Merge pull request #136 from InformationIntegrationGroup/pytransform_…

…glue

Pytransform glue

README.md

@@ -82,7 +82,27 @@ Yes. Due to Oracles binary license issues, we can't distribute the JAR file that
     <artifactId>ojdbc</artifactId> 
     <version>14</version> 
     <scope>system</scope> 
-    <systemPath>${project.basedir}/lib/ojdbc14.jar</systemPath> 
+    <systemPath>/Users/karma/Web-Karma/lib/ojdbc14.jar</systemPath> 
 </dependency> 
 ```
-Make sure that the filename mentioned in the `systemPath` element matches with your downloaded JAR file.
+Make sure that the filename mentioned in the `systemPath` element matches with your downloaded JAR file; it is likely that your installation folder is different from `/Users/karma` so make sure you use the correct one.
+
+### Are there additional steps required to import data from MySQL database? ###
+Yes. Due to MySQL binary license issues, we can't distribute the JAR file that is required for importing data from an MySQL database. Following are the steps to resolve the runtime error that you will get if you try to do it with the current source code:
+
+1. Download the appropriate MySQL driver JAR file (for JDK 1.5 and above) that matches your MySQL version. Link: http://dev.mysql.com/downloads/connector/j/
+2. Put the downloaded JAR file inside `lib` folder of the Karma source code. 
+3. Add the following snippet in the `pom.xml` file of the `karma-jdbc` project inside the dependencies XML element: 
+
+```
+<dependency> 
+    <groupId>mysql</groupId> 
+    <artifactId>mysql-connector-java</artifactId> 
+    <version>5.1.32</version> 
+    <scope>system</scope> 
+    <systemPath>/Users/karma/Web-Karma/lib/mysql-connector-java-5.1.32-bin.jar</systemPath> 
+</dependency> 
+```
+Make sure that the filename mentioned in the `systemPath` element matches with your downloaded JAR file; it is likely that your installation folder is different from `/Users/karma` so make sure you use the correct one. The `version` will be the version of the JAR that you downloaded.
+
+

karma-common/src/main/java/edu/isi/karma/er/helper/PythonRepository.java

@@ -37,7 +37,9 @@ private void initialize()
 		scripts = new ConcurrentHashMap<String, PyCode>();
 		PythonInterpreter interpreter = new PythonInterpreter();
 		compileAndAddToRepository(interpreter, PythonTransformationHelper.getImportStatements());
+		compileAndAddToRepository(interpreter, PythonTransformationHelper.getRowIndexDefStatement());
 		compileAndAddToRepository(interpreter, PythonTransformationHelper.getGetValueDefStatement());
+		compileAndAddToRepository(interpreter, PythonTransformationHelper.getGetValueFromNestedColumnByIndexDefStatement());
 		compileAndAddToRepository(interpreter, PythonTransformationHelper.getIsEmptyDefStatement());
 		compileAndAddToRepository(interpreter, PythonTransformationHelper.getVDefStatement());
 		compileAndAddToRepository(interpreter, PythonTransformationHelper.getTransformStatement());
@@ -67,7 +69,9 @@ private PyCode compile(PythonInterpreter interpreter, String statement) {
 	public void initializeInterperter(PythonInterpreter interpreter)
 	{
 		interpreter.exec(scripts.get(PythonTransformationHelper.getImportStatements()));
+		interpreter.exec(scripts.get(PythonTransformationHelper.getRowIndexDefStatement()));
 		interpreter.exec(scripts.get(PythonTransformationHelper.getGetValueDefStatement()));
+		interpreter.exec(scripts.get(PythonTransformationHelper.getGetValueFromNestedColumnByIndexDefStatement()));
 		interpreter.exec(scripts.get(PythonTransformationHelper.getIsEmptyDefStatement()));
 		interpreter.exec(scripts.get(PythonTransformationHelper.getVDefStatement()));
 

karma-common/src/main/java/edu/isi/karma/er/helper/PythonTransformationHelper.java

@@ -37,6 +37,8 @@ public class PythonTransformationHelper {
 	private static String valueDefStatement = null;
 	private static String isEmptyDefStatement = null;
 	private static String importStatement = null;
+	private static String valueFromNestedColumnByIndexDefStatement = null;
+	private static String getRowIndexDefStatement = null;
 	public static String getPyObjectValueAsString(PyObject obj) {
 		if (obj == null)
 			return "";
@@ -96,6 +98,19 @@ public static String getImportStatements() {
 		return importStatement;
 	}
 
+	public static String getRowIndexDefStatement()
+	{
+		if(getRowIndexDefStatement == null)
+		{
+			StringBuilder methodStmt = new StringBuilder();
+			methodStmt.append("def getRowIndex():\n");
+			methodStmt.append("	factory = edu.isi.karma.rep.WorkspaceManager.getInstance().getWorkspace(workspaceid).getFactory()\n");
+			methodStmt.append("	node = factory.getNode(nodeid)\n");
+			methodStmt.append("	return node.getRowIndex()\n");
+			getRowIndexDefStatement = methodStmt.toString();
+		}
+		return getRowIndexDefStatement;
+	}
 	public static String getGetValueDefStatement() {
 
 		if(valueDefStatement == null)
@@ -118,6 +133,30 @@ public static String getGetValueDefStatement() {
 		return valueDefStatement;
 	}
 
+	public static String getGetValueFromNestedColumnByIndexDefStatement() {
+
+		if(valueFromNestedColumnByIndexDefStatement == null)
+		{
+			StringBuilder methodStmt = new StringBuilder();
+			methodStmt.append("def getValueFromNestedColumnByIndex(columnName, nestedColumnName, index):\n");
+			methodStmt.append("	factory = edu.isi.karma.rep.WorkspaceManager.getInstance().getWorkspace(workspaceid).getFactory()\n");
+			methodStmt.append("	node = factory.getNode(nodeid)\n");
+			methodStmt.append("	targetNode = node.getNeighborByColumnNameWithNestedColumnByRowIndex(columnName, factory, nestedColumnName, index)\n");
+			methodStmt.append("	if targetNode is not None:\n");
+			methodStmt.append("		command.addInputColumns(targetNode.getHNodeId())\n");
+			methodStmt.append("		value = targetNode.getValue()\n");
+			methodStmt.append("		if value is not None:\n");
+			methodStmt.append("			valueAsString = value.asString()\n");
+			methodStmt.append("			if valueAsString is not None:\n");
+			methodStmt.append("				return valueAsString\n");
+			methodStmt.append("	return ''\n");
+			valueFromNestedColumnByIndexDefStatement = methodStmt.toString();
+		}
+		return valueFromNestedColumnByIndexDefStatement;
+	}
+
+
+
 	public static String getIsEmptyDefStatement() {
 
 		if(isEmptyDefStatement == null)

karma-common/src/main/java/edu/isi/karma/rep/Node.java

@@ -203,4 +203,13 @@ public Node getNeighbor(String hNodeId) {
 	public Node getNeighborByColumnName(String columnName, RepFactory factory) {
 		return belongsToRow.getNeighborByColumnName(columnName, factory);
 	}
+
+	public Node getNeighborByColumnNameWithNestedColumnByRowIndex(String columnName, RepFactory factory, String nestedColumnName, int index) {
+		return belongsToRow.getNeighborByColumnNameWithNestedColumnByRowIndex(columnName, factory, nestedColumnName, index);
+	}
+
+	public int getRowIndex()
+	{
+		return belongsToRow.getBelongsToTable().getRowIndex(belongsToRow);
+	}
 }

karma-common/src/main/java/edu/isi/karma/rep/Row.java

@@ -255,6 +255,44 @@ public Node getNeighborByColumnName(String columnName, RepFactory factory) {
 		return null;
 	}
 
+	public Node getNeighborWithNestedColumnByIndex(String hNodeId, RepFactory factory, String nestedColumnName, int index) {
+		if (nodes.containsKey(hNodeId)) {
+			Node nodeWithNestedColumn = nodes.get(hNodeId);
+			Table nestedTable = nodeWithNestedColumn.getNestedTable();
+			if(nestedTable != null)
+			{
+				String [] nestedColumnPath = nestedColumnName.split("/");
+				String nestedHNodeId = factory.getHTable(nestedTable.getHTableId()).getHNodeIdFromColumnName(nestedColumnPath[0]);
+				if (null != nestedHNodeId && nestedColumnPath.length ==1) {
+					Row r = nestedTable.getRow(index);
+					if(r != null)
+					{
+						return r.getNeighbor(nestedHNodeId);
+					}
+				}
+				else
+				{
+					return nestedTable.getRow(0).getNeighborWithNestedColumnByIndex(nestedHNodeId, factory, nestedColumnName.substring(nestedColumnName.indexOf("/")+1), index);
+				}
+			}
+		}
+		return null;
+	}
+
+	public Node getNeighborByColumnNameWithNestedColumnByRowIndex(String columnName, RepFactory factory, String nestedColumnName, int index) {
+		String hTableId = belongsToTable.getHTableId();
+		HTable hTable = factory.getHTable(hTableId);
+		String hNodeId = hTable.getHNodeIdFromColumnName(columnName);
+		if (null != hNodeId) {
+			return getNeighborWithNestedColumnByIndex(hNodeId, factory, nestedColumnName, index);
+		} else if (belongsToTable.getNestedTableInNode() != null) {
+			return belongsToTable.getNestedTableInNode()
+					.getNeighborByColumnNameWithNestedColumnByRowIndex(columnName, factory, nestedColumnName, index);
+		}
+		return null;
+	}
+
+
 	public boolean collectNodes(HNodePath path, Collection<Node> nodes, SuperSelection sel) {
 		Node n = getNode(path.getFirst().getId());
 		if (n == null) {

karma-common/src/main/java/edu/isi/karma/rep/Table.java

@@ -135,6 +135,19 @@ public void addNestedTableToDataTable(HNode hNode, RepFactory factory) {
 			r.addNestedTableToDataTable(hNode, this, factory);
 		}
 	}
+
+	public int getRowIndex(Row r)
+	{
+		return rows.indexOf(r);
+	}
+	public Row getRow(int index)
+	{
+		if(0 <= index && index < rows.size())
+		{
+			return rows.get(index);
+		}
+		return null;
+	}
 
 	/**
 	 * @param startIndex
@@ -145,7 +158,7 @@ public void addNestedTableToDataTable(HNode hNode, RepFactory factory) {
 	 */
 	public ArrayList<Row> getRows(int startIndex, int count, SuperSelection sel) {
 		ArrayList<Row> result = new ArrayList<Row>();
-		Iterator<Row> itr = rows.iterator();
+		Iterator<Row> itr = rows.listIterator(startIndex);
 		int sum = 0;
 		while(itr.hasNext()) {
 			Row r = itr.next();