Merge branch 'servlets'

[proteocache.git] / server / compbio / statistic / CassandraRequester.java

diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index b7f83a8..4bb1966 100755 (executable)
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -10,12 +10,14 @@ import java.util.List;
 import java.util.Map;
 
 import compbio.cassandra.CassandraNativeConnector;
+import compbio.cassandra.CassandraReader;
 import compbio.cassandra.DataBase;
 import compbio.cassandra.Pair;
+import compbio.cassandra.StructureJobLog;
 import compbio.cassandra.StructureProteinPrediction;
 
 public class CassandraRequester {
-       private CassandraNativeConnector DBInstance = new CassandraNativeConnector();
+       private CassandraReader db = new CassandraReader();
        private ArrayList<DataBase> query;
        private static long currentDate = 0;
        private static long earlestDate = 0;
@@ -53,7 +55,7 @@ public class CassandraRequester {
                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) {
@@ -139,14 +141,14 @@ public class CassandraRequester {
                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());
+                       Integer res = db.ReadDateTable(date.getTime());
                        if (res == null)
                                continue;
                        DataBase db = new DataBase();
                        db.setTotal(res);
                        db.setDate(DateFormat(date.getTime()));
                        query.add(db);
-               }                       
+               }
                System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
                return query;
        }
@@ -157,9 +159,9 @@ public class CassandraRequester {
                query = new ArrayList<DataBase>();
                List<StructureProteinPrediction> res;
                if (flag.equals("whole")) 
-                       res = DBInstance.ReadWholeSequence(protIn);
+                       res = db.ReadWholeSequence(protIn);
                 else 
-                       res = DBInstance.ReadPartOfSequence(protIn);
+                       res = db.ReadPartOfSequence(protIn);
                for (StructureProteinPrediction entry : res) {
                        Map<String,String> pred = entry.getPrediction();
                        Iterator it = pred.entrySet().iterator();
@@ -182,12 +184,32 @@ public class CassandraRequester {
         * */
        public List<DataBase> readProteinByCounter(int counter) {
                query = new ArrayList<DataBase>();
-       //      List<Pair<String, String>> res = DBInstance.ReadProteinDataByCounter(counter);
-               
+               Map<String, Integer> map = db.ReadProteinDataByCounter();
+               for (Map.Entry<String, Integer> entry : map.entrySet()) {
+                       if (entry.getValue() > counter) {
+                               DataBase db = new DataBase();
+                               db.setTotalId(entry.getValue());
+                               db.setProt(entry.getKey());
+                               query.add(db);
+                       }
+               }
                return query;
        }
        
-       
+       /*
+        * query jobs log info
+        */
+       public DataBase readJobLog(String jobid) {
+       //      query = new ArrayList<DataBase>();
+               StructureJobLog res = db.ReadJobLog(jobid);
+               DataBase query = new DataBase();
+               query.setLogInfo(res);
+       //      query.setres);
+               return query;
+       }
+       /*
+        * create list of parts of protein sequence;
+        */
        private static List<String> CreateSubprot (String protein, String subprot) {
                List<String> sub = new ArrayList<String>();
                String subStr = protein;
@@ -260,7 +282,7 @@ public class CassandraRequester {
         * find the earliest date in the database
         */
        public long earliestDate() {
-               earlestDate =  DBInstance.getEarliestDateInDB();
+               earlestDate = CassandraNativeConnector.getEarliestDateInDB();
                return earlestDate;
        }