Author: pwang
Date: 2011-01-21 17:29:17 -0800 (Fri, 21 Jan 2011)
New Revision: 23563
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeLineParser.java
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeMappingParameters.java
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/DefaultAttributeTableReader.java
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTextTableDialog.java
Log:
Updated
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeLineParser.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeLineParser.java
2011-01-22 01:27:49 UTC (rev 23562)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeLineParser.java
2011-01-22 01:29:17 UTC (rev 23563)
@@ -34,12 +34,7 @@
*/
package org.cytoscape.tableimport.internal.reader;
-//import cytoscape.Cytoscape;
-//import cytoscape.data.CyAttributes;
-
-//import cytoscape.giny.CytoscapeRootGraph;
-
import org.cytoscape.tableimport.internal.reader.TextTableReader.ObjectType;
import org.cytoscape.model.CyEdge;
@@ -80,6 +75,9 @@
* @param parts entries in a line.
*/
public void parseAll(String[] parts) {
+
+ System.out.println("AttributeLineParser.parseAll()...");
+
// Get key
final String primaryKey = parts[mapping.getKeyIndex()].trim();
final int partsLen = parts.length;
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeMappingParameters.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeMappingParameters.java
2011-01-22 01:27:49 UTC (rev 23562)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeMappingParameters.java
2011-01-22 01:29:17 UTC (rev 23563)
@@ -35,9 +35,7 @@
package org.cytoscape.tableimport.internal.reader;
import org.cytoscape.model.CyNetwork;
-//import cytoscape.Cytoscape;
-//import cytoscape.data.CyAttributes;
//import cytoscape.data.CyAttributesUtils;
//import cytoscape.data.synonyms.Aliases;
@@ -58,8 +56,8 @@
import java.util.Set;
import org.cytoscape.tableimport.internal.util.AttributeTypes;
import org.cytoscape.tableimport.internal.util.CytoscapeServices;
+import org.cytoscape.model.CyTable;
-
/**
* Parameter object for text table <---> CyAttributes mapping.<br>
* <p>
@@ -75,7 +73,7 @@
/**
*
*/
- public static final String ID = "ID";
+ public static final String ID = "name";
private static final String DEF_LIST_DELIMITER = PIPE.toString();
private static final String DEF_DELIMITER = TAB.toString();
private final ObjectType objectType;
@@ -89,7 +87,7 @@
private String listDelimiter;
private boolean[] importFlag;
private Map<String, List<String>> attr2id;
- //private CyAttributes attributes;
+ private CyTable attributes;
//private Aliases existingAliases;
private Map<String, String> networkTitle2ID = null;
@@ -176,7 +174,7 @@
for (CyNetwork net : networkSet) {
//networkTitle2ID.put(net.getTitle(),
net.getIdentifier());
-
networkTitle2ID.put(net.getDefaultNetworkTable().getTitle(),
Long.toString(net.getSUID()));
+
//networkTitle2ID.put(net.getDefaultNetworkTable().getTitle(),
Long.toString(net.getSUID()));
}
} else {
networkTitle2ID = null;
@@ -186,7 +184,7 @@
* If attribute mapping is null, use ID for mapping.
*/
if (mappingAttribute == null) {
- this.mappingAttribute = ID;
+ this.mappingAttribute = ID; // Note: ID = 'name'
} else {
this.mappingAttribute = mappingAttribute;
}
@@ -248,8 +246,11 @@
switch (objectType) {
case NODE:
//attributes = Cytoscape.getNodeAttributes();
+ CyNetwork network =
CytoscapeServices.appMgr.getCurrentNetwork();
+ attributes =
CytoscapeServices.tblMgr.getTableMap(CyNode.class,
network).get(CyNetwork.DEFAULT_ATTRS);
+
//existingAliases =
Cytoscape.getOntologyServer().getNodeAliases();
- //it = Cytoscape.getRootGraph().nodesIterator();
+ it = network.getNodeList().iterator();
//Cytoscape.getRootGraph().nodesIterator();
break;
@@ -441,7 +442,6 @@
// Mapping from attribute value to object ID.
attr2id = new HashMap<String, List<String>>();
- //String objectID = null;
String objectID = null;
Object valObj = null;
@@ -458,6 +458,8 @@
// valObj =
attributes.getAttribute(objectID, mappingAttribute);
//}
+ valObj =
node.getCyRow(mappingAttribute);
+
break;
case EDGE:
@@ -493,17 +495,9 @@
}
}
} else {
- //putAttrValue(valObj.toString(),
objectID);
+ putAttrValue(valObj.toString(),
objectID);
}
- // if
(attr2id.containsKey(attributeValue)) {
- //
objIdList = (List<String>) attr2id.get(attributeValue);
- // } else {
- //
objIdList = new ArrayList<String>();
- // }
- //
- //
objIdList.add(objectID);
- //
attr2id.put(attributeValue, objIdList);
}
}
}
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/DefaultAttributeTableReader.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/DefaultAttributeTableReader.java
2011-01-22 01:27:49 UTC (rev 23562)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/DefaultAttributeTableReader.java
2011-01-22 01:29:17 UTC (rev 23563)
@@ -49,7 +49,6 @@
import org.slf4j.LoggerFactory;
import org.cytoscape.tableimport.internal.util.URLUtil;
-//import cytoscape.logger.CyLogger;
/**
@@ -70,7 +69,6 @@
private final URL source;
private AttributeMappingParameters mapping;
private final AttributeLineParser parser;
- //private static CyLogger logger =
CyLogger.getLogger(DefaultAttributeTableReader.class);
private static final Logger logger =
LoggerFactory.getLogger(DefaultAttributeTableReader.class);
// Number of mapped attributes.
@@ -139,10 +137,10 @@
throws Exception {
this.source = source;
this.startLineNumber = startLineNumber;
- //this.mapping = new AttributeMappingParameters(objectType,
delimiters, listDelimiter,
- // keyIndex,
mappingAttribute, aliasIndexList,
- // attributeNames,
attributeTypes, null,
- // importFlag);
+ this.mapping = new AttributeMappingParameters(objectType,
delimiters, listDelimiter,
+ keyIndex,
mappingAttribute, aliasIndexList,
+ attributeNames,
attributeTypes, null,
+ importFlag);
this.parser = new AttributeLineParser(mapping);
}
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTextTableDialog.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTextTableDialog.java
2011-01-22 01:27:49 UTC (rev 23562)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTextTableDialog.java
2011-01-22 01:29:17 UTC (rev 23563)
@@ -211,7 +211,7 @@
+
"%AttributeTable%</table></p></body></html>";
private static final String DEF_ANNOTATION_ITEM = "Please select an
annotation data source...";
private static final String[] keyTable = { "Alias?", "Column (Attribute
Name)", "Data Type" };
- private static final String ID = "ID";
+ private static final String ID = "name";
private static final String GENE_ASSOCIATION = "gene_association";
// Key column index
@@ -250,6 +250,8 @@
private File[] inputFiles;
private static final Logger logger =
LoggerFactory.getLogger(ImportTextTableDialog.class);
+
+ private CyNetwork network;
/**
* Creates new form ImportAttributesDialog
@@ -268,7 +270,8 @@
// Default Attribute is node attr.
//selectedAttributes = Cytoscape.getNodeAttributes();
selectedAttributes = null;
- CyNetwork network =
CytoscapeServices.appMgr.getCurrentNetwork();
+
+ network = CytoscapeServices.appMgr.getCurrentNetwork();
if (network != null){
selectedAttributes =
CytoscapeServices.tblMgr.getTableMap(CyNode.class,
network).get(CyNetwork.DEFAULT_ATTRS);
}
@@ -1710,7 +1713,7 @@
private void importButtonActionPerformed(ActionEvent evt) throws
Exception {
if (checkDataSourceError() == false)
return;
-
+
boolean importAll = importAllCheckBox.isSelected();
/*
@@ -1832,6 +1835,7 @@
}
}
+
/*
* Switch readers based on the dialog type.
*/
@@ -1857,13 +1861,15 @@
} else {
del = checkDelimiter();
}
+
+ //TODO -- Need to fix problem in
AttributeMappingParameters
mapping = new
AttributeMappingParameters(objType, del,
listDelimiter, keyInFile,
mappingAttribute, aliasList,
attributeNames, attributeTypes,
listDataTypes, importFlag,
caseSensitive);
-
+
if
(source.toString().endsWith(SupportedFileType.EXCEL.getExtension()) ||
source.toString().endsWith(SupportedFileType.OOXML.getExtension())) {
/*
@@ -2771,7 +2777,7 @@
*
*/
private void setKeyList() {
- /*
+
if (mappingAttributeComboBox.getSelectedItem() == null) {
return;
}
@@ -2782,32 +2788,33 @@
Set<Object> valueSet = new TreeSet<Object>();
+ //TODO -- setKeyList
if (selectedKeyAttribute.equals(ID)) {
if (objType == NODE) {
- it = Cytoscape.getRootGraph().nodesIterator();
-
+ //it = Cytoscape.getRootGraph().nodesIterator();
+ it = network.getNodeList().iterator();
while (it.hasNext()) {
CyNode node = (CyNode) it.next();
- valueSet.add(node.getIdentifier());
+ valueSet.add(node.getCyRow().get(ID,
String.class)); // ID = "name"
}
} else if (objType == EDGE) {
- it = Cytoscape.getRootGraph().edgesIterator();
+ //it = Cytoscape.getRootGraph().edgesIterator();
- while (it.hasNext()) {
- valueSet.add(((CyEdge)
it.next()).getIdentifier());
- }
+ //while (it.hasNext()) {
+ // valueSet.add(((CyEdge)
it.next()).getIdentifier());
+ //}
} else {
- it = Cytoscape.getNetworkSet().iterator();
+ //it = Cytoscape.getNetworkSet().iterator();
- while (it.hasNext()) {
- valueSet.add(((CyNetwork)
it.next()).getTitle());
- }
+ //while (it.hasNext()) {
+ // valueSet.add(((CyNetwork)
it.next()).getTitle());
+ //}
}
+ } else {
-
-
- } else {
+ //TODO
+ /*
final byte attrType =
selectedAttributes.getType(selectedKeyAttribute);
Object value = null;
@@ -2869,13 +2876,14 @@
}
}
-
+ */
}
+
previewPanel.setKeyAttributeList(valueSet);
- nodeKeyList.setListData(valueSet.toArray());
- */
+ //nodeKeyList.setListData(valueSet.toArray());
+
}
private void updateAliasTableCell(String name, int columnIndex) {
@@ -2993,7 +3001,7 @@
}
private void updateMappingAttributeComboBox() {
- /*
+
mappingAttributeComboBox.removeAllItems();
final ListCellRenderer lcr =
mappingAttributeComboBox.getRenderer();
@@ -3007,7 +3015,7 @@
if (value.equals(ID)) {
cmp.setIcon(ID_ICON.getIcon());
} else {
-
//cmp.setIcon(getDataTypeIcon(selectedAttributes.getType(value.toString())));
+
//cmp.setIcon(getDataTypeIcon(selectedAttributes.getColumnTypeMap().get(value.toString())));
}
return cmp;
@@ -3016,14 +3024,32 @@
mappingAttributeComboBox.addItem(ID);
- for (String name : selectedAttributes.getAttributeNames()) {
- if ((selectedAttributes.getType(name) !=
AttributeTypes.TYPE_COMPLEX)
- && (selectedAttributes.getType(name) !=
AttributeTypes.TYPE_SIMPLE_MAP)
- && (selectedAttributes.getType(name) !=
AttributeTypes.TYPE_UNDEFINED)) {
- mappingAttributeComboBox.addItem(name);
+ Set<String> keySet =
this.selectedAttributes.getColumnTypeMap().keySet();
+
+ Iterator<String> it = keySet.iterator();
+ Map<String, Class<?>> columnTypeMap =
this.selectedAttributes.getColumnTypeMap();
+
+ while (it.hasNext()){
+ String columnName = it.next();
+
+ if (columnName.equalsIgnoreCase(ID)){
+ continue;
}
+
+ Class<?> type =columnTypeMap.get(columnName);
+ if ( type == String.class || type == Integer.class ||
type == Double.class || type == List.class){
+ mappingAttributeComboBox.addItem(columnName);
+ }
}
- */
+
+ //for (String name : selectedAttributes.getAttributeNames()) {
+ // if ((selectedAttributes.getColumnTypeMap().get(name) !=
AttributeTypes.TYPE_COMPLEX)
+ // && (selectedAttributes.getColumnTypeMap().get(name)
!= AttributeTypes.TYPE_SIMPLE_MAP)
+ // && (selectedAttributes.getColumnTypeMap().get(name)
!= AttributeTypes.TYPE_UNDEFINED)) {
+ // mappingAttributeComboBox.addItem(name);
+ // }
+ //}
+
}
private TableCellRenderer getRenderer(FileTypes type) {
@@ -3067,22 +3093,11 @@
*/
private void loadAnnotation(TextTableReader reader, String source) {
-
System.out.println("\nImporttextTableDialog.loadAnnotation()....\n\n");
-
- /*
- // Create LoadNetwork Task
+ // Create loadAnnotation Task
ImportAttributeTableTask task = new
ImportAttributeTableTask(reader, source);
+ ImportAttributeTableTaskFactory taskFactory = new
ImportAttributeTableTaskFactory(task);
- // Configure JTask Dialog Pop-Up Box
- JTaskConfig jTaskConfig = new JTaskConfig();
- jTaskConfig.setOwner(CytoscapeServices.desktop.getJFrame());
- jTaskConfig.displayCloseButton(true);
- jTaskConfig.displayStatus(true);
- jTaskConfig.setAutoDispose(false);
-
- // Execute Task in New Thread; pops open JTask Dialog Box.
- TaskManager.executeTask(task, jTaskConfig);
- */
+ CytoscapeServices.guiTaskManagerServiceRef.execute(taskFactory);
}
/**
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