Merge branch 'development'

karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/DeleteLinkCommand.java

@@ -101,6 +101,8 @@ private UpdateContainer deleteLink(Alignment alignment, OntologyManager ontMgr,
 		LabeledLink delLink = alignment.getLinkById(linkId);
 		if(delLink != null) {
 			this.displayLabel = delLink.getLabel().getDisplayName();
+		} else {
+			this.displayLabel = edgeUri;
 		}
 
 		alignment.removeLink(linkId);

karma-commands/commands-bloom/pom.xml

@@ -12,7 +12,7 @@
 
     <artifactId>commands-bloom</artifactId>
 	<properties>
-        <hadoop.version>2.4.0.2.1.3.0-563</hadoop.version>
+        <hadoop.version>2.9.0</hadoop.version>
     </properties>
 
 	<repositories>
@@ -102,4 +102,4 @@
 		</dependency>       
 	</dependencies>
 
-</project>
+</project>

karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetHeadersUpdate.java

@@ -46,7 +46,7 @@ public class WorksheetHeadersUpdate extends AbstractUpdate {
 	private enum JsonKeys {
 		worksheetId, columns, columnName, characterLength, hasNestedTable, 
 		columnClass, hNodeId, pythonTransformation, previousCommandId, 
-		columnDerivedFrom, hNodeType, status, onError
+		columnDerivedFrom, hNodeType, status, onError, selectionPyCode
 	}
 
 	public WorksheetHeadersUpdate(String worksheetId, SuperSelection selection) {
@@ -101,7 +101,10 @@ private JSONObject getColumnJsonObject(VHNode hNode, ColumnMetadata colMeta) thr
 		if (t.hasNestedTable()) {
 			Selection sel = selection.getSelection(t.getNestedTable().getId());
 			if (sel != null)
+			{
 				hNodeObj.put(JsonKeys.status.name(), sel.getStatus().name());
+				hNodeObj.put(JsonKeys.selectionPyCode.name(), colMeta.getSelectionPythonCode(t.getNestedTable().getId()));
+			}
 		}
 		hNodeObj.put(JsonKeys.hNodeType.name(), t.getHNodeType().name());
 		Integer colLength = colMeta.getColumnPreferredLength(hNode.getId());

karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/AddColumnConsolidator.java

@@ -0,0 +1,47 @@
+package edu.isi.karma.controller.command.transformation;
+
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.commons.lang3.tuple.ImmutablePair;
+import org.apache.commons.lang3.tuple.Pair;
+import org.json.JSONArray;
+
+import edu.isi.karma.controller.command.Command;
+import edu.isi.karma.controller.command.ICommand;
+import edu.isi.karma.controller.command.worksheet.AddColumnCommand;
+import edu.isi.karma.controller.history.CommandConsolidator;
+import edu.isi.karma.controller.history.HistoryJsonUtil;
+import edu.isi.karma.rep.Workspace;
+
+public class AddColumnConsolidator extends CommandConsolidator {
+
+	@Override
+	public Pair<ICommand, Object> consolidateCommand(List<ICommand> commands,
+			ICommand newCommand, Workspace workspace) {
+		if (newCommand instanceof SubmitPythonTransformationCommand) {
+            String model = newCommand.getModel();
+
+            Iterator<ICommand> itr = commands.iterator();
+            while(itr.hasNext()) {
+                ICommand tmp = itr.next();
+                if (((Command)tmp).getOutputColumns().equals(((Command)newCommand).getOutputColumns())
+                    && tmp.getModel().equals(model)
+                        && (tmp instanceof AddColumnCommand)) {
+                	SubmitPythonTransformationCommand py = ((SubmitPythonTransformationCommand)newCommand);
+                	JSONArray inputJSON = new JSONArray(py.getInputParameterJson());
+
+                	JSONArray tmpInputJSON = new JSONArray(tmp.getInputParameterJson());
+        			String hNodeId = HistoryJsonUtil.getStringValue("hNodeId", tmpInputJSON);
+
+					HistoryJsonUtil.setArgumentValue("hNodeId", hNodeId, inputJSON);
+					py.setInputParameterJson(inputJSON.toString());
+
+                    return new ImmutablePair<>(tmp, (Object)py);
+                }
+            }
+        }
+        return null;
+	}
+
+}

karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/PyTransformConsolidator.java

@@ -1,20 +1,17 @@
 package edu.isi.karma.controller.command.transformation;
 
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.commons.lang3.tuple.ImmutablePair;
+import org.apache.commons.lang3.tuple.Pair;
+import org.json.JSONArray;
+
 import edu.isi.karma.controller.command.Command;
-import edu.isi.karma.controller.command.CommandException;
 import edu.isi.karma.controller.command.ICommand;
 import edu.isi.karma.controller.history.CommandConsolidator;
 import edu.isi.karma.controller.history.HistoryJsonUtil;
-import edu.isi.karma.controller.history.WorksheetCommandHistoryExecutor;
 import edu.isi.karma.rep.Workspace;
-import org.apache.commons.lang3.tuple.ImmutablePair;
-import org.apache.commons.lang3.tuple.Pair;
-import org.json.JSONArray;
-import org.json.JSONObject;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
 
 public class PyTransformConsolidator extends CommandConsolidator {
 

karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/PythonTransformationCommand.java

@@ -130,7 +130,8 @@ protected void generateTransformedValues(Workspace workspace,
 		repo.initializeInterpreter(interpreter);
 		Collection<Node> nodes = new ArrayList<>(Math.max(1000, worksheet
 				.getDataTable().getNumRows()));
-		worksheet.getDataTable().collectNodes(hNode.getHNodePath(f), nodes, selection);
+		SuperSelection tmpSelection = new SuperSelection("TEMP_SUPER_SELECTION");
+		worksheet.getDataTable().collectNodes(hNode.getHNodePath(f), nodes, tmpSelection);
 
 		Map<String, String> rowToValueMap = new HashMap<>();
 

karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/SubmitPythonTransformationCommand.java

@@ -70,7 +70,7 @@ public SubmitPythonTransformationCommand(String id, String model, String newColu
 		//logger.info("SubmitPythonTranformationCommand:" + id + " newColumnName:" + newColumnName + ", code=" + transformationCode);
 		this.pythonNodeId = hNodeId;
 	}
-
+	
 	@Override
 	public String getCommandName() {
 		return this.getClass().getSimpleName();
@@ -124,6 +124,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 					Map<String, String> mapping = gatherTransformedResults(workspace, nodeId);
 					handleJSONOutput(workspace, mapping, newColumnNameHNode);
 				}
+				newColumnAbsoluteName = newColumnNameHNode.getAbsoluteColumnName(f);
 				WorksheetUpdateFactory.detectSelectionStatusChange(worksheetId, workspace, this);
 				return c;
 			} else {

karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/AddColumnCommand.java

@@ -156,7 +156,6 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 
 			c.append(WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId, getSuperSelection(worksheet), workspace.getContextId()));
 			c.append(computeAlignmentAndSemanticTypesAndCreateUpdates(workspace));
-			inputColumns.add(hNodeId);
 			outputColumns.add(newHNodeId);
 			newColumnAbsoluteName = ndid.getAbsoluteColumnName(workspace.getFactory());
 			return c;
@@ -194,10 +193,7 @@ public UpdateContainer undoIt(Workspace workspace) {
 		return WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId, getSuperSelection(worksheet), workspace.getContextId());
 	}
 
-
 	public String getNewHNodeId() {
 		return newHNodeId;
 	}
-
-
 }

karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/ClearSelectionCommand.java

@@ -79,6 +79,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			}
 		}
 
+		worksheet.getMetadataContainer().getColumnMetadata().removeSelectionPythonCode(hTable.getId());
 		WorksheetUpdateFactory.detectSelectionStatusChange(worksheetId, workspace, this);
 		if(!this.isExecutedInBatch()) {
 			UpdateContainer uc = WorksheetUpdateFactory.createWorksheetHierarchicalAndCleaningResultsUpdates(worksheetId, superSel, workspace.getContextId());

karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/OperateSelectionCommand.java

@@ -3,11 +3,8 @@
 import edu.isi.karma.controller.command.CommandException;
 import edu.isi.karma.controller.command.CommandType;
 import edu.isi.karma.controller.command.WorksheetSelectionCommand;
-import edu.isi.karma.controller.command.selection.LargeSelection;
-import edu.isi.karma.controller.command.selection.LargeSelection.Operation;
 import edu.isi.karma.controller.command.selection.MiniSelection;
 import edu.isi.karma.controller.command.selection.Selection;
-import edu.isi.karma.controller.command.selection.SelectionManager;
 import edu.isi.karma.controller.command.selection.SuperSelection;
 import edu.isi.karma.controller.update.ErrorUpdate;
 import edu.isi.karma.controller.update.UpdateContainer;
@@ -65,28 +62,18 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		RepFactory factory = workspace.getFactory();
 		SuperSelection superSel = this.getSuperSelection(worksheet);
 		HTable hTable = factory.getHTable(factory.getHNode(hNodeId).getHTableId());
-		Selection currentSel = superSel.getSelection(hTable.getId());
 		Selection anotherSel = null;
-		if (!operation.equalsIgnoreCase(Operation.Invert.name())) {
-			anotherSel = new MiniSelection(workspace, worksheetId, hTable.getId(), factory.getNewId("SEL"), superSel.getName(), pythonCode, onError);
-			worksheet.getSelectionManager().addSelection(anotherSel);
-		}
-		if (currentSel == null && operation.equalsIgnoreCase(Operation.Invert.name()) ) {
-			return getErrorUpdate("No defined Selection");
-		}
-		if (currentSel == null) {
-			currentSel = new MiniSelection(workspace, worksheetId, hTable.getId(), factory.getNewId("SEL"), superSel.getName(), SelectionManager.defaultCode, onError);
-			worksheet.getSelectionManager().addSelection(currentSel);
-		}
+
+		anotherSel = new MiniSelection(workspace, worksheetId, hTable.getId(), factory.getNewId("SEL"), superSel.getName(), pythonCode, onError);
+		worksheet.getSelectionManager().addSelection(anotherSel);
+		worksheet.getMetadataContainer().getColumnMetadata().addSelectionPythonCode(hTable.getId(), this.pythonCode);
+
 		try {
-			Operation operation = Operation.valueOf(Operation.class, this.operation);
-			Selection t = new LargeSelection(workspace, worksheetId, hTable.getId(), factory.getNewId("SEL"), superSel.getName(), currentSel, anotherSel, operation);
-			worksheet.getSelectionManager().addSelection(t);
-			outputColumns.addAll(t.getInputColumns());
-			previousSelection = superSel.getSelection(t.getHTableId());
+			outputColumns.addAll(anotherSel.getInputColumns());
+			previousSelection = superSel.getSelection(hTable.getId());
 			if (previousSelection != null)
 				superSel.removeSelection(previousSelection);
-			superSel.addSelection(t);
+			superSel.addSelection(anotherSel);
 
 		}catch (Exception e) {
 			return getErrorUpdate("The operation is undefined");
@@ -104,6 +91,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 	public UpdateContainer undoIt(Workspace workspace) {
 		inputColumns.clear();
 		outputColumns.clear();
+		RepFactory factory = workspace.getFactory();
 		Worksheet worksheet = workspace.getWorksheet(worksheetId);
 		SuperSelection superSel = getSuperSelection(worksheet);
 		HNode hNode = workspace.getFactory().getHNode(hNodeId);
@@ -116,6 +104,8 @@ public UpdateContainer undoIt(Workspace workspace) {
 			worksheet.getSelectionManager().removeSelection(currentSel);
 			superSel.removeSelection(currentSel);
 		}
+		worksheet.getMetadataContainer().getColumnMetadata().removeSelectionPythonCode(factory.getHTable(factory.getHNode(hNodeId).getHTableId()).getId());
+
 		WorksheetUpdateFactory.detectSelectionStatusChange(worksheetId, workspace, this);
 		UpdateContainer uc = WorksheetUpdateFactory.createWorksheetHierarchicalAndCleaningResultsUpdates(worksheetId, superSel, workspace.getContextId());	
 		uc.add(new WorksheetSuperSelectionListUpdate(worksheetId));