Merge branch 'development'

usc-isi-i2 · Aug 18, 2014 · df3114b · df3114b
2 parents 5173bed + 98f8a3e
commit df3114b
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Showing 352 changed files with 16,617 additions and 13,506 deletions.
diff --git a/.gitignore b/.gitignore
@@ -82,3 +82,5 @@ Thumbs.db
 
 
 *.log
+
+*.avro
diff --git a/...in/java/edu/isi/karma/controller/command/worksheet/ApplyHistoryFromR2RMLModelCommand.java b/...in/java/edu/isi/karma/controller/command/worksheet/ApplyHistoryFromR2RMLModelCommand.java
@@ -40,10 +40,9 @@
 import edu.isi.karma.controller.history.WorksheetCommandHistoryExecutor;
 import edu.isi.karma.controller.update.AbstractUpdate;
 import edu.isi.karma.controller.update.ErrorUpdate;
+import edu.isi.karma.controller.update.HistoryAddCommandUpdate;
 import edu.isi.karma.controller.update.InfoUpdate;
 import edu.isi.karma.controller.update.UpdateContainer;
-import edu.isi.karma.controller.update.WorksheetListUpdate;
-import edu.isi.karma.controller.update.WorksheetUpdateFactory;
 import edu.isi.karma.kr2rml.KR2RMLVersion;
 import edu.isi.karma.kr2rml.mapping.KR2RMLMapping;
 import edu.isi.karma.kr2rml.mapping.R2RMLMappingIdentifier;
@@ -62,7 +61,8 @@ public class ApplyHistoryFromR2RMLModelCommand extends WorksheetCommand {
 	private boolean override;
 	private static Logger logger = LoggerFactory.getLogger(ApplyHistoryFromR2RMLModelCommand.class);
 
-	protected ApplyHistoryFromR2RMLModelCommand(String id, File uploadedFile, String worksheetId, boolean override) {
+	protected ApplyHistoryFromR2RMLModelCommand(String id, File uploadedFile, 
+			String worksheetId, boolean override) {
 		super(id, worksheetId);
 		this.r2rmlModelFile = uploadedFile;
 		this.override = override;
@@ -96,13 +96,7 @@ public CommandType getCommandType() {
 	public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		final Worksheet worksheet = workspace.getWorksheet(worksheetId);
 		UpdateContainer c = new UpdateContainer();
-		c.add(new WorksheetListUpdate());
-		UpdateContainer rwu = WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId);
-		if(rwu != null)
-		{
-			c.append(rwu);
-		}
-
+
 		try {
 			JSONArray historyJson  = extractHistoryFromModel(workspace, c);
 			HistoryJSONEditor editor = new HistoryJSONEditor(new JSONArray(historyJson.toString()), workspace, worksheetId);
@@ -126,23 +120,17 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			}
 			System.out.println(editor.getHistoryJSON().toString(4));
 			UpdateContainer hc = histExecutor.executeAllCommands(historyJson);
-			if(hc != null)
+			if(hc != null) {
+				hc.removeUpdateByClass(HistoryAddCommandUpdate.class);
+				hc.removeUpdateByClass(InfoUpdate.class);
+				hc.removeUpdateByClass(ErrorUpdate.class);
 				c.append(hc);
+			}
 		} catch (Exception e) {
 			String msg = "Error occured while applying history!";
 			logger.error(msg, e);
 			return new UpdateContainer(new ErrorUpdate(msg));
 		}
-
-		// Add worksheet updates that could have resulted out of the transformation commands
-		for (Worksheet newws : workspace.getWorksheets()) {
-			if (newws.getId().compareTo(worksheetId) != 0) {
-				c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(newws.getId()));
-				Alignment alignment = AlignmentManager.Instance().getAlignmentOrCreateIt(workspace.getId(), newws.getId(), workspace.getOntologyManager());
-				c.append(WorksheetUpdateFactory.createSemanticTypesAndSVGAlignmentUpdates(newws.getId(), workspace, alignment));
-			}
-		}
-		c.append(computeAlignmentAndSemanticTypesAndCreateUpdates(workspace));	
 		c.add(new InfoUpdate("Model successfully applied!"));
 		c.add(new AbstractUpdate() {
 
@@ -169,6 +157,7 @@ public void generateJson(String prefix, PrintWriter pw,
 			}
 
 		});
+
 		return c;
 	}
 

diff --git a/...ds-alignment/src/main/java/edu/isi/karma/controller/command/alignment/AddNodeCommand.java b/...ds-alignment/src/main/java/edu/isi/karma/controller/command/alignment/AddNodeCommand.java
@@ -7,7 +7,6 @@
 
 import edu.isi.karma.controller.command.CommandException;
 import edu.isi.karma.controller.command.CommandType;
-import edu.isi.karma.controller.command.ICommand.CommandTag;
 import edu.isi.karma.controller.command.WorksheetCommand;
 import edu.isi.karma.controller.update.UpdateContainer;
 import edu.isi.karma.controller.update.WorksheetUpdateFactory;

diff --git a/...c/main/java/edu/isi/karma/controller/command/alignment/AddUserLinkToAlignmentCommand.java b/...c/main/java/edu/isi/karma/controller/command/alignment/AddUserLinkToAlignmentCommand.java
@@ -56,6 +56,7 @@ public class AddUserLinkToAlignmentCommand extends WorksheetCommand {
 
 	public AddUserLinkToAlignmentCommand(String id, String edgeId,
 			String alignmentId, String worksheetId) {
+
 		super(id, worksheetId);
 		this.edgeId = edgeId;
 		this.alignmentId = alignmentId;

diff --git a/...java/edu/isi/karma/controller/command/alignment/AddUserLinkToAlignmentCommandFactory.java b/...java/edu/isi/karma/controller/command/alignment/AddUserLinkToAlignmentCommandFactory.java
@@ -20,15 +20,16 @@
  ******************************************************************************/
 package edu.isi.karma.controller.command.alignment;
 
+import javax.servlet.http.HttpServletRequest;
+
+import org.json.JSONArray;
+import org.json.JSONException;
+
 import edu.isi.karma.controller.command.Command;
 import edu.isi.karma.controller.command.JSONInputCommandFactory;
 import edu.isi.karma.controller.history.HistoryJsonUtil;
 import edu.isi.karma.modeling.alignment.AlignmentManager;
 import edu.isi.karma.rep.Workspace;
-import org.json.JSONArray;
-import org.json.JSONException;
-
-import javax.servlet.http.HttpServletRequest;
 
 public class AddUserLinkToAlignmentCommandFactory extends JSONInputCommandFactory {
 	private enum Arguments {

diff --git a/...ain/java/edu/isi/karma/controller/command/alignment/ApplyModelFromTripleStoreCommand.java b/...ain/java/edu/isi/karma/controller/command/alignment/ApplyModelFromTripleStoreCommand.java
@@ -21,20 +21,22 @@
 
 package edu.isi.karma.controller.command.alignment;
 
+import org.json.JSONArray;
+import org.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import edu.isi.karma.controller.command.CommandException;
 import edu.isi.karma.controller.command.CommandType;
 import edu.isi.karma.controller.command.WorksheetCommand;
+import edu.isi.karma.controller.command.selection.SuperSelectionManager;
 import edu.isi.karma.controller.history.WorksheetCommandHistoryExecutor;
 import edu.isi.karma.controller.update.ErrorUpdate;
 import edu.isi.karma.controller.update.InfoUpdate;
 import edu.isi.karma.controller.update.UpdateContainer;
 import edu.isi.karma.controller.update.WorksheetUpdateFactory;
 import edu.isi.karma.er.helper.TripleStoreUtil;
 import edu.isi.karma.rep.Workspace;
-import org.json.JSONArray;
-import org.json.JSONObject;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 public class ApplyModelFromTripleStoreCommand extends WorksheetCommand {
 
@@ -115,7 +117,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			histExecutor.executeAllCommands(historyJson);
 
 			// Add worksheet updates that could have resulted out of the transformation commands
-			UpdateContainer c = WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId);
+			UpdateContainer c = WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId, SuperSelectionManager.DEFAULT_SELECTION);
 			c.append(computeAlignmentAndSemanticTypesAndCreateUpdates(workspace));
 			c.add(new InfoUpdate("Model successfully applied!"));
 			return c;

diff --git a/...a/edu/isi/karma/controller/command/alignment/ApplyModelFromTripleStoreCommandFactory.java b/...a/edu/isi/karma/controller/command/alignment/ApplyModelFromTripleStoreCommandFactory.java
@@ -21,12 +21,12 @@
 
 package edu.isi.karma.controller.command.alignment;
 
+import javax.servlet.http.HttpServletRequest;
+
 import edu.isi.karma.controller.command.Command;
 import edu.isi.karma.controller.command.CommandFactory;
 import edu.isi.karma.rep.Workspace;
 
-import javax.servlet.http.HttpServletRequest;
-
 public class ApplyModelFromTripleStoreCommandFactory extends CommandFactory {
 
 	private enum Arguments {

diff --git a/...lignment/src/main/java/edu/isi/karma/controller/command/alignment/AugmentDataCommand.java b/...lignment/src/main/java/edu/isi/karma/controller/command/alignment/AugmentDataCommand.java
@@ -20,7 +20,8 @@
 import edu.isi.karma.controller.command.Command;
 import edu.isi.karma.controller.command.CommandException;
 import edu.isi.karma.controller.command.CommandType;
-import edu.isi.karma.controller.command.WorksheetCommand;
+import edu.isi.karma.controller.command.WorksheetSelectionCommand;
+import edu.isi.karma.controller.command.selection.SuperSelection;
 import edu.isi.karma.controller.command.worksheet.AddValuesCommand;
 import edu.isi.karma.controller.command.worksheet.AddValuesCommandFactory;
 import edu.isi.karma.controller.update.ErrorUpdate;
@@ -48,7 +49,7 @@
 import edu.isi.karma.rep.metadata.WorksheetProperties.Property;
 import edu.isi.karma.webserver.KarmaException;
 
-public class AugmentDataCommand extends WorksheetCommand{
+public class AugmentDataCommand extends WorksheetSelectionCommand{
 
 	private static Logger LOG = LoggerFactory.getLogger(AugmentDataCommand.class);
 	private String predicate;
@@ -62,8 +63,8 @@ public class AugmentDataCommand extends WorksheetCommand{
 	private String sameAsPredicate;
 	private final Integer limit = 200;
 	Stack<Command> appliedCommands;
-	public AugmentDataCommand(String id, String dataRepoUrl, String worksheetId, String columnUri, String predicate, String otherClass, String hNodeId, Boolean incoming, String sameAsPredicate) {
-		super(id, worksheetId);
+	public AugmentDataCommand(String id, String dataRepoUrl, String worksheetId, String columnUri, String predicate, String otherClass, String hNodeId, Boolean incoming, String sameAsPredicate, String selectionId) {
+		super(id, worksheetId, selectionId);
 		this.predicate = predicate;
 		this.columnUri = columnUri;
 		this.otherClass = otherClass;
@@ -111,10 +112,11 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		Alignment alignment = AlignmentManager.Instance().getAlignment(alignmentId);
 		RepFactory factory = workspace.getFactory();
 		Worksheet worksheet = factory.getWorksheet(worksheetId);
+		SuperSelection selection = getSuperSelection(worksheet);
 		if (alignment.GetTreeRoot() != null)
 			hNodeId = FetchHNodeIdFromAlignmentCommand.gethNodeId(alignmentId, columnUri);
 		if (hNodeId == null) {
-			c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId));
+			c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId, getSuperSelection(worksheet)));
 			c.append(computeAlignmentAndSemanticTypesAndCreateUpdates(workspace));
 			return c;
 		}
@@ -123,11 +125,11 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		hNodeIds.add(hNodeId);
 		inputColumns.addAll(hNodeIds);
 		List<Table> dataTables = new ArrayList<Table>();
-		CloneTableUtils.getDatatable(worksheet.getDataTable(), factory.getHTable(hnode.getHTableId()), dataTables);
+		CloneTableUtils.getDatatable(worksheet.getDataTable(), factory.getHTable(hnode.getHTableId()), dataTables, selection);
 		Map<String, String> rowHashToSubjectURI = new HashMap<String, String>();
 		Map<String, List<String>> SubjectURIToRowId = new HashMap<String, List<String>>();
 		for(Table t : dataTables) {
-			for(Row r : t.getRows(0, t.getNumRows())) {
+			for(Row r : t.getRows(0, t.getNumRows(), selection)) {
 				Node n = r.getNode(hNodeId);
 				if(n != null && n.getValue() != null && !n.getValue().isEmptyValue() && n.getValue().asString() != null && !n.getValue().asString().trim().isEmpty() ) {
 					String uri = n.getValue().asString().trim().replace(" ", "");
@@ -230,7 +232,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 				try {
 					OntologyManager ontMgr = workspace.getOntologyManager();
 					Label label = ontMgr.getUriLabel(incoming ? otherClass : predicate);
-					AddValuesCommand command = (AddValuesCommand) addFactory.createCommand(input, workspace, hNodeId, worksheetId, hnode.getHTableId(), label.getDisplayName(), HNodeType.AugmentData);
+					AddValuesCommand command = (AddValuesCommand) addFactory.createCommand(input, workspace, hNodeId, worksheetId, hnode.getHTableId(), label.getDisplayName(), HNodeType.AugmentData, selection.getName());
 					command.doIt(workspace);
 					outputColumns.addAll(command.getOutputColumns());
 					isNewNode |= command.isNewNode();
@@ -272,7 +274,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 
 
 				semanticTypesArray.put(semanticType);
-				Command sstCommand = sstFactory.createCommand(workspace, worksheetId, nestedHNodeId, false, semanticTypesArray, false, "");
+				Command sstCommand = sstFactory.createCommand(workspace, worksheetId, nestedHNodeId, false, semanticTypesArray, false, "", selection.getName());
 				appliedCommands.push(sstCommand);
 				sstCommand.doIt(workspace);
 				if(!resultClass.get(i).trim().isEmpty())
@@ -302,16 +304,16 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 					Command changeInternalNodeLinksCommand = cinlcf.createCommand(worksheetId, alignmentId, new JSONArray(), newEdges, workspace);
 					changeInternalNodeLinksCommand.doIt(workspace);
 					appliedCommands.push(changeInternalNodeLinksCommand);
-					Command setMetaDataCommand = smpcf.createCommand(workspace, nestedHNodeId, worksheetId, "isUriOfClass", targetId, "");
+					Command setMetaDataCommand = smpcf.createCommand(workspace, nestedHNodeId, worksheetId, "isUriOfClass", targetId, "", selection.getName());
 					setMetaDataCommand.doIt(workspace);
 					appliedCommands.push(setMetaDataCommand);
 				}
 			}
 
 		}
 
-
-		c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId));
+		WorksheetUpdateFactory.detectSelectionStatusChange(worksheetId, workspace, this);
+		c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId, getSuperSelection(worksheet)));
 		c.append(computeAlignmentAndSemanticTypesAndCreateUpdates(workspace));
 		return c;
 	}
@@ -323,7 +325,7 @@ public UpdateContainer undoIt(Workspace workspace) {
 			Command command = appliedCommands.pop();
 			command.undoIt(workspace);
 		}
-		c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId));
+		c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId, getSuperSelection(workspace)));
 		c.append(computeAlignmentAndSemanticTypesAndCreateUpdates(workspace));
 		return c;
 	}

diff --git a/...t/src/main/java/edu/isi/karma/controller/command/alignment/AugmentDataCommandFactory.java b/...t/src/main/java/edu/isi/karma/controller/command/alignment/AugmentDataCommandFactory.java
@@ -14,7 +14,10 @@
 public class AugmentDataCommandFactory extends JSONInputCommandFactory{
 
 	private enum Arguments {
-		worksheetId, predicate, triplesMap, alignmentId, columnUri, otherClass, tripleStoreUrl, hNodeId, incoming, sameAsPredicate
+		worksheetId, predicate, triplesMap, 
+		alignmentId, columnUri, otherClass, 
+		tripleStoreUrl, hNodeId, incoming, 
+		sameAsPredicate, selectionName
 	}
 
 	@Override
@@ -27,7 +30,12 @@ public Command createCommand(HttpServletRequest request, Workspace workspace) {
 		String hNodeId = request.getParameter(Arguments.hNodeId.name());
 		String incoming = request.getParameter(Arguments.incoming.name());
 		String sameAsPredicate = request.getParameter(Arguments.sameAsPredicate.name());
-		return new AugmentDataCommand(getNewId(workspace), dataRepoUrl, worksheetId, columnUri, predicate, otherClass, hNodeId, Boolean.parseBoolean(incoming), sameAsPredicate);
+		String selectionName = request.getParameter(Arguments.selectionName.name());
+		return new AugmentDataCommand(getNewId(workspace), dataRepoUrl, worksheetId, 
+				columnUri, predicate, otherClass, 
+				hNodeId, Boolean.parseBoolean(incoming), 
+				sameAsPredicate, 
+				selectionName);
 	}
 
 	@Override
@@ -47,7 +55,13 @@ public Command createCommand(JSONArray inputJson, Workspace workspace)
 		String hNodeId = CommandInputJSONUtil.getStringValue(Arguments.hNodeId.name(), inputJson);
 		String incoming = CommandInputJSONUtil.getStringValue(Arguments.incoming.name(), inputJson);
 		String sameAsPredicate = CommandInputJSONUtil.getStringValue(Arguments.sameAsPredicate.name(), inputJson);
-		AugmentDataCommand cmd = new AugmentDataCommand(getNewId(workspace), dataRepoUrl, worksheetId, columnUri, predicate, otherClass, hNodeId, Boolean.parseBoolean(incoming),sameAsPredicate);
+		this.normalizeSelectionId(worksheetId, inputJson, workspace);
+		String selectionName = CommandInputJSONUtil.getStringValue(Arguments.selectionName.name(), inputJson);
+		AugmentDataCommand cmd = new AugmentDataCommand(getNewId(workspace), dataRepoUrl, worksheetId, 
+				columnUri, predicate, otherClass, hNodeId, 
+				Boolean.parseBoolean(incoming), 
+				sameAsPredicate, 
+				selectionName);
 
 		cmd.setInputParameterJson(inputJson.toString());
 		return cmd;

diff --git a/...t/src/main/java/edu/isi/karma/controller/command/alignment/AugmentDataDispachCommand.java b/...t/src/main/java/edu/isi/karma/controller/command/alignment/AugmentDataDispachCommand.java
@@ -4,21 +4,24 @@
 
 import edu.isi.karma.controller.command.CommandException;
 import edu.isi.karma.controller.command.CommandType;
-import edu.isi.karma.controller.command.WorksheetCommand;
+import edu.isi.karma.controller.command.WorksheetSelectionCommand;
 import edu.isi.karma.controller.update.UpdateContainer;
 import edu.isi.karma.controller.update.WorksheetUpdateFactory;
 import edu.isi.karma.rep.Workspace;
 
-public class AugmentDataDispachCommand extends WorksheetCommand {
+public class AugmentDataDispachCommand extends WorksheetSelectionCommand {
 	private String predicateIncoming, predicateOutgoing;
 	private AugmentDataCommand incoming;
 	private AugmentDataCommand outgoing;
-	public AugmentDataDispachCommand(String id, String dataRepoUrl, String worksheetId, String columnUri, String predicateIncoming, String otherClassIncoming, String predicateOutgoing, String otherClassOutgoing, String hNodeId, String sameAsPredicate) {
-		super(id, worksheetId);
+	public AugmentDataDispachCommand(String id, String dataRepoUrl, String worksheetId, 
+			String columnUri, String predicateIncoming, String otherClassIncoming, 
+			String predicateOutgoing, String otherClassOutgoing, 
+			String hNodeId, String sameAsPredicate, String selectionId) {
+		super(id, worksheetId, selectionId);
 		this.predicateIncoming = predicateIncoming;
 		this.predicateOutgoing = predicateOutgoing;
-		incoming = new AugmentDataCommand(id, dataRepoUrl, worksheetId, columnUri, predicateIncoming, otherClassIncoming, hNodeId, true, sameAsPredicate);
-		outgoing = new AugmentDataCommand(id, dataRepoUrl, worksheetId, columnUri, predicateOutgoing, otherClassOutgoing, hNodeId, false, sameAsPredicate);
+		incoming = new AugmentDataCommand(id, dataRepoUrl, worksheetId, columnUri, predicateIncoming, otherClassIncoming, hNodeId, true, sameAsPredicate, selectionId);
+		outgoing = new AugmentDataCommand(id, dataRepoUrl, worksheetId, columnUri, predicateOutgoing, otherClassOutgoing, hNodeId, false, sameAsPredicate, selectionId);
 		addTag(CommandTag.Transformation);
 	}
 
@@ -73,7 +76,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			incoming.doIt(workspace);
 		if (predicatesoutgoingarray.length() > 0)
 			outgoing.doIt(workspace);
-		c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId));
+		c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId, getSuperSelection(workspace)));
 		c.append(computeAlignmentAndSemanticTypesAndCreateUpdates(workspace));
 		return c;
 	}
@@ -87,7 +90,7 @@ public UpdateContainer undoIt(Workspace workspace) {
 			incoming.undoIt(workspace);
 		if (predicatesoutgoingarray.length() > 0)
 			outgoing.undoIt(workspace);
-		c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId));
+		c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId, getSuperSelection(workspace)));
 		c.append(computeAlignmentAndSemanticTypesAndCreateUpdates(workspace));
 		return c;
 	}