import java.util.List;
import java.util.Map;
+import compbio.cassandra.AnnotatedProteinSequenceBean;
import compbio.cassandra.CassandraNativeConnector;
+import compbio.cassandra.CassandraReader;
import compbio.cassandra.DataBase;
import compbio.cassandra.Pair;
-import compbio.cassandra.StructureProteinPrediction;
+import compbio.cassandra.StructureJobLog;
public class CassandraRequester {
- private CassandraNativeConnector DBInstance = new CassandraNativeConnector();
+ private CassandraReader db = new CassandraReader();
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
if (null == date2) {
date1 = "2100/1/1";
}
- if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+ if (!isThisDateValid(date1,formatYYMMDD) || !isThisDateValid(date2,formatYYMMDD)) {
System.out.println("Wrong date: point 3");
return null;
}
SetDateRange();
int nbins = 5;
- long dateStart = DateParsing(date1);
- long dateEnd = DateParsing(date2);
+ long dateStart = DateParsing(date1, formatYYMMDD);
+ long dateEnd = DateParsing(date2, formatYYMMDD);
if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
return null;
if (dateStart < earlestDate)
List<Integer> totalTime = new ArrayList<Integer>();
for (int i = 0; i < nbins; i++)
totalTime.add(i, 0);
- List<Pair<String, String>> res = DBInstance.ReadProteinDataTable();
+ List<Pair<String, String>> res = db.ReadProteinDataTable();
List<Pair<Date, Long>> numres = new ArrayList<Pair<Date, Long>>();
for (Pair<String, String> entry : res) {
if (null == date2) {
date1 = "2100/1/1";
}
- if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+ if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
System.out.println("Wrong date: point 3");
return null;
}
SetDateRange();
- long dateStart = DateParsing(date1);
- long dateEnd = DateParsing(date2);
+ long dateStart = DateParsing(date1, formatYYMMDD);
+ long dateEnd = DateParsing(date2, formatYYMMDD);
if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
return null;
if (dateStart < earlestDate)
end.setTime(new Date(dateEnd));
query = new ArrayList<DataBase>();
for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
- Integer res = DBInstance.ReadDateTable(date.getTime());
+ List<Long> res = db.ReadDateTable(date.getTime());
if (res == null)
continue;
- DataBase db = new DataBase();
- db.setTotal(res);
- db.setDate(DateFormat(date.getTime()));
- query.add(db);
- }
+ DataBase bean = new DataBase();
+ bean.setTotal((int)(long)res.get(0));
+ bean.setTotalOK((int)(long)res.get(1));
+ bean.setTotalStopped((int)(long)res.get(2));
+ bean.setTotalError((int)(long)res.get(3));
+ bean.setTotalTimeOut((int)(long)res.get(4));
+ bean.setDate(DateFormat(date.getTime()));
+ query.add(bean);
+ }
System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
return query;
}
+
/*
* query: protein sequence
* */
public List<DataBase> readProteins(String protIn, String flag) {
+ if (protIn == null)
+ return null;
+ System.out.println(protIn.length());
query = new ArrayList<DataBase>();
- List<StructureProteinPrediction> res;
+ List<AnnotatedProteinSequenceBean> res;
if (flag.equals("whole"))
- res = DBInstance.ReadWholeSequence(protIn);
+ res = db.ReadWholeSequence(protIn);
else
- res = DBInstance.ReadPartOfSequence(protIn);
- for (StructureProteinPrediction entry : res) {
- Map<String,String> pred = entry.getPrediction();
- Iterator it = pred.entrySet().iterator();
- while (it.hasNext()) {
- DataBase db = new DataBase();
- db.setProt(entry.getSequence());
- Map.Entry pairs = (Map.Entry)it.next();
- db.setId(entry.getJobid());
- db.setJpred(pairs.getValue().toString());
- if (flag.equals("part"))
- db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
- query.add(db);
+ res = (protIn.length() > 0) ? db.ReadPartOfSequence(protIn) : null;
+ if (res == null)
+ return null;
+ for (AnnotatedProteinSequenceBean entry : res) {
+ DataBase db = new DataBase();
+ db.setProt(entry.getSequence());
+ db.setPredictions(entry);
+ db.setId(entry.getJobid());
+ if (flag.equals("part")) {
+ db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
}
+ query.add(db);
}
return query;
}
-
+
/*
- * query protein sequences with number of jobs
- * */
- public List<DataBase> readProteinByCounter(int counter) {
+ * query protein sequences with number of jobs
+ */
+ public List<DataBase> readProteinByCounter(int minimalcounter) {
query = new ArrayList<DataBase>();
- // List<Pair<String, String>> res = DBInstance.ReadProteinDataByCounter(counter);
-
+ Map<String, Integer> map = db.ReadProteinSequenceByCounter();
+ for (Map.Entry<String, Integer> entry : map.entrySet()) {
+ if (entry.getValue() > minimalcounter && entry.getKey().length() > 0) {
+ DataBase bean = new DataBase();
+ bean.setTotalId(entry.getValue());
+ bean.setProt(entry.getKey());
+ query.add(bean);
+ }
+ }
return query;
}
+ /*
+ * query jobs log info
+ */
+ public DataBase readJobLog(String jobid) {
+ if (jobid == null)
+ return null;
+ StructureJobLog res = db.ReadJobLog(jobid);
+ if (res == null)
+ return null;
+ DataBase query = new DataBase();
+ query.setLogInfo(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;
/*
* convert String date into long date (miliseconds since the epoch start)
*/
- private static long DateParsing(String datInput) {
+ private static long DateParsing(String datInput, SimpleDateFormat formatter) {
if (datInput == null) {
return 0;
}
long dateWorkSt = 0;
- SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
+
try {
dateWorkSt = formatter.parse(datInput).getTime();
} catch (ParseException e) {
*/
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));
+ 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) {
+ public boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) {
if (dateToValidate == null || dateToValidate.equals("")) {
System.out.println("Undefined date");
return false;
}
- SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd");
try {
// if not valid, this will throw ParseException
sdf.setLenient(false);
* find the earliest date in the database
*/
public long earliestDate() {
- earlestDate = DBInstance.getEarliestDateInDB();
+ earlestDate = CassandraNativeConnector.getEarliestDateInDB();
return earlestDate;
}
git://source.jalview.org / proteocache.git / blobdiff