Merge branch 'development'

usc-isi-i2 · Aug 8, 2014 · 5173bed · 5173bed
2 parents ad4ce60 + 23e7745
commit 5173bed
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Showing 169 changed files with 4,889 additions and 3,561 deletions.
diff --git a/.gitignore b/.gitignore
@@ -80,3 +80,5 @@ Thumbs.db
 
 *.sh
 
+
+*.log
diff --git a/...in/java/edu/isi/karma/controller/command/worksheet/ApplyHistoryFromR2RMLModelCommand.java b/...in/java/edu/isi/karma/controller/command/worksheet/ApplyHistoryFromR2RMLModelCommand.java
@@ -59,14 +59,12 @@
 
 public class ApplyHistoryFromR2RMLModelCommand extends WorksheetCommand {
 	private final File r2rmlModelFile;
-	private final String worksheetId;
 	private boolean override;
 	private static Logger logger = LoggerFactory.getLogger(ApplyHistoryFromR2RMLModelCommand.class);
 
 	protected ApplyHistoryFromR2RMLModelCommand(String id, File uploadedFile, String worksheetId, boolean override) {
 		super(id, worksheetId);
 		this.r2rmlModelFile = uploadedFile;
-		this.worksheetId = worksheetId;
 		this.override = override;
 	}
 
@@ -116,7 +114,8 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			AlignmentManager alignMgr = AlignmentManager.Instance();
 			Alignment alignment = alignMgr.getAlignment(workspace.getId(), worksheetId);
 			if (override || alignment == null || alignment.GetTreeRoot() == null) {
-				alignMgr.removeWorkspaceAlignments(workspace.getId());
+				String alignmentId = alignMgr.constructAlignmentId(workspace.getId(), worksheetId);
+				alignMgr.removeAlignment(alignmentId);
 				alignMgr.getAlignmentOrCreateIt(workspace.getId(), worksheetId, workspace.getOntologyManager());
 				editor.deleteExistingTransformationCommands();
 				historyJson = editor.getHistoryJSON();

diff --git a/...ds/commands-alignment-openrdf/src/main/java/edu/isi/karma/kr2rml/KR2RMLMappingWriter.java b/...ds/commands-alignment-openrdf/src/main/java/edu/isi/karma/kr2rml/KR2RMLMappingWriter.java
@@ -91,6 +91,8 @@ private Resource addKR2RMLMappingResource(Worksheet worksheet, KR2RMLMapping map
 				Property.inputColumns);
 		String outputColumns = worksheet.getMetadataContainer().getWorksheetProperties().getPropertyValue(
 				Property.outputColumns);
+		String oldHistory = worksheet.getMetadataContainer().getWorksheetProperties().getPropertyValue(
+				Property.oldCommandHistory);
 		String graphLabel = worksheet.getMetadataContainer().getWorksheetProperties().getPropertyValue(
 				Property.graphLabel);
 		String baseURI = worksheet.getMetadataContainer().getWorksheetProperties().getPropertyValue(
@@ -104,7 +106,9 @@ private Resource addKR2RMLMappingResource(Worksheet worksheet, KR2RMLMapping map
 		if (graphLabel != null && !graphLabel.trim().isEmpty())
 			con.add(mappingRes, repoURIs.get(Uris.KM_HAS_MODELLABEL), f.createLiteral(graphLabel));	
 		if (baseURI != null && !baseURI.trim().isEmpty())
-			con.add(mappingRes, repoURIs.get(Uris.KM_HAS_BASEURI), f.createLiteral(baseURI));	
+			con.add(mappingRes, repoURIs.get(Uris.KM_HAS_BASEURI), f.createLiteral(baseURI));
+		if (oldHistory != null && !oldHistory.trim().isEmpty())
+			con.add(mappingRes, repoURIs.get(Uris.KM_HAS_OLDHISTORY), f.createLiteral(oldHistory));
 		addWorksheetProperties(worksheet, mappingRes);
 		addCompleteWorksheetHistory(mapping, mappingRes);
 		return mappingRes;

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
@@ -5,9 +5,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-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.ICommand.CommandTag;
+import edu.isi.karma.controller.command.WorksheetCommand;
 import edu.isi.karma.controller.update.UpdateContainer;
 import edu.isi.karma.controller.update.WorksheetUpdateFactory;
 import edu.isi.karma.modeling.alignment.Alignment;
@@ -24,8 +25,8 @@
  * @author dipsy
  *
  */
-public class AddNodeCommand extends Command {
-	private String worksheetId;
+public class AddNodeCommand extends WorksheetCommand {
+
 	private String nodeUri;
 	private String nodeLabel;
 	private String alignmentId;
@@ -37,8 +38,7 @@ public class AddNodeCommand extends Command {
 	private DirectedWeightedMultigraph<Node, DefaultLink> oldGraph;
 
 	protected AddNodeCommand(String id, String worksheetId, String alignmentId, String uri, String label) {
-		super(id);
-		this.worksheetId = worksheetId;
+		super(id, worksheetId);
 		this.alignmentId = alignmentId;
 		this.nodeUri = uri;
 		this.nodeLabel = label;

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
@@ -20,9 +20,15 @@
  ******************************************************************************/
 package edu.isi.karma.controller.command.alignment;
 
-import edu.isi.karma.controller.command.Command;
+import java.util.Set;
+
+import org.jgrapht.graph.DirectedWeightedMultigraph;
+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.update.AlignmentSVGVisualizationUpdate;
 import edu.isi.karma.controller.update.ErrorUpdate;
 import edu.isi.karma.controller.update.SemanticTypesUpdate;
@@ -32,19 +38,13 @@
 import edu.isi.karma.modeling.alignment.LinkIdFactory;
 import edu.isi.karma.rep.Worksheet;
 import edu.isi.karma.rep.Workspace;
-import edu.isi.karma.rep.alignment.LabeledLink;
 import edu.isi.karma.rep.alignment.DefaultLink;
+import edu.isi.karma.rep.alignment.LabeledLink;
 import edu.isi.karma.rep.alignment.LinkStatus;
 import edu.isi.karma.rep.alignment.Node;
-import org.jgrapht.graph.DirectedWeightedMultigraph;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.Set;
 
-public class AddUserLinkToAlignmentCommand extends Command {
+public class AddUserLinkToAlignmentCommand extends WorksheetCommand {
 
-	private final String worksheetId;
 	private final String edgeId;
 	private final String alignmentId;
 	private Alignment 	 oldAlignment;
@@ -56,10 +56,9 @@ public class AddUserLinkToAlignmentCommand extends Command {
 
 	public AddUserLinkToAlignmentCommand(String id, String edgeId,
 			String alignmentId, String worksheetId) {
-		super(id);
+		super(id, worksheetId);
 		this.edgeId = edgeId;
 		this.alignmentId = alignmentId;
-		this.worksheetId = worksheetId;
 
 		addTag(CommandTag.Modeling);
 	}

diff --git a/.../main/java/edu/isi/karma/controller/command/alignment/ChangeInternalNodeLinksCommand.java b/.../main/java/edu/isi/karma/controller/command/alignment/ChangeInternalNodeLinksCommand.java
@@ -21,9 +21,16 @@
 
 package edu.isi.karma.controller.command.alignment;
 
-import edu.isi.karma.controller.command.Command;
+import org.jgrapht.graph.DirectedWeightedMultigraph;
+import org.json.JSONArray;
+import org.json.JSONException;
+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.alignment.ChangeInternalNodeLinksCommandFactory.Arguments;
 import edu.isi.karma.controller.update.AlignmentSVGVisualizationUpdate;
 import edu.isi.karma.controller.update.SemanticTypesUpdate;
@@ -34,20 +41,14 @@
 import edu.isi.karma.modeling.ontology.OntologyManager;
 import edu.isi.karma.rep.Worksheet;
 import edu.isi.karma.rep.Workspace;
-import edu.isi.karma.rep.alignment.LabeledLink;
-import edu.isi.karma.rep.alignment.Label;
 import edu.isi.karma.rep.alignment.DefaultLink;
+import edu.isi.karma.rep.alignment.Label;
+import edu.isi.karma.rep.alignment.LabeledLink;
 import edu.isi.karma.rep.alignment.LinkStatus;
 import edu.isi.karma.rep.alignment.Node;
-import org.jgrapht.graph.DirectedWeightedMultigraph;
-import org.json.JSONArray;
-import org.json.JSONException;
-import org.json.JSONObject;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
-public class ChangeInternalNodeLinksCommand extends Command {
-	private final String worksheetId;
+public class ChangeInternalNodeLinksCommand extends WorksheetCommand {
+
 	private final String alignmentId;
 	private JSONArray initialEdges;
 	private JSONArray newEdges;
@@ -66,8 +67,7 @@ public enum JsonKeys {
 
 	public ChangeInternalNodeLinksCommand(String id, String worksheetId,
 			String alignmentId, JSONArray initialEdges, JSONArray newEdges) {
-		super(id);
-		this.worksheetId = worksheetId;
+		super(id, worksheetId);
 		this.alignmentId = alignmentId;
 		this.initialEdges = initialEdges;
 		this.newEdges = newEdges;

diff --git a/.../src/main/java/edu/isi/karma/controller/command/alignment/CheckModelExistenceCommand.java b/.../src/main/java/edu/isi/karma/controller/command/alignment/CheckModelExistenceCommand.java
@@ -4,21 +4,20 @@
 
 import org.json.JSONObject;
 
-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.update.AbstractUpdate;
 import edu.isi.karma.controller.update.UpdateContainer;
 import edu.isi.karma.modeling.alignment.Alignment;
 import edu.isi.karma.modeling.alignment.AlignmentManager;
 import edu.isi.karma.rep.Workspace;
 import edu.isi.karma.view.VWorkspace;
 
-public class CheckModelExistenceCommand extends Command {
-	private String worksheetId;
+public class CheckModelExistenceCommand extends WorksheetCommand {
+
 	protected CheckModelExistenceCommand(String id, String worksheetId) {
-		super(id);
-		this.worksheetId = worksheetId;
+		super(id, worksheetId);
 	}
 
 	@Override

diff --git a/...alignment/src/main/java/edu/isi/karma/controller/command/alignment/DeleteNodeCommand.java b/...alignment/src/main/java/edu/isi/karma/controller/command/alignment/DeleteNodeCommand.java
@@ -5,9 +5,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-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.update.UpdateContainer;
 import edu.isi.karma.controller.update.WorksheetUpdateFactory;
 import edu.isi.karma.modeling.alignment.Alignment;
@@ -23,8 +23,8 @@
  * @author dipsy
  *
  */
-public class DeleteNodeCommand extends Command {
-	private String worksheetId;
+public class DeleteNodeCommand extends WorksheetCommand {
+
 	private String nodeId;
 	private String nodeLabel;
 	private String alignmentId;
@@ -36,8 +36,7 @@ public class DeleteNodeCommand extends Command {
 	private DirectedWeightedMultigraph<Node, DefaultLink> oldGraph;
 
 	protected DeleteNodeCommand(String id, String worksheetId, String alignmentId, String nodeId, String nodeLabel) {
-		super(id);
-		this.worksheetId = worksheetId;
+		super(id, worksheetId);
 		this.alignmentId = alignmentId;
 		this.nodeId = nodeId;
 		this.nodeLabel = nodeLabel;

diff --git a/...src/main/java/edu/isi/karma/controller/command/alignment/FetchR2RMLModelsListCommand.java b/...src/main/java/edu/isi/karma/controller/command/alignment/FetchR2RMLModelsListCommand.java
@@ -15,9 +15,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-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.update.AbstractUpdate;
 import edu.isi.karma.controller.update.ErrorUpdate;
 import edu.isi.karma.controller.update.UpdateContainer;
@@ -28,36 +28,31 @@
 import edu.isi.karma.rep.Workspace;
 import edu.isi.karma.view.VWorkspace;
 
-public class FetchR2RMLModelsListCommand extends Command{
+public class FetchR2RMLModelsListCommand extends WorksheetCommand{
 
 	private String TripleStoreUrl;
 	private String context;
-	private String worksheetId;
 	private static Logger logger = LoggerFactory.getLogger(FetchR2RMLModelsListCommand.class);
 
 	public FetchR2RMLModelsListCommand(String id, String TripleStoreUrl, String context, String worksheetId) {
-		super(id);
+		super(id, worksheetId);
 		this.TripleStoreUrl = TripleStoreUrl;
 		this.context = context;
-		this.worksheetId = worksheetId;
 	}
 
 	@Override
 	public String getCommandName() {
-		// TODO Auto-generated method stub
 		return FetchR2RMLModelsListCommand.class.getSimpleName();
 	}
 
 	@Override
 	public String getTitle() {
-		// TODO Auto-generated method stub
 		return "Fetch R2RML from Triple Store";
 	}
 
 	@Override
 	public String getDescription() {
-		// TODO Auto-generated method stub
-		return null;
+		return "";
 	}
 
 	@Override

diff --git a/...alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetClassesCommand.java b/...alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetClassesCommand.java
@@ -12,9 +12,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-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.update.AbstractUpdate;
 import edu.isi.karma.controller.update.UpdateContainer;
 import edu.isi.karma.modeling.alignment.Alignment;
@@ -27,9 +27,8 @@
 import edu.isi.karma.rep.alignment.NodeType;
 import edu.isi.karma.view.VWorkspace;
 
-public class GetClassesCommand extends Command {
+public class GetClassesCommand extends WorksheetCommand {
 
-	final private String worksheetId;
 	final private INTERNAL_NODES_RANGE range;
 
 	public enum INTERNAL_NODES_RANGE {
@@ -45,8 +44,7 @@ private enum JsonKeys {
 	private static Logger logger = LoggerFactory.getLogger(GetClassesCommand.class.getSimpleName());
 
 	protected GetClassesCommand(String id, String worksheetId, INTERNAL_NODES_RANGE range, String propertyURI) {
-		super(id);
-		this.worksheetId = worksheetId;
+		super(id, worksheetId);
 		this.range = range;
 		this.propertyURI = propertyURI;
 	}

diff --git a/...gnment/src/main/java/edu/isi/karma/controller/command/alignment/GetPropertiesCommand.java b/...gnment/src/main/java/edu/isi/karma/controller/command/alignment/GetPropertiesCommand.java
@@ -14,9 +14,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-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.update.AbstractUpdate;
 import edu.isi.karma.controller.update.UpdateContainer;
 import edu.isi.karma.modeling.alignment.Alignment;
@@ -32,9 +32,8 @@
 import edu.isi.karma.rep.alignment.ObjectPropertyLink;
 import edu.isi.karma.view.VWorkspace;
 
-public class GetPropertiesCommand extends Command {
+public class GetPropertiesCommand extends WorksheetCommand {
 
-	final private String worksheetId;
 	final private INTERNAL_PROP_RANGE propertiesRange;
 
 	public enum INTERNAL_PROP_RANGE {
@@ -50,8 +49,7 @@ private enum JsonKeys {
 	private static Logger logger = LoggerFactory.getLogger(GetPropertiesCommand.class.getSimpleName());
 
 	protected GetPropertiesCommand(String id, String worksheetId, INTERNAL_PROP_RANGE propertiesRange, String classURI, String domainURI, String rangeURI) {
-		super(id);
-		this.worksheetId = worksheetId;
+		super(id, worksheetId);
 		this.propertiesRange = propertiesRange;
 		this.classURI = classURI;
 		this.domainURI = domainURI;

diff --git a/...c/main/java/edu/isi/karma/controller/command/alignment/GetSemanticSuggestionsCommand.java b/...c/main/java/edu/isi/karma/controller/command/alignment/GetSemanticSuggestionsCommand.java
@@ -7,9 +7,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-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.update.AbstractUpdate;
 import edu.isi.karma.controller.update.UpdateContainer;
 import edu.isi.karma.modeling.alignment.Alignment;
@@ -22,15 +22,13 @@
 import edu.isi.karma.rep.Workspace;
 import edu.isi.karma.view.VWorkspace;
 
-public class GetSemanticSuggestionsCommand extends Command {
+public class GetSemanticSuggestionsCommand extends WorksheetCommand {
 	private final String hNodeId;
-	private final String worksheetId;
 	private static Logger logger = LoggerFactory.getLogger(GetSemanticSuggestionsCommand.class.getSimpleName());
 
 	protected GetSemanticSuggestionsCommand(String id, String worksheetId, String hNodeId) {
-		super(id);
+		super(id, worksheetId);
 		this.hNodeId = hNodeId;
-		this.worksheetId = worksheetId;
 	}
 
 	@Override