Add Jpred archive table

diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java
index be90b05..7109c78 100644 (file)
--- a/datadb/compbio/cassandra/CassandraNativeConnector.java
+++ b/datadb/compbio/cassandra/CassandraNativeConnector.java
@@ -2,7 +2,6 @@ package compbio.cassandra;
 
 import java.io.IOException;
 import java.util.Calendar;
-import java.util.HashMap;
 import java.util.List;
 import java.util.ArrayList;
 
@@ -16,6 +15,7 @@ import com.datastax.driver.core.ResultSet;
 public class CassandraNativeConnector {
        private static Cluster cluster;
        private static Session session;
+
        /*
         * connect to the cluster and look weather the dababase has any data inside
         */
@@ -36,6 +36,8 @@ public class CassandraNativeConnector {
                session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.ProteinLog "
                                + "(JobID ascii, DataBegin ascii, DataEnd ascii, ip ascii, FinalStatus ascii, ExecutionStatus ascii, Protein ascii, PRIMARY KEY(JobID));");
                session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.ProteinData (jobtime bigint, JobID ascii, Protein ascii, PRIMARY KEY(JobID));");
+               session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.JpredArchive " + 
+               "(JobID ascii, Protein varchar, IP ascii, StartTime bigint, ExecTime int, alignment map<ascii,ascii>, predictions map<ascii,ascii>, archive blob, LOG varchar, PRIMARY KEY(JobID));");
 
                session.execute("CREATE INDEX IF NOT EXISTS ProteinSeq ON ProteinKeyspace.ProteinRow (protein);");
                session.execute("CREATE INDEX IF NOT EXISTS JobDateStamp ON ProteinKeyspace.ProteinData (jobtime);");
@@ -76,7 +78,7 @@ public class CassandraNativeConnector {
        /*
         * inserting data into the db
         */
-       public void InsertData(long jobtime, String startdate, String enddate, String ip, String jobid, String statusEx, String statusFinal,
+       public void FormQueryTables(long jobtime, String startdate, String enddate, String ip, String jobid, String statusEx, String statusFinal,
                        String protein, List<FastaSequence> predictions) {
 
                String check1 = "SELECT * FROM ProteinKeyspace.ProteinLog WHERE JobID = '" + jobid + "';";
@@ -105,13 +107,51 @@ public class CassandraNativeConnector {
                        String check2 = "SELECT * FROM ProteinKeyspace.ProteinRow WHERE JobID = '" + jobid + "';";
                        ResultSet results2 = session.execute(check2);
                        if (results2.isExhausted()) {
-                               String com3 = "INSERT INTO ProteinKeyspace.ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" 
-                       + protein + "','" + jobid + "',{" + final_prediction + "});";
+                               String com3 = "INSERT INTO ProteinKeyspace.ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','"
+                                               + jobid + "',{" + final_prediction + "});";
                                session.execute(com3);
                        }
                }
        }
 
+       public void ArchiveData(long starttime, int exectime, String ip, String jobid, String statusEx, String statusFinal,
+                       String protein, List<FastaSequence> predictions, List<FastaSequence> seqs, String LogFile) {
+
+               String check1 = "SELECT * FROM ProteinKeyspace.JpredArchive WHERE JobID = '" + jobid + "';";
+               ResultSet results1 = session.execute(check1);
+               if (results1.isExhausted()) {
+                       String allpredictions = "";
+                       for (FastaSequence pred : predictions) {
+                               String predictionname = pred.getId();
+                               String prediction = pred.getSequence().replaceAll("\n", "");
+                               allpredictions += "'" + predictionname + "':'" + prediction + "',";
+                       }
+                       String final_allpredictions = "";
+                       if (null != allpredictions) {
+                               final_allpredictions = allpredictions.substring(0, allpredictions.length() - 1);
+                       }
+                       String alignment = "";
+                       for (FastaSequence seq : seqs) {
+                               String predictionname = seq.getId();
+                               String prediction = seq.getSequence().replaceAll("\n", "");
+                               alignment += "'" + predictionname + "':'" + prediction + "',";
+                       }
+                       String final_alignment = "";
+                       if (null != allpredictions) {
+                               final_alignment = alignment.substring(0, allpredictions.length() - 1);
+                       }
+                       
+                       String com1 = "INSERT INTO ProteinKeyspace.JpredArchive "
+                                       + "(JobID, Protein, IP, StartTime, ExecTime, alignment, predictions, LOG))"
+                                       + " VALUES ('" 
+                                       + jobid + "','" + protein + "','" + ip + "'," + starttime + "," + exectime
+                                       + "',[" + final_allpredictions + "],[" + final_alignment + "],'" + LogFile + "]);";
+                       session.execute(com1);
+               }
+       }
+
+       
+       
        /*
         * getting data from the db
         */
@@ -122,17 +162,17 @@ public class CassandraNativeConnector {
                ResultSet results = session.execute(com);
                final long queryTime = System.currentTimeMillis();
                List<Row> rows = results.all();
-               System.out.println ("Query time is " + (queryTime - startTime) + " msec");
+               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"));
+                       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");
+               System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
                return res;
        }
 
@@ -145,7 +185,7 @@ public class CassandraNativeConnector {
                System.out.println("Command: " + com);
                ResultSet results = session.execute(com);
                final long queryTime = System.currentTimeMillis();
-               System.out.println ("Query time is " + (queryTime - startTime) + " msec");
+               System.out.println("Query time is " + (queryTime - startTime) + " msec");
 
                Calendar cal = Calendar.getInstance();
                long res = cal.getTimeInMillis();
@@ -159,8 +199,8 @@ public class CassandraNativeConnector {
                        ++c;
                }
                final long endTime = System.currentTimeMillis();
-               System.out.println (c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+               System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
                return res;
        }
-       
+
 }

diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index b780ddf..51fc8e3 100644 (file)
--- a/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@ -100,14 +100,9 @@ public class JpredParserHTTP implements JpredParser {
                                                                } catch (ParseException e) {
                                                                        e.printStackTrace();
                                                                }
-                                                               cc.InsertData(dateWork1, table[0], table[1], table[2], id, "OK", "OK", newprotein, seqs);
+                                                               cc.FormQueryTables(dateWork1, table[0], table[1], table[2], id, "OK", "OK", newprotein, seqs);
                                                                ++countinsertions;
                                                                ++njobs;
-                                                               // flush every 50 insertions
-                                                               // if (0 == countinsertions % 50) {
-                                                               // cc.flushData();
-                                                               // njobs -= 50;
-                                                               // }
                                                        }
                                                } catch (IOException e) {
                                                        e.printStackTrace();

diff --git a/datadb/compbio/cassandra/JpredParserLocalFile.java b/datadb/compbio/cassandra/JpredParserLocalFile.java
index 281a20b..54e50ab 100644 (file)
--- a/datadb/compbio/cassandra/JpredParserLocalFile.java
+++ b/datadb/compbio/cassandra/JpredParserLocalFile.java
@@ -104,7 +104,7 @@ public class JpredParserLocalFile implements JpredParser {
                                                        } catch (ParseException e) {
                                                                e.printStackTrace();
                                                        }
-                                                       cc.InsertData(insertdate, starttime, finishtime, ip, id, "OK", "OK", newprotein, seqs);
+                                                       cc.FormQueryTables(insertdate, starttime, finishtime, ip, id, "OK", "OK", newprotein, seqs);
                                                        ++countinsertions;
                                                        ++njobs;
                                                }

diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index 9885d64..83c8a7a 100755 (executable)
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -164,7 +164,7 @@ public class CassandraRequester {
         * find the earliest date in the database
         */
        public long earliestDate() {
-               earlestDate =  DBInstance.getEarliestDateInDB();
+               earlestDate = DBInstance.getEarliestDateInDB();
                return earlestDate;
        }
 }