public Set<String> getSamples() {
HashSet<String> uniqueSamples = new HashSet<String>(table.size());
for (Entry e : table) uniqueSamples.add(e.getSampleId());
return uniqueSamples;
}
public Set<String> getSamplesInLane(int lane) {
if (lane <= 0) throw new IllegalArgumentException("Invalid negative lane number " + lane);
HashSet<String> samples = new HashSet<String>(table.size() / 8);
for (Entry e : this) {
if (lane == e.getLane()) samples.add(e.getSampleId());
}
return samples;
}
/**
* Return a string that describes the statistics for the top n entries, sorted by descending
* order of total time spent dealing with the query. This will always include the totals entry
* in the first position.
*
* @param n the desired number of entries to describe
* @return a string describing the statistics for the top n entries
*/
public synchronized String toStringTop(int n) {
StringBuilder out = new StringBuilder();
List<Entry> list = entries();
if (list.isEmpty()) return "<no queries executed>";
Collections.sort(list, TOTAL_TIME_DESCENDING);
int maxCountLength = COUNT_FORMAT.format(list.get(0).numQueries).length();
double totalDuration = list.get(0).queryTime;
for (Entry entry : list.subList(0, Math.min(n, list.size())))
out.append(entry.toString(maxCountLength, totalDuration)).append('\n');
return out.toString();
}
public void run() {
while (true) {
try {
// System.out.println(r+": Take(wait)");
// String[] info = q.take();
String blogID = q.poll(60, TimeUnit.SECONDS);
if (blogID == null) {
System.out.println("Poll.Timeout");
continue;
}
// System.out.println(r+": Take(get) : "+blogID);
if (blogID == NO_MORE_WORK) {
break;
}
URL feedUrl = new URL("http://www.blogger.com/feeds/" + blogID + "/comments/default");
Query myQuery = new Query(feedUrl);
myQuery.setMaxResults(25);
System.out.print(r + "+,");
Feed resultFeed = myService.query(myQuery, Feed.class);
for (Entry entry : resultFeed.getEntries()) {
if (entry.getAuthors().get(0).getUri() != null) {
String profileID = entry.getAuthors().get(0).getUri().replaceAll("[^\\d]", "");
if (profileID.length() == 20) {
try {
myStm.executeUpdate(
"INSERT IGNORE INTO author SET profileID = '" + profileID + "'");
// System.out.print(r+"+,");
} catch (Exception e) {
}
}
}
}
} catch (Exception e) {
System.out.print(r + "ERR,");
}
}
System.out.println("Bye(" + r + ")");
try {
myStm.close();
} catch (Exception e) {
}
}
private void insertRecord(String line) throws FormatException {
String[] fields = line.split(",");
if (fields.length < 9)
throw new FormatException(
"Too few columns in sample sheet. Expecing at least 9 but found "
+ fields.length
+ ". Line: "
+ line);
// Format is CSV with these columns:
// "FCID","Lane","SampleID","SampleRef","Index","Description","Control","Recipe","Operator"
// All text fields are quoted (all except Lane)
// remove external quotes and whitespace from all string fields (even spaces within the quotes)
for (int i = 0; i < fields.length; ++i) {
quoteMatcher.reset(fields[i]);
fields[i] = quoteMatcher.replaceAll("").trim();
}
Entry entry;
try {
entry = Entry.createEntry(fields);
} catch (IllegalArgumentException e) {
throw new FormatException(e.getMessage() + ". Line: " + line);
}
table.add(entry);
}
public static Entry createEntry(String[] fields) {
if (fields.length < 9)
throw new IllegalArgumentException(
"Too few fields to build a sample sheet entry. Expecing at least 9 but found "
+ fields.length
+ ".");
Entry e = new Entry();
e.setFlowcellId(fields[0]);
e.setLane(Integer.parseInt(fields[1]));
e.setSampleId(fields[2]);
e.setSampleRef(fields[3]);
e.setIndex(fields[4]);
e.setDescription(fields[5]);
e.setControl(fields[6]);
e.setRecipe(fields[7]);
e.setOperator(fields[8]);
return e;
}
public void loadTable(Reader in) throws IOException, FormatException {
table = new ArrayList<Entry>(InitNumEntries);
String line = null;
LineNumberReader input = new LineNumberReader(in);
line = input.readLine();
if (line == null) throw new FormatException("Empty sample sheet");
// Verify that heading is as expected, ignoring quotes and case
if (!line.replaceAll("\"", "").toLowerCase().startsWith(ExpectedHeading))
throw new FormatException(
"Unexpected heading! Expected:\n" + ExpectedHeading + "\nFound:\n" + line);
line = input.readLine();
while (line != null) {
insertRecord(line);
line = input.readLine();
}
if (table.size() > 1) {
// Check for duplicates barcodes in the same lane
// start by sorting the table by lane
Collections.sort(
table,
new Comparator<Entry>() {
@Override
public int compare(Entry a, Entry b) {
return a.getLane() - b.getLane();
}
});
HashSet<String> samplesInLane = new HashSet<String>();
int currentLane = table.get(0).getLane();
for (Entry e : table) // table is an ArrayList of Entries
{
if (e.getLane() == currentLane) {
if (samplesInLane.contains(e.getIndex()))
throw new FormatException(
"index " + e.getIndex() + " appears twice for the same lane " + currentLane);
else samplesInLane.add(e.getIndex());
} else {
// lane change
samplesInLane.clear();
samplesInLane.add(e.getIndex());
currentLane = e.getLane();
}
}
}
}