/** Read table from the data source. */
public void readTable(CyTable table) throws IOException {
// InputStream is = null;
try {
BufferedReader bufRd = null;
if (is == null) {
is = URLUtil.getInputStream(source);
}
try {
// This data is shared by both the OpenCSV and the old method of reading files.
int lineCount = 0;
bufRd =
new BufferedReader(new InputStreamReader(is, Charset.forName("UTF-8").newDecoder()));
/*
* Read & extract one line at a time. The line can be Tab delimited,
*/
final String delimiter = mapping.getDelimiterRegEx();
// If the delimiter contains a comma, treat the file as a CSV file.
if (delimiter.contains(TextFileDelimiters.COMMA.toString())
&& mapping.getDelimiters().size() == 1) {
// Use OpenCSV.. New method...
CSVReader reader = new CSVReader(bufRd);
String[] rowData; // Note that rowData is roughly equivalent to "parts" in the old code.
while ((rowData = reader.readNext()) != null) {
// If key dos not exists, ignore the line.
if (lineCount >= startLineNumber && rowData.length >= mapping.getKeyIndex() + 1) {
try {
// if(importAll) {
parser.parseAll(table, rowData);
// } else
// parser.parseEntry(table, parts);
} catch (Exception ex) {
logger.warn("Couldn't parse row from OpenCSV: " + lineCount);
}
globalCounter++;
}
lineCount++;
}
} else // Use the "old" method for splitting the lines.
{
String line;
String[] parts = null;
while ((line = bufRd.readLine()) != null) {
/*
* Ignore Empty & Commnet lines.
*/
if ((commentChar != null) && line.startsWith(commentChar)) {
// Do nothing
} else if ((lineCount >= startLineNumber) && (line.trim().length() > 0)) {
parts = line.split(delimiter);
// If key dos not exists, ignore the line.
if (parts.length >= mapping.getKeyIndex() + 1) {
try {
// if(importAll) {
parser.parseAll(table, parts);
// } else
// parser.parseEntry(table, parts);
} catch (Exception ex) {
logger.warn("Couldn't parse row: " + lineCount);
}
globalCounter++;
}
}
lineCount++;
}
}
} finally {
if (bufRd != null) {
bufRd.close();
}
}
} finally {
if (is != null) {
is.close();
}
}
}
