Author: mes
Date: 2011-11-15 12:08:29 -0800 (Tue, 15 Nov 2011)
New Revision: 27470
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/MapNetworkAttrTask.java
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/MergeDataTask.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/UnrecognizedVisualPropertyManager.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumn.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyTableProjection.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
Log:
made virtual columns only join on the source primary key rather than an
arbitrary key
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/MapNetworkAttrTask.java
===================================================================
---
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/MapNetworkAttrTask.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/MapNetworkAttrTask.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -114,7 +114,7 @@
for (final CyTable targetTable : targetTables) {
if (cancelled)
return;
- targetTable.addVirtualColumns(newGlobalTable,
sourceTableJoinColumn, mappingKey, false);
+ targetTable.addVirtualColumns(newGlobalTable,
mappingKey, false);
}
}
}
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
===================================================================
--- core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
2011-11-15 18:53:49 UTC (rev 27469)
+++ core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -223,35 +223,36 @@
*/
int getRowCount();
- /** Adds a "virtual" column to the the current table.
- * @param virtualColumn the name of the new virtual column, if this
name already exists,
- * new column names with -1, -2 and so appended
to this name on will
- * be tried until a non-existing name will be
found
- * @param sourceColumn the name of the column in "sourceTable" that
will be mapped to
- * "virtualColumn"
- * @param sourceTable the table that really contains the column
that we're adding (all
- * updates and lookups of this new column will
be redirected to here)
- * @param sourceJoinKey the column in "sourceTable" that will be used
for the join
- * @param targetJoinKey the column in current table that will be used
for the join
- * @param isImmutable if true, this column cannot be deleted
- * @return the actual name of the new virtual column
- * Note: The types of "sourceJoinKey" and "targetJoinKey" have to be
identical.
+ /**
+ * Adds a "virtual" column to the the current table.
+ * @param virtualColumn The name of the new virtual column, if this
name already exists,
+ * new column names with -1, -2 and so appended
to this name on will
+ * be tried until a non-existing name will be
found.
+ * @param sourceColumn The name of the column in "sourceTable" that
will be mapped to
+ * "virtualColumn".
+ * @param sourceTable The table that really contains the column that
we're adding (all
+ * updates and lookups of this new column will be
redirected to here).
+ * The table will be joined on the primary key
column of this table.
+ * @param targetJoinKey The column in current table that will be used
for the join. This
+ * column will be joined with the primary key
column of the source
+ * table. These columns must be of the same type!
+ * @param isImmutable If true, this column cannot be deleted.
+ * @return The actual name of the new virtual column.
*/
String addVirtualColumn(String virtualColumn, String sourceColumn,
CyTable sourceTable,
- String sourceJoinKey, String targetJoinKey,
- boolean isImmutable);
+ String targetJoinKey, boolean isImmutable);
/** Adds all columns in another table as "virtual" columns to the the
current table.
- * @param sourceTable the table that really contains the column
that we're adding (all
- * updates and lookups of this new column will
be redirected to here)
- * @param sourceJoinKey the column in "sourceTable" that will be used
for the join
- * @param targetJoinKey the column in current table that will be used
for the join
- * @param isImmutable if true, these columns cannot be deleted
- * Note: The types of "sourceJoinKey" and "targetJoinKey" have to be
identical. Also none
- * of the column names in "sourceTable" must exist in the
current table!
+ * @param sourceTable The table that really contains the column
that we're adding (all
+ * updates and lookups of this new column will
be redirected to here).
+ * The table will be joined on the primary key
column of this table.
+ * None of the column names in "sourceTable"
must exist in the current table!
+ * @param targetJoinKey The column in current table that will be used
for the join. This
+ * column will be joined with the primary key
column of the source
+ * table. These columns must be of the same type!
+ * @param isImmutable If true, these columns cannot be deleted.
*/
- void addVirtualColumns(CyTable sourceTable, String sourceJoinKey,
String targetJoinKey,
- boolean isImmutable);
+ void addVirtualColumns(CyTable sourceTable, String targetJoinKey,
boolean isImmutable);
/**
* Returns how (or if) this CyTable should be saved.
Modified:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
===================================================================
---
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -541,26 +541,21 @@
@Test
public void testVirtualColumn() {
table.createColumn("x", Long.class, false);
- table2.createColumn("x2", Long.class, false);
table2.createColumn("s", String.class, false);
- assertEquals(table.addVirtualColumn("s1", "s", table2, "x2",
"x", false), "s1");
+ assertEquals(table.addVirtualColumn("s1", "s", table2, "x",
false), "s1");
assertEquals("Virtual column type should have been String!",
String.class, table.getColumn("s1").getType());
- assertEquals(table.addVirtualColumn("s1", "s", table2, "x2",
"x", false), "s1-1");
+ assertEquals(table.addVirtualColumn("s1", "s", table2, "x",
false), "s1-1");
assertEquals("Virtual column type should have been String!",
String.class, table.getColumn("s1-1").getType());
}
@Test
public void testVirtualColumnIsSet() {
- table.createColumn("x", Integer.class, false);
CyRow row1 = table.getRow(1L);
- row1.set("x", 33);
- table2.createColumn("x2", Integer.class, false);
CyRow row2 = table2.getRow(1L);
- row2.set("x2", 33);
table2.createColumn("s", String.class, false);
- table.addVirtualColumn("s1", "s", table2, "x2", "x", true);
+ table.addVirtualColumn("s1", "s", table2,
table.getPrimaryKey().getName(), true);
assertFalse(row1.isSet("s1"));
row2.set("s", "abc");
assertTrue(row1.isSet("s1"));
@@ -568,14 +563,10 @@
@Test
public void testVirtualColumnGet() {
- table.createColumn("x", Integer.class, false);
CyRow row1 = table.getRow(1L);
- row1.set("x", 33);
- table2.createColumn("x2", Integer.class, false);
CyRow row2 = table2.getRow(1L);
- row2.set("x2", 33);
table2.createColumn("s", String.class, false);
- table.addVirtualColumn("s1", "s", table2, "x2", "x", false);
+ table.addVirtualColumn("s1", "s", table2,
table.getPrimaryKey().getName(), false);
assertFalse(row1.isSet("s1"));
row2.set("s", "abc");
assertEquals(row1.get("s1", String.class), "abc");
@@ -583,14 +574,10 @@
@Test
public void testVirtualColumnSetWithAReplacementValue() {
- table.createColumn("x", Integer.class, false);
CyRow row1 = table.getRow(1L);
- row1.set("x", 33);
- table2.createColumn("x2", Integer.class, false);
CyRow row2 = table2.getRow(1L);
- row2.set("x2", 33);
table2.createColumn("s", String.class, false);
- table.addVirtualColumn("s1", "s", table2, "x2", "x", true);
+ table.addVirtualColumn("s1", "s", table2,
table.getPrimaryKey().getName(), true);
assertFalse(row1.isSet("s1"));
row2.set("s", "abc");
assertEquals(row1.get("s1", String.class), "abc");
@@ -600,14 +587,10 @@
@Test
public void testVirtualColumnUnset() {
- table.createColumn("x", Integer.class, false);
CyRow row1 = table.getRow(1L);
- row1.set("x", 33);
- table2.createColumn("x2", Integer.class, false);
CyRow row2 = table2.getRow(1L);
- row2.set("x2", 33);
table2.createColumn("s", String.class, false);
- table.addVirtualColumn("s1", "s", table2, "x2", "x", false);
+ table.addVirtualColumn("s1", "s", table2,
table.getPrimaryKey().getName(), false);
row2.set("s", "abc");
assertTrue(row1.isSet("s1"));
row1.set("s1", null);
@@ -619,11 +602,9 @@
table.createColumn("x", Integer.class, false);
CyRow row1 = table.getRow(1L);
row1.set("x", 33);
- table2.createColumn("x2", Integer.class, false);
CyRow row2 = table2.getRow(1L);
- row2.set("x2", 33);
table2.createColumn("s", String.class, false);
- table.addVirtualColumn("s1", "s", table2, "x2", "x", true);
+ table.addVirtualColumn("s1", "s", table2,
table.getPrimaryKey().getName(), true);
assertFalse(row1.isSet("s1"));
row2.set("s", "abc");
Collection<CyRow> matchingRows = table.getMatchingRows("s1",
"abc");
@@ -636,9 +617,8 @@
@Test
public void testVirtualColumnDelete() {
table.createColumn("x", Long.class, false);
- table2.createColumn("x2", Long.class, false);
table2.createColumn("s", String.class, false);
- table.addVirtualColumn("s1", "s", table2, "x2", "x", false);
+ table.addVirtualColumn("s1", "s", table2, "x", false);
assertNotNull(table.getColumn("s1"));
table.deleteColumn("s1");
assertNull(table.getColumn("s1"));
@@ -646,14 +626,10 @@
@Test
public void testVirtualColumnColumnSize() {
- table.createColumn("x", Integer.class, false);
CyRow row1 = table.getRow(1L);
- row1.set("x", 33);
- table2.createColumn("x2", Integer.class, false);
CyRow row2 = table2.getRow(1L);
- row2.set("x2", 33);
table2.createColumn("s", String.class, false);
- table.addVirtualColumn("s1", "s", table2, "x2", "x", true);
+ table.addVirtualColumn("s1", "s", table2,
table.getPrimaryKey().getName(), true);
assertFalse(row1.isSet("s1"));
row2.set("s", "abc");
List<String> columnValues =
table.getColumn("s1").getValues(String.class);
@@ -664,9 +640,8 @@
@Test
public void testVirtualColumnGetColumnValues() {
table.createColumn("x", Long.class, false);
- table2.createColumn("x2", Long.class, false);
table2.createListColumn("b", Boolean.class, false);
- table.addVirtualColumn("b1", "b", table2, "x2", "x", false);
+ table.addVirtualColumn("b1", "b", table2, "x", false);
assertEquals("Virtual column list element type should have been
Boolean!",
Boolean.class,
table.getColumn("b1").getListElementType());
}
@@ -674,9 +649,8 @@
@Test
public void testIsVirtual() {
table.createColumn("x", Long.class, false);
- table2.createColumn("x2", Long.class, false);
table2.createListColumn("b", Boolean.class, false);
- table.addVirtualColumn("b1", "b", table2, "x2", "x", true);
+ table.addVirtualColumn("b1", "b", table2, "x", true);
assertTrue(table.getColumn("b1").getVirtualColumnInfo().isVirtual());
assertFalse(table.getColumn("x").getVirtualColumnInfo().isVirtual());
assertFalse(table2.getColumn("b").getVirtualColumnInfo().isVirtual());
@@ -709,9 +683,8 @@
table.createColumn("x", Long.class, false);
CyColumn column = table.getColumn("x");
assertNull(column.getVirtualColumnInfo().getSourceTable());
- table2.createColumn("x2", Long.class, false);
table2.createListColumn("b", Boolean.class, false);
- table.addVirtualColumn("b1", "b", table2, "x2", "x", true);
+ table.addVirtualColumn("b1", "b", table2, "x", true);
CyColumn column2 = table.getColumn("b1");
assertEquals(table2,
column2.getVirtualColumnInfo().getSourceTable());
}
@@ -719,10 +692,9 @@
@Test
public void testTableMutability() {
table.createColumn("x", Long.class, false);
- table2.createColumn("x2", Long.class, false);
table2.createListColumn("b", Boolean.class, false);
assertEquals(Mutability.MUTABLE, table2.getMutability());
- table.addVirtualColumn("b1", "b", table2, "x2", "x", true);
+ table.addVirtualColumn("b1", "b", table2, "x", true);
assertEquals(Mutability.IMMUTABLE_DUE_TO_VIRT_COLUMN_REFERENCES,
table2.getMutability());
}
@@ -927,4 +899,80 @@
public void testGetAttrBeforeColumnExists() {
assertNull(attrs.get("nonexistentColumnX",Integer.class));
}
+
+ @Test
+ public void testVirtualColumns() {
+ table2.createColumn("s", String.class, false);
+ table2.createColumn("t", Integer.class, false);
+ table2.createColumn("u", Long.class, false);
+ table2.createColumn("v", Boolean.class, false);
+ table2.createColumn("w", Double.class, false);
+ table2.createListColumn("x", String.class, false);
+ table.addVirtualColumns( table2,
table.getPrimaryKey().getName(), false);
+
+ CyColumn scol = table.getColumn("s");
+ assertNotNull(scol);
+ assertEquals(String.class,scol.getType());
+
+ CyColumn tcol = table.getColumn("t");
+ assertNotNull(tcol);
+ assertEquals(Integer.class,tcol.getType());
+
+ CyColumn ucol = table.getColumn("u");
+ assertNotNull(ucol);
+ assertEquals(Long.class,ucol.getType());
+
+ CyColumn vcol = table.getColumn("v");
+ assertNotNull(vcol);
+ assertEquals(Boolean.class,vcol.getType());
+
+ CyColumn wcol = table.getColumn("w");
+ assertNotNull(wcol);
+ assertEquals(Double.class,wcol.getType());
+
+ CyColumn xcol = table.getColumn("x");
+ assertNotNull(xcol);
+ assertEquals(List.class,xcol.getType());
+ assertEquals(String.class,xcol.getListElementType());
+ }
+
+ @Test
+ public void testVirtualColumnWithDupe() {
+ table2.createColumn("s", String.class, false);
+ table.createColumn("s", String.class, false);
+ table.addVirtualColumns( table2,
table.getPrimaryKey().getName(), false);
+
+ CyColumn scol = table.getColumn("s");
+ assertFalse( scol.getVirtualColumnInfo().isVirtual() );
+
+ CyColumn s1col = table.getColumn("s-1");
+ assertTrue( s1col.getVirtualColumnInfo().isVirtual() );
+ }
+
+ @Test
+ public void testVirtualColumnsNoPrimaryKey() {
+ table2.createColumn("s", String.class, false);
+ table.addVirtualColumns( table2,
table.getPrimaryKey().getName(), false);
+
+ CyColumn scol = table.getColumn("s");
+ assertNotNull(scol);
+
+ // If the tables have the same name for the primary key column,
then verify that
+ // we don't get new column with the expected new column name
for source table
+ // primary key. Also make sure that the existing column for
the primary key
+ // is not virtual.
+ if ( table.getPrimaryKey().getName().equals(
table2.getPrimaryKey().getName() ) ) {
+ String expectedNewName =
table2.getPrimaryKey().getName() + "-1";
+ CyColumn npkcol = table.getColumn( expectedNewName );
+ assertNull(npkcol);
+ CyColumn pkcol = table.getColumn(
table.getPrimaryKey().getName() );
+ assertFalse( pkcol.getVirtualColumnInfo().isVirtual() );
+
+ // Otherwise, just make sure that the primary key column of the
source table
+ // isn't added.
+ } else {
+ CyColumn npkcol = table.getColumn(
table2.getPrimaryKey().getName() );
+ assertNull(npkcol);
+ }
+ }
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/MergeDataTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/MergeDataTask.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/MergeDataTask.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -37,9 +37,9 @@
taskMonitor.setProgress(0.2);
// "Copy" Name column to ID type name.
final CyColumn pKey = table.getPrimaryKey();
- table.addVirtualColumn(columnName, pKey.getName(), table,
pKey.getName(), pKey.getName(), false);
+ table.addVirtualColumn(columnName, pKey.getName(), table,
pKey.getName(), false);
taskMonitor.setProgress(0.5);
- nodeTable.addVirtualColumn(columnName, pKey.getName(), table,
pKey.getName(), pKey.getName(), false);
+ nodeTable.addVirtualColumn(columnName, pKey.getName(), table,
pKey.getName(), false);
taskMonitor.setStatusMessage("Finished!");
taskMonitor.setProgress(1.0);
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -287,7 +287,6 @@
targetTable.addVirtualColumn(columnData.getName(),
columnData.getSourceColumn(),
sourceTable,
-
columnData.getSourceJoinKey(),
columnData.getTargetJoinKey(),
columnData.isImmutable());
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/UnrecognizedVisualPropertyManager.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/UnrecognizedVisualPropertyManager.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/UnrecognizedVisualPropertyManager.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -178,7 +178,7 @@
vpTbl.createColumn("att_id", Long.class, false);
vpTbl.createColumn("att_value", String.class, false);
vpTbl.createColumn("target_id", Long.class, false);
- vpTbl.addVirtualColumn("att_name_vc", "att_name", rendererTbl,
RENDERER_TABLE_PK, "att_id", false);
+ vpTbl.addVirtualColumn("att_name_vc", "att_name", rendererTbl,
"att_id", false);
// add tables to the internal maps
rendererTablesMap.put(netViewId, rendererTbl);
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -195,7 +195,7 @@
private void linkDefaultTables(CyTable srcTable, CyTable tgtTable) {
// Add all columns from source table as virtual columns in
target table.
-
tgtTable.addVirtualColumns(srcTable,Identifiable.SUID,Identifiable.SUID,true);
+ tgtTable.addVirtualColumns(srcTable,Identifiable.SUID,true);
// Now add a listener for column created events to add
// virtual columns to any subsequent source columns added.
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -715,24 +715,40 @@
logger.debug("risky use of get() instead of getList()
for retrieving list");
lastInternalError = null;
+ final Object value = getValue(key,columnName,type);
+
+ if ( value == null )
+ return getDefaultValue(columnName,defaultValue);
+ else
+ return type.cast(value);
+ }
+
+ Object getValue(Object key, String columnName) {
+ return getValue(key,columnName,null);
+ }
+
+ private Object getValue(Object key, String columnName, Class<?> type) {
final VirtualColumn virtColumn =
virtualColumnMap.get(columnName);
if (virtColumn != null)
- return (T)virtColumn.getValue(key);
+ return virtColumn.getValue(key);
final Object vl = getValueOrEquation(key, columnName);
if (vl == null)
- return getDefaultValue(columnName,defaultValue);
+ return null;
if (vl instanceof Equation) {
final StringBuilder errorMsg = new StringBuilder();
- final Object result =
+ final Object value =
EqnSupport.evalEquation((Equation)vl, key,
interpreter,
currentlyActiveAttributes, columnName,
errorMsg, this);
lastInternalError = errorMsg.toString();
- return result == null ?
getDefaultValue(columnName,defaultValue) :
(T)EqnSupport.convertEqnResultToColumnType(type, result);
+ if ( type == null )
+ return value;
+ else
+ return
EqnSupport.convertEqnResultToColumnType(type, value);
} else
- return type.cast(vl);
+ return vl;
}
private <T> T getDefaultValue(final String columnName, final T
defaultValue) {
@@ -747,27 +763,7 @@
}
}
- Object getValue(Object key, String columnName) {
- final VirtualColumn virtColumn =
virtualColumnMap.get(columnName);
- if (virtColumn != null)
- return virtColumn.getValue(key);
- final Object vl = getValueOrEquation(key, columnName);
- if (vl == null)
- return null;
-
- if (vl instanceof Equation) {
- final StringBuilder errorMsg = new StringBuilder();
- final Object value =
- EqnSupport.evalEquation((Equation)vl, key,
interpreter,
-
currentlyActiveAttributes, columnName,
- errorMsg, this);
- lastInternalError = errorMsg.toString();
- return value;
- } else
- return vl;
- }
-
synchronized private <T> List<T> getListX(final Object key, final
String columnName,
final Class<?
extends T> listElementType, final List<T> defaultValue)
{
@@ -845,8 +841,7 @@
@Override
public final String addVirtualColumn(final String virtualColumnName,
final String sourceColumnName,
- final CyTable sourceTable, final
String sourceJoinKeyName,
- final String targetJoinKeyName,
final boolean isImmutable)
+ final CyTable sourceTable, final
String targetJoinKeyName, final boolean isImmutable)
{
if (virtualColumnName == null)
throw new NullPointerException("\"virtualColumn\"
argument must never be null!");
@@ -857,8 +852,6 @@
throw new
NullPointerException("\"sourceColumn\" argument must never be null!");
if (sourceTable == null)
throw new NullPointerException("\"sourceTable\"
argument must never be null!");
- if (sourceJoinKeyName == null)
- throw new
NullPointerException("\"sourceJoinKey\" argument must never be null!");
if (targetJoinKeyName == null)
throw new
NullPointerException("\"targetJoinKey\" argument must never be null!");
@@ -866,19 +859,16 @@
if (sourceColumn == null)
throw new
IllegalArgumentException("\"sourceColumn\" is not a column in
\"sourceColumn\"!");
- final CyColumn sourceJoinKeyType =
sourceTable.getColumn(sourceJoinKeyName);
- if (sourceJoinKeyType == null)
- throw new
IllegalArgumentException("\"sourceJoinKey\" is not a known column in
\"sourceTable\"!");
-
final CyColumn targetJoinKeyType =
this.getColumn(targetJoinKeyName);
if (targetJoinKeyType == null)
throw new
IllegalArgumentException("\"targetJoinKey\" is not a known column in this
table!");
+ final CyColumn sourceJoinKeyType =
sourceTable.getPrimaryKey();
if (sourceJoinKeyType.getType() !=
targetJoinKeyType.getType())
throw new
IllegalArgumentException("\"sourceJoinKey\" has a different type from
\"targetJoinKey\"!");
++((CyTableImpl)sourceTable).virtualColumnReferenceCount;
- VirtualColumnInfo virtualInfo = new
VirtualColumnInfoImpl(true, sourceTable, sourceColumnName, sourceJoinKeyName,
targetJoinKeyName, isImmutable);
+ VirtualColumnInfo virtualInfo = new
VirtualColumnInfoImpl(true, sourceTable, sourceColumnName,
sourceTable.getPrimaryKey().getName(), targetJoinKeyName, isImmutable);
final CyColumn targetColumn =
new CyColumnImpl(this, virtualColumnName,
sourceColumn.getType(),
sourceColumn.getListElementType(),
@@ -889,7 +879,7 @@
types.put(targetName, targetColumn);
virtualColumnMap.put(targetName,
new VirtualColumn(sourceTable,
sourceColumnName, this,
-
sourceJoinKeyName, targetJoinKeyName));
+
sourceTable.getPrimaryKey().getName(), targetJoinKeyName));
}
eventHelper.fireEvent(new ColumnCreatedEvent(this, targetName));
@@ -927,39 +917,33 @@
@Override
synchronized public final void addVirtualColumns(final CyTable
sourceTable,
- final String
sourceJoinKeyName,
final String
targetJoinKeyName,
final boolean
isImmutable)
{
if (sourceTable == null)
throw new NullPointerException("\"sourceTable\"
argument must never be null!");
- if (sourceJoinKeyName == null)
- throw new NullPointerException("\"sourceJoinKeyName\"
argument must never be null!");
if (targetJoinKeyName == null)
throw new NullPointerException("\"targetJoinKeyName\"
argument must never be null!");
- final CyColumn sourceJoinKey =
sourceTable.getColumn(sourceJoinKeyName);
- if (sourceJoinKey == null)
- throw new IllegalArgumentException("\"sourceJoinKey\"
is not a known column in \"sourceTable\"!");
-
final CyColumn targetJoinKey =
this.getColumn(targetJoinKeyName);
if (targetJoinKey == null)
throw new IllegalArgumentException("\"" +
targetJoinKeyName
+ "\" is not a known
column in this table!");
+ final CyColumn sourceJoinKey = sourceTable.getPrimaryKey();
if (sourceJoinKey.getType() != targetJoinKey.getType())
- throw new IllegalArgumentException("\"" +
sourceJoinKeyName
+ throw new IllegalArgumentException("\"" +
sourceJoinKey.getName()
+ "\" has a
different type from \""
+ targetJoinKeyName
+ "\"!");
final Collection<CyColumn> columns = sourceTable.getColumns();
for (final CyColumn column : columns) {
final String columnName = column.getName();
- if (columnName.equals(sourceJoinKeyName))
+ // skip the primary key
+ if (columnName.equals(sourceJoinKey.getName()))
continue;
- addVirtualColumn(columnName, columnName, sourceTable,
sourceJoinKeyName,
- targetJoinKeyName, isImmutable);
+ addVirtualColumn(columnName, columnName, sourceTable,
targetJoinKeyName, isImmutable);
}
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumn.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumn.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumn.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -97,10 +97,11 @@
}
private CyRow getSourceRow(final Object targetKey) {
- final Object joinKey =
- targetTable.getValue(targetKey,
targetJoinColumn.getName());
+ final Object joinKey = targetTable.getValue(targetKey,
targetJoinColumn.getName());
if (joinKey == null)
return null;
+ return sourceTable.getRow(joinKey);
+ /*
final Collection<CyRow> sourceRows =
sourceTable.getMatchingRows(sourceJoinColumn.getName(),
joinKey);
@@ -108,6 +109,7 @@
return null;
return sourceRows.iterator().next();
+ */
}
Collection<CyRow> getMatchingRows(final Object value) {
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -62,7 +62,7 @@
if ( tgt.getColumn(srcName) != null )
return;
CyColumn srcCol = src.getColumn(srcName);
- tgt.addVirtualColumn(srcName,srcName,src,Identifiable.SUID,
Identifiable.SUID,srcCol.isImmutable());
+
tgt.addVirtualColumn(srcName,srcName,src,Identifiable.SUID,srcCol.isImmutable());
}
}
Modified:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -98,9 +98,8 @@
table.createColumn("x", Long.class, false);
CyColumn column = table.getColumn("x");
assertNull(column.getVirtualColumnInfo().getSourceTable());
- table2.createColumn("x2", Long.class, false);
table2.createListColumn("b", Boolean.class, false);
- table.addVirtualColumn("b1", "b", table2, "x2", "x", true);
+ table.addVirtualColumn("b1", "b", table2, "x", true);
mgrImpl.addTable(table2);
boolean caughtException = false;
Modified:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -201,15 +201,11 @@
@Test
public void testVirtualColumnWithAnEquationReference() {
- table.createColumn("x", Integer.class, false);
table.createColumn("ss", String.class, false);
CyRow row1 = table.getRow(1L);
- row1.set("x", 33);
- table2.createColumn("x2", Integer.class, false);
CyRow row2 = table2.getRow(1L);
- row2.set("x2", 33);
table2.createColumn("s", String.class, true);
- table.addVirtualColumn("s1", "s", table2, "x2", "x", true);
+ table.addVirtualColumn("s1", "s", table2,
table.getPrimaryKey().getName(), true);
row2.set("s", "abc");
final Map<String, Class<?>> varnameToTypeMap = new
HashMap<String, Class<?>>();
Modified:
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyTableProjection.java
===================================================================
---
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyTableProjection.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/impl/trunk/table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyTableProjection.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -317,7 +317,6 @@
* "virtualColumn"
* @param sourceTable the table that really contains the column
that we're adding (all
* updates and lookups of this new column will
be redirected to here)
- * @param sourceJoinKey the column in "sourceTable" that will be used
for the join
* @param targetJoinKey the column in current table that will be used
for the join
* @param isImmutable if true, this column cannot be deleted
* @return the actual name of the new virtual column
@@ -325,8 +324,7 @@
*/
@Override
public String addVirtualColumn(String virtualColumn, String
sourceColumn,
- CyTable sourceTable, String
sourceJoinKey,
- String targetJoinKey, boolean
isImmutable)
+ CyTable sourceTable, String
targetJoinKey, boolean isImmutable)
{
throw new UnsupportedOperationException("addVirtualColumn()
method not supported!");
}
@@ -334,17 +332,15 @@
/** Adds all columns in another table as "virtual" columns to the the
current table.
* @param sourceTable the table that really contains the column
that we're adding (all
* updates and lookups of this new column will
be redirected to here)
- * @param sourceJoinKey the column in "sourceTable" that will be used
for the join
* @param targetJoinKey the column in current table that will be used
for the join
* @param isImmutable if true, these columns cannot be deleted
* Note: The types of "sourceJoinKey" and "targetJoinKey" have to be
identical. Also none
* of the column names in "sourceTable" must exist in the
current table!
*/
@Override
- public void addVirtualColumns(CyTable sourceTable, String sourceJoinKey,
- String targetJoinKey, boolean isImmutable)
+ public void addVirtualColumns(CyTable sourceTable, String
targetJoinKey, boolean isImmutable)
{
- throw new UnsupportedOperationException("addVirtualColumn()
method not supported!");
+ throw new UnsupportedOperationException("addVirtualColumns()
method not supported!");
}
/**
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
2011-11-15 18:53:49 UTC (rev 27469)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
2011-11-15 20:08:29 UTC (rev 27470)
@@ -87,6 +87,6 @@
taskMonitor.setProgress(progress);
}
- nodeTable.addVirtualColumns(globalTable, colName,
CyTableEntry.NAME, false);
+ nodeTable.addVirtualColumns(globalTable, CyTableEntry.NAME,
false);
}
}
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