Fixed data id for workflow run

Author: hvarg

server/src/main/java/org/diskproject/server/adapters/AirFlowAdapter.java

@@ -87,7 +87,7 @@ public String getWorkflowLink(String id) {
     }
 
     @Override
-    public Map<String, String> areFilesAvailable(Set<String> filelist, String dType) {
+    public List<String> areFilesAvailable(Set<String> filelist, String dType) {
         // Auto-generated method stub
         return null;
     }

server/src/main/java/org/diskproject/server/repository/DiskRepository.java

@@ -1544,27 +1544,14 @@ private Map<String, String> addData(List<String> dsUrls, MethodAdapter methodAda
 
         // avoid to duplicate files
         Set<String> names = nameToUrl.keySet();
-        Map<String, String> availableFiles = methodAdapter.areFilesAvailable(names, dType);
-        names.removeAll(availableFiles.keySet());
+        List<String> availableFiles = methodAdapter.areFilesAvailable(names, dType);
+        names.removeAll(availableFiles);
 
         // upload the files
         for (String newFilename : names) {
             String newFile = nameToUrl.get(newFilename);
             System.out.println("Uploading to " + methodAdapter.getName() + ": " + newFile + " as " + newFilename + " (" + dType + ")");
-            String dataId = methodAdapter.addData(newFile, newFilename, dType);
-            urlToName.put(newFile, dataId);
-        }
-
-        // Set current available urls
-        for (String existingFilename: availableFiles.keySet()) {
-            for (String newName: urlToName.keySet()) {
-                if (urlToName.get(newName).equals(existingFilename)) {
-                    String newFile = availableFiles.get(existingFilename);
-                    System.out.println("Replaced " + existingFilename + " -> " + newFile);
-                    urlToName.put(newName, newFile);
-                }
-            }
-
+            methodAdapter.addData(newFile, newFilename, dType);
         }
 
         return urlToName;
@@ -1896,8 +1883,16 @@ public void run() {
                     System.out.println("[R] Executing " + bindings.getWorkflow() + " with:");
                     for (VariableBinding v : vBindings) {
                         String[] l = v.isCollection() ? v.getBindingAsArray() : null;
-                        System.out.println("[R] - " + v.getVariable() + ": "
-                                + (l == null ? v.getBinding() : l[0] + " (" + l.length + ")"));
+                        int i = 0;
+                        if (l != null) {
+                            System.out.println("[R] - " + v.getVariable() + ": ");
+                            for (String b: l) {
+                                System.out.println("[R]    " + String.valueOf(i) + ") " + b);
+                                i++;
+                            }
+                        } else {
+                            System.out.println("[R] - " + v.getVariable() + ": " + v.getBinding());
+                        }
                     }
 
                     List<String> runIds = methodAdapter.runWorkflow(bindings.getWorkflow(), sendbindings, inputs);
@@ -1949,7 +1944,6 @@ private void processWorkflowOutputs (TriggeredLOI tloi, LineOfInquiry loi, Workf
             if (id.contains(wb.getWorkflow())) {
                 for (VariableBinding b: wb.getBindings()) {
                     String varName = b.getVariable();
-                    System.out.println("> " + varName);
                     if (outputAssignations.containsKey(varName)) {
                         outputAssignations.put(varName, b.getBinding());
                     }

server/src/main/java/org/diskproject/server/repository/WingsAdapter.java

@@ -998,7 +998,7 @@ public String addRemoteDataToWings(String url, String name, String dType) throws
 		return dataid;
 	}
 
-	public Map<String, String> isFileListOnWings(Set<String> filelist, String filetype) {
+	public List<String> isFileListOnWings(Set<String> filelist, String filetype) {
 		List<String> returnValue = new ArrayList<String>();
 		//String filetype = this.internal_server + "/export/users/" + getUsername() + "/" + domain + "/data/ontology.owl#File";
 		String fileprefix = "<" + this.internal_server + "/export/users/" + getUsername() + "/" + domain
@@ -1045,7 +1045,7 @@ public Map<String, String> isFileListOnWings(Set<String> filelist, String filety
 			formdata.add(new BasicNameValuePair("format", "json"));
 			String resultjson = get(pageId, formdata);
 			if (resultjson == null || resultjson.equals(""))
-				return createFilesUrl(returnValue);
+				return returnValue;
 
 			JsonObject result = null;
 			try {
@@ -1069,15 +1069,7 @@ public Map<String, String> isFileListOnWings(Set<String> filelist, String filety
 			}
 		}
 
-		return createFilesUrl(returnValue);
-	}
-
-	private Map<String,String> createFilesUrl (List<String> names) {
-		Map<String,String> r = new HashMap<String,String>();
-		for (String name: names) {
-			r.put(name, this.DATAID(name));
-		}
-		return r;
+		return returnValue;
 	}
 
 	public boolean isFileOnWings(String url) {
@@ -1274,7 +1266,7 @@ private String toPlanAcceptableFormat(String wfName, List<VariableBinding> vbl,
 					String bindingValue = vb.getBinding();
 
 					if (v.getDimensionality() ==  0) { // && !bindingValue.startsWith("[")) { FIXME!
-						curBinding += "\"" + bindingValue + "\"";
+						curBinding += "\"" + (v.isParam() ? "" : dataID) + bindingValue + "\"";
 					} else {
 						if (v.getDimensionality() == 0) {
 							System.err.println("WARNING: Variable " + v.getName() + " has dimensionality 0 but the binding is an array");
@@ -1427,7 +1419,7 @@ public boolean ping() {
 	}
 
 	@Override
-	public Map<String, String> areFilesAvailable(Set<String> filelist, String dType) {
+	public List<String> areFilesAvailable(Set<String> filelist, String dType) {
 		return this.isFileListOnWings(filelist, dType);
 	}
 

shared/src/main/java/org/diskproject/shared/classes/adapters/MethodAdapter.java

@@ -86,7 +86,7 @@ public String toString () {
 
 	public abstract String getDataUri (String id);
 
-	public abstract Map<String, String> areFilesAvailable (Set<String> fileList, String dType);
+	public abstract List<String> areFilesAvailable (Set<String> fileList, String dType);
 
 	public abstract String addData (String url, String name, String dType) throws Exception;