private void mergeTables(
final CyTable source, final CyTable target, final Class<? extends CyIdentifiable> type) {
CyColumn sourceKey = source.getPrimaryKey();
CyColumn targetKey = target.getPrimaryKey();
String keyName = sourceKey.getName();
// Make sure keys match
if (keyName.equals(targetKey.getName())) {
// Merge columns first, because even if the source table has no rows to merge,
// the columns have to be restored
mergeColumns(keyName, source, target);
for (CyRow sourceRow : source.getAllRows()) {
if (cancelled) return;
Long key = sourceRow.get(keyName, Long.class);
CyIdentifiable entry = cache.getObjectById(key, type);
Long mappedKey = entry != null ? entry.getSUID() : null;
if (mappedKey == null) mappedKey = key;
CyRow targetRow = target.getRow(mappedKey);
mergeRow(keyName, sourceRow, targetRow);
}
}
}
@Override
public boolean handleIt(
final CyIdentifiable to,
final CyColumn toColumn,
final Map<CyIdentifiable, CyColumn> mapFromGOFromAttr) {
if (to == null || toColumn == null || mapFromGOFromAttr == null) {
throw new java.lang.NullPointerException("All parameters should not be null.");
}
final CyTable table = toColumn.getTable();
final CyRow row = table.getRow(to.getSUID());
final ColumnType type = ColumnType.getType(toColumn);
if (type == ColumnType.STRING) {
final String toValue = row.get(toColumn.getName(), String.class);
final Set<String> values = new TreeSet<String>();
values.add(toValue);
for (Map.Entry<CyIdentifiable, CyColumn> entry : mapFromGOFromAttr.entrySet()) {
final CyIdentifiable from = entry.getKey();
final CyColumn fromColumn = entry.getValue();
final CyRow fromRow = fromColumn.getTable().getRow(from.getSUID());
// TODO figure out which network to be using
String fromValue = fromRow.get(fromColumn.getName(), String.class);
if (fromValue != null) {
values.add(fromValue.toString());
}
}
StringBuilder str = new StringBuilder();
for (String v : values) {
str.append(v + ";");
}
str.deleteCharAt(str.length() - 1);
row.set(toColumn.getName(), str.toString());
return true;
}
// FIXME: how about Integer, Double, Boolean?
return false;
}
private String convertToName(final String id) {
final Collection<CyRow> rows =
ontologyDAG.getDefaultNodeTable().getMatchingRows(CyNetwork.NAME, id);
if (!rows.isEmpty()) {
final CyRow row = rows.iterator().next();
final String termName = row.get(OBOReader.TERM_NAME, String.class);
if (termName != null) return termName;
else return id;
} else return id;
}
/** {@inheritDoc} */
@Override
public Evidence[] mapFromTable(CyEdge edge, CyTable table) {
if (edge == null) throw new NullPointerException("edge cannot be null");
if (table == null) throw new NullPointerException("table cannot be null");
Set<String> nonAnnotationColumns =
new HashSet<String>(
asList(
CyNetwork.SUID,
NETWORK_SUID,
NETWORK_NAME,
EDGE_SUID,
BEL_STATEMENT,
SUMMARY_TEXT,
CITATION_ID,
CITATION_NAME,
CITATION_TYPE,
SPECIES));
Collection<CyRow> evidenceRows = table.getMatchingRows(EDGE_SUID, edge.getSUID());
List<Evidence> evidences = new ArrayList<Evidence>(evidenceRows.size());
if (!evidenceRows.isEmpty()) {
for (CyRow evRow : evidenceRows) {
Evidence e = new Evidence();
e.belStatement = evRow.get(BEL_STATEMENT, String.class);
e.summaryText = evRow.get(SUMMARY_TEXT, String.class);
e.citation = new Citation();
e.citation.id = evRow.get(CITATION_ID, String.class);
e.citation.name = evRow.get(CITATION_NAME, String.class);
e.citation.type = evRow.get(CITATION_TYPE, String.class);
e.biologicalContext = new BiologicalContext();
e.biologicalContext.speciesCommonName = evRow.get(SPECIES, String.class);
e.biologicalContext.variedAnnotations = new HashMap<String, Object>();
for (Entry<String, Object> columnValue : evRow.getAllValues().entrySet()) {
if (nonAnnotationColumns.contains(columnValue.getKey())) continue;
e.biologicalContext.variedAnnotations.put(columnValue.getKey(), columnValue.getValue());
}
evidences.add(e);
}
}
return evidences.toArray(new Evidence[evidences.size()]);
}
/** {@inheritDoc} */
@Override
public void mapToTable(Graph graph, Edge edge, Evidence evidence, CyTable table) {
if (graph == null) throw new NullPointerException("graph cannot be null");
if (edge == null) throw new NullPointerException("edge cannot be null");
if (evidence == null) throw new NullPointerException("evidence cannot be null");
if (table == null) throw new NullPointerException("table cannot be null");
if (graph.cyNetwork == null)
throw new IllegalArgumentException("graph's cyNetwork cannot be null");
if (edge.cyEdge == null) throw new IllegalArgumentException("edge's cyEdge cannot be null");
CyNetwork cyN = graph.cyNetwork;
CyEdge cyE = edge.cyEdge;
CyRow networkRow = cyN.getRow(cyN);
String networkName = networkRow.get(CyNetwork.NAME, String.class);
CyRow row = table.getRow(SUIDFactory.getNextSUID());
row.set(NETWORK_SUID, cyN.getSUID());
row.set(NETWORK_NAME, networkName);
row.set(EDGE_SUID, cyE.getSUID());
row.set(BEL_STATEMENT, evidence.belStatement);
row.set(SUMMARY_TEXT, evidence.summaryText);
if (evidence.citation != null) {
row.set(CITATION_TYPE, evidence.citation.type);
row.set(CITATION_ID, evidence.citation.id);
row.set(CITATION_NAME, evidence.citation.name);
}
if (evidence.biologicalContext != null) {
// create any annotation columns that do not already exist
BiologicalContext bc = evidence.biologicalContext;
for (String varyingKey : bc.variedAnnotations.keySet()) {
getOrCreateColumn(varyingKey, String.class, false, table);
}
// set annotation values
row.set(SPECIES, bc.speciesCommonName);
Map<String, Object> varying = bc.variedAnnotations;
for (Entry<String, Object> entry : varying.entrySet()) {
row.set(entry.getKey(), getOrEmptyString(entry.getKey(), varying));
}
}
}
private void guessHumanReadableName(final CyRow row) {
boolean found = false;
// Special handler for STRING. This is a hack...
if (row.getTable().getColumn(STRING_ATTR_NAME) != null) {
final List<String> stringList = row.getList(STRING_ATTR_NAME, String.class);
if (stringList != null) found = findHumanReadableName(row, stringList, ncbiPattern, true);
}
if (found) return;
// try NCBI
if (row.getTable().getColumn(ENTREZ_GENE_ATTR_NAME) != null) {
final List<String> ncbiList = row.getList(ENTREZ_GENE_ATTR_NAME, String.class);
if (ncbiList != null) found = findHumanReadableName(row, ncbiList, ncbiPattern, true);
}
if (found) return;
// Try Uniprot
List<String> uniprotList = null;
if (row.getTable().getColumn(UNIPROT_ATTR_NAME) != null) {
uniprotList = row.getList(UNIPROT_ATTR_NAME, String.class);
if (uniprotList != null) found = findHumanReadableName(row, uniprotList, exact1Pattern, true);
}
if (found) return;
if (uniprotList != null) found = findHumanReadableName(row, uniprotList, uniprotPattern, false);
if (found) return;
// Unknown
if (row.getTable().getColumn("unknown") != null) {
final List<String> unknownList = row.getList("unknown", String.class);
if (unknownList != null)
found = findHumanReadableName(row, unknownList, uniprotPattern, false);
}
if (found) return;
if (found == false) {
// Give up. Use primary key
row.set(PREDICTED_GENE_NAME, row.get(CyNetwork.NAME, String.class));
}
}
private void mergeRow(String keyName, CyRow sourceRow, CyRow targetRow) {
for (CyColumn column : sourceRow.getTable().getColumns()) {
if (cancelled) return;
String columnName = column.getName();
if (columnName.equals(keyName)) continue;
Class<?> type = column.getType();
if (type.equals(List.class)) {
Class<?> elementType = column.getListElementType();
List<?> list = sourceRow.getList(columnName, elementType);
targetRow.set(columnName, list);
} else {
Object value = sourceRow.get(columnName, type);
targetRow.set(columnName, value);
}
}
}
@Test
public void gaReaderTest() throws Exception {
File file = new File("./src/test/resources/" + GA_YEAST);
GeneAssociationReader reader =
new GeneAssociationReader(
"dummy dag", file.toURI().toURL().openStream(), "yeast GA", serviceRegistrar);
System.out.print("Start read: ");
reader.run(tm);
final CyTable[] tables = reader.getTables();
assertNotNull(tables);
assertEquals(1, tables.length);
assertNotNull(tables[0]);
// All 22 Columns + NAME primary key + synonyms
assertEquals(24, tables[0].getColumns().size());
// For yeast test file.
assertEquals(6359, tables[0].getRowCount());
// Check table contents
final CyTable table = tables[0];
final CyRow row1 = table.getRow("S000003319");
assertNotNull(row1);
final List<String> bpList1 = row1.getList("biological process", String.class);
assertNotNull(bpList1);
assertFalse(bpList1.contains("GO:0000287"));
assertTrue(bpList1.contains("GO:0006067"));
assertFalse(bpList1.contains("fake value"));
final String taxName = row1.get(GeneAssociationTag.TAXON.toString(), String.class);
assertNotNull(taxName);
assertEquals("Saccharomyces cerevisiae", taxName);
final List<String> referenceList1 =
row1.getList("biological process DB Reference", String.class);
// assertNotNull(referenceList1);
// assertEquals(2, referenceList1.size());
}
public void handleEvent(RowsSetEvent e) {
final CyTable local = e.getSource();
synchronized (lock) {
final List<CyTable> sharedList = tables.get(local);
for (CyTable shared : sharedList) {
for (RowSetRecord record : e.getColumnRecords(columnName)) {
// assume payload collection is for same column
final CyRow r = shared.getRow(record.getRow().get(CyIdentifiable.SUID, Long.class));
if (r != null) {
final Object name = record.getValue();
String sharedName = r.get(sharedColumnName, String.class);
if (sharedName == null) {
r.set(sharedColumnName, name);
}
}
}
}
}
}
