--- /dev/null
+package compbio.statistic;
+
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import compbio.cassandra.CassandraNativeConnector;
+import compbio.cassandra.CassandraReader;
+import compbio.cassandra.DataBase;
+import compbio.cassandra.Pair;
+import compbio.cassandra.StructureJobLog;
+import compbio.cassandra.StructureProteinPrediction;
+
+public class CassandraRequester {
+ private CassandraReader db = new CassandraReader();
+ private ArrayList<DataBase> query;
+ private static long currentDate = 0;
+ private static long earlestDate = 0;
+
+ /*
+ * query: execution time for the period from date1 till date2
+ */
+ public List<DataBase> extractExecutionTime(String date1, String date2) {
+ if (null == date1) {
+ date1 = "1970/1/1";
+ }
+ if (null == date2) {
+ date1 = "2100/1/1";
+ }
+ if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+ System.out.println("Wrong date: point 3");
+ return null;
+ }
+ SetDateRange();
+ int nbins = 5;
+ long dateStart = DateParsing(date1);
+ long dateEnd = DateParsing(date2);
+ if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
+ return null;
+ if (dateStart < earlestDate)
+ dateStart = earlestDate;
+ if (dateEnd > currentDate)
+ dateStart = currentDate;
+
+ Calendar start = Calendar.getInstance();
+ start.setTime(new Date(dateStart));
+ Calendar end = Calendar.getInstance();
+ end.setTime(new Date(dateEnd));
+ query = new ArrayList<DataBase>();
+ List<Integer> totalTime = new ArrayList<Integer>();
+ for (int i = 0; i < nbins; i++)
+ totalTime.add(i, 0);
+ List<Pair<String, String>> res = db.ReadProteinDataTable();
+ List<Pair<Date, Long>> numres = new ArrayList<Pair<Date, Long>>();
+
+ for (Pair<String, String> entry : res) {
+ SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
+ try {
+ Date jobstartdate = dateformatter.parse(entry.getElement0());
+ long date = jobstartdate.getTime();
+ if (dateStart <= date && date <= dateEnd) {
+ SimpleDateFormat datetimeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
+ Date jobstarttime = datetimeformatter.parse(entry.getElement0());
+ Date jobendtime = datetimeformatter.parse(entry.getElement1());
+ long diff = (jobendtime.getTime() - jobstarttime.getTime()) / 1000;
+ Pair<Date, Long> pair = new Pair<Date, Long>(jobstartdate, Long.valueOf(diff));
+ numres.add(pair);
+ }
+ } catch (ParseException e) {
+ e.printStackTrace();
+ }
+ }
+
+ for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
+ List<Integer> timeResult = new ArrayList<Integer>();
+ for (int i = 0; i < nbins; i++)
+ timeResult.add(i, 0);
+ for (Pair<Date, Long> p : numres) {
+ if (date.equals(p.getElement0())) {
+ long lenResult = p.getElement1().longValue();
+ if (lenResult <= 30)
+ timeResult.set(0, timeResult.get(0) + 1);
+ else if (lenResult > 30 && lenResult <= 60)
+ timeResult.set(1, timeResult.get(1) + 1);
+ else if (lenResult > 60 && lenResult <= 120)
+ timeResult.set(2, timeResult.get(2) + 1);
+ else if (lenResult > 120 && lenResult <= 600)
+ timeResult.set(3, timeResult.get(3) + 1);
+ else {
+ timeResult.set(4, timeResult.get(4) + 1);
+ }
+ }
+ }
+ for (int i = 0; i < nbins; i++)
+ totalTime.set(i, totalTime.get(i) + timeResult.get(i));
+ DataBase db = new DataBase();
+ db.setTimeRez(timeResult);
+ db.setDate(DateFormat(date.getTime()));
+ query.add(db);
+ }
+
+ DataBase db = new DataBase();
+ db.setTimeTotalExec(totalTime);
+ query.add(db);
+ System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
+ return query;
+ }
+
+ /*
+ * query: total number of jobs for the period from date1 till date2
+ */
+ public List<DataBase> countJobs(String date1, String date2) {
+ if (null == date1) {
+ date1 = "1970/1/1";
+ }
+ if (null == date2) {
+ date1 = "2100/1/1";
+ }
+ if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+ System.out.println("Wrong date: point 3");
+ return null;
+ }
+ SetDateRange();
+ long dateStart = DateParsing(date1);
+ long dateEnd = DateParsing(date2);
+ if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
+ return null;
+ if (dateStart < earlestDate)
+ dateStart = earlestDate;
+ if (dateEnd > currentDate)
+ dateStart = currentDate;
+
+ Calendar start = Calendar.getInstance();
+ start.setTime(new Date(dateStart));
+ Calendar end = Calendar.getInstance();
+ end.setTime(new Date(dateEnd));
+ query = new ArrayList<DataBase>();
+ for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
+ long res = db.ReadDateTable(date.getTime());
+ DataBase db = new DataBase();
+ db.setTotal((int)res);
+ db.setDate(DateFormat(date.getTime()));
+ query.add(db);
+ }
+ System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
+ return query;
+ }
+ /*
+ * query: protein sequence
+ * */
+ public List<DataBase> readProteins(String protIn, String flag) {
+ query = new ArrayList<DataBase>();
+ List<StructureProteinPrediction> res;
+ if (flag.equals("whole"))
+ res = db.ReadWholeSequence(protIn);
+ else
+ res = db.ReadPartOfSequence(protIn);
+ for (StructureProteinPrediction entry : res) {
+ Map<String,String> pred = entry.getPrediction();
+ Iterator it = pred.entrySet().iterator();
+ while (it.hasNext()) {
+ DataBase db = new DataBase();
+ db.setProt(entry.getSequence());
+ Map.Entry pairs = (Map.Entry)it.next();
+ db.setId(entry.getJobid());
+ db.setJpred(pairs.getValue().toString());
+ if (flag.equals("part"))
+ db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
+ query.add(db);
+ }
+ }
+ return query;
+ }
+
+ /*
+ * query protein sequences with number of jobs
+ */
+ public List<DataBase> readProteinByCounter(int minimalcounter) {
+ query = new ArrayList<DataBase>();
+ Map<String, Integer> map = db.ReadProteinSequenceByCounter();
+ for (Map.Entry<String, Integer> entry : map.entrySet()) {
+ if (entry.getValue() > minimalcounter) {
+ DataBase db = new DataBase();
+ db.setTotalId(entry.getValue());
+ db.setProt(entry.getKey());
+ query.add(db);
+ }
+ }
+ return query;
+ }
+
+ /*
+ * query jobs log info
+ */
+ public DataBase readJobLog(String jobid) {
+ // query = new ArrayList<DataBase>();
+ StructureJobLog res = db.ReadJobLog(jobid);
+ DataBase query = new DataBase();
+ query.setLogInfo(res);
+ // query.setres);
+ return query;
+ }
+ /*
+ * create list of parts of protein sequence;
+ */
+ private static List<String> CreateSubprot (String protein, String subprot) {
+ List<String> sub = new ArrayList<String>();
+ String subStr = protein;
+ while (subStr.length() > 0 && subStr.contains(subprot)) {
+ String first = subStr.substring(0, subStr.indexOf(subprot));
+ if (first.length() > 0)
+ sub.add(first);
+ sub.add(subprot);
+ subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
+ }
+ if (subStr.length() > 0)
+ sub.add(subStr);
+ return sub;
+ }
+ /*
+ * convert String date into long date (miliseconds since the epoch start)
+ */
+ private static long DateParsing(String datInput) {
+ if (datInput == null) {
+ return 0;
+ }
+ long dateWorkSt = 0;
+ SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
+ try {
+ dateWorkSt = formatter.parse(datInput).getTime();
+ } catch (ParseException e) {
+ e.printStackTrace();
+ }
+ return dateWorkSt;
+ }
+
+ // convert long to date in string format
+ private static String DateFormat(long inDate) {
+ SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
+ return datformat.format(new Date(inDate));
+ }
+
+ /*
+ * set earlest date and current dates. earlestDate is static and should be
+ * set at the 1st call currentDate should be re-calculated every time
+ */
+ private static void SetDateRange() {
+ Calendar cal = Calendar.getInstance();
+ currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH));
+ if (0 == earlestDate) {
+ CassandraRequester cr = new CassandraRequester();
+ earlestDate = cr.earliestDate();
+ System.out.println("Set earlest Date = " + earlestDate);
+ }
+ }
+
+ public boolean isThisDateValid(String dateToValidate) {
+ if (dateToValidate == null || dateToValidate.equals("")) {
+ System.out.println("Undefined date");
+ return false;
+ }
+ SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd");
+ try {
+ // if not valid, this will throw ParseException
+ sdf.setLenient(false);
+ Date date = sdf.parse(dateToValidate);
+ } catch (ParseException e) {
+ e.printStackTrace();
+ return false;
+ }
+ return true;
+ }
+
+ /*
+ * find the earliest date in the database
+ */
+ public long earliestDate() {
+ earlestDate = CassandraNativeConnector.getEarliestDateInDB();
+ return earlestDate;
+ }
+
+}
git://source.jalview.org / proteocache.git / blobdiff