+++ /dev/null
-package compbio.cassandra;
-
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.ArrayList;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import com.datastax.driver.core.Row;
-import com.datastax.driver.core.Session;
-import com.datastax.driver.core.ResultSet;
-
-import compbio.beans.DateBean;
-import compbio.beans.JobBean;
-import compbio.beans.ProteinBean;
-import compbio.beans.Total;
-import compbio.engine.JobStatus;
-import compbio.engine.Pair;
-
-public class CassandraReaderOld {
- private Session session;
- private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
-
- public CassandraReaderOld() {
- Session inis = CassandraNativeConnector.getSession();
- setSession(inis);
- }
-
- public void setSession(Session s) {
- assert s != null;
- session = s;
- }
-
- /*
- * getting data from the db
- */
- public List<Pair<String, String>> ReadProteinDataTable() {
- final long startTime = System.currentTimeMillis();
- String com = "SELECT DataBegin,DataEnd FROM ProteinLog;";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
- final long queryTime = System.currentTimeMillis();
- List<Row> rows = results.all();
- System.out.println("Query time is " + (queryTime - startTime) + " msec");
-
- List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
- int c = 0;
- for (Row r : rows) {
- Pair<String, String> pair = new Pair<String, String>(r.getString("DataBegin"), r.getString("DataEnd"));
- res.add(pair);
- ++c;
- }
- final long endTime = System.currentTimeMillis();
- System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
- return res;
- }
-
- /*
- * getting data from the db
- */
- public DateBean ReadProteinData(long day, String date) {
- String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
- if (results.isExhausted())
- return null;
- List<Row> rows = results.all();
- DateBean res = new DateBean(date);
- for (Row r : rows) {
- res.setJobidAndSeq(r.getString("JobID"), r.getString("Protein"));
- }
- return res;
- }
-
- /**
- * getting data from the db
- */
- public DateBean ReadFailedJobs(long day, String date, JobStatus status) {
- // FailLog (jobtime, JobID, ExecTime, ip, FinalStatus)
- String com = "SELECT JobID FROM FailLog WHERE jobtime = " + day + " and FinalStatus = '" + status.name() + "';";
- ResultSet results = session.execute(com);
- if (results.isExhausted())
- return null;
- List<Row> rows = results.all();
- DateBean res = new DateBean(date);
- for (Row r : rows) {
- String jobid = r.getString("JobID");
- String com1 = "SELECT Protein FROM ProteinLog WHERE JobID = '" + jobid + "';";
- System.out.println("Command: " + com1);
- ResultSet results2 = session.execute(com1);
- List<Row> jrows = results2.all();
- if (1 == jrows.size()) {
- String protein = jrows.get(0).getString("Protein");
- res.setJobidAndSeq(jobid, protein);
- }
- }
- return res;
- }
-
- /*
- * getting data from the db JobDateInfo
- */
- public Total ReadDateTable(long queryDate) {
- ResultSet results = session.execute("SELECT * FROM JobDateInfo WHERE jobday = " + queryDate + ";");
- if (results.isExhausted())
- return null;
- Row therow = results.one();
- Total res = new Total(therow.getLong("Total"), therow.getLong("TotalOK"), therow.getLong("TotalStopped"),
- therow.getLong("TotalError"), therow.getLong("TotalTimeOut"));
- if (!results.isExhausted()) {
- Date date = new Date(queryDate);
- log.warn("CassandraReader.ReadDateTable: date row for " + date.toString() + " (" + queryDate + ") duplicated ");
- }
- return res;
- }
-
- /*
- * getting whole protein sequence from the db ProteinRow
- */
- public List<ProteinBean> ReadWholeSequence(String queryProtein) {
- final long startTime = System.currentTimeMillis();
- String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
- if (results.isExhausted())
- return null;
- final long queryTime = System.currentTimeMillis();
- List<Row> rows = results.all();
- System.out.println("first size : " + rows.size());
- System.out.println("Query time is " + (queryTime - startTime) + " msec");
- System.out.println(" rows analysed, " + rows.size());
- List<ProteinBean> res = new ArrayList<ProteinBean>();
- ProteinBean structure = new ProteinBean(queryProtein, rows.get(0).getMap("Predictions", String.class, String.class));
- System.out.println("second size : " + rows.size());
- int c = 0;
- for (Row r : rows) {
- structure.setJobid(r.getString("JobID"));
- ++c;
- }
- res.add(structure);
- final long endTime = System.currentTimeMillis();
- System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
- return res;
- }
-
- /*
- * getting jobs by ip
- */
- public Map<String, String[]> ReadIpWithJobs(String ip) {
- final long startTime = System.currentTimeMillis();
- String com = "SELECT JobID, Protein, FinalStatus, DataBegin FROM ProteinLog WHERE ip = '" + ip + "';";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
- if (results.isExhausted())
- return null;
- final long queryTime = System.currentTimeMillis();
- List<Row> rows = results.all();
- Map<String, String[]> res = new HashMap<String, String[]>();
- System.out.println("Query time is " + (queryTime - startTime) + " msec");
- System.out.println(" rows analysed, " + rows.size());
- int c = 0;
- for (Row r : rows) {
- if (r.getString("FinalStatus").equals("OK")) {
- String date = r.getString("DataBegin");
- res.put(r.getString("JobID"), new String[] { date.substring(0, date.indexOf(":")), r.getString("Protein") });
- ++c;
- }
- }
- final long endTime = System.currentTimeMillis();
- System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
- return res;
- }
-
- /*
- * getting part of protein sequence from the db ProteinRow
- */
- public List<ProteinBean> ReadPartOfSequence(String queryProtein) {
- final long startTime = System.currentTimeMillis();
- String com = "SELECT * FROM ProteinRow;";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
- if (results.isExhausted())
- return null;
- final long queryTime = System.currentTimeMillis();
- List<Row> rows = results.all();
- System.out.println("Query time is " + (queryTime - startTime) + " msec");
- System.out.println(" rows analysed, " + rows.size());
- List<ProteinBean> res = new ArrayList<ProteinBean>();
- int c = 0;
- for (Row r : rows) {
- String prot = r.getString("Protein");
- if (prot.matches("(.*)" + queryProtein + "(.*)")) {
- ProteinBean structure = new ProteinBean(prot, r.getMap("Predictions", String.class, String.class));
- structure.setJobid(r.getString("JobID"));
- res.add(structure);
- ++c;
- }
- }
- final long endTime = System.currentTimeMillis();
- System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
- return res;
- }
-
- /*
- * getting protein sequence from the db ProteinRow
- */
- public Map<String, String> ReadProtein() {
- //final long startTime = System.currentTimeMillis();
- String com = "SELECT * FROM ProteinRow;";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
- if (results.isExhausted())
- return null;
- //final long queryTime = System.currentTimeMillis();
- List<Row> rows = results.all();
- Map<String, String> output = new HashMap<String, String>();
- for (Row r : rows) {
- String protein = r.getString("Protein");
- String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class));
- if (protein != null && prediction != null) {
- output.put(protein, prediction);
- }
- }
- //final long endTime = System.currentTimeMillis();
- return output;
- }
-
- private String findJnetpred(Map<String, String> pred) {
- if (pred != null) {
- if (pred.containsKey("jnetpred"))
- return pred.get("jnetpred");
- }
- return null;
- }
-
- /*
- * getting protein sequences by counter
- */
- public Map<String, Integer> ReadProteinSequenceByCounter() {
- final long startTime = System.currentTimeMillis();
- String com = "SELECT Protein, JobID FROM ProteinRow;";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
- if (results.isExhausted())
- return null;
- final long queryTime = System.currentTimeMillis();
- List<Row> rows = results.all();
- System.out.println("Query time is " + (queryTime - startTime) + " msec");
- System.out.println(" rows analysed, " + rows.size());
- Map<String, Integer> res = new HashMap<String, Integer>();
- int c = 0;
- for (Row r : rows) {
- String protein = r.getString("Protein");
- if (res.containsKey(protein))
- res.put(protein, res.get(protein) + 1);
- else
- res.put(protein, 1);
- }
- final long endTime = System.currentTimeMillis();
- System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
- return res;
- }
-
- /*
- * getting ip by counter
- */
- public Map<String, Integer> ReadIpByCounter() {
- final long startTime = System.currentTimeMillis();
- String com = "SELECT JobID, ip FROM ProteinLog;";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
- if (results.isExhausted())
- return null;
- final long queryTime = System.currentTimeMillis();
- List<Row> rows = results.all();
- System.out.println("Query time is " + (queryTime - startTime) + " msec");
- System.out.println(" rows analysed, " + rows.size());
- Map<String, Integer> res = new HashMap<String, Integer>();
- int c = 0;
- for (Row r : rows) {
- String ip = r.getString("ip");
- if (res.containsKey(ip))
- res.put(ip, res.get(ip) + 1);
- else
- res.put(ip, 1);
- }
- final long endTime = System.currentTimeMillis();
- System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
- return res;
- }
-
- /*
- * getting log info for jobid
- */
- public JobBean ReadJobLog(String jobid) {
- final long startTime = System.currentTimeMillis();
- String com = "SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
- if (results.isExhausted())
- return null;
- final long queryTime = System.currentTimeMillis();
- Row row = results.one();
- String com1 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;";
- System.out.println("Command: " + com1);
- ResultSet results1 = session.execute(com1);
- if (results1.isExhausted())
- return null;
- Row row1 = results1.one();
- JobBean res = new JobBean(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"), row.getString("DataEnd"),
- row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
- String program = row.getString("ProgramName");
- String version = row.getString("ProgramVersion");
- if (null != program && null != version) {
- res.setProgramName(program);
- res.setProgramVersion(version);
- }
- System.out.println("Query time is " + (queryTime - startTime) + " msec");
- final long endTime = System.currentTimeMillis();
- System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec");
- return res;
- }
-}
import com.datastax.driver.core.Session;
import com.datastax.driver.core.exceptions.QueryExecutionException;
import com.datastax.driver.core.exceptions.QueryValidationException;
+
import compbio.cassandra.CassandraNativeConnector;
public class CassandraReader {
earlestDate = CassandraNativeConnector.getEarliestDateInDB();
return earlestDate;
}
+
+ /**
+ * prepares an example of either job id or IP for the DB
+ *
+ * @param exampletype
+ * defines which example you need (an existing job from the DB -
+ * jobid, an IP - "ip")
+ * @return a string representation of the requested example, if the example
+ * type is not known empty string is returned
+ */
+ public String getExample(String exampletype) {
+ if (exampletype.equals("jobid")) {
+ return "jp_NzBOJKo";
+ } else if (exampletype.equals("ip")) {
+ return "127.0.0.1";
+ }
+ return "";
+ }
}
--- /dev/null
+package compbio.cassandra.readers;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import com.datastax.driver.core.ResultSet;
+import com.datastax.driver.core.Row;
+
+
+public class FeaturesReader extends CassandraReader {
+
+ public FeaturesReader() {
+ super();
+ }
+
+ /**
+ * query protein feature
+ *
+ * @param feature
+ * protein SS feature
+ *
+ * @param percent
+ * percent SS feature in protein sequence
+ *
+ * @return UserBean to the controller SSFeaturesController
+ **/
+
+ public Map<String, String> readProteinsPrediction(String feature, int percent) {
+ ResultSet results = CassandraQuery("SELECT * FROM ProteinRow;");
+ if (results.isExhausted())
+ return null;
+ List<Row> rows = results.all();
+ Map<String, String> query = new HashMap<String, String>();
+ for (Row r : rows) {
+ String prot = r.getString("Protein");
+ String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class));
+ if (prot != null && prediction != null && (!prot.equals(""))) {
+ if (prediction.replaceAll("[^" + feature + "]", "").length() > prediction.length() * percent / 100 ) {
+ query.put(prot, prediction);
+ }
+ }
+ }
+ return query;
+ }
+
+
+ private String findJnetpred(Map<String, String> pred) {
+ if (pred != null) {
+ if (pred.containsKey("jnetpred"))
+ return pred.get("jnetpred");
+ }
+ return null;
+ }
+
+
+}
import compbio.beans.TotalByCounterBean;
import compbio.beans.UserBean;
+import compbio.cassandra.readers.CassandraReader;
import compbio.cassandra.readers.IpReader;
import compbio.cassandra.readers.ReaderByCounter;
-import compbio.statistic.CassandraRequester;
/**
* @author Alexander Sherstnev
@RequestMapping(value = "/admin/ip/query", method = RequestMethod.GET)
public String initOneIPForm(Map<String, Object> model) {
model.put("username", getPrincipalName());
- CassandraRequester cr = new CassandraRequester();
+ CassandraReader cr = new CassandraReader();
model.put("value", cr.getExample("ip"));
return "query/IP";
}
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
-import compbio.statistic.CassandraRequester;
import compbio.beans.DateBean;
import compbio.beans.ExecutionTimeBean;
import compbio.beans.JobBean;
@RequestMapping(value = "/job/query", method = RequestMethod.GET)
public String initFindForm(Map<String, Object> model) {
model.put("username", getPrincipalName());
- CassandraRequester cr = new CassandraRequester();
+ CassandraReader cr = new CassandraReader();
model.put("value", cr.getExample("jobid"));
return "query/JobLog";
}
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
-import compbio.statistic.CassandraRequester;
+import compbio.cassandra.readers.FeaturesReader;
+
/**
* Spring controller for dealing with proteomes. This version works in the
return "query/SSFeatures";
}
- CassandraRequester cr = new CassandraRequester();
- Map<String, String> r = cr.readProteinsPrediction(typeFeature, realpercent);
+ FeaturesReader reader = new FeaturesReader();
+ Map<String, String> r = reader.readProteinsPrediction(typeFeature, realpercent);
model.put("results", r);
model.put("njobs", 0);
if (null != r) {
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
-import compbio.statistic.CassandraRequester;
+import compbio.cassandra.readers.FeaturesReader;
/**
* Spring controller for protein secondary structure features. This version
return "query/SSFeatures";
}
- CassandraRequester cr = new CassandraRequester();
- Map<String, String> r = cr.readProteinsPrediction(typeFeature, realpercent);
+ FeaturesReader reader = new FeaturesReader();
+ Map<String, String> r = reader.readProteinsPrediction(typeFeature, realpercent);
model.put("results", r);
model.put("njobs", 0);
StringBuilder csvline = new StringBuilder("");
+++ /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.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import compbio.beans.DateBean;
-import compbio.beans.JobBean;
-import compbio.beans.ProteinBean;
-import compbio.beans.Total;
-import compbio.beans.TotalByCounterBean;
-import compbio.beans.TotalJobsStatisticBean;
-import compbio.beans.UserBean;
-import compbio.cassandra.CassandraNativeConnector;
-import compbio.cassandra.CassandraReaderOld;
-import compbio.cassandra.DataBase;
-import compbio.engine.JobStatus;
-import compbio.engine.Pair;
-
-public class CassandraRequester {
- private CassandraReaderOld db = new CassandraReaderOld();
- private ArrayList<DataBase> query;
- private static long currentDate = 0;
- private static long earlestDate = 0;
- private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
- private final static SimpleDateFormat formatDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
-
- /*
- * 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, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
- System.out.println("CassandraRequester.extractExecutionTime: wrong format for date1 " + date1 + "or date2 " + date2);
- return null;
- }
- SetDateRange();
- int nbins = 5;
- long dateStart = DateParsing(date1, formatYYMMDD);
- long dateEnd = DateParsing(date2, formatYYMMDD);
- 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);
- }
-
- /*
- * ???? Very strange code... DataBase db = new DataBase();
- * db.setTimeTotalExec(totalTime); query.add(db);
- */
- return query;
- }
-
- /*
- * query: total number of jobs for the period from date1 till date2
- */
- public TotalJobsStatisticBean countJobs(String date1, String date2) {
- /*
- * if (null == date1) { date1 = "1970/1/1"; } if (null == date2) { date1
- * = "2100/1/1"; } if (!isThisDateValid(date1, formatYYMMDD) ||
- * !isThisDateValid(date2, formatYYMMDD)) { System.out.println(
- * "CassandraRequester.countJobs: wrong format for date1 " + date1 +
- * "or date2 " + date2); return null; }
- */
- SetDateRange();
- long dateStart = DateParsing(date1, formatYYMMDD);
- long dateEnd = DateParsing(date2, formatYYMMDD);
- /*
- * 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));
- TotalJobsStatisticBean query = new TotalJobsStatisticBean();
- Total wholeTotal = new Total(0, 0, 0, 0, 0);
- for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
- Total res = db.ReadDateTable(date.getTime());
- if (res == null)
- continue;
- query.setDateTotal(DateFormat(date.getTime()), res);
- wholeTotal.setTotal(res.getTotal() + wholeTotal.getTotal());
- wholeTotal.setTotalOK(res.getTotalOK() + wholeTotal.getTotalOK());
- wholeTotal.setTotalStopped(res.getTotalStopped() + wholeTotal.getTotalStopped());
- wholeTotal.setTotalError(res.getTotalError() + wholeTotal.getTotalError());
- wholeTotal.setTotalTimeOut(res.getTotalTimeOut() + wholeTotal.getTotalTimeOut());
- }
- query.setWholeTotal(wholeTotal);
- return query;
- }
-
- /*
- * query: jobs and sequence at date
- */
- public DateBean readJobByDay(String date, JobStatus status) {
- if (!isThisDateValid(date, formatDDMMYY)) {
- System.out.println("CassandraRequester.readJobByDay: Wrong date format for " + date);
- return null;
- }
- SetDateRange();
- long day = DateParsing(date, formatDDMMYY);
- if (day < earlestDate || day > currentDate)
- return null;
-
- if (status == JobStatus.OK) {
- return db.ReadProteinData(day, date);
- }
- return db.ReadFailedJobs(day, date, status);
- }
-
- /*
- * query: protein sequence
- */
- public List<ProteinBean> readProteins(String protIn, String searchtype) {
- List<ProteinBean> result;
- if (searchtype.equals("whole"))
- result = db.ReadWholeSequence(protIn);
- else
- result = db.ReadPartOfSequence(protIn);
- if (result == null)
- return null;
-
- if (searchtype.equals("partial")) {
- for (ProteinBean entry : result) {
- entry.setSubProt(CreateSubprot(entry.getSequence(), protIn));
- }
- }
- return result;
- }
-
- /*
- * query: protein feature
- */
-
- public Map<String, String> readProteinsPrediction(String feature, int percent) {
- Map<String, String> results = db.ReadProtein();
- if (results == null)
- return null;
- Map<String, String> query = new HashMap<String, String>();
- for (Map.Entry<String, String> entry : results.entrySet()) {
- String prediction = entry.getValue();
- String protein = entry.getKey();
- if (prediction.replaceAll("[^" + feature + "]", "").length() > prediction.length() * percent / 100 && !protein.equals("")) {
- query.put(protein, prediction);
- }
- }
- return query;
- }
-
- /*
- * query protein sequences with number of jobs
- */
- public List<TotalByCounterBean> readProteinByCounter(int minimalcounter) {
- List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
- Map<String, Integer> map = db.ReadProteinSequenceByCounter();
- if (map == null)
- return null;
- for (Map.Entry<String, Integer> entry : map.entrySet()) {
- if (entry.getValue() > minimalcounter) {
- TotalByCounterBean bean = new TotalByCounterBean();
- bean.setTotaljobs(entry.getValue());
- bean.setName(entry.getKey());
- query.add(bean);
- }
- }
- return query;
- }
-
- /*
- * query ip with number of jobs
- */
- public List<TotalByCounterBean> readIpByCounter(Integer minimalcounter) {
- List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
- Map<String, Integer> map = db.ReadIpByCounter();
- if (minimalcounter == null)
- minimalcounter = 0;
- if (map == null)
- return null;
- for (Map.Entry<String, Integer> entry : map.entrySet()) {
- if (entry.getValue() > minimalcounter) {
- TotalByCounterBean bean = new TotalByCounterBean();
- bean.setTotaljobs(entry.getValue());
- bean.setName(entry.getKey());
- query.add(bean);
- }
- }
- return query;
- }
-
- /*
- * query jobs log info
- */
- public JobBean readJobLog(String jobid) {
- if (jobid == null)
- return null;
- return db.ReadJobLog(jobid);
- }
-
- /*
- * query jobs by ipStructureJobLog
- */
- public UserBean readIp(String ip) {
- if (ip == null)
- return null;
- Map<String, String[]> res = db.ReadIpWithJobs(ip);
- if (res == null)
- return null;
- UserBean query = new UserBean(ip);
- query.setMainInfo(res);
- 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, SimpleDateFormat formatter) {
- if (datInput == null) {
- return 0;
- }
- long dateWorkSt = 0;
-
- 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),
- formatYYMMDD);
- if (0 == earlestDate) {
- CassandraRequester cr = new CassandraRequester();
- earlestDate = cr.earliestDate();
- }
- }
-
- public boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) {
- if (dateToValidate == null || dateToValidate.equals("")) {
- return false;
- }
- 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;
- }
-
- /**
- * prepares an example of either job id or IP for the DB
- *
- * @param exampletype
- * defines which example you need (an existing job from the DB -
- * jobid, an IP - "ip")
- * @return a string representation of the requested example, if the example
- * type is not known empty string is returned
- */
- public String getExample(String exampletype) {
- if (exampletype.equals("jobid")) {
- return "jp_NzBOJKo";
- } else if (exampletype.equals("ip")) {
- return "127.0.0.1";
- }
- return "";
- }
-
-}
--- /dev/null
+
+package compbio.ws.jpred.jaxws;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+@XmlRootElement(name = "findJobForSequence", namespace = "http://server.proteocache.ws")
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "findJobForSequence", namespace = "http://server.proteocache.ws", propOrder = {
+ "sequence",
+ "program",
+ "version"
+})
+public class FindJobForSequence {
+
+ @XmlElement(name = "sequence", namespace = "")
+ private String sequence;
+ @XmlElement(name = "program", namespace = "")
+ private String program;
+ @XmlElement(name = "version", namespace = "")
+ private String version;
+
+ /**
+ *
+ * @return
+ * returns String
+ */
+ public String getSequence() {
+ return this.sequence;
+ }
+
+ /**
+ *
+ * @param sequence
+ * the value for the sequence property
+ */
+ public void setSequence(String sequence) {
+ this.sequence = sequence;
+ }
+
+ /**
+ *
+ * @return
+ * returns String
+ */
+ public String getProgram() {
+ return this.program;
+ }
+
+ /**
+ *
+ * @param program
+ * the value for the program property
+ */
+ public void setProgram(String program) {
+ this.program = program;
+ }
+
+ /**
+ *
+ * @return
+ * returns String
+ */
+ public String getVersion() {
+ return this.version;
+ }
+
+ /**
+ *
+ * @param version
+ * the value for the version property
+ */
+ public void setVersion(String version) {
+ this.version = version;
+ }
+
+}
--- /dev/null
+
+package compbio.ws.jpred.jaxws;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+@XmlRootElement(name = "findJobForSequenceResponse", namespace = "http://server.proteocache.ws")
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "findJobForSequenceResponse", namespace = "http://server.proteocache.ws")
+public class FindJobForSequenceResponse {
+
+ @XmlElement(name = "return", namespace = "")
+ private String _return;
+
+ /**
+ *
+ * @return
+ * returns String
+ */
+ public String getReturn() {
+ return this._return;
+ }
+
+ /**
+ *
+ * @param _return
+ * the value for the _return property
+ */
+ public void setReturn(String _return) {
+ this._return = _return;
+ }
+
+}
--- /dev/null
+
+package compbio.ws.jpred.jaxws;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+@XmlRootElement(name = "getArchive", namespace = "http://server.proteocache.ws")
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "getArchive", namespace = "http://server.proteocache.ws")
+public class GetArchive {
+
+ @XmlElement(name = "job", namespace = "")
+ private String job;
+
+ /**
+ *
+ * @return
+ * returns String
+ */
+ public String getJob() {
+ return this.job;
+ }
+
+ /**
+ *
+ * @param job
+ * the value for the job property
+ */
+ public void setJob(String job) {
+ this.job = job;
+ }
+
+}
--- /dev/null
+
+package compbio.ws.jpred.jaxws;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+@XmlRootElement(name = "getArchiveResponse", namespace = "http://server.proteocache.ws")
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "getArchiveResponse", namespace = "http://server.proteocache.ws")
+public class GetArchiveResponse {
+
+ @XmlElement(name = "return", namespace = "")
+ private String _return;
+
+ /**
+ *
+ * @return
+ * returns String
+ */
+ public String getReturn() {
+ return this._return;
+ }
+
+ /**
+ *
+ * @param _return
+ * the value for the _return property
+ */
+ public void setReturn(String _return) {
+ this._return = _return;
+ }
+
+}
git://source.jalview.org / proteocache.git / commitdiff