From c0a1ee97e2126b8be6e8cbaeeee2315d52090f14 Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Fri, 8 Nov 2013 13:28:29 +0000 Subject: [PATCH 1/1] Fix problems with Natasha's code --- .../cassandra/CassandraNativeConnector.java | 117 +------------------- datadb/compbio/cassandra/StructureJobLog.java | 45 ++++++++ 2 files changed, 46 insertions(+), 116 deletions(-) create mode 100644 datadb/compbio/cassandra/StructureJobLog.java diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java index 8e86624..4ba9377 100644 --- a/datadb/compbio/cassandra/CassandraNativeConnector.java +++ b/datadb/compbio/cassandra/CassandraNativeConnector.java @@ -268,121 +268,6 @@ public class CassandraNativeConnector { } /* - * getting data from the db ProteinData - */ - public Integer ReadDateTable(long queryDate) { - final long startTime = System.currentTimeMillis(); - String com = "SELECT jobtime, JobID FROM ProteinKeyspace.ProteinData WHERE jobtime = " + queryDate + ";"; - 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"); - return rows.size(); - } - - /* - * getting part of protein sequence from the db ProteinRow - */ - public List ReadPartOfSequence(String queryProtein) { - final long startTime = System.currentTimeMillis(); - String com = "SELECT * FROM ProteinKeyspace.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(); - 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)); - res.add(structure); - ++c; - } - } - final long endTime = System.currentTimeMillis(); - System.out.println (c + " rows analysed, execution time is " + (endTime - startTime) + " msec"); - return res; - } - - /* - * getting protein sequences by counter - */ - public Map ReadProteinDataByCounter() { - final long startTime = System.currentTimeMillis(); - String com = "SELECT Protein FROM ProteinKeyspace.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()); - Map res = new HashMap(); - int c = 0; - for (Row r : rows) { - String protein = r.getString("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"); - return res; - } - - /* - * getting data from the db ProteinData - */ - public Integer ReadDateTable(long queryDate) { - final long startTime = System.currentTimeMillis(); - String com = "SELECT jobtime, JobID FROM ProteinKeyspace.ProteinData WHERE jobtime = " + queryDate + ";"; - 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"); - return rows.size(); - } - - /* - * getting whole protein sequence from the db ProteinRow - */ - public List ReadWholeSequence(String queryProtein) { - final long startTime = System.currentTimeMillis(); - String com = "SELECT JobID, Predictions FROM ProteinKeyspace.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()); - 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)); - res.add(structure); - ++c; - } - final long endTime = System.currentTimeMillis(); - 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) { @@ -464,7 +349,7 @@ public class CassandraNativeConnector { return res; } - + /* * getting earlest date of jobs from the db */ public long getEarliestDateInDB() { diff --git a/datadb/compbio/cassandra/StructureJobLog.java b/datadb/compbio/cassandra/StructureJobLog.java new file mode 100644 index 0000000..4f2414b --- /dev/null +++ b/datadb/compbio/cassandra/StructureJobLog.java @@ -0,0 +1,45 @@ +package compbio.cassandra; + +import java.util.Map; + +public class StructureJobLog { + private String jobid; + private String dateStart; + private String dateEnd; + private String sequence; + private String ip; + private Map prediction; + + public StructureJobLog (String seq, String id, String dateStart, String dateEnd, String ip, Map pred) { + this.sequence = seq; + this.jobid = id; + this.dateStart = dateStart; + this.dateEnd = dateEnd; + this.ip = ip; + this.prediction = pred; + } + + public String getSequence () { + return sequence; + } + + public String getJobid () { + return jobid; + } + + public String getDateStart () { + return dateStart; + } + + public String getDateEnd () { + return dateEnd; + } + + public String getIP () { + return ip; + } + + public Map getPrediction () { + return prediction; + } +} -- 1.7.10.2