#################################################################################
# Cassandra host or IP
# test server is 10.0.115.190
-cassandra.host=localhost
+#cassandra.host=localhost
+cassandra.host=Main-laptop2.dyn.lifesci.dundee.ac.uk
#cassandra.host=gjb-www-1.cluster.lifesci.dundee.ac.uk
#cassandra.host=c6100-1.cluster.lifesci.dundee.ac.uk
cassandra.jpred.web.update=true
cassandra.jpred.web.inidelay=0
cassandra.jpred.web.updaterate=30
+#cassandra.jpred.web.prefix=http://gjb-www-1.cluster.lifesci.dundee.ac.uk:3209/results
# update time period (in days)
# by defauls for 100 past days
package compbio.beans;
import java.util.HashMap;
-import java.util.LinkedHashMap;
import java.util.Map;
public class DateBean {
private String ip;
private String ProgramName;
private String ProgramVersion;
+ private String ProgramLink;
private LinkedHashMap<String, String> predictions;
- public JobBean(String seq, String id, String dateStart, String dateEnd, String ip, Map<String, String> pred, String program, String version) {
+ public JobBean(String seq, String id, String dateStart, String dateEnd, String ip, Map<String, String> pred) {
this.sequence = seq;
- this.ProgramName = program;
- this.ProgramVersion = version;
+ this.ProgramName = "";
+ this.ProgramVersion = "";
this.jobid = id;
this.dateStart = dateStart;
this.dateEnd = dateEnd;
this.ip = ip;
+ this.ProgramLink = "";
this.predictions = new LinkedHashMap<String, String>();
setPredictions(pred);
}
return ProgramVersion;
}
+ public String getProgramLink() {
+ return ProgramLink;
+ }
+
+ public void setProgramName(String name) {
+ ProgramName = name;
+ }
+
+ public void setProgramVersion(String version) {
+ ProgramVersion = version;
+ }
+
+ public void setProgramLink(String link) {
+ ProgramLink = link;
+ }
+
public Map<String, String> getPrediction() {
return predictions;
}
this.predictions = new LinkedHashMap<String, String>();
this.jobid = new ArrayList<String>();
setPredictions(pred);
+ setJnetpred(pred);
}
public void setSequence(String seq) {
session.execute("CREATE TABLE IF NOT EXISTS JobDateInfo "
+ "(jobday bigint, Total bigint, TotalOK bigint, TotalStopped bigint, TotalError bigint, TotalTimeOut bigint, Program varchar, Version varchar, PRIMARY KEY(jobday));");
- String com = "CREATE TABLE IF NOT EXISTS Users "
- + "(name varchar, id bigint, email varchar, password varchar, organisation varchar, position varchar, signedtolist boolean, registrationdate bigint, PRIMARY KEY(id));";
+ session.execute("CREATE TABLE IF NOT EXISTS Programs "
+ + "(Program varchar, Version varchar, Description varchar, weblink varchar, PRIMARY KEY(Program,Version));");
+
+ session.execute("CREATE TABLE IF NOT EXISTS Users "
+ + "(name varchar, id bigint, email varchar, password varchar, organisation varchar, position varchar, signedtolist boolean, registrationdate bigint, PRIMARY KEY(id));");
// session.execute("ALTER TABLE ProteinLog ADD ProgramName ascii;");
// session.execute("ALTER TABLE ProteinLog ADD ProgramVersion ascii;");
import com.datastax.driver.core.Row;
import com.datastax.driver.core.Session;
import com.datastax.driver.core.ResultSet;
-import com.datastax.driver.core.PreparedStatement;
-import com.datastax.driver.core.BoundStatement;
import com.datastax.driver.core.exceptions.QueryExecutionException;
-import compbio.engine.ProteoCachePropertyHelperManager;
import compbio.cassandra.CassandraNativeConnector;
public class CassandraNewTableWriter {
Calendar endcal = Calendar.getInstance();
long endTime = endcal.getTime().getTime();
for (Date date = runnicCal.getTime(); date.getTime() < endTime; runnicCal.add(Calendar.DATE, 1), date = runnicCal.getTime()) {
- try {
+ try {
String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + date.getTime() + ";";
System.out.println(com);
ResultSet results = session.execute(com);
continue;
List<Row> rows = results.all();
System.out.println(rows.size());
- int k=0;
for (Row r : rows) {
session.execute("UPDATE ProteinLog SET ProgramName = 'Jpred', ProgramVersion = '3.0.1' WHERE JobID = '"
+ r.getString("JobID") + "';");
session.execute("UPDATE JpredArchive SET ProgramName = 'Jpred', ProgramVersion = '3.0.1' WHERE JobID = '"
- + r.getString("JobID") + "';");
+ + r.getString("JobID") + "';");
}
} catch (QueryExecutionException e) {
e.printStackTrace();
import java.util.Date;
import java.util.List;
-import org.apache.log4j.Logger;
-
import com.datastax.driver.core.ResultSet;
import com.datastax.driver.core.Row;
-import com.datastax.driver.core.Session;
-import com.datastax.driver.core.exceptions.QueryExecutionException;
-import com.datastax.driver.core.exceptions.QueryValidationException;
+import compbio.cassandra.readers.CassandraReader;
-public class CassandraRemover {
- private Session session;
+/**
+ * The class removes jobs from the cassandra database. 4 different strategies
+ * are possiable: 1. remove 1 job with given job ID 2. remove jobs launched from
+ * an IP 3. remove jobs with particular protein sequence 4. remove jobs launched
+ * within a time range (date1, data2)
+ *
+ * @author Alexander Sherstnev
+ * @author Natasha Sherstneva
+ * @version 1.0
+ * @since Nov 2013
+ */
+public class CassandraRemover extends CassandraReader {
static SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
- private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
- public CassandraRemover() {
- Session inis = CassandraNativeConnector.getSession();
- setSession(inis);
- }
+ /**
+ * private method for real deleting one job
+ *
+ * @param jobid
+ * job ID
+ * @param date
+ * job execution date
+ *
+ * @return nothing
+ */
+ private int RemoveJob(String jobid, long date) {
- public void setSession(Session s) {
- assert s != null;
- session = s;
- }
+ if (date < 0L) {
+ log.error("CassandraRemover error: job " + jobid + " with date " + date
+ + " can not be deleted in JobDateInfo. Daily statistics is inconsistent");
+ return 0;
+ }
- /*
- * delete a record from CF for current jobId
- */
- private void RemoveJob(String jobid, long date) {
String status = FindStatus(jobid);
- String com0 = "DELETE FROM ProteinLog WHERE JobID = '" + jobid + "';";
- System.out.println("Command: " + com0);
- session.execute(com0);
- String com3 = "UPDATE jpredarchive SET finalstatus = 'DELETED' WHERE JobID = '" + jobid + "' ;";
+ String com1 = "DELETE FROM ProteinLog WHERE JobID = '" + jobid + "';";
+ System.out.println("Command: " + com1);
+ CassandraQuery(com1);
+
+ String com2 = "UPDATE jpredarchive SET finalstatus = 'DELETED' WHERE JobID = '" + jobid + "' ;";
+ System.out.println("Command: " + com2);
+ CassandraQuery(com2);
+
+ String com3 = "SELECT * FROM JobDateInfo WHERE jobday = " + date + ";";
System.out.println("Command: " + com3);
- session.execute(com3);
- String com = "SELECT * FROM JobDateInfo WHERE jobday = " + date + ";";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
+ ResultSet results = CassandraQuery(com3);
+ if (results.isExhausted()) {
+ log.error("CassandraRemover error: job " + jobid + " with date " + date
+ + " can not be deleted in JobDateInfo. Daily statistics is inconsistent");
+ return 0;
+ }
Row row = results.one();
long njobs = row.getLong("Total") - 1;
if (status.equals("OK")) {
long njobsOK = row.getLong("TotalOK") - 1;
- String com1 = "DELETE FROM ProteinRow WHERE JobID = '" + jobid + "';";
- System.out.println("Command: " + com1);
- session.execute(com1);
- String com2 = "DELETE FROM ProteinData WHERE JobID = '" + jobid + "' AND jobtime = " + date + ";";
- System.out.println("Command: " + com2);
- session.execute(com2);
+ String com4 = "DELETE FROM ProteinRow WHERE JobID = '" + jobid + "';";
+ System.out.println("Command: " + com4);
+ CassandraQuery(com4);
+
+ String com5 = "DELETE FROM ProteinData WHERE JobID = '" + jobid + "' AND jobtime = " + date + ";";
+ System.out.println("Command: " + com5);
+ CassandraQuery(com5);
UpdateJobDateInfo(date, "TotalOK", njobsOK, njobs);
} else {
String com6 = "DELETE FROM FailLog WHERE JobID = '" + jobid + "' AND jobtime = " + date + ";";
System.out.println("Command: " + com6);
- session.execute(com6);
+ CassandraQuery(com6);
if (status.equals("STOPPED")) {
long njobsStopped = row.getLong("TotalStopped") - 1;
UpdateJobDateInfo(date, "TotalStopped", njobsStopped, njobs);
UpdateJobDateInfo(date, "TotalTimeOut", njobsTimeOut, njobs);
}
}
- System.out.println("Remove jobs: " + jobid);
+ System.out.println("Job " + jobid + " removed...");
+ return 1;
}
+ /**
+ * update a pariticular column in the JobDateInfo table
+ *
+ * @param jobid
+ * job ID
+ *
+ * @return nothing
+ *
+ */
private void UpdateJobDateInfo(long date, String ColumnName, long totalcol, long total) {
- String com4 = "UPDATE JobDateInfo SET " + ColumnName + " = " + totalcol + ", Total = " + total + " WHERE jobday = " + date + ";";
- System.out.println("Command: " + com4);
- session.execute(com4);
+ String com = "UPDATE JobDateInfo SET " + ColumnName + " = " + totalcol + ", Total = " + total + " WHERE jobday = " + date + ";";
+ System.out.println("Command: " + com);
+ CassandraQuery(com);
}
+ /**
+ * external method for deleting job with given job ID (strategy 1)
+ *
+ * @param jobid
+ * job ID
+ *
+ * @return a number of deleted jobs
+ *
+ */
public int RemoveJobById(String jobid) {
if (jobid == null)
return 0;
- Long date = FindDate(jobid);
- RemoveJob(jobid, date);
- return 1;
+ long date = FindJobDate(jobid);
+ return RemoveJob(jobid, date);
}
+ /**
+ * external method for deleting jobs within a time range (strategy 4)
+ *
+ * @param date1
+ * starting date
+ *
+ * @param date2
+ * ending date
+ *
+ * @return a number of deleted jobs
+ *
+ */
public int RemoveJobByDate(String date1, String date2) {
- int numremover = 0;
if (date1 == null || date2 == null)
return 0;
+
+ int njobs = 0;
Long dateBegin = convertDate(date1);
Long dateEnd = convertDate(date2);
Calendar start = Calendar.getInstance();
start.setTime(new Date(dateBegin));
Calendar end = Calendar.getInstance();
end.setTime(new Date(dateEnd));
+
for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
- System.out.println("--------------------------------------------------------------------: ");
- String com = "SELECT JobID FROM ProteinData WHERE jobtime = " + date.getTime() + ";";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
+ String com1 = "SELECT JobID FROM ProteinData WHERE jobtime = " + date.getTime() + ";";
+ System.out.println("Command: " + com1);
+ ResultSet results = CassandraQuery(com1);
if (!results.isExhausted()) {
List<Row> rows = results.all();
for (Row r : rows) {
String jobid = r.getString("JobID");
if (jobid != null) {
- RemoveJob(jobid, date.getTime());
- numremover++;
+ njobs += RemoveJob(jobid, date.getTime());
}
}
}
- String comm = "SELECT JobID FROM FailLog WHERE jobtime = " + date.getTime() + ";";
- ResultSet resultsfail = session.execute(comm);
+
+ String com2 = "SELECT JobID FROM FailLog WHERE jobtime = " + date.getTime() + ";";
+ ResultSet resultsfail = CassandraQuery(com2);
if (!resultsfail.isExhausted()) {
List<Row> rows = resultsfail.all();
for (Row r : rows) {
String jobid = r.getString("JobID");
if (jobid != null) {
- RemoveJob(jobid, date.getTime());
- numremover++;
+ njobs += RemoveJob(jobid, date.getTime());
}
}
}
}
- return numremover;
+ return njobs;
}
+ /**
+ * external method for deleting jobs launched from a particular IP (strategy
+ * 2)
+ *
+ * @param ip
+ * the IP
+ *
+ * @return a number of deleted jobs
+ *
+ */
public int RemoveJobByIp(String ip) {
- int numremover = 0;
+ int njobs = 0;
if (ip == null)
return 0;
String com = "SELECT databegin, JobID FROM ProteinLog WHERE ip = '" + ip + "';";
- ResultSet results = session.execute(com);
+ ResultSet results = CassandraQuery(com);
if (!results.isExhausted()) {
List<Row> rows = results.all();
for (Row r : rows) {
Long date = convertDate(r.getString("databegin"));
String jobid = r.getString("JobID");
- if (date == null || jobid == null)
- continue;
- RemoveJob(jobid, date);
- numremover++;
+ if (date != null || jobid != null) {
+ njobs += RemoveJob(jobid, date);
+ }
}
}
- return numremover;
+ return njobs;
}
- public int RemoveJobBySequence(String seq) {
- int numremover = 0;
- if (seq == null)
+ /**
+ * external method for deleting jobs with a protein sequence (strategy 3)
+ *
+ * @param sequence
+ * the sequence
+ *
+ * @return a number of deleted jobs
+ *
+ */
+ public int RemoveJobBySequence(String sequence) {
+ int njobs = 0;
+ if (sequence == null)
return 0;
- String com = "SELECT JobID FROM ProteinRow WHERE Protein = '" + seq + "';";
- ResultSet results = session.execute(com);
+ String com = "SELECT JobID FROM ProteinRow WHERE Protein = '" + sequence + "';";
+ ResultSet results = CassandraQuery(com);
if (!results.isExhausted()) {
List<Row> rows = results.all();
for (Row r : rows) {
String jobid = r.getString("JobID");
- Long date = FindDate(jobid);
- RemoveJob(jobid, date);
- numremover++;
+ long date = FindJobDate(jobid);
+ njobs += RemoveJob(jobid, date);
}
}
- return numremover;
+ return njobs;
}
- private Long FindDate(String jobid) {
+ private long FindJobDate(String jobid) {
String com = "SELECT databegin FROM ProteinLog WHERE JobID = '" + jobid + "';";
- ResultSet results = session.execute(com);
- Long date = convertDate(results.one().getString("databegin"));
- return date;
+ ResultSet results = CassandraQuery(com);
+ if (!results.isExhausted()) {
+ return convertDate(results.one().getString("databegin"));
+ }
+ return -1L;
}
private String FindStatus(String jobid) {
- String status = "UNKNOWN";
- String command = "SELECT FinalStatus FROM ProteinLog WHERE JobID = '" + jobid + "';";
- try {
- System.out.println("Command: " + command);
- ResultSet results = session.execute(command);
- Row raw = results.one();
- if (null != raw) {
- status = raw.getString("FinalStatus");
- }
- } catch (QueryExecutionException e) {
- String mess = "CassandraRemover: query execution exception...";
- System.out.println(mess);
- log.error(mess);
- log.error(e.getLocalizedMessage(), e.getCause());
- } catch (QueryValidationException e) {
- String mess = "CassandraRemover: query validation exception... Command: " + command;
- System.out.println(mess);
- log.error(mess);
- log.error(e.getLocalizedMessage(), e.getCause());
+ String com = "SELECT FinalStatus FROM ProteinLog WHERE JobID = '" + jobid + "';";
+ System.out.println("Command: " + com);
+ ResultSet results = CassandraQuery(com);
+ if (!results.isExhausted()) {
+ return results.one().getString("FinalStatus");
}
- System.out.println("*****status: " + status);
- return status;
+ return "UNKNOWN";
}
protected long convertDate(String d) {
package compbio.cassandra;
import java.util.List;
-import java.util.ArrayList;
-import java.util.Collections;
import compbio.beans.JobBean;
import compbio.beans.ProteinBean;
import java.io.BufferedReader;
import java.io.File;
-import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
import java.io.FileInputStream;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import compbio.data.sequence.FastaSequence;
public class JpredParserLocalFile implements JpredParser {
- private CassandraWriter cw = new CassandraWriter();
private String dirprefix;
public void setSource(String newsourceprefix) {
if (in.matches(date + ":(.*)jp_[^\\s]+")) {
String[] table = in.split("\\s+");
String starttime = table[0];
- String finishtime = table[1];
- String ip = table[2];
String id = table[table.length - 1];
totalcount++;
String confilename = dirprefix + "/" + id + "/" + id + ".concise";
} else {
SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
String dateInString1 = starttime.substring(0, starttime.indexOf(":"));
- long insertdate = 0;
try {
Date dat = formatter.parse(dateInString1);
- insertdate = dat.getTime();
} catch (ParseException e) {
e.printStackTrace();
}
import compbio.cassandra.CassandraNativeConnector;
public class CassandraReader {
- private static long earlestDate = 0;
- private Session session;
+ protected static long earlestDate = 0;
+ protected Session session;
protected static Logger log = Logger.getLogger(CassandraNativeConnector.class);
public CassandraReader() {
ResultSet results = session.execute(command);
return results;
} catch (QueryExecutionException e) {
- String mess = "CassandraUserManagerImpl.findAllUsers: query execution exception...";
+ String mess = "ProteoCache Cassandra DB interface: query execution exception...\n Command: " + command;
System.out.println(mess);
log.error(mess);
log.error(e.getLocalizedMessage(), e.getCause());
return null;
} catch (QueryValidationException e) {
- String mess = "CassandraUserManagerImpl.findAllUsers: query validation exception... Command: " + command;
+ String mess = "CProteoCache Cassandra DB interface: query validation exception...\n Command: " + command;
System.out.println(mess);
log.error(mess);
log.error(e.getLocalizedMessage(), e.getCause());
import com.datastax.driver.core.Session;
import com.datastax.driver.core.ResultSet;
-import compbio.cassandra.Pair;
+import compbio.engine.Pair;
public class CassandraReaderExecutionTime {
private Session session;
session = s;
}
- private void setConditions() {
-
- }
-
public boolean JobisNotInsterted(String jobid) {
ResultSet results1 = session.execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
if (results1.isExhausted()) {
import compbio.beans.ExecutionTimeBean;
import compbio.beans.TotalExecutionTime;
import compbio.cassandra.DateFormatter;
-import compbio.cassandra.Pair;
+import compbio.engine.Pair;
public class ExecutionTimeReader extends CassandraReader {
ResultSet results = CassandraQuery("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
if (results.isExhausted())
return null;
- Row row = results.one();
+ Row row1 = results.one();
ResultSet results1 = CassandraQuery("SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;");
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), row.getString("ProgramName"),
- row.getString("ProgramVersion"));
+ Row row2 = results1.one();
+ String program = row1.getString("ProgramName");
+ String version = row1.getString("ProgramVersion");
+ JobBean res = new JobBean(row1.getString("Protein"), row1.getString("JobID"), row1.getString("DataBegin"),
+ row1.getString("DataEnd"), row1.getString("ip"), row2.getMap("Predictions", String.class, String.class));
+
+ if (null != program && null != version) {
+ res.setProgramName(program);
+ res.setProgramVersion(version);
+ ResultSet results3 = CassandraQuery("SELECT * FROM Programs WHERE Program = '" + program + "' and Version = '" + version
+ + "' ALLOW FILTERING;");
+ if (results3.isExhausted())
+ return null;
+ Row row3 = results3.one();
+ String link = row3.getString("weblink");
+ if (null != link) {
+ res.setProgramLink(link);
+ }
+ }
+
return res;
}
}
import compbio.beans.ProteinBean;
+/**
+ * Reader class for making requests on protein sequences to cassandra.
+ *
+ * @author Alexander Sherstnev
+ * @author Natasha Sherstneva
+ *
+ * @since 0.5
+ * @version 1.0
+ * @since December 2013
+ */
public class SequenceReader extends CassandraReader {
public SequenceReader() {
/**
* query: protein sequence
*
- * @param protIn
+ * @param sequence
* protein sequence or partial of protein sequence
* @param searchtype
* "whole" or "partial" of protein sequence
* @return List<ProteinBean> to the controller SequenceController
*
**/
- public List<ProteinBean> readProteins(String protIn, String searchtype) {
+ public List<ProteinBean> readProteins(String sequence, String searchtype) {
List<ProteinBean> query = new ArrayList<ProteinBean>();
if (searchtype.equals("whole")) {
- ResultSet results = CassandraQuery("SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + protIn + "';");
+ ResultSet results = CassandraQuery("SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + sequence + "';");
if (results.isExhausted())
return null;
List<Row> rows = results.all();
- ProteinBean structure = new ProteinBean(protIn, rows.get(0).getMap("Predictions", String.class, String.class));
+ ProteinBean structure = new ProteinBean(sequence, rows.get(0).getMap("Predictions", String.class, String.class));
for (Row r : rows) {
structure.setJobid(r.getString("JobID"));
}
query.add(structure);
} else {
- ResultSet results = CassandraQuery("SELECT * FROM ProteinRow;");
+ ResultSet results = CassandraQuery("SELECT * FROM ProteinRow;");
if (results.isExhausted())
return null;
List<Row> rows = results.all();
for (Row r : rows) {
- String prot = r.getString("Protein");
- if (prot.matches("(.*)" + protIn + "(.*)")) {
- ProteinBean structure = new ProteinBean(prot, r.getMap("Predictions", String.class, String.class));
- structure.setJobid(r.getString("JobID"));
- query.add(structure);
+ String protein = r.getString("Protein");
+ if (protein.matches("(.*)" + sequence + "(.*)")) {
+ ProteinBean foundsequence = new ProteinBean(protein, r.getMap("Predictions", String.class, String.class));
+ foundsequence.setJobid(r.getString("JobID"));
+ query.add(foundsequence);
}
}
}
if (searchtype.equals("partial")) {
for (ProteinBean entry : query) {
- entry.setSubProt(CreateSubprotein(entry.getSequence(), protIn));
+ entry.setSubProt(CreateSubprotein(entry.getSequence(), sequence));
}
}
return query;
package compbio.engine;
-import compbio.cassandra.Pair;
/**
public JpredJob(String jobid, String date1, String date2) {
super(jobid, date1, date2);
- this.protein = protein;
predictions = new ArrayList<FastaSequence>();
alignment = new ArrayList<FastaSequence>();
log = "";
public JpredJob(String jobid, String date1, String date2, List<FastaSequence> alignment, List<FastaSequence> predictions) {
super(jobid, date1, date2);
- this.protein = protein;
this.alignment = alignment;
this.predictions = predictions;
}
-package compbio.cassandra;
+package compbio.engine;
public class Pair<K, V> {
import compbio.cassandra.readers.CassandraReader;
/**
- *
+ * ProteoCache Basic controller. All other controllers should inherit this
+ * controller. Currently BasicController provides user role checks and some
+ * global dates for the system (current and the earliest date of executing job)
*
* @author Alexander Sherstnev
* @version 1.0
public class BasicController {
final protected SimpleDateFormat formaterDDMMYY = DateFormatter.getFormatDDMMYY();
final protected SimpleDateFormat formaterYYMMDD = DateFormatter.getFormatYYMMDD();
- protected Calendar cal = Calendar.getInstance();
- protected String theEaerlistDate = DateFormatter.DateLongToString(CassandraReader.earliestDate(), formaterYYMMDD);
- protected String theCurrentDate = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
+ /**
+ * give the user (principal) name
+ *
+ * @return the user name. If the user uses LDAP credentials LDAP prefix is
+ * set
+ */
protected String getPrincipalName() {
Object principal = SecurityContextHolder.getContext().getAuthentication().getPrincipal();
if (principal instanceof UserDetails) {
return principal.toString();
}
+ /**
+ * check whether the current user has standard user permissions (ROLE_USER
+ * or ROLE_LDAP_USER)
+ *
+ * @return true if this is a ROLE_USER/ROLE_LDAP_USER user, false otherwise
+ */
protected boolean isUserRole() {
Object principal = SecurityContextHolder.getContext().getAuthentication().getPrincipal();
if (principal instanceof UserDetails) {
return false;
}
+ /**
+ * check whether the current user has administrator permissions (ROLE_ADMIN)
+ *
+ * @return true if this is a ROLE_ADMIN user, false otherwise
+ */
protected boolean isAdminRole() {
Object principal = SecurityContextHolder.getContext().getAuthentication().getPrincipal();
if (principal instanceof UserDetails) {
return false;
}
- protected String DateChecking(String trimmeddate1, String trimmeddate2, long longDate1, long longDate2) {
+ /**
+ * check whether provided dates are ordered properly and within permitted
+ * time range
+ *
+ * @param date1
+ * early limit of the time range)
+ *
+ * * @param date2 late limit of the time range)
+ *
+ * * @param longDate1 date 1 in the numerical represenation (in
+ * milliseconds)
+ *
+ * * @param longDate2 date 2 in the numerical represenation (in
+ * milliseconds)
+ *
+ * @return true if these dates are correct, false otherwise
+ */
+ protected String checkDates(String date1, String date2, long longDate1, long longDate2) {
Calendar cal2 = Calendar.getInstance();
- if (trimmeddate1.equalsIgnoreCase("") || trimmeddate2.equalsIgnoreCase(""))
- return "The date cann't be empty";
- else if (!DateFormatter.isThisDateValid(trimmeddate1, formaterYYMMDD)
- || !DateFormatter.isThisDateValid(trimmeddate2, formaterYYMMDD))
- return "The date format in invalid. Try format yyyy/mm/dd";
+ if (date1.equalsIgnoreCase("") || date2.equalsIgnoreCase(""))
+ return "The date can not be empty strinfs";
+ else if (!DateFormatter.isThisDateValid(date1, formaterYYMMDD) || !DateFormatter.isThisDateValid(date2, formaterYYMMDD))
+ return "The date format in invalid. The format yyyy/mm/dd should be used";
else if (longDate2 < CassandraReader.earliestDate())
- return "The date2 is after the earlestDate " + theEaerlistDate;
+ return "The date2 is earlier than the earliest date in the system " + getEarliestDate();
else if (longDate1 > cal2.getTimeInMillis())
- return "The date1 is before the current date " + theCurrentDate;
+ return "The date1 is later than the current date " + getCurrentDate();
else if (longDate1 > longDate2)
- return "Wrong date's diaposon. The date1 is more than date2.";
- else
- return null;
+ return "Wrong date range. The date1 is later than date2.";
+
+ return null;
+ }
+
+ /**
+ * gives the current date in the form of string (yyyy/mm/dd)
+ *
+ * @return the current date
+ */
+ protected String getCurrentDate() {
+ Calendar cal = Calendar.getInstance();
+ String date = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
+ return date;
+ }
+
+ /**
+ * gives the earliest date in the system (through a direct call of a
+ * Cassandra related class) in the form of string (yyyy/mm/dd)
+ *
+ * @return the current date
+ */
+ protected String getEarliestDate() {
+ return DateFormatter.DateLongToString(CassandraReader.earliestDate(), formaterYYMMDD);
}
}
import compbio.cassandra.readers.DailyStatisticsReader;
/**
+ * MVC controller for collecting and showing job statistics
+ *
* @author Alexander Sherstnev
* @author Natasha Sherstneva
- * @version 1.0 Dec 2013
+ *
+ * @version 1.0
+ * @since Dec 2013
*/
@Controller
public class DailyStatisticsController extends BasicController {
final long startTime = System.currentTimeMillis();
DailyStatisticsReader reader = new DailyStatisticsReader();
if (option.equals("AllDates,off")) {
- date1 = theEaerlistDate;
- date2 = theCurrentDate;
+ date1 = getEarliestDate();
+ date2 = getCurrentDate();
}
// dates in string format
// dates in long format
long longDate1 = DateFormatter.DateParsing(date1, formaterYYMMDD);
long longDate2 = DateFormatter.DateParsing(date2, formaterYYMMDD);
- String error = DateChecking(trimmeddate1, trimmeddate2, longDate1, longDate2);
+ String error = checkDates(trimmeddate1, trimmeddate2, longDate1, longDate2);
if (error != null) {
model.put("error", error);
model.put("date1", date1);
thetime = formaterDDMMYY.parse(realdate).getTime();
}
- if (null == JobStatus.getJobStatus(status))
+ if (null == JobStatus.getJobStatus(status))
return "support/Notimplemented";
-
DailyStatisticsReader reader = new DailyStatisticsReader();
// IMPORTANT: input should be suppied in the format: DD/MM/YYYY
DateBean r = reader.readJobByDay(thetime, realdate, JobStatus.getJobStatus(status));
import compbio.cassandra.DateFormatter;
/**
+ * MVC controller for direct interaction with the internal DB
+ *
* @author Alexander Sherstnev
* @author Natasha Sherstneva
+ *
+ * @version 1.0
+ * @since Nov 2013
*/
@Controller
public class DatabaseController extends BasicController {
model.put("seq", sequence);
CassandraRemover cr = new CassandraRemover();
- int njobs = 0;
+ int njobs1 = 0;
+ int njobs2 = 0;
+ int njobs3 = 0;
+ int njobs4 = 0;
if (byId.equals("on,off"))
- njobs = cr.RemoveJobById(jobid);
+ njobs1 = cr.RemoveJobById(jobid);
if (byDate.equals("on,off")) {
long longDate1 = DateFormatter.DateParsing(date1, formaterYYMMDD) / 1000;
long longDate2 = DateFormatter.DateParsing(date2, formaterYYMMDD) / 1000;
int timerange = (int)(longDate2 - longDate1) /24 / 3600 + 1;
model.put("ndays", timerange);
- njobs = cr.RemoveJobByDate(date1, date2);
+ njobs2 = cr.RemoveJobByDate(date1, date2);
}
if (byIp.equals("on,off"))
- njobs = cr.RemoveJobByIp(ip);
+ njobs3 = cr.RemoveJobByIp(ip);
if (bySequence.equals("on,off"))
- njobs = cr.RemoveJobBySequence(sequence);
- model.put("njobs", njobs);
+ njobs4 = cr.RemoveJobBySequence(sequence);
+ model.put("njobs", njobs1 + njobs2 + njobs3 + njobs4);
+ model.put("njobsbyDate", njobs2);
+ model.put("njobsbyIP", njobs3);
+ model.put("njobsbySeq", njobs4);
return "reports/RemoveJobs";
}
import java.net.HttpURLConnection;
import java.net.URL;
import java.text.ParseException;
-import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.Date;
-import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
import compbio.beans.DateBean;
import compbio.beans.ExecutionTimeBean;
-import compbio.beans.Total;
+import compbio.beans.JobBean;
import compbio.beans.TotalExecutionTime;
-import compbio.beans.TotalJobsStatisticBean;
-import compbio.cassandra.DataBase;
import compbio.cassandra.DateFormatter;
import compbio.cassandra.readers.CassandraReader;
-import compbio.cassandra.readers.DailyStatisticsReader;
import compbio.cassandra.readers.ExecutionTimeReader;
import compbio.cassandra.readers.JobReader;
import compbio.engine.ExecutionInterval;
-import compbio.engine.JobStatus;
import compbio.engine.archive.ArchivedJob;
/**
+ * Spring controller for supporting job queries. This version works in the
+ * servlet style.
+ *
* @author Alexander Sherstnev
* @author Natasha Sherstneva
- * @version 1.0 Dec 2013
+ * @version 1.0
+ * @since Dec 2013
*/
@Controller
public class JobController extends BasicController {
/**
* form a report page for a job execution time statistics.
*
+ * @param date1
+ * initial date for requested statistics
+ * @param date2
+ * final date for requested statistics
+ * @param alldates
+ * All available jobs are analyzed if alldates="AllDates,off"
* @param model
* MVC model
* @return link to the JSP query page
*/
@RequestMapping(value = "/stat/exectime/results", method = RequestMethod.GET)
public String findExecTimeData(@RequestParam("date1") String date1, @RequestParam("date2") String date2,
- @RequestParam(value = "option", required = false) String option, Map<String, Object> model) {
+ @RequestParam(value = "option", required = false) String alldates, Map<String, Object> model) {
model.put("username", getPrincipalName());
final long startTime = System.currentTimeMillis();
Calendar loccal = Calendar.getInstance();
ExecutionTimeReader reader = new ExecutionTimeReader();
- if (option.equals("AllDates,off")) {
- date1 = theEaerlistDate;
- date2 = theCurrentDate;
+ if (alldates.equals("AllDates,off")) {
+ date1 = getEarliestDate();
+ date2 = getCurrentDate();
}
-
+
// dates in string format
String trimmeddate1 = date1.replaceAll("\\s", "");
String trimmeddate2 = date2.replaceAll("\\s", "");
// dates in long format
long longDate1 = DateFormatter.DateParsing(date1, formaterYYMMDD);
long longDate2 = DateFormatter.DateParsing(date2, formaterYYMMDD);
- String error = DateChecking(trimmeddate1, trimmeddate2, longDate1, longDate2);
+ String error = checkDates(trimmeddate1, trimmeddate2, longDate1, longDate2);
if (error != null) {
model.put("error", error);
model.put("date1", date1);
model.put("date2", date2);
return "query/JobTimeExecution";
}
-
+
if (longDate1 < CassandraReader.earliestDate())
longDate1 = CassandraReader.earliestDate();
if (longDate2 > loccal.getTimeInMillis())
date2 = DateFormatter.DateLongToString(longDate2, formaterYYMMDD);
model.put("date1", date1);
model.put("date2", date2);
- model.put("option", option);
- ExecutionTimeBean res = reader.query(longDate1, longDate2);;
+ model.put("option", alldates);
+ ExecutionTimeBean res = reader.query(longDate1, longDate2);
+ ;
model.put("result", res);
Map<String, TotalExecutionTime> results = res.getDateTotal();
- String csvline = "";
+ StringBuilder csvline = new StringBuilder("");
if (0 < res.getDateTotal().size()) {
- csvline = "\'Date\',\'Total\',\'0-30 sec\',\'30-60 sec\',\'1-2 min\',\'2-10 min\',\'more 10 min\'%0A";
+ csvline.append("\'Date\',\'Total\',\'0-30 sec\',\'30-60 sec\',\'1-2 min\',\'2-10 min\',\'more 10 min\'%0A");
for (Map.Entry<String, TotalExecutionTime> entry : results.entrySet()) {
- csvline += "\'" + entry.getKey() + "\',\'" + entry.getValue().getTotal() + "\',\'" + entry.getValue().getTotal0_30s() + "\',\'"
- + entry.getValue().getTotal30_60s() + "\',\'" + entry.getValue().getTotal1_2m() + "\',\'"
- + entry.getValue().getTotal2_10m() + "\',\'" + entry.getValue().getTotal10m() + "\'%0A";
+ csvline.append("\'" + entry.getKey() + "\',\'" + entry.getValue().getTotal() + "\',\'" + entry.getValue().getTotal0_30s()
+ + "\',\'" + entry.getValue().getTotal30_60s() + "\',\'" + entry.getValue().getTotal1_2m() + "\',\'"
+ + entry.getValue().getTotal2_10m() + "\',\'" + entry.getValue().getTotal10m() + "\'%0A");
}
}
- model.put("csvfile", csvline);
+ model.put("csvfile", csvline.toString());
model.put("ndays", res.getDateTotal().size() - 1);
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
if (null == ExecutionInterval.getExecutionInterval(interval))
return "support/Notimplemented";
-
ExecutionTimeReader reader = new ExecutionTimeReader();
// IMPORTANT: input should be suppied in the format: DD/MM/YYYY
DateBean r = reader.readJobByDay(thetime, realdate, ExecutionInterval.getBoundsInterval(interval));
}
/**
- * form a query page for a job. The servlet should no be visible to users at
- * all.
+ * form result page for one job with a given job ID.
*
+ * @param jobid
+ * job ID
* @param model
* MVC model
+ *
* @return link to the JSP query page
* @throws IOException
*/
model.put("username", getPrincipalName());
final long startTime = System.currentTimeMillis();
JobReader reader = new JobReader();
- model.put("result", reader.readJobLog(jobid));
+ JobBean job = reader.readJobLog(jobid);
+ if (null == job) {
+ model.put("jobnotfound", "yes");
+ } else {
+ model.put("result", job);
+ }
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
model.put("IdJob", jobid);
+ // prepare archive file for the job for downloading
ArchivedJob aj = new ArchivedJob(jobid);
try {
model.put("jobarchive", aj.prepareJobArchiveToWeb());
log.error("JobController.prepareJobArchiveToWeb: IO exception with job archive file");
log.error(e.getLocalizedMessage(), e.getCause());
}
+
// add a direct link to the job
String remotelink = "http://www.compbio.dundee.ac.uk/www-jpred/results/" + jobid + "/" + jobid + ".results.html";
URL remotelinkurl = new URL(remotelink);
return "reports/Job";
}
- /**
- * convert date from the standard long representation (milliseconds from 1
- * Jan 1970) to yyyy/mm/dd
- *
- * @param indate
- * date in milliseconds from 1 Jan 1970
- * @return date in the form of yyyy/mm/dd
- */
- private String DateFormatYYMMDD(long indate) {
- SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd");
- String dateString = datformat.format(new Date(indate));
- return dateString;
- }
-
}
package compbio.controllers;
+import java.util.Calendar;
+
import org.springframework.stereotype.Controller;
import org.springframework.ui.ModelMap;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
+import compbio.beans.Total;
+import compbio.beans.TotalJobsStatisticBean;
+import compbio.cassandra.DateFormatter;
+import compbio.cassandra.readers.DailyStatisticsReader;
+
+/**
+ * The main system controller with most general functionality (home page, login
+ * and logout pages)
+ *
+ * @author Alexander Sherstnev
+ * @author Natasha Sherstneva
+ *
+ * @version 1.0
+ * @since Dec 2013
+ */
@Controller
public class MainController extends BasicController {
+ /**
+ * Form the project home page
+ *
+ * @param model
+ * MVC model object
+ *
+ * @return JSP template for the page
+ */
@RequestMapping(value = "/index", method = RequestMethod.GET)
public String printPublicHome(ModelMap model) {
model.addAttribute("username", getPrincipalName());
+ model = getStatistics(model);
if (isUserRole())
return "home";
return "public";
}
+ /**
+ * Form login page
+ *
+ * @param model
+ * MVC model object
+ *
+ * @return JSP template for the page
+ */
@RequestMapping(value = "/login", method = RequestMethod.GET)
public String login(ModelMap model) {
return "login";
}
+ /**
+ * Form a page with failed login
+ *
+ * @param model
+ * MVC model object
+ *
+ * @return JSP template for the page
+ */
@RequestMapping(value = "/loginfailed", method = RequestMethod.GET)
public String loginerror(ModelMap model) {
model.addAttribute("error", "Wrong user name or password");
return "login";
}
+ /**
+ * Form a page after log out
+ *
+ * @param model
+ * MVC model object
+ *
+ * @return JSP template for the page
+ */
@RequestMapping(value = "/logout", method = RequestMethod.GET)
public String logout(ModelMap model) {
+ model = getStatistics(model);
return "public";
}
+ /**
+ * Form a page with denial of service
+ *
+ * @param model
+ * MVC model object
+ *
+ * @return JSP template for the page
+ */
@RequestMapping(value = "/denied", method = RequestMethod.GET)
public String denied(ModelMap model) {
model.put("username", getPrincipalName());
return "support/Denied";
}
+ /**
+ * Form the project home page
+ *
+ * @param model
+ * MVC model object
+ *
+ * @return JSP template for the page
+ */
@RequestMapping(value = "/home", method = RequestMethod.GET)
public String printHome(ModelMap model) {
model.addAttribute("username", getPrincipalName());
+ model = getStatistics(model);
return "home";
}
+ /**
+ * collect job execution statiustics for the last 7 days.
+ *
+ * @param model
+ * MVC model object
+ *
+ * @return the the same model, but with additional parameters with the job
+ * statistics
+ */
+ private ModelMap getStatistics(ModelMap model) {
+ int ndays = 7;
+ model.addAttribute("ndays", ndays);
+
+ Calendar cal = Calendar.getInstance();
+ String date2 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
+ long longDate2 = DateFormatter.DateParsing(date2, formaterYYMMDD);
+ cal.add(Calendar.DATE, -ndays);
+ String date1 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
+ long longDate1 = DateFormatter.DateParsing(date1, formaterYYMMDD);
+
+ DailyStatisticsReader reader = new DailyStatisticsReader();
+ TotalJobsStatisticBean res = reader.query(longDate1, longDate2);
+ Total total = res.getWholeTotal();
+ model.addAttribute("total", total.getTotal());
+ model.addAttribute("totalOK", total.getTotalOK());
+ model.addAttribute("totalTimeout", total.getTotalOK());
+ model.addAttribute("totalError", total.getTotalError());
+ model.addAttribute("totalStopped", total.getTotalStopped());
+ return model;
+ }
+
}
import compbio.cassandra.readers.FeaturesReader;
/**
- * Spring controller for sequence queries. This version works in the servlet
- * style.
+ * Spring controller for protein secondary structure features. This version
+ * works in the servlet style.
*
* @author Alexander Sherstnev
* @author Natasha Sherstneva
@RequestMapping("/features")
public class SSFeaturesController extends BasicController {
+ /**
+ * form a query page for protein secondary structure feaatures: Proteins
+ * with given fraction of H/E (helix/beta sheets)
+ *
+ * @param model
+ * MVC model object
+ *
+ * @return link to the report JSP page
+ */
@RequestMapping(value = "query", method = RequestMethod.GET)
public String formCounterQuery(Map<String, Object> model) {
model.put("username", getPrincipalName());
return "query/SSFeatures";
}
+ /**
+ * form a results page for protein secondary structure features: Proteins
+ * with given fraction of H/E (helix/beta sheets) All proteins with E/H
+ * higher than a given percent of the length are returned
+ *
+ * @param model
+ * MVC model object
+ * @param typeFeature
+ * type of SS: H/E (helix/beta sheets)
+ * @param percent
+ * fraction of the protein length predicted as H/E (helix/beta
+ * sheets)
+ *
+ * @return link to the report JSP page
+ */
@RequestMapping(value = "results", method = RequestMethod.GET)
public String countSequences(@RequestParam("TypeFeatures") String typeFeature, @RequestParam("Percent") String percent,
Map<String, Object> model) {
Map<String, String> r = reader.readProteinsPrediction(typeFeature, realpercent);
model.put("results", r);
model.put("njobs", 0);
- String csvline = "";
+ StringBuilder csvline = new StringBuilder("");
if (null != r) {
model.put("njobs", r.size());
- csvline = "\'Prediction%20number\',\'Protein%20Sequence\', \'Secondary%20Structure%20Prediction\'%0A";
- }
+ csvline.append("\'Prediction%20number\',\'Protein%20Sequence\', \'Secondary%20Structure%20Prediction\'%0A");
- // form line for CSV file
- int counter = 1;
- for (Map.Entry<String, String> entry : r.entrySet()) {
- csvline += "\'" + counter + "\',\'" + entry.getKey() + "\',\'" + entry.getValue() + "\'%0A";
- ++counter;
+ // form line for CSV file
+ int counter = 1;
+ for (Map.Entry<String, String> entry : r.entrySet()) {
+ csvline.append("\'" + counter + "\',\'" + entry.getKey() + "\',\'" + entry.getValue() + "\'%0A");
+ ++counter;
+ }
}
- model.put("csvfile", csvline);
+ model.put("csvfile", csvline.toString());
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
import compbio.cassandra.readers.SequenceReader;
/**
- * Spring controller for sequence queries. This version works in the servlet
- * style.
+ * Spring controller for supporting sequence queries. This version works in the
+ * servlet style.
*
* @author Alexander Sherstnev
* @author Natasha Sherstneva
* be searched
* @return link to the report JSP page
*/
- @RequestMapping(value = "sequence/results", method = RequestMethod.GET)
+ @RequestMapping(value = "results", method = RequestMethod.GET)
public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("searchtype") String searchtype,
Map<String, Object> model) {
model.put("username", getPrincipalName());
model.put("njobs", 0);
model.put("prot", trimmedsequence);
model.put("searchtype", searchtype);
- String csvline = "";
+ StringBuilder csvline = new StringBuilder("");
if (0 < trimmedsequence.length()) {
SequenceReader reader = new SequenceReader();
List<ProteinBean> result = reader.readProteins(trimmedsequence, searchtype);
model.put("results", result);
if (null != result) {
- if (searchtype.equals("whole"))
+ if (searchtype.equals("whole")) {
model.put("njobs", result.get(0).getJobid().size());
- else
+ } else {
model.put("njobs", result.size());
- csvline = "\'Job\',\'Annotation\',\'Sequence\'%0A";
- // form CSV file string
+ }
+ csvline.append("\'Job\',\'Annotation\',\'Sequence\'%0A");
for (ProteinBean entry : result) {
List<String> jobs = entry.getJobid();
String protein = entry.getSequence();
LinkedHashMap<String, String> predictions = entry.getPredictions();
+ StringBuilder jobline = new StringBuilder();
+ for (Map.Entry<String, String> pr : predictions.entrySet()) {
+ jobline.append("\'\',\'" + pr.getKey() + "\',\'" + pr.getValue() + "\'%0A");
+ }
for (String job : jobs) {
- csvline += "\'" + job + "\',\'Sequence\',\'" + protein + "\',\'%0A";
- for (Map.Entry<String, String> pr : predictions.entrySet()) {
- csvline += "\'\',\'" + pr.getKey() + "\',\'" + pr.getValue() + "\'%0A";
- }
+ csvline.append("\'" + job + "\',\'Sequence\',\'" + protein + "\',\'%0A" + jobline.toString());
}
}
}
+ } else {
+ model.put("error", "The sequence after trimming is empty");
+ model.put("value", sequence);
+ return "query/Sequence";
}
- model.put("csvfile", csvline);
+ model.put("csvfile", csvline.toString());
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
List<TotalByCounterBean> r = reader.readProteinByCounter(realcounter);
model.put("results", r);
model.put("njobs", 0);
- String csvline = "";
+ StringBuilder csvline = new StringBuilder("");
if (null != r) {
model.put("njobs", r.size());
- csvline = "\'Job%20 count\', \'Protein%20Sequence\'%0A";
- }
- // form line for CSV file
-
- for (TotalByCounterBean b : r) {
- if (b.getName().equals("")) {
- csvline += "\'" + b.getTotaljobs() + "\',\'Alignment%20job\'%0A";
- // fix problem with records without protein sequence (alignment
- // jobs)
- b.setName("Alignment job");
- } else {
- csvline += "\'" + b.getTotaljobs() + "\',\'" + b.getName() + "\'%0A";
+ // form line for CSV file
+ csvline.append("\'Job%20 count\', \'Protein%20Sequence\'%0A");
+ for (TotalByCounterBean b : r) {
+ if (b.getName().equals("")) {
+ // fix problem with records without protein sequence
+ // (alignment jobs)
+ csvline.append("\'" + b.getTotaljobs() + "\',\'Alignment%20job\'%0A");
+ b.setName("Alignment job");
+ } else {
+ csvline.append("\'" + b.getTotaljobs() + "\',\'" + b.getName() + "\'%0A");
+ }
}
}
- model.put("csvfile", csvline);
+ model.put("csvfile", csvline.toString());
model.put("results", r);
final long endTime = System.currentTimeMillis();
if (READ_WEB_JPRED) {
// get data from real Jpred production server
- final String datasrc = "http://www.compbio.dundee.ac.uk/www-jpred/results/usage-new/alljobs.dat";
- final String prefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
+ String theprefix = ph.getProperty("cassandra.jpred.web.prefix");
+ if (null == theprefix) {
+ theprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
+ }
+
+ final String datasrc = theprefix + "/usage-new/alljobs.dat";
+ final String prefix = theprefix;
final JpredParserHTTP parser = new JpredParserHTTP(prefix);
int initialdelay = 300;
<div class="panel panel-default">
<div class="panel-heading">Execution statistics for the last days</div>
<div class="panel-body">
- Statistics plot
+ <p style="font-weight:bold;">${total} jobs have been calculated with Jped over the last ${ndays} days:</p>
+ <ul>
+ <li>${totalOK} jobs have been done without problems (status: OK)</li>
+ <li>${totalStopped} jobs have been stopped (status: Stopped)</li>
+ <li>${totalTimeout} jobs haven't had enough time to complete (status: Time Out)</li>
+ <li>${totalError} jobs have been failed (status: Internal Error)</li>
+ </ul>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">Overview</div>
<div class="panel-body">
- ProteoCache is as a repository of the result of running all tools in the Dundee Resource on
- complete proteomes. The data are updated on a regular basis as tools are improved and genomes newly
- sequenced or updated.
+ ProteoCache is as a repository and a caching system for Jpred and other tools of the Dundee Resource.
+ ProteoCache deals with both single proteins and complete proteomes. The internal data are updated
+ on a regular basis as the tools are improved and proteomes are published and updated.
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">Execution statistics for the last days</div>
<div class="panel-body">
- bla-bla
+ <p style="font-weight:bold;">${total} jobs have been calculated with Jped over the last ${ndays} days:</p>
+ <ul>
+ <li>${totalOK} jobs have been done without problems (status: OK)</li>
+ <li>${totalStopped} jobs have been stopped (status: Stopped)</li>
+ <li>${totalTimeout} jobs haven't had enough time to complete (status: Time Out)</li>
+ <li>${totalError} jobs have been failed (status: Internal Error)</li>
+ </ul>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">Overview</div>
<div class="panel-body">
- ProteoCache is as a repository of the result of running all tools in the Dundee Resource on
- complete proteomes. The data are updated on a regular basis as tools are improved and genomes newly
- sequenced or updated.
+ ProteoCache is as a repository and a caching system for Jpred and other tools of the Dundee Resource.
+ ProteoCache deals with both single proteins and complete proteomes. The internal data are updated
+ on a regular basis as the tools are improved and proteomes are published and updated.
</div>
</div>
</div>
<body>
<div class="container">
<jsp:include page="../fragments/mainmenu.jsp" />
- <spring:url value="/sequence/sequence/results" var="query"/>
+ <spring:url value="/sequence/results" var="query"/>
<div class="panel panel-default">
<div class="panel-heading">
<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
-<%@page import="java.util.ArrayList"%>
+<%@ taglib prefix="sec" uri="http://www.springframework.org/security/tags"%>
<html>
<jsp:include page="../fragments/header.jsp" />
<p style="font-weight:bold;">IP Statistics</p>
</div>
<div class="panel-body">
-
+<sec:authorize access="hasRole('ROLE_ADMIN')">
+ <p>Servlet execution time: ${timeExecution} milliseconds</p>
+</sec:authorize>
<c:choose>
<c:when test="${njobs == 0}">
<p>No IP with at least ${counter} jobs ever launched found</p>
</c:when>
<c:otherwise>
- <p>${njobs} IP with at least ${counter} jobs ever launched</p>
+ <p>${njobs} IPs with at least ${counter} jobs ever launched</p>
<div class="table-responsive">
<table class="table table-striped table-hover table-bordered" id="counts">
<thead>
<body>
<div class="container">
<jsp:include page="../fragments/mainmenu.jsp" />
- <spring:url value="/sequence/sequence/results" var="sequence_query" />
+ <spring:url value="/sequence/results" var="sequence_query" />
<spring:url value="/admin/ip/results" var="ip_query" />
+ <spring:url value="/job/results?IdJob=${IdJob}" var="the_query" />
+ <spring:url value="/database/remove/go?byId=on&id=${IdJob}&byId=off&date1=&date2=&byDate=off&ip=&byIp=off&seq=&bySequence=off" var="remove_query" />
+
+ <!-- reload and CSV buttons -->
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="${the_query}" class="btn btn-default active">Reload</a>
+ </li>
+<sec:authorize access="hasRole('ROLE_ADMIN')">
+ <li>
+ <a href="${remove_query}" class="btn btn-default active">Delete</a>
+ </li>
+</sec:authorize>
+ </ul>
<div class="panel panel-default">
<div class="panel-heading">
<p style="font-weight:bold;">Information for the job ${IdJob}</p>
</div>
<div class="panel-body">
+ <c:choose><c:when test="${jobnotfound == 'yes'}">
+ <p>The job not found</p>
+ </c:when><c:otherwise>
<p>Start timestamp : ${result.dateStart}</p>
<p>End timestamp : ${result.dateEnd}</p>
- <c:if test='${jobarchive != null}'>
- <p>Program name : ${result.programName}</p>
- <p>Program version : ${result.programVersion}</p>
+ <c:if test='${result.programName != null}'>
+ <c:choose>
+ <c:when test="${result.programLink != ''}">
+ <p style="font-weight:bold;">
+ Program: <a href="${result.programLink}">${result.programName}</a> (version : ${result.programVersion})
+ </p>
+ </c:when>
+ <c:otherwise>
+ <p style="font-weight:bold;">Program : ${result.programName} (version : ${result.programVersion})</p>
+ </c:otherwise>
+ </c:choose>
</c:if>
<sec:authorize access="hasRole('ROLE_ADMIN')">
<p>IP: <a title="Click to view other jobs" href="${ip_query}?ip=${result.ip}">${result.ip}</a></p>
</tbody>
</table>
</div>
+ </c:otherwise></c:choose>
</div>
</div>
<jsp:include page="../fragments/footer.jsp" />
</div>
</body>
-</html>
\ No newline at end of file
+</html>
<jsp:include page="../fragments/mainmenu.jsp" />
<spring:url value="/job/results" var="job_query" />
<spring:url value="/stat/jobsoneday/results?date=${date}&status=${status}" var="the_query" />
- <spring:url value="/sequence/sequence/results" var="sequence_query" />
+ <spring:url value="/sequence/results" var="sequence_query" />
<ul class="nav navbar-nav navbar-right">
<li>
<jsp:include page="../fragments/footer.jsp" />
</div>
</body>
-</html>
\ No newline at end of file
+</html>
<body>
<div class="container">
<jsp:include page="../fragments/mainmenu.jsp" />
- <spring:url value="/sequence/sequence/results" var="sequence_query" />
+ <spring:url value="/sequence/results" var="sequence_query" />
<spring:url value="/admin/ip/results" var="ip_query" />
<div class="panel panel-default">
- <div class="panel-heading">
- <p style="font-weight:bold;">Information for removed jobs</p>
- </div>
- <div class="panel-body">
- <!-- <div class="grid-wrapper-div">-->
- <c:if test="${byDate != 'off'}">
- <p>${njobs} jobs have been removed for time period: <c:out value="${date1}" /> to <c:out value="${date2}"/> (${ndays} days)</p>
- </c:if>
- <c:if test="${byId != 'off'}">
- <p>Job ${id} has been removed.</p>
- </c:if>
- <c:if test="${byIp != 'off'}">
- <p>Jobs launched from ${ip} have been removed. ${njobs} jobs have been removed.</p>
- </c:if>
- <c:if test="${bySequence != 'off'}">
- <p>Jobs launched with sequence ${seq} have been removed. ${njobs} jobs have been removed.</p>
- </c:if>
- <!-- </div>-->
- </div>
+ <div class="panel-heading">
+ <p style="font-weight:bold;">Information on removed jobs</p>
+ </div>
+ <div class="panel-body">
+ <c:choose>
+ <c:when test="${njobs > 0}">
+ <c:if test="${byDate != 'off'}">
+ <p>${njobsbyDate} jobs have been removed for the time period: ${date1} to ${date2} (${ndays} days)</p>
+ </c:if>
+ <c:if test="${byId != 'off'}">
+ <p>Job ${id} has been removed.</p>
+ </c:if>
+ <c:if test="${byIp != 'off'}">
+ <p>Jobs launched from ${ip} have been removed. ${njobsbyIp} jobs have been removed.</p>
+ </c:if>
+ <c:if test="${bySequence != 'off'}">
+ <p>Jobs launched with sequence ${seq} have been removed. ${njobsbySeq} jobs have been removed.</p>
+ </c:if>
+ </c:when>
+ <c:otherwise>
+ <p>No jobs has been removed.</p>
+ </c:otherwise>
+ </c:choose>
+ </div>
</div>
<jsp:include page="../fragments/footer.jsp" />
</div>
</body>
-</html>
\ No newline at end of file
+</html>
<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
-<%@page import="java.util.ArrayList"%>
+<%@ taglib prefix="sec" uri="http://www.springframework.org/security/tags"%>
<html>
<jsp:include page="../fragments/header.jsp" />
<body>
<div class="container">
<jsp:include page="../fragments/mainmenu.jsp" />
- <spring:url value="/sequence/sequence/results" var="sequence_query" />
+ <spring:url value="/sequence/results" var="sequence_query" />
<spring:url value="/features/results" var="the_query"/>
<spring:url value="/features/results?TypeFeatures=${feature}&Percent=${percent}" var="the_query" />
</div>
<div class="panel-body">
+<sec:authorize access="hasRole('ROLE_ADMIN')">
+ <p>Servlet execution time: ${timeExecution} milliseconds</p>
+</sec:authorize>
<c:choose>
<c:when test="${njobs == 0}">
<p>No proteins with feature ${feature} more then ${percent}% of the protein sequence found</p>
<jsp:include page="../fragments/footer.jsp" />
</div>
</body>
-</html>
\ No newline at end of file
+</html>
<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
-<%@page import="java.util.ArrayList"%>
+<%@ taglib prefix="sec" uri="http://www.springframework.org/security/tags"%>
<html>
<jsp:include page="../fragments/header.jsp" />
<div class="container">
<jsp:include page="../fragments/mainmenu.jsp" />
<spring:url value="/job/results" var="job_query" />
- <spring:url value="/sequence/sequence/results?sequence=${prot}&searchtype=${searchtype}" var="the_query"/>
+ <spring:url value="/sequence/results?sequence=${prot}&searchtype=${searchtype}" var="the_query"/>
<c:set var="shortensequencelength" value="108"/>
<!-- reload and CSV buttons -->
</div>
<div class="panel-body">
+<sec:authorize access="hasRole('ROLE_ADMIN')">
+ <p>Servlet execution time: ${timeExecution} milliseconds</p>
+</sec:authorize>
<c:choose>
<c:when test="${njobs == 0}">
<p>No jobs found</p>
<c:forEach items="${results}" var="res" varStatus="status">
<c:forEach items="${res.jobid}" var="id" varStatus="status">
<tr>
- <th rowspan="${res.size + 2}"><a
+ <th rowspan="3"><a
title="Click to view the job log"
href="${job_query}?IdJob=${id}">${id}</a></th>
</tr>
<tr>
<td style="text-align: center; font-weight: bold; font-family: monospace">Sequence</td>
<c:if test="${searchtype == 'whole'}">
- <td
- style="text-align: left; border-buttom: dotted; font-family: monospace"><c:out
- value="${res.sequence}" /></td>
+ <td style="text-align: left; font-family: monospace">
+ ${res.sequence}</td>
</c:if>
<c:if test="${searchtype == 'partial'}">
- <td
- style="text-align: left; border-buttom: dotted; font-family: monospace">
+ <td style="text-align: left; border-buttom: dotted; font-family: monospace">
<c:forEach items="${res.subProt}" var="seq">
<c:choose>
- <c:when test="${fn:contains(seq, prot)}">
- <span style="background-color: blue">${seq}</span></c:when>
- <c:otherwise>${seq}</c:otherwise>
+ <c:when test="${fn:contains(seq, prot)}">
+ <span style="background-color: blue">${seq}</span></c:when>
+ <c:otherwise>${seq}</c:otherwise>
</c:choose>
</c:forEach>
</td>
</c:if>
</tr>
- <c:forEach items="${res.predictions}" var="seq"
- varStatus="status">
- <tr>
- <td
- style="text-align: center; font-weight: bold; font-family: monospace"><c:out
- value="${seq.key}" /></td>
- <td
- style="text-align: left; border-buttom: dotted; font-family: monospace"><c:out
- value="${seq.value}" /></td>
- </tr>
- </c:forEach>
+ <tr>
+ <td style="text-align: center; font-weight: bold; font-family: monospace">
+ Jnetpred
+ </td>
+ <td style="text-align: left; border-buttom: dotted; font-family: monospace">
+ ${res.jnetpred}
+ </td>
+ </tr>
</c:forEach>
</c:forEach>
</tbody>
<jsp:include page="../fragments/footer.jsp" />
</div>
</body>
-</html>
\ No newline at end of file
+</html>
<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
+<%@ taglib prefix="sec" uri="http://www.springframework.org/security/tags"%>
<html>
<jsp:include page="../fragments/header.jsp" />
<body>
<div class="container">
<jsp:include page="../fragments/mainmenu.jsp" />
- <spring:url value="/sequence/sequence/results" var="sequence_query" />
+ <spring:url value="/sequence/results" var="sequence_query" />
<spring:url value="/sequence/counts/results?counterJob=${counter}" var="the_query" />
<c:set var="shortensequencelength" value="108"/>
</div>
<div class="panel-body">
+<sec:authorize access="hasRole('ROLE_ADMIN')">
+ <p>Servlet execution time: ${timeExecution} milliseconds</p>
+</sec:authorize>
<c:choose>
<c:when test="${njobs == 0}">
<p>No proteins with at least ${counter} jobs found</p>
<jsp:include page="../fragments/footer.jsp" />
</div>
</body>
-</html>
\ No newline at end of file
+</html>
git://source.jalview.org / proteocache.git / commitdiff