
     return true;
   }
 
   public String runSensorWorkflow(
-    String dataid,
-    HttpServletRequest request,
-    ServletContext context
-  ) {
+      String dataid,
+      HttpServletRequest request,
+      ServletContext context) {
     try {
       DataItem dtype = this.dc.getDatatypeForData(dataid);
       if (dtype == null) {
@@ -818,34 +744,29 @@ public String runSensorWorkflow(
       Variable[] invars = this.tc.getTemplate(tplid).getInputVariables();
       if (invars.length != 1) {
         System.err.println(
-          "Template should have exactly 1 input variable. Has " + invars.length
-        );
+            "Template should have exactly 1 input variable. Has " + invars.length);
         return null;
       }
-      HashMap<String, ArrayList<String>> dataBindings =
-        new HashMap<String, ArrayList<String>>();
+      HashMap<String, ArrayList<String>> dataBindings = new HashMap<String, ArrayList<String>>();
       ArrayList<String> inputfiles = new ArrayList<String>();
       inputfiles.add(dataid);
       dataBindings.put(invars[0].getID(), inputfiles);
 
       TemplateBindings tbindings = new TemplateBindings();
       tbindings.setCallbackUrl(
-        this.config.portalConfig.mainConfig.getServerUrl() +
-        this.config.getUserDomainUrl() +
-        "/data/setMetadataFromSensorOutput?data_id=" +
-        URLEncoder.encode(dataid, "UTF-8")
-      );
+          this.config.portalConfig.mainConfig.getServerUrl() +
+              this.config.getUserDomainUrl() +
+              "/data/setMetadataFromSensorOutput?data_id=" +
+              URLEncoder.encode(dataid, "UTF-8"));
       tbindings.setCallbackCookies(
-        CookieHandler.httpCookiesFromServlet(request)
-      );
+          CookieHandler.httpCookiesFromServlet(request));
       tbindings.setDataBindings(dataBindings);
       tbindings.setParameterBindings(new HashMap<String, ArrayList<Object>>());
       tbindings.setParameterTypes(new HashMap<String, String>());
       tbindings.setComponentBindings(new HashMap<String, String>());
       tbindings.setTemplateId(tplid);
 
-      ArrayList<String> runids =
-        this.rc.expandAndRunTemplate(tbindings, context);
+      ArrayList<String> runids = this.rc.expandAndRunTemplate(tbindings, context);
       if (runids != null && runids.size() > 0) {
         return runids.get(0);
       }
@@ -859,10 +780,9 @@ public String runSensorWorkflow(
   }
 
   public String runSensorComponent(
-    String dataid,
-    HttpServletRequest request,
-    ServletContext context
-  ) {
+      String dataid,
+      HttpServletRequest request,
+      ServletContext context) {
     try {
       DataItem dtype = this.dc.getDatatypeForData(dataid);
       if (dtype == null) {
@@ -879,15 +799,13 @@ public String runSensorComponent(
       ArrayList<ComponentRole> outroles = c.getOutputs();
       if (inroles.size() != 1) {
         System.err.println(
-          "Sensor component should have exactly 1 input. Has " + inroles.size()
-        );
+            "Sensor component should have exactly 1 input. Has " + inroles.size());
         return null;
       }
       if (outroles.size() != 1) {
         System.err.println(
-          "Sensor component should have exactly 1 output. Has " +
-          outroles.size()
-        );
+            "Sensor component should have exactly 1 output. Has " +
+                outroles.size());
         return null;
       }
 
@@ -901,23 +819,21 @@ public String runSensorComponent(
       role_bindings.put(inroles.get(0).getRoleName(), b);
       role_bindings.put(outroles.get(0).getRoleName(), bout);
 
-      String callbackUrl =
-        request.getScheme() +
-        "://" +
-        request.getServerName() +
-        ":" +
-        request.getServerPort() +
-        this.config.getUserDomainUrl() +
-        "/data/setMetadataFromSensorOutput?data_id=" +
-        URLEncoder.encode(dataid, "UTF-8");
+      String callbackUrl = request.getScheme() +
+          "://" +
+          request.getServerName() +
+          ":" +
+          request.getServerPort() +
+          this.config.getUserDomainUrl() +
+          "/data/setMetadataFromSensorOutput?data_id=" +
+          URLEncoder.encode(dataid, "UTF-8");
 
       this.rc.runComponent(
           cid,
           role_bindings,
           callbackUrl,
           CookieHandler.httpCookiesFromServlet(request),
-          context
-        );
+          context);
     } catch (Exception e) {
       e.printStackTrace();
       this.rc.end();
@@ -928,10 +844,9 @@ public String runSensorComponent(
   }
 
   public String setMetadataFromSensorOutput(
-    String data_id,
-    ExecutionPlan plan
-  ) {
-    //System.out.println(plan);
+      String data_id,
+      ExecutionPlan plan) {
+    // System.out.println(plan);
     for (ExecutionStep step : plan.getAllExecutionSteps()) {
       for (ExecutionFile file : step.getOutputFiles()) {
         file.loadMetadataFromFileContents();
@@ -946,11 +861,10 @@ public synchronized boolean delData(String dataid) {
   }
 
   public synchronized boolean renameData(String dataid, String newid) {
-    String provlog =
-      "Renaming " +
-      KBUtils.getLocalName(dataid) +
-      " to " +
-      KBUtils.getLocalName(newid);
+    String provlog = "Renaming " +
+        KBUtils.getLocalName(dataid) +
+        " to " +
+        KBUtils.getLocalName(newid);
     Provenance p = new Provenance(dataid);
     p.addActivity(new ProvActivity(ProvActivity.UPDATE, provlog));
 
@@ -966,19 +880,16 @@ public synchronized boolean setDataLocation(String dataid, String location) {
   }
 
   public synchronized boolean renameDataType(String dtypeid, String newid) {
-    String provlog =
-      "Renaming " +
-      KBUtils.getLocalName(dtypeid) +
-      " to " +
-      KBUtils.getLocalName(newid);
+    String provlog = "Renaming " +
+        KBUtils.getLocalName(dtypeid) +
+        " to " +
+        KBUtils.getLocalName(newid);
     Provenance p = new Provenance(dtypeid);
     p.addActivity(new ProvActivity(ProvActivity.UPDATE, provlog));
 
-    return (
-      dc.renameDatatype(newid, dtypeid) &&
-      dc.renameDatatypeInLibrary(newid, dtypeid) &&
-      prov.addProvenance(p)
-    );
+    return (dc.renameDatatype(newid, dtypeid) &&
+        dc.renameDatatypeInLibrary(newid, dtypeid) &&
+        prov.addProvenance(p));
   }
 
   public void end() {
@@ -991,12 +902,12 @@ public void end() {
   }
 
   public synchronized boolean importFromExternalCatalog(
-    String dataid,
-    String dtypeid,
-    String propvals_json,
-    String location
-  ) {
-    if (dc == null) return false;
+      String dataid,
+      String dtypeid,
+      String propvals_json,
+      String location) {
+    if (dc == null)
+      return false;
 
     try {
       JsonParser parser = new JsonParser();
@@ -1007,8 +918,8 @@ public synchronized boolean importFromExternalCatalog(
         dc.addData(dataid, dtypeid);
       }
       for (Map.Entry<String, JsonElement> entry : propvals
-        .getAsJsonObject()
-        .entrySet()) {
+          .getAsJsonObject()
+          .entrySet()) {
         String propid = entry.getKey();
         String value = entry.getValue().getAsString();
 
@@ -1039,21 +950,21 @@ public synchronized boolean importFromExternalCatalog(
   private void trustAllCertificates() {
     // Create a new trust manager that trust all certificates
     TrustManager[] trustAllCerts = new TrustManager[] {
-      new X509TrustManager() {
-        public java.security.cert.X509Certificate[] getAcceptedIssuers() {
-          return null;
-        }
+        new X509TrustManager() {
+          public java.security.cert.X509Certificate[] getAcceptedIssuers() {
+            return null;
+          }
 
-        public void checkClientTrusted(
-          java.security.cert.X509Certificate[] certs,
-          String authType
-        ) {}
+          public void checkClientTrusted(
+              java.security.cert.X509Certificate[] certs,
+              String authType) {
+          }
 
-        public void checkServerTrusted(
-          java.security.cert.X509Certificate[] certs,
-          String authType
-        ) {}
-      },
+          public void checkServerTrusted(
+              java.security.cert.X509Certificate[] certs,
+              String authType) {
+          }
+        },
     };
 
     // Activate the new trust manager
@@ -1061,6 +972,7 @@ public void checkServerTrusted(
       SSLContext sc = SSLContext.getInstance("SSL");
       sc.init(null, trustAllCerts, new java.security.SecureRandom());
       HttpsURLConnection.setDefaultSSLSocketFactory(sc.getSocketFactory());
-    } catch (Exception e) {}
+    } catch (Exception e) {
+    }
   }
 }
diff --git a/portal/src/main/java/edu/isi/wings/portal/controllers/PlanController.java b/portal/src/main/java/edu/isi/wings/portal/controllers/PlanController.java
index 452dcd6b..43df94ce 100644
--- a/portal/src/main/java/edu/isi/wings/portal/controllers/PlanController.java
+++ b/portal/src/main/java/edu/isi/wings/portal/controllers/PlanController.java
@@ -376,13 +376,15 @@ private void printEncodedResults(
   private ArrayList<ArrayList<TreeMap<String, Binding>>> getDataBindings(
     VariableBindingsListSet bindingsets
   ) {
-    ArrayList<ArrayList<TreeMap<String, Binding>>> blistsets =
-      new ArrayList<ArrayList<TreeMap<String, Binding>>>();
+    ArrayList<ArrayList<TreeMap<String, Binding>>> blistsets = new ArrayList<
+      ArrayList<TreeMap<String, Binding>>
+    >();
 
     for (ArrayList<VariableBindingsList> bindings : bindingsets) {
       HashMap<String, Boolean> bindingstrs = new HashMap<String, Boolean>();
-      ArrayList<TreeMap<String, Binding>> blist =
-        new ArrayList<TreeMap<String, Binding>>();
+      ArrayList<TreeMap<String, Binding>> blist = new ArrayList<
+        TreeMap<String, Binding>
+      >();
       for (VariableBindingsList binding : bindings) {
         TreeMap<String, Binding> xbindings = new TreeMap<String, Binding>();
 
@@ -412,8 +414,9 @@ private ArrayList<ArrayList<TreeMap<String, Binding>>> getDataBindings(
   private ArrayList<TreeMap<String, Binding>> getParameterBindings(
     ArrayList<Template> cts
   ) {
-    ArrayList<TreeMap<String, Binding>> bindings_b =
-      new ArrayList<TreeMap<String, Binding>>();
+    ArrayList<TreeMap<String, Binding>> bindings_b = new ArrayList<
+      TreeMap<String, Binding>
+    >();
     for (Template bt : cts) {
       TreeMap<String, Binding> binding_b = new TreeMap<String, Binding>();
       for (Variable v : bt.getInputVariables()) {
@@ -426,8 +429,9 @@ private ArrayList<TreeMap<String, Binding>> getParameterBindings(
 
     // Expanding collections into multiple configurations
     // FIXME: Cannot handle parameter collections right now
-    ArrayList<TreeMap<String, Binding>> bindings =
-      new ArrayList<TreeMap<String, Binding>>();
+    ArrayList<TreeMap<String, Binding>> bindings = new ArrayList<
+      TreeMap<String, Binding>
+    >();
     HashMap<String, Boolean> bstrs = new HashMap<String, Boolean>();
     while (!bindings_b.isEmpty()) {
       boolean hasSets = false;
@@ -538,8 +542,10 @@ private Double getEstimatedExecutionTime(Template t, String tplid) {
     usermetrics.add(nl);
 
     //FIXME: Hardcoding the coefficients as well for now
-    HashMap<String, HashMap<String, Double>> tcoeffs =
-      new HashMap<String, HashMap<String, Double>>();
+    HashMap<String, HashMap<String, Double>> tcoeffs = new HashMap<
+      String,
+      HashMap<String, Double>
+    >();
     HashMap<String, Double> onlineLDA = new HashMap<String, Double>();
     HashMap<String, Double> parallelLDA = new HashMap<String, Double>();
     HashMap<String, Double> malletLDA = new HashMap<String, Double>();
@@ -578,8 +584,10 @@ private HashMap<String, Integer> getRegressionVariableValues(
     ArrayList<String> userparams
   ) {
     // FIXME: Assuming value is Integer
-    HashMap<String, Integer> regressionVariables =
-      new HashMap<String, Integer>();
+    HashMap<String, Integer> regressionVariables = new HashMap<
+      String,
+      Integer
+    >();
     for (Variable v : t.getInputVariables()) {
       if (v.isDataVariable() && v.getBinding() != null) {
         Metrics metrics = v.getBinding().getMetrics();
diff --git a/portal/src/main/java/edu/isi/wings/portal/controllers/RunController.java b/portal/src/main/java/edu/isi/wings/portal/controllers/RunController.java
index 77802d95..2fde1c1d 100644
--- a/portal/src/main/java/edu/isi/wings/portal/controllers/RunController.java
+++ b/portal/src/main/java/edu/isi/wings/portal/controllers/RunController.java
@@ -23,6 +23,12 @@
 import com.google.gson.JsonParser;
 import edu.isi.kcap.ontapi.KBTriple;
 import edu.isi.kcap.wings.opmm.Catalog;
+import edu.isi.kcap.wings.opmm.Constants;
+import edu.isi.kcap.wings.opmm.DataTypes.Links;
+import edu.isi.kcap.wings.opmm.DataTypes.ProvenanceResponseSchema;
+import edu.isi.kcap.wings.opmm.Publisher.TriplesPublisher;
+import edu.isi.kcap.wings.opmm.FilePublisher;
+import edu.isi.kcap.wings.opmm.Mapper;
 import edu.isi.kcap.wings.opmm.WorkflowExecutionExport;
 import edu.isi.kcap.wings.opmm.WorkflowTemplateExport;
 import edu.isi.wings.catalog.component.ComponentFactory;
@@ -40,7 +46,6 @@
 import edu.isi.wings.planner.api.impl.kb.WorkflowGenerationKB;
 import edu.isi.wings.portal.classes.JsonHandler;
 import edu.isi.wings.portal.classes.config.ConfigLoader;
-import edu.isi.wings.portal.classes.config.FileUploadServerConfig;
 import edu.isi.wings.portal.classes.config.PublisherConfig;
 import edu.isi.wings.portal.classes.util.ComponentExecutingThread;
 import edu.isi.wings.portal.classes.util.PlanningAPIBindings;
@@ -72,6 +77,8 @@
 import org.apache.http.entity.StringEntity;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClients;
+import org.apache.jena.base.Sys;
+import org.apache.jena.riot.Lang;
 
 public class RunController {
 
@@ -84,8 +91,7 @@ public class RunController {
   private Properties props;
 
   public static ExecutorService executor;
-  public static HashMap<String, PlanningAPIBindings> apiBindings =
-    new HashMap<String, PlanningAPIBindings>();
+  public static HashMap<String, PlanningAPIBindings> apiBindings = new HashMap<String, PlanningAPIBindings>();
 
   public RunController(ConfigLoader config) {
     this.config = config;
@@ -96,14 +102,13 @@ public RunController(ConfigLoader config) {
 
     if (executor == null) {
       // System.out.println("Parallel:" + config.getPlannerConfig().getParallelism());
-      executor =
-        Executors.newFixedThreadPool(
-          config.portalConfig.getPlannerConfig().getParallelism()
-        );
+      executor = Executors.newFixedThreadPool(
+          config.portalConfig.getPlannerConfig().getParallelism());
     }
   }
 
-  public void end() {}
+  public void end() {
+  }
 
   /**
    * Get the run list json.
@@ -116,57 +121,50 @@ public void end() {}
    * @return
    */
   public String getRunListJSON(
-    String pattern,
-    String status,
-    int start,
-    int limit
-  ) {
+      String pattern,
+      String status,
+      int start,
+      int limit) {
     HashMap<String, Object> result = new HashMap<String, Object>();
     int numberOfRuns = this.getNumberOfRuns(pattern, status, null);
     boolean fasterQuery = numberOfRuns > 1000;
     result.put("success", true);
     result.put("results", numberOfRuns);
     result.put(
-      "rows",
-      this.getRunList(pattern, status, start, limit, fasterQuery)
-    );
+        "rows",
+        this.getRunList(pattern, status, start, limit, fasterQuery));
     return json.toJson(result);
   }
 
   public String getRunListSimpleJSON(
-    String pattern,
-    String status,
-    int start,
-    int limit,
-    Date started_after
-  ) {
+      String pattern,
+      String status,
+      int start,
+      int limit,
+      Date started_after) {
     HashMap<String, Object> result = new HashMap<String, Object>();
     result.put("success", true);
     result.put("results", this.getNumberOfRuns(pattern, status, started_after));
     result.put(
-      "rows",
-      this.getRunListSimple(pattern, status, start, limit, started_after)
-    );
+        "rows",
+        this.getRunListSimple(pattern, status, start, limit, started_after));
     return json.toJson(result);
   }
 
   public ArrayList<HashMap<String, Object>> getRunListSimple(
-    String pattern,
-    String status,
-    int start,
-    int limit,
-    Date started_after
-  ) {
+      String pattern,
+      String status,
+      int start,
+      int limit,
+      Date started_after) {
     ExecutionMonitorAPI monitor = config.getDomainExecutionMonitor();
-    ArrayList<HashMap<String, Object>> list =
-      new ArrayList<HashMap<String, Object>>();
+    ArrayList<HashMap<String, Object>> list = new ArrayList<HashMap<String, Object>>();
     for (RuntimePlan exe : monitor.getRunListSimple(
-      pattern,
-      status,
-      start,
-      limit,
-      started_after
-    )) {
+        pattern,
+        status,
+        start,
+        limit,
+        started_after)) {
       HashMap<String, Object> map = new HashMap<String, Object>();
       map.put("runtimeInfo", exe.getRuntimeInfo());
       map.put("template_id", exe.getOriginalTemplateID());
@@ -177,22 +175,19 @@ public ArrayList<HashMap<String, Object>> getRunListSimple(
   }
 
   public ArrayList<HashMap<String, Object>> getRunList(
-    String pattern,
-    String status,
-    int start,
-    int limit,
-    boolean fasterQuery
-  ) {
+      String pattern,
+      String status,
+      int start,
+      int limit,
+      boolean fasterQuery) {
     ExecutionMonitorAPI monitor = config.getDomainExecutionMonitor();
-    ArrayList<HashMap<String, Object>> list =
-      new ArrayList<HashMap<String, Object>>();
+    ArrayList<HashMap<String, Object>> list = new ArrayList<HashMap<String, Object>>();
     for (RuntimePlan exe : monitor.getRunList(
-      pattern,
-      status,
-      start,
-      limit,
-      fasterQuery
-    )) {
+        pattern,
+        status,
+        start,
+        limit,
+        fasterQuery)) {
       HashMap<String, Object> map = new HashMap<String, Object>();
 
       map.put("runtimeInfo", exe.getRuntimeInfo());
@@ -207,9 +202,9 @@ public ArrayList<HashMap<String, Object>> getRunList(
         map.put("running_jobs", this.getStepIds(running_steps));
         map.put("failed_jobs", this.getStepIds(failed_steps));
         if (numtotal > 0) {
-          map.put("percent_done", numdone * 100.0 / numtotal);
-          map.put("percent_running", running_steps.size() * 100.0 / numtotal);
-          map.put("percent_failed", failed_steps.size() * 100.0 / numtotal);
+          map.put("percent_done", (numdone * 100.0) / numtotal);
+          map.put("percent_running", (running_steps.size() * 100.0) / numtotal);
+          map.put("percent_failed", (failed_steps.size() * 100.0) / numtotal);
         }
       }
       list.add(map);
@@ -218,10 +213,9 @@ public ArrayList<HashMap<String, Object>> getRunList(
   }
 
   public int getNumberOfRuns(
-    String pattern,
-    String status,
-    Date started_after
-  ) {
+      String pattern,
+      String status,
+      Date started_after) {
     ExecutionMonitorAPI monitor = config.getDomainExecutionMonitor();
     return monitor.getNumberOfRuns(pattern, status, started_after);
   }
@@ -273,7 +267,8 @@ public String getRunPlanJSON(String runid) {
 
   private String getPublishedURL(String runid) {
     PublisherConfig publisher = config.portalConfig.getPublisher();
-    if (publisher == null) return null;
+    if (publisher == null)
+      return null;
 
     /* TODO: Return already published url for the run id if possible */
     /*
@@ -297,10 +292,12 @@ private Map<String, Object> getShortConstraints(Template tpl) {
     Map<String, Object> varbindings = new HashMap<String, Object>();
     for (Variable v : tpl.getVariables()) {
       List<Object> constraints = new ArrayList<Object>();
-      if (v.isParameterVariable()) continue;
+      if (v.isParameterVariable())
+        continue;
       for (KBTriple t : tpl.getConstraintEngine().getConstraints(v.getID())) {
         Map<String, Object> cons = new HashMap<String, Object>();
-        if (t.getPredicate().getName().equals("hasDataBinding")) continue;
+        if (t.getPredicate().getName().equals("hasDataBinding"))
+          continue;
         cons.put("p", t.getPredicate().getName());
         cons.put("o", t.getObject());
         constraints.add(cons);
@@ -314,7 +311,8 @@ public String deleteRuns(String rjson, ServletContext context) {
     HashMap<String, Object> ret = new HashMap<String, Object>();
     ret.put("success", false);
     JsonElement listel = new JsonParser().parse(rjson);
-    if (listel == null) return json.toJson(ret);
+    if (listel == null)
+      return json.toJson(ret);
 
     if (listel.isJsonObject()) {
       return this.deleteRun(rjson, context);
@@ -327,9 +325,8 @@ public String deleteRuns(String rjson, ServletContext context) {
       JsonElement el = list.get(i);
       String runid = el.getAsJsonObject().get("id").getAsString();
       monitor.deleteRun(
-        runid,
-        config.portalConfig.storageConfig.isDeleteRunOutputs()
-      );
+          runid,
+          config.portalConfig.storageConfig.isDeleteRunOutputs());
     }
 
     ret.put("success", true);
@@ -340,16 +337,15 @@ public String deleteRun(String rjson, ServletContext context) {
     HashMap<String, Object> ret = new HashMap<String, Object>();
     ret.put("success", false);
     JsonElement el = new JsonParser().parse(rjson);
-    if (el == null) return json.toJson(ret);
+    if (el == null)
+      return json.toJson(ret);
 
     String runid = el.getAsJsonObject().get("id").getAsString();
     ExecutionMonitorAPI monitor = config.getDomainExecutionMonitor();
-    if (
-      !monitor.deleteRun(
+    if (!monitor.deleteRun(
         runid,
-        config.portalConfig.storageConfig.isDeleteRunOutputs()
-      )
-    ) return json.toJson(ret);
+        config.portalConfig.storageConfig.isDeleteRunOutputs()))
+      return json.toJson(ret);
     /*
      * if (monitor.runExists(runid)) {
      * this.stopRun(runid, context);
@@ -364,13 +360,9 @@ public String deleteRun(String rjson, ServletContext context) {
 
   public boolean stopRun(String runid, ServletContext context) {
     ExecutionMonitorAPI monitor = config.getDomainExecutionMonitor();
-    if (
-      monitor.getRunDetails(runid).getRuntimeInfo().getStatus() ==
-      RuntimeInfo.Status.RUNNING
-    ) {
+    if (monitor.getRunDetails(runid).getRuntimeInfo().getStatus() == RuntimeInfo.Status.RUNNING) {
       PlanExecutionEngine engine = (PlanExecutionEngine) context.getAttribute(
-        "engine_" + runid
-      );
+          "engine_" + runid);
       RuntimePlan rplan = (RuntimePlan) context.getAttribute("plan_" + runid);
       if (engine != null && rplan != null) {
         engine.abort(rplan);
@@ -386,9 +378,8 @@ public boolean stopRun(String runid, ServletContext context) {
    * - Puts the rest of the processing in a Queue to be processed sequentially
    */
   public ArrayList<String> expandAndRunTemplate(
-    TemplateBindings template_bindings,
-    ServletContext context
-  ) {
+      TemplateBindings template_bindings,
+      ServletContext context) {
     // Create a runid
     String ex_prefix = props.getProperty("domain.executions.dir.url");
     String template_id = template_bindings.getTemplateId();
@@ -404,15 +395,14 @@ public ArrayList<String> expandAndRunTemplate(
     // Submit the planning and execution thread
     try {
       PlanningAndExecutingThread thread = new PlanningAndExecutingThread(
-        ex_prefix,
-        template_id,
-        this.config,
-        config.portalConfig.getPlannerConfig().getMaxQueueSize(),
-        template_bindings,
-        apis,
-        executor,
-        context
-      );
+          ex_prefix,
+          template_id,
+          this.config,
+          config.portalConfig.getPlannerConfig().getMaxQueueSize(),
+          template_bindings,
+          apis,
+          executor,
+          context);
       executor.submit(thread).get();
 
       // Return the runids
@@ -424,12 +414,11 @@ public ArrayList<String> expandAndRunTemplate(
   }
 
   public Future<?> runComponent(
-    String cid,
-    HashMap<String, Binding> role_bindings,
-    String callbackUrl,
-    Cookie[] callbackCookies,
-    ServletContext context
-  ) {
+      String cid,
+      HashMap<String, Binding> role_bindings,
+      String callbackUrl,
+      Cookie[] callbackCookies,
+      ServletContext context) {
     PlanningAPIBindings apis = null;
     String exPrefix = props.getProperty("domain.executions.dir.url");
     if (apiBindings.containsKey(exPrefix)) {
@@ -441,15 +430,13 @@ public Future<?> runComponent(
 
     // Submit the planning and execution thread
     return executor.submit(
-      new ComponentExecutingThread(
-        cid,
-        this.config,
-        role_bindings,
-        apis,
-        callbackUrl,
-        callbackCookies
-      )
-    );
+        new ComponentExecutingThread(
+            cid,
+            this.config,
+            role_bindings,
+            apis,
+            callbackUrl,
+            callbackCookies));
   }
 
   public static void invalidateCachedAPIs() {
@@ -457,56 +444,53 @@ public static void invalidateCachedAPIs() {
   }
 
   public String runExpandedTemplate(
-    String origtplid,
-    String templatejson,
-    String consjson,
-    String seedjson,
-    String seedconsjson,
-    String callbackUrl,
-    ServletContext context
-  ) {
+      String origtplid,
+      String templatejson,
+      String consjson,
+      String seedjson,
+      String seedconsjson,
+      String callbackUrl,
+      ServletContext context) {
     Gson json = JsonHandler.createTemplateGson();
     Template xtpl = JsonHandler.getTemplateFromJSON(
-      json,
-      templatejson,
-      consjson
-    );
+        json,
+        templatejson,
+        consjson);
     xtpl.autoLayout();
     Template seedtpl = JsonHandler.getTemplateFromJSON(
-      json,
-      seedjson,
-      seedconsjson
-    );
+        json,
+        seedjson,
+        seedconsjson);
 
     return createPlan(origtplid, context, xtpl, seedtpl, callbackUrl);
   }
 
   private String createPlan(
-    String origtplid,
-    ServletContext context,
-    Template xtpl,
-    Template seedtpl,
-    String callbackUrl
-  ) {
+      String origtplid,
+      ServletContext context,
+      Template xtpl,
+      Template seedtpl,
+      String callbackUrl) {
     String requestid = UuidGen.generateAUuid("");
     WorkflowGenerationAPI wg = new WorkflowGenerationKB(
-      props,
-      DataFactory.getReasoningAPI(props),
-      DataFactory.getCreationAPI(props),
-      ComponentFactory.getReasoningAPI(props),
-      ComponentFactory.getCreationAPI(props),
-      ResourceFactory.getAPI(props),
-      requestid
-    );
+        props,
+        DataFactory.getReasoningAPI(props),
+        DataFactory.getCreationAPI(props),
+        ComponentFactory.getReasoningAPI(props),
+        ComponentFactory.getCreationAPI(props),
+        ResourceFactory.getAPI(props),
+        requestid);
 
     ExecutionPlan plan = wg.getExecutionPlan(xtpl);
 
     String seedid = UuidGen.generateURIUuid((URIEntity) seedtpl);
     if (plan != null) {
       // Save the expanded template, seeded template and plan
-      if (!xtpl.save()) return "";
+      if (!xtpl.save())
+        return "";
 
-      if (!seedtpl.saveAs(seedid)) return "";
+      if (!seedtpl.saveAs(seedid))
+        return "";
 
       if (plan.save()) {
         RuntimePlan rplan = new RuntimePlan(plan);
@@ -532,12 +516,11 @@ public Response reRunPlan(String run_id, ServletContext context) {
     String callbackUrl = plan.getCallbackUrl();
     tc.end();
 
-    if (
-      createPlan(orig_tp_id, context, xtpl, seedtpl, callbackUrl) == ""
-    ) return Response
-      .status(Response.Status.INTERNAL_SERVER_ERROR)
-      .entity("Internal error")
-      .build();
+    if (createPlan(orig_tp_id, context, xtpl, seedtpl, callbackUrl) == "")
+      return Response
+          .status(Response.Status.INTERNAL_SERVER_ERROR)
+          .entity("Internal error")
+          .build();
     return Response.status(Response.Status.CREATED).entity("CREATED").build();
   }
 
@@ -597,11 +580,10 @@ private String urlToString(URL url) {
       // normally, 3xx is redirect
       int status = conn.getResponseCode();
       if (status != HttpURLConnection.HTTP_OK) {
-        if (
-          status == HttpURLConnection.HTTP_MOVED_TEMP ||
-          status == HttpURLConnection.HTTP_MOVED_PERM ||
-          status == HttpURLConnection.HTTP_SEE_OTHER
-        ) redirect = true;
+        if (status == HttpURLConnection.HTTP_MOVED_TEMP ||
+            status == HttpURLConnection.HTTP_MOVED_PERM ||
+            status == HttpURLConnection.HTTP_SEE_OTHER)
+          redirect = true;
       }
 
       if (redirect) {
@@ -613,8 +595,7 @@ private String urlToString(URL url) {
       }
 
       BufferedReader in = new BufferedReader(
-        new InputStreamReader(conn.getInputStream())
-      );
+          new InputStreamReader(conn.getInputStream()));
       String inputLine;
       StringBuffer html = new StringBuffer();
 
@@ -629,197 +610,164 @@ private String urlToString(URL url) {
     return null;
   }
 
-  public String publishRun(String runid) {
+  /**
+   * @param runid
+   * @return
+   * @throws Exception
+   */
+  public ProvenanceResponseSchema publishRun(String runid) throws Exception {
     HashMap<String, String> retmap = new HashMap<String, String>();
     ExecutionMonitorAPI monitor = config.getDomainExecutionMonitor();
     RuntimePlan plan = monitor.getRunDetails(runid);
+    ProvenanceResponseSchema response = null;
     if (plan.getRuntimeInfo().getStatus() != Status.SUCCESS) {
-      retmap.put("error", "Can only publish successfully completed runs");
-    } else try {
-      // Mapper opmm = new Mapper();
-
-      PublisherConfig publisher = config.portalConfig.getPublisher();
-
-      FileUploadServerConfig publishUrl = publisher.getUploadServer();
-      String tstoreurl = publisher.getTstorePublishUrl();
-      String tstorequery = publisher.getTstoreQueryUrl();
-      String exportName = publisher.getExportName();
-      String exportUrl = publisher.getUrl();
-
-      String uploadURL = publishUrl.getUrl();
-      String uploadUsername = publishUrl.getUsername();
-      String uploadDirectory = publishUrl.getDirectory();
-      String uploadPassword = publishUrl.getPassword();
-      long uploadMaxSize = publishUrl.getMaxUploadSize();
-      // opmm.setPublishExportPrefix(puburl);
-
-      String rname = runid.substring(runid.indexOf('#') + 1);
-      // String runurl = opmm.getRunUrl(rname);
-
-      // Fetch expanded template (to get data binding ids)
-      TemplateCreationAPI tc = TemplateFactory.getCreationAPI(props);
-      Template xtpl = tc.getTemplate(plan.getExpandedTemplateID());
-      tc.end();
-
-      HashMap<String, String> varBindings = new HashMap<String, String>();
-      for (Variable var : xtpl.getVariables()) {
-        varBindings.put(var.getID(), var.getBinding().getID());
-      }
+      throw new Exception("Can only publish successfully completed runs");
+    } else
+      try {
+        // Mapper opmm = new Mapper();
+        String webServerDirectory = "/tmp/";
+        String webServerDomain = "http://localhost";
+        FilePublisher.Type type = FilePublisher.Type.FILE_SYSTEM;
+        FilePublisher filePublisher = new FilePublisher(type, webServerDirectory,
+            webServerDomain);
+        String domain = config.getDomainId();
+        String catalogRepositoryDirectory = "domains";
+        PublisherConfig publisher = config.portalConfig.getPublisher();
+
+        String runName = runid.substring(runid.indexOf('#') + 1);
+        // String runurl = opmm.getRunUrl(rname);
+
+        // Fetch expanded template (to get data binding ids)
+        TemplateCreationAPI tc = TemplateFactory.getCreationAPI(props);
+        Template xtpl = tc.getTemplate(plan.getExpandedTemplateID());
+        tc.end();
+
+        HashMap<String, String> varBindings = new HashMap<String, String>();
+        for (Variable var : xtpl.getVariables()) {
+          varBindings.put(var.getID(), var.getBinding().getID());
+        }
 
-      // Create a temporary directory to upload/move
-      File _tmpdir = File.createTempFile("temp", "");
-      File tempdir = new File(_tmpdir.getParent() + "/" + rname);
-      FileUtils.deleteQuietly(tempdir);
-      if (!_tmpdir.delete() || !tempdir.mkdirs()) throw new Exception(
-        "Cannot create temp directory"
-      );
-
-      File datadir = new File(tempdir.getAbsolutePath() + "/data");
-      File codedir = new File(tempdir.getAbsolutePath() + "/code");
-      datadir.mkdirs();
-      codedir.mkdirs();
-
-      /*
-       * String tupurl = upurl + "/" + tempdir.getName();
-       * String dataurl = tupurl + "/data";
-       * String codeurl = tupurl + "/code";
-       * String cdir = props.getProperty("lib.domain.code.storage");
-       * String ddir = props.getProperty("lib.domain.data.storage");
-       */
-
-      FileUtils.deleteQuietly(tempdir);
-
-      // Create the temporal directory to store data, components, workflow and
-      // exection
-      tempdir.mkdirs();
-      File dcontdir = new File(tempdir.getAbsolutePath() + "/ont/data");
-      File acontdir = new File(tempdir.getAbsolutePath() + "/ont/components");
-      File wflowdir = new File(tempdir.getAbsolutePath() + "/ont/workflows");
-      File execsdir = new File(tempdir.getAbsolutePath() + "/ont/executions");
-
-      File run_exportdir = new File(tempdir.getAbsolutePath() + "/export/run");
-      File tpl_exportdir = new File(
-        tempdir.getAbsolutePath() + "/export/template"
-      );
-      dcontdir.mkdirs();
-      acontdir.mkdirs();
-      wflowdir.mkdirs();
-      execsdir.mkdirs();
-      run_exportdir.mkdirs();
-      tpl_exportdir.mkdirs();
-
-      // Merge both concrete and abstract component libraries from WINGS
-      String aclib = props.getProperty("lib.concrete.url");
-      String abslib = props.getProperty("lib.abstract.url");
-      // String workflow_lib = props.getProperty("lib.domain.workflow.url");
-
-      String aclibdata = urlToString(new URL(aclib));
-      String abslibdata = urlToString(new URL(abslib));
-      // String workflow_lib_data = urlToString(new URL(workflow_lib));
-
-      abslibdata = abslibdata.replaceFirst("<\\?xml.+?>", "");
-      abslibdata =
-        Pattern
-          .compile("<rdf:RDF.+?>", Pattern.DOTALL)
-          .matcher(abslibdata)
-          .replaceFirst("");
-      abslibdata = abslibdata.replaceFirst("<\\/rdf:RDF>", "");
-      aclibdata = aclibdata.replaceFirst("<\\/rdf:RDF>", "");
-
-      String rplandata = urlToString(new URL(runid));
-
-      // write aclibfie and rplanfile
-      aclibdata += abslibdata + "</rdf:RDF>\n";
-      File aclibfile = new File(acontdir.getAbsolutePath() + "/library.owl");
-      File rplanfile = new File(
-        execsdir.getAbsolutePath() + "/" + plan.getName() + ".owl"
-      );
-      FileUtils.write(aclibfile, aclibdata);
-      FileUtils.write(rplanfile, rplandata);
-
-      // workflow file?
-      URL otplurl = new URL(plan.getOriginalTemplateID());
-      File otplfile = new File(
-        wflowdir.getAbsolutePath() + "/" + otplurl.getRef() + ".owl"
-      );
-      String otpldata = urlToString(otplurl);
-      FileUtils.write(otplfile, otpldata);
-
-      Catalog catalog = new Catalog(
-        config.getDomainId(),
-        exportName,
-        publisher.getDomainsDir(),
-        aclibfile.getAbsolutePath()
-      );
-
-      WorkflowExecutionExport exp = new WorkflowExecutionExport(
-        rplanfile.getAbsolutePath(),
-        catalog,
-        exportUrl,
-        exportName,
-        tstorequery,
-        config.getDomainId()
-      );
-      exp.setUploadURL(uploadURL);
-      exp.setUploadUsername(uploadUsername);
-      exp.setUploadPassword(uploadPassword);
-      exp.setUploadMaxSize(uploadMaxSize);
-      exp.setUploadDirectory(uploadDirectory);
-      String serialization = "TURTLE";
-
-      // publish the catalog
-      String domainPath = catalog.exportCatalog(null, serialization);
-      File domainFile = new File(domainPath);
-      this.publishFile(
-          tstoreurl,
-          catalog.getDomainGraphURI(),
-          domainFile.getAbsolutePath()
-        );
-
-      // execution
-      String executionFilePath = run_exportdir + File.separator + "execution";
-      String graphUri = exp.exportAsOPMW(executionFilePath, serialization);
-      if (!exp.isExecPublished()) {
-        this.publishFile(tstoreurl, graphUri, executionFilePath);
-
-        // expandedTemplate
-        String expandedTemplateFilePath =
-          run_exportdir + File.separator + "expandedTemplate";
-        String expandedTemplateGraphUri = exp
-          .getConcreteTemplateExport()
-          .exportAsOPMW(expandedTemplateFilePath, serialization);
-        if (
-          !exp.getConcreteTemplateExport().isTemplatePublished()
-        ) this.publishFile(
-            tstoreurl,
-            expandedTemplateGraphUri,
-            expandedTemplateFilePath
-          );
-
-        // abstract
-        WorkflowTemplateExport abstractTemplateExport = exp
-          .getConcreteTemplateExport()
-          .getAbstractTemplateExport();
-        if (abstractTemplateExport != null) {
-          String abstractFilePath = run_exportdir + File.separator + "abstract";
-          String abstractGraphUri = abstractTemplateExport.exportAsOPMW(
-            abstractFilePath,
-            serialization
-          );
-          if (!abstractTemplateExport.isTemplatePublished()) this.publishFile(
-              tstoreurl,
-              abstractGraphUri,
-              abstractFilePath
-            );
+        // Create a temporary directory to upload/move
+        File _tmpdir = File.createTempFile("temp", "");
+        File runTmpDirectory = new File(_tmpdir.getParent() + "/" + runName);
+        FileUtils.deleteQuietly(runTmpDirectory);
+        if (!_tmpdir.delete() || !runTmpDirectory.mkdirs())
+          throw new Exception(
+              "Cannot create temp directory");
+
+        File datadir = new File(runTmpDirectory.getAbsolutePath() + "/data");
+        File codedir = new File(runTmpDirectory.getAbsolutePath() + "/code");
+        datadir.mkdirs();
+        codedir.mkdirs();
+
+        /*
+         * String tupurl = upurl + "/" + tempdir.getName();
+         * String dataurl = tupurl + "/data";
+         * String codeurl = tupurl + "/code";
+         * String cdir = props.getProperty("lib.domain.code.storage");
+         * String ddir = props.getProperty("lib.domain.data.storage");
+         */
+
+        FileUtils.deleteQuietly(runTmpDirectory);
+
+        // Create the temporal directory to store data, components, workflow and
+        // exection
+        runTmpDirectory.mkdirs();
+        File dcontdir = new File(runTmpDirectory.getAbsolutePath() + "/ont/data");
+        File acontdir = new File(runTmpDirectory.getAbsolutePath() + "/ont/components");
+        File wflowdir = new File(runTmpDirectory.getAbsolutePath() + "/ont/workflows");
+        File execsdir = new File(runTmpDirectory.getAbsolutePath() + "/ont/executions");
+
+        File run_exportdir = new File(runTmpDirectory.getAbsolutePath() + "/export/run");
+        File tpl_exportdir = new File(
+            runTmpDirectory.getAbsolutePath() + "/export/template");
+        dcontdir.mkdirs();
+        acontdir.mkdirs();
+        wflowdir.mkdirs();
+        execsdir.mkdirs();
+        run_exportdir.mkdirs();
+        tpl_exportdir.mkdirs();
+
+        // Merge both concrete and abstract component libraries from WINGS
+        String aclib = props.getProperty("lib.concrete.url");
+        String abslib = props.getProperty("lib.abstract.url");
+        // String workflow_lib = props.getProperty("lib.domain.workflow.url");
+
+        String aclibdata = urlToString(new URL(aclib));
+        String abslibdata = urlToString(new URL(abslib));
+        // String workflow_lib_data = urlToString(new URL(workflow_lib));
+
+        abslibdata = abslibdata.replaceFirst("<\\?xml.+?>", "");
+        abslibdata = Pattern
+            .compile("<rdf:RDF.+?>", Pattern.DOTALL)
+            .matcher(abslibdata)
+            .replaceFirst("");
+        abslibdata = abslibdata.replaceFirst("<\\/rdf:RDF>", "");
+        aclibdata = aclibdata.replaceFirst("<\\/rdf:RDF>", "");
+
+        String rplandata = urlToString(new URL(runid));
+
+        // write aclibfie and rplanfile
+        aclibdata += abslibdata + "</rdf:RDF>\n";
+        File componentLibraryFilePath = new File(
+            acontdir.getAbsolutePath() + "/library.owl");
+        File planFilePath = new File(
+            execsdir.getAbsolutePath() + "/" + plan.getName() + ".owl");
+        FileUtils.write(componentLibraryFilePath, aclibdata);
+        FileUtils.write(planFilePath, rplandata);
+
+        // workflow file?
+        URL otplurl = new URL(plan.getOriginalTemplateID());
+        File otplfile = new File(
+            wflowdir.getAbsolutePath() + "/" + otplurl.getRef() + ".owl");
+        String otpldata = urlToString(otplurl);
+        FileUtils.write(otplfile, otpldata);
+
+        String executionFilePath = run_exportdir + File.separator + "execution";
+        String expandedTemplateFilePath = run_exportdir + File.separator + "expandedTemplate";
+        String abstractFilePath = run_exportdir + File.separator + "abstract";
+
+        /**
+         * Publisher configuration
+         */
+        Lang serialization = Lang.TURTLE;
+        String exportUrl = config.portalConfig.getPublisher().getTripleStore().getExportUrl();
+        String exportPath = config.portalConfig.getPublisher().getTripleStore().getExportPath();
+        String endpointQueryURI = config.portalConfig.getPublisher().getTripleStore().getQueryUrl();
+        String endpointPostURI = config.portalConfig.getPublisher().getTripleStore().getPublishUrl();
+        TriplesPublisher executionPublisher = new TriplesPublisher(
+            endpointQueryURI,
+            endpointPostURI,
+            exportUrl,
+            exportPath,
+            serialization);
+
+        TriplesPublisher catalogPublisher = new TriplesPublisher(
+            endpointQueryURI,
+            endpointPostURI,
+            Constants.CATALOG_URI,
+            exportPath,
+            serialization);
+
+        try {
+          response = Mapper.main(
+              domain,
+              catalogRepositoryDirectory,
+              componentLibraryFilePath.getAbsolutePath(),
+              planFilePath.getAbsolutePath(),
+              executionFilePath,
+              expandedTemplateFilePath,
+              abstractFilePath,
+              filePublisher,
+              executionPublisher,
+              catalogPublisher);
+        } catch (Exception e) {
+          throw new Exception("Error publishing run: " + e.getMessage());
         }
+      } catch (Exception e) {
+        throw new Exception("Error publishing run: " + e.getMessage());
       }
-
-      retmap.put("url", exp.getTransformedExecutionURI());
-    } catch (Exception e) {
-      e.printStackTrace();
-      retmap.put("error", e.getMessage());
-    }
-    return json.toJson(retmap);
+    return response;
   }
 
   /*
@@ -858,8 +806,7 @@ public String publishRun(String runid) {
    */
   private void publishFile(String tstoreurl, String graphurl, String filepath) {
     System.out.println(
-      "Publishing the filepath " + filepath + " on graph " + graphurl
-    );
+        "Publishing the filepath " + filepath + " on graph " + graphurl);
     try {
       CloseableHttpClient httpClient = HttpClients.createDefault();
       HttpPut putRequest = new HttpPut(tstoreurl + "?graph=" + graphurl);
@@ -868,11 +815,11 @@ private void publishFile(String tstoreurl, String graphurl, String filepath) {
       int timeoutSeconds = 10;
       int CONNECTION_TIMEOUT_MS = timeoutSeconds * 1000;
       RequestConfig requestConfig = RequestConfig
-        .custom()
-        .setConnectionRequestTimeout(CONNECTION_TIMEOUT_MS)
-        .setConnectTimeout(CONNECTION_TIMEOUT_MS)
-        .setSocketTimeout(CONNECTION_TIMEOUT_MS)
-        .build();
+          .custom()
+          .setConnectionRequestTimeout(CONNECTION_TIMEOUT_MS)
+          .setConnectTimeout(CONNECTION_TIMEOUT_MS)
+          .setSocketTimeout(CONNECTION_TIMEOUT_MS)
+          .build();
       putRequest.setConfig(requestConfig);
 
       File file = new File(filepath);
diff --git a/portal/src/main/java/edu/isi/wings/portal/controllers/TemplateController.java b/portal/src/main/java/edu/isi/wings/portal/controllers/TemplateController.java
index 92792dd4..e8b319e4 100644
--- a/portal/src/main/java/edu/isi/wings/portal/controllers/TemplateController.java
+++ b/portal/src/main/java/edu/isi/wings/portal/controllers/TemplateController.java
@@ -218,8 +218,9 @@ private ArrayList<HashMap<String, Object>> getTemplateInputs(
       varDims.put(varid, r.getDimensionality());
     }
 
-    ArrayList<HashMap<String, Object>> returnList =
-      new ArrayList<HashMap<String, Object>>();
+    ArrayList<HashMap<String, Object>> returnList = new ArrayList<
+      HashMap<String, Object>
+    >();
 
     // Some caches
     HashMap<String, Boolean> varsDone = new HashMap<String, Boolean>();
diff --git a/portal/src/main/java/edu/isi/wings/portal/filters/servlets/CompressionFilter.java b/portal/src/main/java/edu/isi/wings/portal/filters/servlets/CompressionFilter.java
index af682b52..0c1e70bd 100644
--- a/portal/src/main/java/edu/isi/wings/portal/filters/servlets/CompressionFilter.java
+++ b/portal/src/main/java/edu/isi/wings/portal/filters/servlets/CompressionFilter.java
@@ -35,13 +35,9 @@ public void doFilter(
           String ctype = request.getHeader("content-type");
           if (
             (ctype != null) &&
-            (
-              (
-                ctype.contains("zip") ||
+            ((ctype.contains("zip") ||
                 ctype.contains("compress") ||
-                ctype.contains("image")
-              )
-            )
+                ctype.contains("image")))
           ) compress = false;
         }
         if (compress) {
diff --git a/portal/src/main/java/edu/isi/wings/portal/resources/DataResource.java b/portal/src/main/java/edu/isi/wings/portal/resources/DataResource.java
index a0f1282d..6bb5dd9e 100644
--- a/portal/src/main/java/edu/isi/wings/portal/resources/DataResource.java
+++ b/portal/src/main/java/edu/isi/wings/portal/resources/DataResource.java
@@ -32,8 +32,8 @@ public class DataResource extends WingsResource {
   public void init() {
     super.init();
     this.loadExternal = ("/external".equals(external));
-    if (this.hasPermissions() && !this.isPage("intro")) this.dc =
-      new DataController(config, this.loadExternal);
+    if (this.hasPermissions() && !this.isPage("intro"))
+      this.dc = new DataController(config, this.loadExternal);
   }
 
   @PreDestroy
@@ -64,7 +64,8 @@ public void getIntroduction() {
   @Path("getDataJSON")
   @Produces(MediaType.APPLICATION_JSON)
   public String getDataJSON(@QueryParam("data_id") String data_id) {
-    if (this.dc != null) return this.dc.getDataJSON(data_id);
+    if (this.dc != null)
+      return this.dc.getDataJSON(data_id);
     return null;
   }
 
@@ -92,7 +93,8 @@ public String runSensorComponent(@QueryParam("data_id") final String dataid) {
   @Path("getDataTypeJSON")
   @Produces(MediaType.APPLICATION_JSON)
   public String getDataTypeJSON(@QueryParam("data_type") String data_type) {
-    if (this.dc != null) return this.dc.getDatatypeJSON(data_type);
+    if (this.dc != null)
+      return this.dc.getDatatypeJSON(data_type);
     return null;
   }
 
@@ -100,7 +102,8 @@ public String getDataTypeJSON(@QueryParam("data_type") String data_type) {
   @Path("getDataHierarchyJSON")
   @Produces(MediaType.APPLICATION_JSON)
   public String getDataHierarchyJSON() {
-    if (this.dc != null) return this.dc.getDataHierarchyJSON();
+    if (this.dc != null)
+      return this.dc.getDataHierarchyJSON();
     return null;
   }
 
@@ -108,7 +111,8 @@ public String getDataHierarchyJSON() {
   @Path("getNodeDataHierarchyJSON")
   @Produces(MediaType.APPLICATION_JSON)
   public String getNodeDataHierarchyJSON(@QueryParam("node") String nodeid) {
-    if (this.dc != null) return this.dc.getNodeDataHierarchyJSON(nodeid);
+    if (this.dc != null)
+      return this.dc.getNodeDataHierarchyJSON(nodeid);
     return null;
   }
 
@@ -116,7 +120,8 @@ public String getNodeDataHierarchyJSON(@QueryParam("node") String nodeid) {
   @Path("getDataListJSON")
   @Produces(MediaType.APPLICATION_JSON)
   public String getDataListJSON() {
-    if (this.dc != null) return this.dc.getDataListJSON();
+    if (this.dc != null)
+      return this.dc.getDataListJSON();
     return null;
   }
 
@@ -124,7 +129,8 @@ public String getDataListJSON() {
   @Path("fetch")
   @Produces(MediaType.APPLICATION_OCTET_STREAM)
   public Response fetchData(@QueryParam("data_id") String data_id) {
-    if (this.dc != null) return this.dc.streamData(data_id, this.context);
+    if (this.dc != null)
+      return this.dc.streamData(data_id, this.context);
     return Response.status(Status.FORBIDDEN).build();
   }
 
@@ -132,21 +138,21 @@ public Response fetchData(@QueryParam("data_id") String data_id) {
   @Path("setMetadataFromSensorOutput")
   @Produces(MediaType.TEXT_PLAIN)
   public String setMetadataFromSensorOutput(
-    @QueryParam("data_id") String data_id,
-    @JsonProperty("plan") ExecutionPlan plan
-  ) {
-    if (this.dc != null) return this.dc.setMetadataFromSensorOutput(
-        data_id,
-        plan
-      );
+      @QueryParam("data_id") String data_id,
+      @JsonProperty("plan") ExecutionPlan plan) {
+    if (this.dc != null)
+      return this.dc.setMetadataFromSensorOutput(
+          data_id,
+          plan);
     return null;
   }
 
   @POST
   @Path("publish")
   @Produces(MediaType.TEXT_PLAIN)
-  public String publishData(@FormParam("data_id") String data_id) {
-    if (this.dc != null) return this.dc.publishData(data_id);
+  public String publishData(@FormParam("data_id") String data_id) throws Exception {
+    if (this.dc != null)
+      return this.dc.publishData(data_id);
     return null;
   }
 
@@ -154,12 +160,9 @@ public String publishData(@FormParam("data_id") String data_id) {
   @Path("saveDataJSON")
   @Produces(MediaType.TEXT_PLAIN)
   public String saveDataJSON(
-    @FormParam("data_id") String data_id,
-    @FormParam("propvals_json") String json
-  ) {
-    if (
-      this.dc != null && this.isOwner() && this.dc.saveDataJSON(data_id, json)
-    ) {
+      @FormParam("data_id") String data_id,
+      @FormParam("propvals_json") String json) {
+    if (this.dc != null && this.isOwner() && this.dc.saveDataJSON(data_id, json)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
@@ -170,12 +173,9 @@ public String saveDataJSON(
   @Path("saveDataTypeJSON")
   @Produces(MediaType.APPLICATION_JSON)
   public String saveDataTypeJSON(
-    @FormParam("data_type") String data_type,
-    @FormParam("props_json") String json
-  ) {
-    if (
-      this.dc != null && this.isOwner() && !config.portalConfig.isSandboxed()
-    ) {
+      @FormParam("data_type") String data_type,
+      @FormParam("props_json") String json) {
+    if (this.dc != null && this.isOwner() && !config.portalConfig.isSandboxed()) {
       RunController.invalidateCachedAPIs();
       return this.dc.saveDatatypeJSON(data_type, json);
     }
@@ -186,15 +186,12 @@ public String saveDataTypeJSON(
   @Path("newDataType")
   @Produces(MediaType.TEXT_PLAIN)
   public String newDataType(
-    @FormParam("data_type") String data_type,
-    @FormParam("parent_type") String parent_type
-  ) {
-    if (
-      this.dc != null &&
-      this.isOwner() &&
-      !config.portalConfig.isSandboxed() &&
-      this.dc.addDatatype(parent_type, data_type)
-    ) {
+      @FormParam("data_type") String data_type,
+      @FormParam("parent_type") String parent_type) {
+    if (this.dc != null &&
+        this.isOwner() &&
+        !config.portalConfig.isSandboxed() &&
+        this.dc.addDatatype(parent_type, data_type)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
@@ -207,12 +204,10 @@ public String newDataType(
   public String delDataTypes(@FormParam("data_type") String dtypes) {
     Gson gson = new Gson();
     String[] data_types = gson.fromJson(dtypes, String[].class);
-    if (
-      this.dc != null &&
-      this.isOwner() &&
-      !config.portalConfig.isSandboxed() &&
-      this.dc.delDatatypes(data_types)
-    ) {
+    if (this.dc != null &&
+        this.isOwner() &&
+        !config.portalConfig.isSandboxed() &&
+        this.dc.delDatatypes(data_types)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
@@ -223,16 +218,13 @@ public String delDataTypes(@FormParam("data_type") String dtypes) {
   @Path("moveDatatypeTo")
   @Produces(MediaType.TEXT_PLAIN)
   public String moveDatatypeTo(
-    @FormParam("data_type") String data_type,
-    @FormParam("from_parent_type") String from_parent_type,
-    @FormParam("to_parent_type") String to_parent_type
-  ) {
-    if (
-      this.dc != null &&
-      this.isOwner() &&
-      !config.portalConfig.isSandboxed() &&
-      this.dc.moveDatatypeTo(data_type, from_parent_type, to_parent_type)
-    ) {
+      @FormParam("data_type") String data_type,
+      @FormParam("from_parent_type") String from_parent_type,
+      @FormParam("to_parent_type") String to_parent_type) {
+    if (this.dc != null &&
+        this.isOwner() &&
+        !config.portalConfig.isSandboxed() &&
+        this.dc.moveDatatypeTo(data_type, from_parent_type, to_parent_type)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
@@ -243,16 +235,13 @@ public String moveDatatypeTo(
   @Path("moveDataTo")
   @Produces(MediaType.TEXT_PLAIN)
   public String moveDataTo(
-    @FormParam("data_id") String data_id,
-    @FormParam("from_parent_type") String from_parent_type,
-    @FormParam("to_parent_type") String to_parent_type
-  ) {
-    if (
-      this.dc != null &&
-      this.isOwner() &&
-      !config.portalConfig.isSandboxed() &&
-      this.dc.moveDataTo(data_id, from_parent_type, to_parent_type)
-    ) {
+      @FormParam("data_id") String data_id,
+      @FormParam("from_parent_type") String from_parent_type,
+      @FormParam("to_parent_type") String to_parent_type) {
+    if (this.dc != null &&
+        this.isOwner() &&
+        !config.portalConfig.isSandboxed() &&
+        this.dc.moveDataTo(data_id, from_parent_type, to_parent_type)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
@@ -263,15 +252,12 @@ public String moveDataTo(
   @Path("addDataForType")
   @Produces(MediaType.TEXT_PLAIN)
   public String addDataForType(
-    @FormParam("data_id") String data_id,
-    @FormParam("data_type") String data_type
-  ) {
-    if (
-      this.dc != null &&
-      this.isOwner() &&
-      !config.portalConfig.isSandboxed() &&
-      this.dc.addDataForDatatype(data_id, data_type)
-    ) {
+      @FormParam("data_id") String data_id,
+      @FormParam("data_type") String data_type) {
+    if (this.dc != null &&
+        this.isOwner() &&
+        !config.portalConfig.isSandboxed() &&
+        this.dc.addDataForDatatype(data_id, data_type)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
@@ -282,12 +268,9 @@ public String addDataForType(
   @Path("addRemoteDataForType")
   @Produces(MediaType.TEXT_PLAIN)
   public String addRemoteDataForType(
-    @FormParam("data_url") String data_url,
-    @FormParam("data_type") String data_type
-  ) {
-    if (
-      this.dc != null && this.isOwner() && !config.portalConfig.isSandboxed()
-    ) {
+      @FormParam("data_url") String data_url,
+      @FormParam("data_type") String data_type) {
+    if (this.dc != null && this.isOwner() && !config.portalConfig.isSandboxed()) {
       RunController.invalidateCachedAPIs();
       return this.dc.addRemoteDataForType(data_url, data_type);
     }
@@ -298,12 +281,10 @@ public String addRemoteDataForType(
   @Path("delData")
   @Produces(MediaType.TEXT_PLAIN)
   public String delData(@FormParam("data_id") String data_id) {
-    if (
-      this.dc != null &&
-      this.isOwner() &&
-      !config.portalConfig.isSandboxed() &&
-      this.dc.delData(data_id)
-    ) {
+    if (this.dc != null &&
+        this.isOwner() &&
+        !config.portalConfig.isSandboxed() &&
+        this.dc.delData(data_id)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
@@ -314,15 +295,12 @@ public String delData(@FormParam("data_id") String data_id) {
   @Path("renameData")
   @Produces(MediaType.TEXT_PLAIN)
   public String renameData(
-    @FormParam("data_id") String data_id,
-    @FormParam("newid") String newid
-  ) {
-    if (
-      this.dc != null &&
-      this.isOwner() &&
-      !config.portalConfig.isSandboxed() &&
-      this.dc.renameData(data_id, newid)
-    ) {
+      @FormParam("data_id") String data_id,
+      @FormParam("newid") String newid) {
+    if (this.dc != null &&
+        this.isOwner() &&
+        !config.portalConfig.isSandboxed() &&
+        this.dc.renameData(data_id, newid)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
@@ -333,15 +311,12 @@ public String renameData(
   @Path("renameDataType")
   @Produces(MediaType.TEXT_PLAIN)
   public String renameDataType(
-    @FormParam("data_type") String data_type,
-    @FormParam("newid") String newid
-  ) {
-    if (
-      this.dc != null &&
-      this.isOwner() &&
-      !config.portalConfig.isSandboxed() &&
-      this.dc.renameDataType(data_type, newid)
-    ) {
+      @FormParam("data_type") String data_type,
+      @FormParam("newid") String newid) {
+    if (this.dc != null &&
+        this.isOwner() &&
+        !config.portalConfig.isSandboxed() &&
+        this.dc.renameDataType(data_type, newid)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
@@ -352,15 +327,12 @@ public String renameDataType(
   @Path("setDataLocation")
   @Produces(MediaType.TEXT_PLAIN)
   public String setDataLocation(
-    @FormParam("data_id") String data_id,
-    @FormParam("location") String location
-  ) {
-    if (
-      this.dc != null &&
-      this.isOwner() &&
-      !config.portalConfig.isSandboxed() &&
-      this.dc.setDataLocation(data_id, location)
-    ) {
+      @FormParam("data_id") String data_id,
+      @FormParam("location") String location) {
+    if (this.dc != null &&
+        this.isOwner() &&
+        !config.portalConfig.isSandboxed() &&
+        this.dc.setDataLocation(data_id, location)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
@@ -371,25 +343,21 @@ public String setDataLocation(
   @Path("addBatchData")
   @Produces(MediaType.TEXT_PLAIN)
   public String addBatchData(
-    @FormParam("data_type") String data_type,
-    @FormParam("data_ids") String dids,
-    @FormParam("data_locations") String locs
-  ) {
+      @FormParam("data_type") String data_type,
+      @FormParam("data_ids") String dids,
+      @FormParam("data_locations") String locs) {
     Gson gson = new Gson();
     String[] data_ids = gson.fromJson(dids, String[].class);
     String[] data_locations = gson.fromJson(locs, String[].class);
-    if (
-      this.dc != null &&
-      this.isOwner() &&
-      !config.portalConfig.isSandboxed() &&
-      this.dc.addBatchData(
-          data_type,
-          data_ids,
-          data_locations,
-          this.request,
-          this.context
-        )
-    ) {
+    if (this.dc != null &&
+        this.isOwner() &&
+        !config.portalConfig.isSandboxed() &&
+        this.dc.addBatchData(
+            data_type,
+            data_ids,
+            data_locations,
+            this.request,
+            this.context)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
@@ -400,13 +368,10 @@ public String addBatchData(
   @Path("registerData")
   @Produces(MediaType.TEXT_PLAIN)
   public String registerData(
-    @FormParam("data_id") String data_id,
-    @FormParam("newname") String newname,
-    @FormParam("metadata_json") String json
-  ) {
-    if (
-      this.dc != null && this.isOwner() && !config.portalConfig.isSandboxed()
-    ) {
+      @FormParam("data_id") String data_id,
+      @FormParam("newname") String newname,
+      @FormParam("metadata_json") String json) {
+    if (this.dc != null && this.isOwner() && !config.portalConfig.isSandboxed()) {
       RunController.invalidateCachedAPIs();
       return this.dc.registerData(data_id, newname, json);
     }
@@ -417,17 +382,14 @@ public String registerData(
   @Path("importFromExternalCatalog")
   @Produces(MediaType.TEXT_PLAIN)
   public String importFromExternalCatalog(
-    @FormParam("data_id") String data_id,
-    @FormParam("data_type") String data_type,
-    @FormParam("propvals_json") String json,
-    @FormParam("location") String location
-  ) {
-    if (
-      this.dc != null &&
-      this.isOwner() &&
-      !config.portalConfig.isSandboxed() &&
-      this.dc.importFromExternalCatalog(data_id, data_type, json, location)
-    ) {
+      @FormParam("data_id") String data_id,
+      @FormParam("data_type") String data_type,
+      @FormParam("propvals_json") String json,
+      @FormParam("location") String location) {
+    if (this.dc != null &&
+        this.isOwner() &&
+        !config.portalConfig.isSandboxed() &&
+        this.dc.importFromExternalCatalog(data_id, data_type, json, location)) {
       RunController.invalidateCachedAPIs();
       return "OK";
     }
diff --git a/portal/src/main/java/edu/isi/wings/portal/resources/RunResource.java b/portal/src/main/java/edu/isi/wings/portal/resources/RunResource.java
index c0fbe775..adb1aec6 100644
--- a/portal/src/main/java/edu/isi/wings/portal/resources/RunResource.java
+++ b/portal/src/main/java/edu/isi/wings/portal/resources/RunResource.java
@@ -1,10 +1,14 @@
 package edu.isi.wings.portal.resources;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
+import com.google.gson.Gson;
+import edu.isi.kcap.wings.opmm.DataTypes.Links;
+import edu.isi.kcap.wings.opmm.DataTypes.ProvenanceResponseSchema;
 import edu.isi.wings.portal.classes.util.TemplateBindings;
 import edu.isi.wings.portal.controllers.RunController;
 import java.util.ArrayList;
 import java.util.Date;
+import java.util.HashMap;
 import javax.annotation.PostConstruct;
 import javax.annotation.PreDestroy;
 import javax.ws.rs.FormParam;
@@ -182,7 +186,17 @@ public String stopRun(@FormParam("run_id") String run_id) {
   @Path("publishRun")
   @Produces(MediaType.TEXT_PLAIN)
   public String publishRun(@FormParam("run_id") String run_id) {
-    if (this.rc != null) return this.rc.publishRun(run_id);
+    if (this.rc != null) {
+      try {
+        ProvenanceResponseSchema responseQuery = this.rc.publishRun(run_id);
+        Gson gson = new Gson();
+        String json = gson.toJson(responseQuery);
+        return json;
+      } catch (Exception e) {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+      }
+    }
     return null;
   }
 }
diff --git a/portal/src/main/java/edu/isi/wings/portal/resources/TemplateResource.java b/portal/src/main/java/edu/isi/wings/portal/resources/TemplateResource.java
index de497700..0ec7e2c2 100644
--- a/portal/src/main/java/edu/isi/wings/portal/resources/TemplateResource.java
+++ b/portal/src/main/java/edu/isi/wings/portal/resources/TemplateResource.java
@@ -67,7 +67,7 @@ public void destroy() {
   public void getIntroduction() {
     String intropage = "Template";
     if (!editor) intropage += "Browser"; else intropage +=
-      "Editor" + (tellme ? "Tellme" : "");
+    "Editor" + (tellme ? "Tellme" : "");
     this.loadIntroduction(intropage);
   }
 
diff --git a/portal/src/main/java/edu/isi/wings/portal/resources/UploadResource.java b/portal/src/main/java/edu/isi/wings/portal/resources/UploadResource.java
index 304c1390..602ad492 100644
--- a/portal/src/main/java/edu/isi/wings/portal/resources/UploadResource.java
+++ b/portal/src/main/java/edu/isi/wings/portal/resources/UploadResource.java
@@ -53,7 +53,7 @@ public String uploadFile(
     boolean isComponent = false;
     String storageDir = dom.getDomainDirectory() + "/";
     if ("data".equals(type)) storageDir +=
-      dom.getDataLibrary().getStorageDirectory(); else if (
+    dom.getDataLibrary().getStorageDirectory(); else if (
       "component".equals(type)
     ) {
       storageDir += dom.getConcreteComponentLibrary().getStorageDirectory();
diff --git a/portal/src/main/java/edu/isi/wings/portal/servlets/ProvenanceFileServlet.java b/portal/src/main/java/edu/isi/wings/portal/servlets/ProvenanceFileServlet.java
new file mode 100644
index 00000000..63398f83
--- /dev/null
+++ b/portal/src/main/java/edu/isi/wings/portal/servlets/ProvenanceFileServlet.java
@@ -0,0 +1,71 @@
+package edu.isi.wings.portal.servlets;
+
+import edu.isi.wings.portal.classes.config.Config;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import edu.isi.wings.portal.classes.config.ConfigLoader;
+
+public class ProvenanceFileServlet extends HttpServlet {
+
+  @Override
+  protected void doGet(HttpServletRequest request, HttpServletResponse response)
+      throws ServletException, IOException {
+    ConfigLoader configLoader = new ConfigLoader(request, null, null);
+    // TODO: replace the following with
+    // configLoader.portalConfig.getProvenanceDirectory();
+    String provenanceDirectoryPath = "/tmp" + File.separator + "wings" + File.separator + "provenance";
+    File provenanceDirectory = new File(provenanceDirectoryPath);
+
+    String requestFile = request.getPathInfo();
+    String filePath = provenanceDirectoryPath + File.separator + requestFile;
+    System.out.println("FileServlet: " + filePath);
+
+    File file = new File(filePath);
+    if (!file.exists()) {
+      response.sendError(HttpServletResponse.SC_NOT_FOUND); // 404.
+      return;
+    }
+    // check if filepath is in allowed directory
+    if (!isInsideDirectory(file, provenanceDirectory)) {
+      response.sendError(HttpServletResponse.SC_FORBIDDEN);
+      return;
+    }
+    // Set content type and headers for the response
+    response.setContentType("application/octet-stream");
+    response.setHeader(
+        "Content-Disposition",
+        "attachment; filename=\"" + file.getName() + "\"");
+
+    // Read the file and write its contents to the response output stream
+    try (
+        FileInputStream fis = new FileInputStream(filePath);
+        OutputStream out = response.getOutputStream()) {
+      byte[] buffer = new byte[4096];
+      int bytesRead;
+      while ((bytesRead = fis.read(buffer)) != -1) {
+        out.write(buffer, 0, bytesRead);
+      }
+    } catch (IOException e) {
+      // Handle exception
+      e.printStackTrace();
+    }
+  }
+
+  private static boolean isInsideDirectory(File file, File directory) {
+    File parent = file.getParentFile();
+    if (parent == null) {
+      return false;
+    } else if (parent.equals(directory)) {
+      return true;
+    } else {
+      return isInsideDirectory(parent, directory);
+    }
+  }
+}
diff --git a/portal/src/main/webapp/WEB-INF/web.xml b/portal/src/main/webapp/WEB-INF/web.xml
index f211dfc2..11c49601 100644
--- a/portal/src/main/webapp/WEB-INF/web.xml
+++ b/portal/src/main/webapp/WEB-INF/web.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <web-app xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee" 
-         xmlns:web="http://xmlns.jcp.org/xml/ns/javaee/web-app_3_1.xsd"
-         version="3.1" xmlns="http://xmlns.jcp.org/xml/ns/javaee">
+  xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee"
+  xmlns:web="http://xmlns.jcp.org/xml/ns/javaee/web-app_3_1.xsd"
+  version="3.1" xmlns="http://xmlns.jcp.org/xml/ns/javaee">
   <display-name>Wings Portal</display-name>
   <servlet>
     <description>Login page</description>
@@ -14,7 +14,7 @@
     <servlet-name>Login</servlet-name>
     <url-pattern>/login/*</url-pattern>
   </servlet-mapping>
-  
+
   <servlet>
     <description>Servlet to Export Graph</description>
     <display-name>Graph Exporter</display-name>
@@ -26,6 +26,17 @@
     <url-pattern>/export/*</url-pattern>
   </servlet-mapping>
 
+  <servlet>
+    <description>Servlet to obtain the Provenance Files</description>
+    <display-name>Provenance Files</display-name>
+    <servlet-name>ProvenanceFile</servlet-name>
+    <servlet-class>edu.isi.wings.portal.servlets.ProvenanceFileServlet</servlet-class>
+  </servlet>
+  <servlet-mapping>
+    <servlet-name>ProvenanceFile</servlet-name>
+    <url-pattern>/provenance/*</url-pattern>
+  </servlet-mapping>
+
   <servlet>
     <description></description>
     <display-name>SparqlEndpoint</display-name>
@@ -36,7 +47,7 @@
     <servlet-name>SparqlEndpoint</servlet-name>
     <url-pattern>/sparql</url-pattern>
   </servlet-mapping>
-  
+
   <servlet>
     <description>Wings Config</description>
     <display-name>Wings config</display-name>
@@ -46,9 +57,9 @@
   <servlet-mapping>
     <servlet-name>ViewConfig</servlet-name>
     <url-pattern>/config</url-pattern>
-  </servlet-mapping>  
-  
-  <!-- 
+  </servlet-mapping>
+
+  <!--
   	CORS & Compression filters for Non-REST-API servlets
   	The Jersey REST-APIs have their own filters and interceptors
   -->
@@ -78,11 +89,11 @@
     <dispatcher>REQUEST</dispatcher>
     <dispatcher>FORWARD</dispatcher>
   </filter-mapping>
-  
+
   <session-config>
     <session-timeout>43200</session-timeout>
   </session-config>
-  
+
   <security-role>
     <role-name>WingsUser</role-name>
   </security-role>
@@ -111,7 +122,7 @@
       <role-name>WingsAdmin</role-name>
     </auth-constraint>
   </security-constraint>
-  
+
   <login-config>
     <auth-method>FORM</auth-method>
     <form-login-config>
@@ -119,5 +130,5 @@
       <form-error-page>/jsp/login/login_failed.jsp</form-error-page>
     </form-login-config>
   </login-config>
-  
-</web-app>
+
+</web-app>
\ No newline at end of file
diff --git a/wings-docker/config/local-mosorio/portal.properties b/wings-docker/config/local-mosorio/portal.properties
deleted file mode 100644
index 1ec6f442..00000000
--- a/wings-docker/config/local-mosorio/portal.properties
+++ /dev/null
@@ -1,54 +0,0 @@
-{
-
-
-    storage = 
-    {
-        local = /Users/mosorio/Downloads/tomcat/wings/storage/default;
-        tdb = /Users/mosorio/Downloads/tomcat/wings/storage/default/TDB;
-    }
-
-    server = http://localhost:8080;
-    graphviz = /usr/bin/dot;
-    light-reasoner = false;
-    ontology = 
-    {
-        data = http://www.wings-workflows.org/ontology/data.owl;
-        component = http://www.wings-workflows.org/ontology/component.owl;
-        workflow = http://www.wings-workflows.org/ontology/workflow.owl;
-        execution = http://www.wings-workflows.org/ontology/execution.owl;
-    }
-
-    execution = 
-    {
-        engine = 
-        {
-            name = Local;
-            implementation = edu.isi.wings.execution.engine.api.impl.local.LocalExecutionEngine;
-            type = BOTH;
-        }
-
-        engine = 
-        {
-            name = Distributed;
-            implementation = edu.isi.wings.execution.engine.api.impl.distributed.DistributedExecutionEngine;
-            type = BOTH;
-        }
-    }
-
-    publisher =
-    {
-        url = "http://ontosoft.isi.edu:7071";
-        name = "exportTest"
-        upload-server =
-        {
-            url = "http://ontosoft.isi.edu:7071";
-            username = "user";
-            password = "password";
-        }
-        triple-store = {
-            publish = http://ontosoft.isi.edu:3030/provenance/data;
-            query = http://ontosoft.isi.edu:3030/provenance/sparql;
-            domains-directory = /Users/mosorio/Downloads/tomcat/wings/storage/default;
-        }
-    }
-}
diff --git a/wings-docker/config/local-mosorio/wings-portal.xml b/wings-docker/config/local-mosorio/wings-portal.xml
deleted file mode 100644
index 272e5c07..00000000
--- a/wings-docker/config/local-mosorio/wings-portal.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<Context debug="0" reloadable="true" crossContext="true">
-   <Parameter name="config.file" value="/etc/wings/portal.properties" />
-   <ResourceLink name="users" global="UserDatabase" type="org.apache.catalina.UserDatabase" />
-</Context>
diff --git a/wings-docker/config/pegasus/portal.properties b/wings-docker/config/pegasus/portal.properties
deleted file mode 100644
index c05f48bc..00000000
--- a/wings-docker/config/pegasus/portal.properties
+++ /dev/null
@@ -1,53 +0,0 @@
-{
-    storage = 
-    {
-        local = /lfs/wings/storage/default;
-        tdb = /lfs/wings/storage/default/TDB;
-    }
-
-    server = http://localhost:8080;
-    graphviz = /usr/bin/dot;
-    light-reasoner = false;
-    ontology = 
-    {
-        data = http://www.wings-workflows.org/ontology/data.owl;
-        component = http://www.wings-workflows.org/ontology/component.owl;
-        workflow = http://www.wings-workflows.org/ontology/workflow.owl;
-        execution = http://www.wings-workflows.org/ontology/execution.owl;
-    }
-
-    execution = 
-    {
-        engine = 
-        {
-            name = Local;
-            implementation = edu.isi.wings.execution.engine.api.impl.local.LocalExecutionEngine;
-            type = BOTH;
-        }
-
-        engine = 
-        {
-            name = Distributed;
-            implementation = edu.isi.wings.execution.engine.api.impl.distributed.DistributedExecutionEngine;
-            type = BOTH;
-        }
-
-
-        engine =
-        {
-            name = Pegasus;
-            implementation = edu.isi.wings.execution.engine.api.impl.pegasus.PegasusExecutionEngine;
-            type = BOTH;
-            properties =
-            {
-                pegasus =
-                {
-                    home         = /usr;
-                    storage-dir  = /lfs/pegasus/storage;
-                    site-catalog = /etc/pegasus/local.sites.xml
-                    site         = local;
-                }
-            }
-        }
-    }
-}
diff --git a/wings-docker/docker/default/Dockerfile b/wings-docker/docker/default/Dockerfile
index 44703398..3695af48 100644
--- a/wings-docker/docker/default/Dockerfile
+++ b/wings-docker/docker/default/Dockerfile
@@ -51,6 +51,5 @@ RUN jar -xvf wings-portal-*.war
 
 # Add wings context file to the wings portal webapp
 COPY ./wings-docker/config/default/wings-portal.xml /usr/local/tomcat/webapps/wings-portal/META-INF/context.xml
-COPY ./wings-docker/config/default/portal.properties /etc/wings/portal.properties
 
 WORKDIR /usr/local/tomcat