private static Map<String, String> nodeAllocationToMap(AssociationEntry entry) {
final HashMap<String, String> map = new HashMap(8);
map.put(FIELD_HOSTNAME, entry.getHostname());
map.put(FIELD_IP, entry.getIpAddress());
map.put(FIELD_MAC, entry.getMac());
map.put(FIELD_BROADCAST, entry.getBroadcast());
map.put(FIELD_SUBNET_MASK, entry.getSubnetMask());
map.put(FIELD_GATEWAY, entry.getGateway());
map.put(FIELD_IN_USE, Boolean.toString(entry.isInUse()));
map.put(FIELD_EXPLICIT_MAC, Boolean.toString(entry.isExplicitMac()));
return map;
}
private static Map<String, String> nodeToMap(VmmNode node) {
final HashMap<String, String> map = new HashMap<String, String>(7);
map.put(FIELD_HOSTNAME, node.getHostname());
map.put(FIELD_POOL, node.getPoolName());
map.put(FIELD_MEMORY, String.valueOf(node.getMemory()));
map.put(FIELD_MEM_REMAIN, String.valueOf(node.getMemRemain()));
map.put(FIELD_NETWORKS, node.getNetworkAssociations());
map.put(FIELD_IN_USE, String.valueOf(!node.isVacant()));
map.put(FIELD_ACTIVE, String.valueOf(node.isActive()));
return map;
}
public static void main(String[] args) throws Exception {
String inputFileName = "";
String inputFileName2 = "";
String outputFileName = "";
String solrServerHost = "";
String keepListFileName = "";
String filterListFileName = "";
String searchTerm = "";
HashMap<String, String> keepGrayList = new HashMap<String, String>();
HashMap<String, String> filterGrayList = new HashMap<String, String>();
boolean useAlias = false;
CommandLineParser parser = new GnuParser();
Options options = createCLIOptions();
try {
CommandLine line = parser.parse(options, args);
if (line.hasOption("f1")) {
// get the input file
inputFileName = line.getOptionValue("f1");
}
if (line.hasOption("f2")) {
inputFileName2 = line.getOptionValue("f2");
}
if (line.hasOption("o")) {
// get the output file
outputFileName = line.getOptionValue("o");
}
if (line.hasOption("s")) {
// get the server host name
solrServerHost = line.getOptionValue("s");
}
if (line.hasOption("term")) {
searchTerm = line.getOptionValue("term");
}
if (line.hasOption("a")) {
useAlias = true;
}
if (line.hasOption("k")) {
keepListFileName = line.getOptionValue("k");
}
if (line.hasOption("r")) {
filterListFileName = line.getOptionValue("r");
}
} catch (ParseException exp) {
log.warning("Command line parsing failed. Reason:" + exp.getMessage());
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("pubcrawl", options);
System.exit(1);
}
if (isEmpty(outputFileName) || isEmpty(inputFileName) && isEmpty(searchTerm)) {
// missing required elements, print usage and exit
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("pubcrawl", options);
System.exit(1);
}
if (!isEmpty(keepListFileName)) {
// need to load the keepList hashmap
FileReader inputReader = new FileReader(keepListFileName);
BufferedReader bufReader = new BufferedReader(inputReader);
String keepTerm = bufReader.readLine();
while (keepTerm != null) {
String[] keepInfoArr = keepTerm.trim().split("\t");
keepGrayList.put(keepInfoArr[0].toLowerCase(), keepInfoArr[1]);
keepTerm = bufReader.readLine();
}
bufReader.close();
}
log.info("loading filterlist filename");
if (!isEmpty(filterListFileName)) {
// need to load the filterlist hashmap
FileReader inputReader = new FileReader(filterListFileName);
BufferedReader bufReader = new BufferedReader(inputReader);
String filterTerm = bufReader.readLine();
while (filterTerm != null) {
String[] filterInfoArr = filterTerm.trim().split("\t");
filterGrayList.put(filterInfoArr[0].toLowerCase(), filterInfoArr[1]);
filterTerm = bufReader.readLine();
}
bufReader.close();
}
SolrServer server = getSolrServer(solrServerHost);
String logname = outputFileName + "_log.out";
// create output files
FileWriter logFileStream = new FileWriter(logname);
BufferedWriter logFileOut = new BufferedWriter(logFileStream);
FileWriter dataResultsStream = new FileWriter(outputFileName);
BufferedWriter dataResultsOut = new BufferedWriter(dataResultsStream);
final Map<String, Integer> singleCountMap = new HashMap<String, Integer>();
final List<String> term2List = new ArrayList<String>();
// now load the appropriate list of gene terms - if the second file name wasn't entered
if (isEmpty(inputFileName2)) {
String sql = "Select term1,count from singletermcount";
if (useAlias) {
sql = "Select alias,count from singletermcount_alias";
}
JdbcTemplate jdbcTemplate = getJdbcTemplate();
jdbcTemplate.query(
sql,
new ResultSetExtractor() {
public Object extractData(ResultSet rs) throws SQLException, DataAccessException {
while (rs.next()) {
String geneName = rs.getString(1).trim();
int count = rs.getInt(2);
singleCountMap.put(geneName.toLowerCase(), count);
if (count > 0) {
term2List.add(geneName.toLowerCase());
}
}
return null;
}
});
} else { // have a second input file, so read the file in and put those as the terms in the
// term2List, set the SingleCountMap to empty
FileReader inputReader2 = new FileReader(inputFileName2);
BufferedReader bufReader2 = new BufferedReader(inputReader2);
String searchTerm2 = bufReader2.readLine();
while (searchTerm2 != null) {
term2List.add(searchTerm2.trim().toLowerCase());
searchTerm2 = bufReader2.readLine();
}
}
Long totalDocCount = getTotalDocCount(server);
logFileOut.write("Total doc count: " + totalDocCount);
Pubcrawl p = new Pubcrawl();
if (isEmpty(inputFileName)) { // entered term option, just have one to calculate
SearchTermAndList searchTermArray = getTermAndTermList(searchTerm.trim(), useAlias, false);
Long searchTermCount =
getTermCount(server, singleCountMap, searchTermArray, filterGrayList, keepGrayList);
ExecutorService pool = Executors.newFixedThreadPool(32);
Set<Future<NGDItem>> set = new HashSet<Future<NGDItem>>();
Date firstTime = new Date();
for (String secondTerm : term2List) {
SearchTermAndList secondTermArray = getTermAndTermList(secondTerm, useAlias, false);
long secondTermCount =
getTermCount(server, singleCountMap, secondTermArray, filterGrayList, keepGrayList);
Callable<NGDItem> callable =
p
.new SolrCallable(
searchTermArray,
secondTermArray,
searchTermCount,
secondTermCount,
server,
useAlias,
filterGrayList,
keepGrayList,
totalDocCount);
Future<NGDItem> future = pool.submit(callable);
set.add(future);
}
for (Future<NGDItem> future : set) {
dataResultsOut.write(future.get().printItem());
}
Date secondTime = new Date();
logFileOut.write(
"First set of queries took "
+ (secondTime.getTime() - firstTime.getTime()) / 1000
+ " seconds.\n");
logFileOut.flush();
logFileOut.close();
dataResultsOut.flush();
dataResultsOut.close();
pool.shutdown();
} else {
FileReader inputReader = new FileReader(inputFileName);
BufferedReader bufReader = new BufferedReader(inputReader);
String fileSearchTerm = bufReader.readLine();
SearchTermAndList searchTermArray = getTermAndTermList(fileSearchTerm, useAlias, false);
Long searchTermCount =
getTermCount(server, singleCountMap, searchTermArray, filterGrayList, keepGrayList);
// do this once with a lower amount of threads, in case we are running on a server where new
// caching is taking place
ExecutorService pool = Executors.newFixedThreadPool(32);
List<Future<NGDItem>> set = new ArrayList<Future<NGDItem>>();
long firstTime = currentTimeMillis();
int count = 0;
for (String secondTerm : term2List) {
count++;
SearchTermAndList secondTermArray = getTermAndTermList(secondTerm, useAlias, false);
long secondTermCount =
getTermCount(server, singleCountMap, secondTermArray, filterGrayList, keepGrayList);
Callable<NGDItem> callable =
p
.new SolrCallable(
searchTermArray,
secondTermArray,
searchTermCount,
secondTermCount,
server,
useAlias,
filterGrayList,
keepGrayList,
totalDocCount);
Future<NGDItem> future = pool.submit(callable);
set.add(future);
if (count > 5000) {
for (Future<NGDItem> futureItem : set) {
dataResultsOut.write(futureItem.get().printItem());
futureItem = null;
}
count = 0;
set.clear();
}
}
for (Future<NGDItem> future : set) {
dataResultsOut.write(future.get().printItem());
}
long secondTime = currentTimeMillis();
logFileOut.write(
"First set of queries took " + (secondTime - firstTime) / 1000 + " seconds.\n");
logFileOut.flush();
set.clear();
pool = Executors.newFixedThreadPool(32);
fileSearchTerm = bufReader.readLine();
count = 0;
while (fileSearchTerm != null) {
searchTermArray = getTermAndTermList(fileSearchTerm, useAlias, false);
searchTermCount =
getTermCount(server, singleCountMap, searchTermArray, filterGrayList, keepGrayList);
secondTime = currentTimeMillis();
for (String secondTerm : term2List) {
SearchTermAndList secondTermArray = getTermAndTermList(secondTerm, useAlias, false);
long secondTermCount =
getTermCount(server, singleCountMap, secondTermArray, filterGrayList, keepGrayList);
Callable<NGDItem> callable =
p
.new SolrCallable(
searchTermArray,
secondTermArray,
searchTermCount,
secondTermCount,
server,
useAlias,
filterGrayList,
keepGrayList,
totalDocCount);
Future<NGDItem> future = pool.submit(callable);
set.add(future);
count++;
if (count > 5000) {
for (Future<NGDItem> futureItem : set) {
dataResultsOut.write(futureItem.get().printItem());
futureItem = null;
}
count = 0;
set.clear();
}
}
for (Future<NGDItem> future : set) {
dataResultsOut.write(future.get().printItem());
future = null;
}
logFileOut.write("Query took " + (currentTimeMillis() - secondTime) / 1000 + " seconds.\n");
logFileOut.flush();
set.clear();
fileSearchTerm = bufReader.readLine();
}
long fourthTime = currentTimeMillis();
logFileOut.write("Final time: " + (fourthTime - firstTime) / 1000 + " seconds.\n");
bufReader.close();
logFileOut.flush();
logFileOut.close();
dataResultsOut.flush();
dataResultsOut.close();
pool.shutdown();
}
System.exit(0);
}
private static Map<String, String> nodeReportToMap(NodeReport nodeReport) {
final HashMap<String, String> map = new HashMap<String, String>(2);
map.put(FIELD_HOSTNAME, nodeReport.getHostname());
map.put(FIELD_RESULT, nodeReport.getState());
final VmmNode node = nodeReport.getNode();
if (node == null) {
map.put(FIELD_POOL, null);
map.put(FIELD_MEMORY, null);
map.put(FIELD_NETWORKS, null);
map.put(FIELD_IN_USE, null);
map.put(FIELD_ACTIVE, null);
} else {
map.put(FIELD_POOL, node.getPoolName());
map.put(FIELD_MEMORY, String.valueOf(node.getMemory()));
map.put(FIELD_NETWORKS, node.getNetworkAssociations());
map.put(FIELD_IN_USE, String.valueOf(!node.isVacant()));
map.put(FIELD_ACTIVE, String.valueOf(node.isActive()));
}
return map;
}
