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Network file IO engine for netroles library
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/*
* This file is part of netroles.
*
* netroles is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* netroles is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with netroles. If not, see
* Example:
*
*
* final CsvNodeListSource source = new CsvEdgeListSource(stream, true);
*
* // configure what to read
* source.monad(NODE, Source.Range.INT);
* source.range(VALUE, Source.Range.INT);
*
* // read
* try (final InputStream in = new ByteArrayInputStream(data.getBytes())) {
* source.parse();
* }
*
*/
public class CsvNodeListSource implements SourceFormat, Source {
private static final Logger LOG = LoggerFactory.getLogger(CsvNodeListSource.class);
private final InputStream in;
private final boolean header;
private final Map> name2range;
private String nameNode;
private Range rangeNodeId;
private Map> monadic;
private IdMapper ids = IdMapper.continous(String.class);
/**
* Constructs the source.
*
* @param in the stream to read from.
* @param header true if the CSV data contains a header line, otherwise false.
*/
public CsvNodeListSource(final InputStream in, final boolean header) {
this.in = in;
this.header = header;
name2range = new HashMap<>();
}
@Override
public boolean isAutoconfig() {
return false;
}
@Override
public void mergeNodes(final ConstMapping ids) {
this.ids = IdMapper.fixed(ids); // TODO hand in mapper?
}
@Override
public void monad(final String varName, final Range range) {
nameNode = varName;
rangeNodeId = range;
}
@Override
public void noderange(final String varName, final Range range) {
name2range.put(varName, range);
}
@Override
public SourceFormat parse() throws IOException {
final CsvParser parser = new CsvParser(UnivocitySettings.SETTINGS);
parser.beginParsing(in);
// parse header
String[] row = parser.parseNext();
final ArrayList header = new ArrayList<>();
if (this.header) {
Collections.addAll(header, row);
row = parser.parseNext();
} else {
IntStream.range(0, row.length).mapToObj(String::valueOf).forEach(header::add);
}
// find source and target columns
final int nodeCol = header.indexOf(nameNode);
if (nodeCol < 0) {
throw new IOException("could not find node column\n" + "known: "
+ String.join(", ", header) + "\n" + "searching: " + nameNode);
}
if (name2range.remove(nameNode) != null) {
LOG.warn("removed node range");
}
// create ranges and lists
final RangedList[] rangedMappings = new RangedList[row.length];
for (int i = 0; i < rangedMappings.length; i++) {
Range range = name2range.get(header.get(i));
if (range != null) {
rangedMappings[i] = new RangedList<>(range);
}
}
// read
try (ProgressSource p = ProgressProvider.getMonitor().newSource()) {
p.updateProgress("read node csv");
int ignored = 0;
do {
final int v = ids.map(row[nodeCol]);
if (v >= 0) {
// add monadic attributes
p.updateProgress(v);
for (int i = 0; i < row.length; i++) {
if (rangedMappings[i] != null) {
if (v >= rangedMappings[i].getList().size()) {
rangedMappings[i].getList().setSize(null, v + 1);
}
rangedMappings[i].setListAt(v, row[i]);
}
}
} else {
ignored++;
}
} while ((row = parser.parseNext()) != null);
LOG.info("{} ids read", ids.size());
LOG.info("{} rows ignored (merging or empty)", ignored);
// fill the monadic mappings map
p.updateProgress(1, 3);
monadic = new LinkedHashMap<>();
int maxId = ids.getMapping().values().stream().mapToInt(Integer::intValue).max().orElse(-1) + 1;
for (int i = 0; i < rangedMappings.length; i++) {
if (rangedMappings[i] != null) {
PrimitiveList mapping = rangedMappings[i].getList();
mapping.setSize(null, maxId);
monadic.put(header.get(i), mapping);
}
}
// save the original node ids
final RangedList nodeIds = new RangedList<>(rangeNodeId, maxId);
for (final Map.Entry e : ids.entrySet()) {
nodeIds.setListAt(e.getValue().intValue(), e.getKey());
}
monadic.put("id", nodeIds.getList());
}
return this;
}
@Override
public Map> monadic() {
return Collections.unmodifiableMap(monadic);
}
@Override
public Map nodeIds() {
return ids.getMapping();
}
@Override
public void close() throws IOException {
in.close();
}
}