@Override
public void write(DataOutput output) throws IOException {
Bytes.writeByteArray(output, name.getBytes());
WritableUtils.writeVInt(output, type.ordinal());
WritableUtils.writeVLong(output, sequenceNumber);
output.writeLong(timeStamp);
Bytes.writeByteArray(
output, pkName == null ? ByteUtil.EMPTY_BYTE_ARRAY : Bytes.toBytes(pkName));
WritableUtils.writeVInt(output, allColumns.size());
for (int i = 0; i < allColumns.size(); i++) {
PColumn column = allColumns.get(i);
column.write(output);
}
stats.write(output);
}
@Override
public PColumn getPKColumn(String name) throws ColumnNotFoundException {
List<PColumn> columns = columnsByName.get(name);
int size = columns.size();
if (size == 0) {
throw new ColumnNotFoundException(name);
}
if (size > 1) {
do {
PColumn column = columns.get(--size);
if (column.getFamilyName() == null) {
return column;
}
} while (size > 0);
throw new ColumnNotFoundException(name);
}
return columns.get(0);
}
@Override
public PColumn getColumn(String name) throws ColumnNotFoundException, AmbiguousColumnException {
List<PColumn> columns = columnsByName.get(name);
int size = columns.size();
if (size == 0) {
throw new ColumnNotFoundException(name);
}
if (size > 1) {
for (PColumn column : columns) {
if (QueryConstants.DEFAULT_COLUMN_FAMILY.equals(column.getFamilyName().getString())) {
// Allow ambiguity with default column, since a user would not know how to prefix it.
return column;
}
}
throw new AmbiguousColumnException(name);
}
return columns.get(0);
}
@Override
public QueryResult<Variant> getAllVariantsByRegionAndStudy(
Region region, String sourceId, QueryOptions options) {
Long start, end, dbstart, dbend;
start = System.currentTimeMillis();
QueryResult<Variant> queryResult =
new QueryResult<>(
String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
List<Variant> results = new LinkedList<>();
boolean includeSamples;
boolean includeStats;
boolean includeEffects;
if (!options.containsKey("samples")
&& !options.containsKey("stats")
&& !options.containsKey("effects")) {
includeSamples = true;
includeStats = true;
includeEffects = true;
} else {
includeSamples = options.containsKey("samples") && options.getBoolean("samples");
includeStats = options.containsKey("stats") && options.getBoolean("stats");
includeEffects = options.containsKey("effects") && options.getBoolean("effects");
}
try {
String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
HTable table = new HTable(admin.getConfiguration(), tableName);
dbstart = System.currentTimeMillis();
Scan regionScan = new Scan(startRow.getBytes(), stopRow.getBytes());
ResultScanner scanres = table.getScanner(regionScan);
dbend = System.currentTimeMillis();
queryResult.setDbTime(dbend - dbstart);
// Iterate over results and, optionally, their samples and statistics
for (Result result : scanres) {
String[] rowkeyParts = new String(result.getRow(), CHARSET_UTF_8).split("_");
String chromosome = rowkeyParts[0].replaceFirst("^0+(?!$)", "");
int position = Integer.parseInt(rowkeyParts[1]);
// Get basic result fields from Protocol Buffers message
NavigableMap<byte[], byte[]> infoMap = result.getFamilyMap("i".getBytes());
byte[] byteInfo = infoMap.get((sourceId + "_data").getBytes());
VariantFieldsProtos.VariantInfo protoInfo =
VariantFieldsProtos.VariantInfo.parseFrom(byteInfo);
String reference = protoInfo.getReference();
String alternate = StringUtils.join(protoInfo.getAlternateList(), ",");
String format = StringUtils.join(protoInfo.getFormatList(), ":");
Variant variant = new Variant(chromosome, position, position, reference, alternate);
// Set samples if requested
if (includeSamples) {
NavigableMap<byte[], byte[]> sampleMap = result.getFamilyMap("d".getBytes());
Map<String, Map<String, String>> resultSampleMap = new HashMap<>();
// Set samples
for (byte[] s : sampleMap.keySet()) {
String sampleName = (new String(s, CHARSET_UTF_8)).replaceAll(sourceId + "_", "");
VariantFieldsProtos.VariantSample sample =
VariantFieldsProtos.VariantSample.parseFrom(sampleMap.get(s));
String sample1 = sample.getSample();
String[] values = sample1.split(":");
String[] fields = format.split(":");
Map<String, String> singleSampleMap = new HashMap<>();
for (int i = 0; i < fields.length; i++) {
singleSampleMap.put(fields[i], values[i]);
}
// TODO
// variant.addSampleData(sampleName, singleSampleMap);
}
}
// Set stats if requested
if (includeStats) {
byte[] byteStats = infoMap.get((sourceId + "_stats").getBytes());
VariantFieldsProtos.VariantStats protoStats =
VariantFieldsProtos.VariantStats.parseFrom(byteStats);
VariantStats variantStats =
new VariantStats(
chromosome,
position,
reference,
alternate,
protoStats.getMaf(),
protoStats.getMgf(),
protoStats.getMafAllele(),
protoStats.getMgfGenotype(),
protoStats.getMissingAlleles(),
protoStats.getMissingGenotypes(),
protoStats.getMendelianErrors(),
protoStats.getIsIndel(),
protoStats.getCasesPercentDominant(),
protoStats.getControlsPercentDominant(),
protoStats.getCasesPercentRecessive(),
protoStats.getControlsPercentRecessive());
variant.setStats(variantStats);
}
if (includeEffects) {
QueryResult<VariantEffect> queryEffects = getEffectsByVariant(variant, options);
variant.setEffect(queryEffects.getResult());
}
results.add(variant);
}
} catch (IOException e) {
System.err.println(e.getClass().getName() + ": " + e.getMessage());
}
queryResult.setResult(results);
queryResult.setNumResults(results.size());
end = System.currentTimeMillis();
queryResult.setTime(end - start);
return queryResult;
}
public QueryResult getSimpleVariantsByRegion(
Region region, String sourceId, QueryOptions options) {
Long start, end, dbstart, dbend;
start = System.currentTimeMillis();
boolean includeStats;
boolean includeEffects;
if (!options.containsKey("stats") && !options.containsKey("effects")) {
includeStats = true;
includeEffects = true;
} else {
includeStats = options.containsKey("stats") && options.getBoolean("stats");
includeEffects = options.containsKey("effects") && options.getBoolean("effects");
}
QueryResult<Variant> queryResult =
new QueryResult<>(
String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
List<Variant> results = new ArrayList<>();
String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
BasicDBObject query =
new BasicDBObject("position", new BasicDBObject("$gte", startRow).append("$lte", stopRow))
.append("sources.sourceId", sourceId);
DBCollection collection = db.getCollection("variants");
dbstart = System.currentTimeMillis();
DBCursor variantInStudies = collection.find(query);
dbend = System.currentTimeMillis();
queryResult.setDbTime(dbend - dbstart);
for (DBObject result : variantInStudies) {
String[] rowkeyParts = result.get("position").toString().split("_");
String chromosome = rowkeyParts[0].replaceFirst("^0+(?!$)", "");
int position = Integer.parseInt(rowkeyParts[1]);
BasicDBList studies = (BasicDBList) result.get("sources");
BasicDBObject st = (BasicDBObject) studies.get(0);
String ref = (String) st.get("ref");
String alt = StringUtils.join((ArrayList<String>) st.get("alt"), ",");
// TODO Needs rework
Variant variant = new Variant(chromosome, position, position, ref, alt);
// Set stats informations
if (includeStats) {
VariantStats stats = new VariantStats();
BasicDBObject mongoStats = (BasicDBObject) st.get("stats");
stats.setMaf((float) (double) mongoStats.get("maf"));
stats.setMafAllele((String) mongoStats.get("alleleMaf"));
stats.setMissingGenotypes((int) mongoStats.get("missing"));
List<Genotype> genotypeCount = new ArrayList<>();
for (BasicDBObject s : (List<BasicDBObject>) mongoStats.get("genotypeCount")) {
for (Map.Entry<String, Object> entry : s.entrySet()) {
Genotype genotype = new Genotype(entry.getKey());
genotype.setCount((Integer) entry.getValue());
genotypeCount.add(genotype);
}
}
stats.setGenotypes(genotypeCount);
variant.setStats(stats);
}
// TODO Set consequence type names
if (includeEffects) {
BasicDBList mongoEffects = (BasicDBList) st.get("effects");
if (mongoEffects != null) {
for (Object e : mongoEffects) {
String effectObo = e.toString();
VariantEffect effect = new VariantEffect();
effect.setConsequenceTypeObo(effectObo);
variant.addEffect(effect);
}
}
}
results.add(variant);
}
queryResult.setResult(results);
queryResult.setNumResults(results.size());
end = System.currentTimeMillis();
queryResult.setTime(end - start);
return queryResult;
}
@Override
public QueryResult getVariantsHistogramByRegion(
Region region, String sourceId, boolean histogramLogarithm, int histogramMax) {
QueryResult<ObjectMap> queryResult =
new QueryResult<>(
String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
List<ObjectMap> data = new ArrayList<>();
String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
long startTime = System.currentTimeMillis();
long startDbTime = System.currentTimeMillis();
BasicDBObject query =
new BasicDBObject("position", new BasicDBObject("$gte", startRow).append("$lte", stopRow))
.append("studies.studyId", sourceId);
DBCollection collection = db.getCollection("variants");
DBCursor queryResults = collection.find(query);
queryResult.setDbTime(System.currentTimeMillis() - startDbTime);
int resultSize = queryResults.size();
if (resultSize > histogramMax) { // Need to group results to fit maximum size of the histogram
int sumChunkSize = resultSize / histogramMax;
int i = 0, j = 0;
int featuresCount = 0;
ObjectMap item = null;
for (DBObject result : queryResults) {
// featuresCount += result.getInt("features_count");
// if (i == 0) {
// item = new ObjectMap("chromosome", result.getString("chromosome"));
// item.put("chunkId", result.getInt("chunk_id"));
// item.put("start", result.getInt("start"));
// } else if (i == sumChunkSize - 1 || j == resultSize - 1) {
// if (histogramLogarithm) {
// item.put("featuresCount", (featuresCount > 0) ?
// Math.log(featuresCount) : 0);
// } else {
// item.put("featuresCount", featuresCount);
// }
// item.put("end", result.getInt("end"));
// data.add(item);
// i = -1;
// featuresCount = 0;
// }
// j++;
// i++;
}
} else {
for (DBObject result : queryResults) {
// ObjectMap item = new ObjectMap("chromosome",
// result.getString("chromosome"));
// item.put("chunkId", result.getInt("chunk_id"));
// item.put("start", result.getInt("start"));
// if (histogramLogarithm) {
// int features_count = result.getInt("features_count");
// result.put("featuresCount", (features_count > 0) ?
// Math.log(features_count) : 0);
// } else {
// item.put("featuresCount", result.getInt("features_count"));
// }
// item.put("end", result.getInt("end"));
// data.add(item);
}
}
queryResult.setResult(data);
queryResult.setNumResults(data.size());
queryResult.setTime(System.currentTimeMillis() - startTime);
return queryResult;
}
public int run(String[] args) throws Exception {
// printUsage();
/*
* SETUP
*/
Configuration argConf = getConf();
Hashtable<String, String> confArg = new Hashtable<String, String>();
setup(confArg, argConf);
Date currentTime = new Date();
Date endDate = new Date(new Long(confArg.get("timestamp_stop")));
Boolean full_run = confArg.get("intermediate").matches("(?i).*true.*");
Boolean quick_add = confArg.get("quick_add").matches("(?i).*true.*");
logger.info("Running GeStore");
// ZooKeeper setup
Configuration config = HBaseConfiguration.create();
zkWatcher = new ZooKeeperWatcher(config, "Testing", new HBaseAdmin(config));
zkInstance =
new ZooKeeper(
ZKConfig.getZKQuorumServersString(config),
config.getInt("zookeeper.session.timeout", -1),
zkWatcher);
if (!confArg.get("task_id").isEmpty()) {
confArg.put("temp_path", confArg.get("temp_path") + confArg.get("task_id"));
}
String lockRequest = confArg.get("file_id");
if (!confArg.get("run_id").isEmpty())
lockRequest = lockRequest + "_" + confArg.get("run_id") + "_";
if (!confArg.get("task_id").isEmpty())
lockRequest = lockRequest + "_" + confArg.get("task_id") + "_";
// Get type of movement
toFrom type_move = checkArgs(confArg);
if (type_move == toFrom.LOCAL2REMOTE && !confArg.get("format").equals("unknown")) {
List<String> arguments = new ArrayList<String>();
arguments.add("-Dinput=" + confArg.get("local_path"));
arguments.add("-Dtable=" + confArg.get("file_id"));
arguments.add("-Dtimestamp=" + confArg.get("timestamp_stop"));
arguments.add("-Dtype=" + confArg.get("format"));
arguments.add("-Dtarget_dir=" + confArg.get("base_path") + "_" + confArg.get("file_id"));
arguments.add("-Dtemp_hdfs_path=" + confArg.get("temp_path"));
arguments.add("-Drun_id=" + confArg.get("run_id"));
if (!confArg.get("run_id").isEmpty()) arguments.add("-Drun_id=" + confArg.get("run_id"));
if (!confArg.get("task_id").isEmpty()) arguments.add("-Dtask_id=" + confArg.get("task_id"));
if (quick_add) arguments.add("-Dquick_add=" + confArg.get("quick_add"));
String lockName = lock(lockRequest);
String[] argumentString = arguments.toArray(new String[arguments.size()]);
adddb.main(argumentString);
unlock(lockName);
System.exit(0);
}
// Database registration
dbutil db_util = new dbutil(config);
db_util.register_database(confArg.get("db_name_files"), true);
db_util.register_database(confArg.get("db_name_runs"), true);
db_util.register_database(confArg.get("db_name_updates"), true);
FileSystem hdfs = FileSystem.get(config);
FileSystem localFS = FileSystem.getLocal(config);
// Get source type
confArg.put("source", getSource(db_util, confArg.get("db_name_files"), confArg.get("file_id")));
confArg.put(
"database", isDatabase(db_util, confArg.get("db_name_files"), confArg.get("file_id")));
if (!confArg.get("source").equals("local")
&& type_move == toFrom.REMOTE2LOCAL
&& !confArg.get("timestamp_stop").equals(Integer.toString(Integer.MAX_VALUE))) {
confArg.put("timestamp_stop", Long.toString(latestVersion(confArg, db_util)));
}
/*
* Get previous timestamp
*/
Get run_id_get = new Get(confArg.get("run_id").getBytes());
Result run_get = db_util.doGet(confArg.get("db_name_runs"), run_id_get);
KeyValue run_file_prev =
run_get.getColumnLatest(
"d".getBytes(), (confArg.get("file_id") + "_db_timestamp").getBytes());
String last_timestamp = new String("0");
if (null != run_file_prev && !confArg.get("source").equals("local")) {
long last_timestamp_real = run_file_prev.getTimestamp();
Long current_timestamp = new Long(confArg.get("timestamp_real"));
if ((current_timestamp - last_timestamp_real) > 36000) {
last_timestamp = new String(run_file_prev.getValue());
Integer lastTimestamp = new Integer(last_timestamp);
lastTimestamp += 1;
last_timestamp = lastTimestamp.toString();
logger.info("Last timestamp: " + last_timestamp + " End data: " + endDate);
Date last_run = new Date(run_file_prev.getTimestamp());
if (last_run.before(endDate) && !full_run) {
confArg.put("timestamp_start", last_timestamp);
}
}
}
Integer tse = new Integer(confArg.get("timestamp_stop"));
Integer tss = new Integer(confArg.get("timestamp_start"));
if (tss > tse) {
logger.info("No new version of requested file.");
return 0;
}
/*
* Generate file
*/
String lockName = lock(lockRequest);
Get file_id_get = new Get(confArg.get("file_id").getBytes());
Result file_get = db_util.doGet(confArg.get("db_name_files"), file_id_get);
if (!file_get.isEmpty()) {
boolean found =
hasFile(
db_util,
hdfs,
confArg.get("db_name_files"),
confArg.get("file_id"),
getFullPath(confArg));
if (confArg.get("source").equals("fullfile")) {
found = false;
}
String filenames_put =
getFileNames(
db_util, confArg.get("db_name_files"), confArg.get("file_id"), getFullPath(confArg));
// Filename not found in file database
if (!found && type_move == toFrom.REMOTE2LOCAL) {
if (!confArg.get("source").equals("local")) {
// Generate intermediate file
if (getFile(hdfs, confArg, db_util) == null) {
unlock(lockName);
return 1;
}
// Put generated file into file database
if (!confArg.get("format").equals("fullfile")) {
putFileEntry(
db_util,
hdfs,
confArg.get("db_name_files"),
confArg.get("file_id"),
confArg.get("full_file_name"),
confArg.get("source"));
}
} else {
logger.warn("Remote file not found, and cannot be generated! File: " + confArg);
unlock(lockName);
return 1;
}
}
} else {
if (type_move == toFrom.REMOTE2LOCAL) {
logger.warn("Remote file not found, and cannot be generated.");
unlock(lockName);
return 1;
}
}
/*
* Copy file
* Update tables
*/
if (type_move == toFrom.LOCAL2REMOTE) {
if (!confArg.get("format").equals("fullfile")) {
putFileEntry(
db_util,
hdfs,
confArg.get("db_name_files"),
confArg.get("file_id"),
getFullPath(confArg),
confArg.get("source"));
}
putRunEntry(
db_util,
confArg.get("db_name_runs"),
confArg.get("run_id"),
confArg.get("file_id"),
confArg.get("type"),
confArg.get("timestamp_real"),
confArg.get("timestamp_stop"),
getFullPath(confArg),
confArg.get("delimiter"));
hdfs.copyFromLocalFile(new Path(confArg.get("local_path")), new Path(getFullPath(confArg)));
} else if (type_move == toFrom.REMOTE2LOCAL) {
FileStatus[] files = hdfs.globStatus(new Path(getFullPath(confArg) + "*"));
putRunEntry(
db_util,
confArg.get("db_name_runs"),
confArg.get("run_id"),
confArg.get("file_id"),
confArg.get("type"),
confArg.get("timestamp_real"),
confArg.get("timestamp_stop"),
getFullPath(confArg),
confArg.get("delimiter"));
unlock(lockName);
for (FileStatus file : files) {
Path cur_file = file.getPath();
Path cur_local_path =
new Path(new String(confArg.get("local_path") + confArg.get("file_id")));
String suffix = getSuffix(getFileName(confArg), cur_file.getName());
if (suffix.length() > 0) {
cur_local_path = cur_local_path.suffix(new String("." + suffix));
}
if (confArg.get("copy").equals("true")) {
String crc = hdfs.getFileChecksum(cur_file).toString();
if (checksumLocalTest(cur_local_path, crc)) {
continue;
} else {
hdfs.copyToLocalFile(cur_file, cur_local_path);
writeChecksum(cur_local_path, crc);
}
} else {
System.out.println(cur_local_path + "\t" + cur_file);
}
}
}
unlock(lockName);
return 0;
}
private void init(
PName name,
PTableType type,
long timeStamp,
long sequenceNumber,
String pkName,
List<PColumn> columns,
PTableStats stats) {
this.name = name;
this.type = type;
this.timeStamp = timeStamp;
this.sequenceNumber = sequenceNumber;
this.columnsByName = ArrayListMultimap.create(columns.size(), 1);
this.pkName = pkName;
List<PColumn> pkColumns = Lists.newArrayListWithExpectedSize(columns.size() - 1);
PColumn[] allColumns = new PColumn[columns.size()];
RowKeySchemaBuilder builder = new RowKeySchemaBuilder();
for (int i = 0; i < allColumns.length; i++) {
PColumn column = columns.get(i);
allColumns[column.getPosition()] = column;
PName familyName = column.getFamilyName();
if (familyName == null) {
pkColumns.add(column);
builder.addField(column);
}
columnsByName.put(column.getName().getString(), column);
}
this.pkColumns = ImmutableList.copyOf(pkColumns);
this.rowKeySchema = builder.setMinNullable(pkColumns.size()).build();
this.allColumns = ImmutableList.copyOf(allColumns);
// Two pass so that column order in column families matches overall column order
// and to ensure that column family order is constant
int maxExpectedSize = allColumns.length - pkColumns.size();
// Maintain iteration order so that column families are ordered as they are listed
Map<PName, List<PColumn>> familyMap = Maps.newLinkedHashMap();
for (PColumn column : allColumns) {
PName familyName = column.getFamilyName();
if (familyName != null) {
List<PColumn> columnsInFamily = familyMap.get(familyName);
if (columnsInFamily == null) {
columnsInFamily = Lists.newArrayListWithExpectedSize(maxExpectedSize);
familyMap.put(familyName, columnsInFamily);
}
columnsInFamily.add(column);
}
}
Iterator<Map.Entry<PName, List<PColumn>>> iterator = familyMap.entrySet().iterator();
PColumnFamily[] families = new PColumnFamily[familyMap.size()];
ImmutableMap.Builder<String, PColumnFamily> familyByString = ImmutableMap.builder();
ImmutableSortedMap.Builder<byte[], PColumnFamily> familyByBytes =
ImmutableSortedMap.orderedBy(Bytes.BYTES_COMPARATOR);
for (int i = 0; i < families.length; i++) {
Map.Entry<PName, List<PColumn>> entry = iterator.next();
PColumnFamily family = new PColumnFamilyImpl(entry.getKey(), entry.getValue());
families[i] = family;
familyByString.put(family.getName().getString(), family);
familyByBytes.put(family.getName().getBytes(), family);
}
this.families = ImmutableList.copyOf(families);
this.familyByBytes = familyByBytes.build();
this.familyByString = familyByString.build();
this.stats = stats;
}
@Override
public int newKey(ImmutableBytesWritable key, byte[][] values) {
int i = 0;
TrustedByteArrayOutputStream os =
new TrustedByteArrayOutputStream(SchemaUtil.estimateKeyLength(this));
try {
List<PColumn> columns = getPKColumns();
int nColumns = columns.size();
PColumn lastPKColumn = columns.get(nColumns - 1);
while (i < values.length && i < nColumns) {
PColumn column = columns.get(i);
PDataType type = column.getDataType();
// This will throw if the value is null and the type doesn't allow null
byte[] byteValue = values[i++];
if (byteValue == null) {
byteValue = ByteUtil.EMPTY_BYTE_ARRAY;
}
// An empty byte array return value means null. Do this,
// since a type may have muliple representations of null.
// For example, VARCHAR treats both null and an empty string
// as null. This way we don't need to leak that part of the
// implementation outside of PDataType by checking the value
// here.
if (byteValue.length == 0 && !column.isNullable()) {
throw new ConstraintViolationException(
name.getString() + "." + column.getName().getString() + " may not be null");
}
Integer byteSize = column.getByteSize();
if (type.isFixedWidth()) { // TODO: handle multi-byte characters
if (byteValue.length != byteSize) {
throw new ConstraintViolationException(
name.getString()
+ "."
+ column.getName().getString()
+ " must be "
+ byteSize
+ " bytes ("
+ SchemaUtil.toString(type, byteValue)
+ ")");
}
} else if (byteSize != null && byteValue.length > byteSize) {
throw new ConstraintViolationException(
name.getString()
+ "."
+ column.getName().getString()
+ " may not exceed "
+ byteSize
+ " bytes ("
+ SchemaUtil.toString(type, byteValue)
+ ")");
}
os.write(byteValue, 0, byteValue.length);
// Separate variable length column values in key with zero byte
if (!type.isFixedWidth() && column != lastPKColumn) {
os.write(SEPARATOR_BYTE);
}
}
// If some non null pk values aren't set, then throw
if (i < nColumns) {
PColumn column = columns.get(i);
PDataType type = column.getDataType();
if (type.isFixedWidth() || !column.isNullable()) {
throw new ConstraintViolationException(
name.getString() + "." + column.getName().getString() + " may not be null");
}
// Separate variable length column values in key with zero byte
if (column != lastPKColumn) {
os.write(SEPARATOR_BYTE);
}
}
key.set(os.getBuffer(), 0, os.size());
return i;
} finally {
try {
os.close();
} catch (IOException e) {
throw new RuntimeException(e); // Impossible
}
}
}
/**
* init station code map
*
* @param file station code file path
*/
private static void initStationCode(String file) {
List<String> lstStation = new Vector<>();
strConfig = file + ".process";
File fsP = new File(strConfig);
if (!fsP.exists()) {
try {
fsP.createNewFile();
} catch (IOException e) {
e.printStackTrace();
}
} else {
BufferedReader readp = null;
try {
String line = null;
readp = new BufferedReader(new FileReader(fsP));
while ((line = readp.readLine()) != null) {
processed.add(line);
}
} catch (IOException e) {
e.printStackTrace();
} finally {
if (readp != null) {
try {
readp.close();
} catch (IOException e) {
e.printStackTrace();
}
}
}
}
File fs = new File(file);
BufferedReader reader = null;
try {
String stationName = null;
String stationCode = null;
String line = null;
String[] splitLine = null;
reader = new BufferedReader(new FileReader(fs));
while ((line = reader.readLine()) != null) {
splitLine = line.split("\t");
if (splitLine.length != 2) {
continue;
}
stationName = splitLine[0];
stationCode = splitLine[1];
mapStationCode.put(stationName, stationCode);
lstStation.add(stationName);
}
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
} finally {
if (reader == null) {
try {
reader.close();
} catch (IOException e1) {
e1.printStackTrace();
}
}
}
int len = lstStation.size();
String start = null;
for (int i = 0; i < len; i++) {
start = lstStation.get(i);
for (String end : lstStation) {
if (start.equals(end) || processed.contains(start + ":" + end)) {
continue;
}
lstAllProcessStation.add(new DefaultKeyValue(start, end));
}
}
}