Examples with CyColumn org.cytoscape.model.CyColumn used on opensource projects

Example 1 with CyColumn

use of org.cytoscape.model.CyColumn in project EnrichmentMapApp by BaderLab.

the class SessionModelIO method clearTable.

private void clearTable(CyTable table) {
    List<Object> rowKeys = new ArrayList<>();
    CyColumn keyColumn = table.getPrimaryKey();
    for (CyRow row : table.getAllRows()) {
        Object key = row.get(keyColumn.getName(), keyColumn.getType());
        rowKeys.add(key);
    }
    table.deleteRows(rowKeys);
}

Example 2 with CyColumn

use of org.cytoscape.model.CyColumn in project EnrichmentMapApp by BaderLab.

the class BaseIntegrationTest method assertEdgeTableRowsEqual.

/**
	 * For edges we need to ignore the directionality.
	 */
private void assertEdgeTableRowsEqual(List<CyColumn> expectedColumns, List<CyRow> expectedRows, List<CyRow> actualRows) {
    Set<String> columnsToIgnore = ImmutableSet.of(CyNetwork.NAME, CyRootNetwork.SHARED_NAME);
    List<CyColumn> columnsToTest = expectedColumns.stream().filter(c -> !columnsToIgnore.contains(c.getName())).collect(Collectors.toList());
    Map<SimilarityKey, CyRow> expectedRowsByKey = new HashMap<>();
    for (CyRow row : expectedRows) {
        SimilarityKey key = SimilarityKey.parse(row.get(CyNetwork.NAME, String.class));
        expectedRowsByKey.put(key, row);
    }
    for (CyRow actual : actualRows) {
        SimilarityKey key = SimilarityKey.parse(actual.get(CyNetwork.NAME, String.class));
        CyRow expected = expectedRowsByKey.remove(key);
        assertNotNull(key.toString(), expected);
        assertAttributesEqual(columnsToTest, expected, actual);
    }
    assertTrue(expectedRowsByKey.isEmpty());
}

Example 3 with CyColumn

use of org.cytoscape.model.CyColumn in project EnrichmentMapApp by BaderLab.

the class BaseIntegrationTest method assertAttributesEqual.

private void assertAttributesEqual(List<CyColumn> columnsToTest, CyRow expected, CyRow actual) {
    for (CyColumn column : columnsToTest) {
        String name = column.getName();
        Class<?> type = column.getType();
        //			if(!CyNetwork.SUID.equals(name)) {
        Object expectedValue = expected.get(name, type);
        Object actualValue = actual.get(name, type);
        String message = "Col: " + name + ",";
        if (type.equals(List.class)) {
            // because CyListImpl doesn't implement equals()
            assertArrayEquals(message, ((List<?>) expectedValue).toArray(), ((List<?>) actualValue).toArray());
        } else {
            assertEquals(message, expectedValue, actualValue);
        }
    //			}
    }
}

Example 4 with CyColumn

use of org.cytoscape.model.CyColumn in project EnrichmentMapApp by BaderLab.

the class BaseIntegrationTest method sort.

/**
	 * I don't need to actually sort the rows in a meaningful way, just make it deterministic.
	 */
public void sort(List<CyColumn> columns, List<CyRow> rows) {
    Comparator<CyRow> rowComparator = null;
    for (CyColumn column : columns) {
        //			if(!CyNetwork.SUID.equals(column.getName())) {
        Comparator<CyRow> c = Comparator.comparing((CyRow row) -> row.get(column.getName(), column.getType()).toString());
        rowComparator = rowComparator == null ? c : rowComparator.thenComparing(c);
    //			}
    }
    Collections.sort(rows, rowComparator);
}

Example 5 with CyColumn

use of org.cytoscape.model.CyColumn in project EnrichmentMapApp by BaderLab.

the class BaseIntegrationTest method assertTablesEqual.

public void assertTablesEqual(CyTable expectedTable, CyTable actualTable, boolean edgeTable, Set<String> columnsToIgnore) {
    List<CyColumn> expectedColumns = new ArrayList<>(expectedTable.getColumns());
    // Remove columns to ignore
    expectedColumns = expectedColumns.stream().filter(c -> !columnsToIgnore.contains(c.getName())).filter(c -> !CyNetwork.SUID.equals(c.getName())).collect(Collectors.toList());
    // Test columns are the same
    for (CyColumn expectedColumn : expectedColumns) {
        String name = expectedColumn.getName();
        //			if(!CyNetwork.SUID.equals(name)) {
        CyColumn actualColumn = actualTable.getColumn(name);
        assertNotNull("Column '" + name + "' does not exist", actualColumn);
        assertEquals("Column '" + name + "' is wrong type", expectedColumn.getType(), actualColumn.getType());
    //			}
    }
    List<CyRow> expectedRows = expectedTable.getAllRows();
    List<CyRow> actualRows = actualTable.getAllRows();
    assertEquals("Tables are not the same size", expectedRows.size(), actualRows.size());
    if (edgeTable) {
        assertEdgeTableRowsEqual(expectedColumns, expectedRows, actualRows);
    } else {
        // node table or other table
        // need to sort both Lists 
        sort(expectedColumns, expectedRows);
        sort(expectedColumns, actualRows);
        for (int i = 0; i < expectedRows.size(); i++) {
            CyRow expectedRow = expectedRows.get(i);
            CyRow actualRow = actualRows.get(i);
            assertAttributesEqual(expectedColumns, expectedRow, actualRow);
        }
    }
}