From e340dab523f648f1dff28b6019d0e5ba97dfb1f7 Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Fri, 8 Nov 2013 13:46:48 +0000 Subject: [PATCH] Remove keyspace name from queries --- .../cassandra/CassandraNativeConnector.java | 59 ++++++++++---------- 1 file changed, 31 insertions(+), 28 deletions(-) diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java index 4ba9377..6e6992d 100644 --- a/datadb/compbio/cassandra/CassandraNativeConnector.java +++ b/datadb/compbio/cassandra/CassandraNativeConnector.java @@ -204,7 +204,7 @@ public class CassandraNativeConnector { */ public List> ReadProteinDataTable() { final long startTime = System.currentTimeMillis(); - String com = "SELECT DataBegin,DataEnd FROM ProteinKeyspace.ProteinLog;"; + String com = "SELECT DataBegin,DataEnd FROM ProteinLog;"; System.out.println("Command: " + com); ResultSet results = session.execute(com); final long queryTime = System.currentTimeMillis(); @@ -228,7 +228,7 @@ public class CassandraNativeConnector { */ public Integer ReadDateTable(long queryDate) { final long startTime = System.currentTimeMillis(); - String com = "SELECT jobtime, JobID FROM ProteinKeyspace.ProteinData WHERE jobtime = " + queryDate + ";"; + String com = "SELECT jobtime, JobID FROM ProteinData WHERE jobtime = " + queryDate + ";"; System.out.println("Command: " + com); ResultSet results = session.execute(com); final long queryTime = System.currentTimeMillis(); @@ -237,7 +237,7 @@ public class CassandraNativeConnector { return 0; List rows = results.all(); final long endTime = System.currentTimeMillis(); - System.out.println ("Processing time is " + (endTime - queryTime) + " msec"); + System.out.println("Processing time is " + (endTime - queryTime) + " msec"); return rows.size(); } @@ -246,81 +246,83 @@ public class CassandraNativeConnector { */ public List ReadWholeSequence(String queryProtein) { final long startTime = System.currentTimeMillis(); - String com = "SELECT JobID, Predictions FROM ProteinKeyspace.ProteinRow WHERE Protein = '" + queryProtein + "';"; + 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 rows = results.all(); - System.out.println ("Query time is " + (queryTime - startTime) + " msec"); - System.out.println (" rows analysed, " + rows.size()); + System.out.println("Query time is " + (queryTime - startTime) + " msec"); + System.out.println(" rows analysed, " + rows.size()); List res = new ArrayList(); int c = 0; for (Row r : rows) { - StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap("Predictions", String.class, String.class)); + StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap( + "Predictions", String.class, String.class)); res.add(structure); ++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; } /* * getting part of protein sequence from the db ProteinRow */ - public List ReadPartOfSequence(String queryProtein) { + public List ReadPartOfSequence(String queryProtein) { final long startTime = System.currentTimeMillis(); - String com = "SELECT * FROM ProteinKeyspace.ProteinRow;"; + 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 rows = results.all(); - System.out.println ("Query time is " + (queryTime - startTime) + " msec"); - System.out.println (" rows analysed, " + rows.size()); - List res = new ArrayList(); + System.out.println("Query time is " + (queryTime - startTime) + " msec"); + System.out.println(" rows analysed, " + rows.size()); + List res = new ArrayList(); int c = 0; for (Row r : rows) { String prot = r.getString("Protein"); if (prot.matches("(.*)" + queryProtein + "(.*)")) { - StructureProteinPrediction structure = new StructureProteinPrediction(prot, r.getString("JobID"), r.getMap("Predictions", String.class, String.class)); + StructureProteinPrediction structure = new StructureProteinPrediction(prot, r.getString("JobID"), r.getMap("Predictions", + String.class, String.class)); res.add(structure); ++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; } - + /* * getting protein sequences by counter */ - public Map ReadProteinDataByCounter() { + public Map ReadProteinDataByCounter() { final long startTime = System.currentTimeMillis(); - String com = "SELECT Protein FROM ProteinKeyspace.ProteinRow;"; + String com = "SELECT Protein FROM ProteinRow;"; System.out.println("Command: " + com); ResultSet results = session.execute(com); if (results.isExhausted()) return null; final long queryTime = System.currentTimeMillis(); List rows = results.all(); - System.out.println ("Query time is " + (queryTime - startTime) + " msec"); - System.out.println (" rows analysed, " + rows.size()); + System.out.println("Query time is " + (queryTime - startTime) + " msec"); + System.out.println(" rows analysed, " + rows.size()); Map res = new HashMap(); int c = 0; for (Row r : rows) { String protein = r.getString("Protein"); - if (res.containsKey(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"); + System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec"); return res; } @@ -342,10 +344,11 @@ public class CassandraNativeConnector { if (results1.isExhausted()) return null; Row row1 = results1.one(); - StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"), row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class)); - System.out.println ("Query time is " + (queryTime - startTime) + " msec"); + StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"), + row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class)); + 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"); + System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec"); return res; } @@ -354,11 +357,11 @@ public class CassandraNativeConnector { */ public long getEarliestDateInDB() { final long startTime = System.currentTimeMillis(); - String com = "SELECT jobtime,JobID FROM ProteinKeyspace.ProteinData;"; + String com = "SELECT jobtime,JobID FROM ProteinData;"; 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(); @@ -372,7 +375,7 @@ 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; } -- 1.7.10.2