X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraCreate.java;fp=datadb%2Fcompbio%2Fcassandra%2FCassandraCreate.java;h=ad1fcbe37db855d96658ceb702904102c1748b9b;hb=6a81b75c020845f9bb94c307a66347e4362da85f;hp=54fffaced07cfe28ac897b6f892dda83c2de3102;hpb=764f0d166bb7651490cbd5181063b6dd00042b07;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraCreate.java b/datadb/compbio/cassandra/CassandraCreate.java
index 54fffac..ad1fcbe 100644
--- a/datadb/compbio/cassandra/CassandraCreate.java
+++ b/datadb/compbio/cassandra/CassandraCreate.java
@@ -26,7 +26,9 @@ public class CassandraCreate {
 	StringSerializer ss = StringSerializer.get();
 	LongSerializer ls = LongSerializer.get();
 
-	// connect to the cluster
+	/*
+	 * connect to the cluster and look weather the dababase has any data inside
+	 */
 	public void Connection() {
 		cluster = HFactory.getOrCreateCluster("Protein Cluster", "127.0.0.1:9160");
 		KeyspaceDefinition keyspaceDef = cluster.describeKeyspace("ProteinKeyspace");
@@ -60,11 +62,12 @@ public class CassandraCreate {
 	}
 
 	/*
-	 * parsing data from
-	 * http://www.compbio.dundee.ac.uk/www-jpred/results/usage-new/alljobs.dat
+	 * parsing data source and filling the database
 	 */
-	public void Parsing() {
-		/* CF ProteinRow store protein and prediction */
+	public void Parsing(String source) {
+		/*
+		 * CF ProteinRow store protein and prediction
+		 */
 		mutatorString = HFactory.createMutator(ksp, ss);
 
 		/*
@@ -72,21 +75,38 @@ public class CassandraCreate {
 		 */
 		mutatorLog = HFactory.createMutator(ksp, ss);
 
-		/* CF ProteinData store id and protein per data */
+		/*
+		 * CF ProteinData store id and protein per data
+		 */
 		mutatorLong = HFactory.createMutator(ksp, ls);
 
-		System.out.println("Parsing......");
-		String in = "http://www.compbio.dundee.ac.uk/www-jpred/results/usage-new/alljobs.dat";
-		DataParsing datParsing = new DataParsing();
-		datParsing.Parsing(in, 4);
-		flushData();
+		if (source.equals("http")) {
+			// get data from real Jpred production server
+			System.out.println("Parsing web data source......");
+			String datasrc = "http://www.compbio.dundee.ac.uk/www-jpred/results/usage-new/alljobs.dat";
+			String prefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
+			JpredParserHTTP parser = new JpredParserHTTP(prefix);
+			parser.setSource("");
+			parser.Parsing(datasrc, 4);
+			flushData();
+		} else if (source.equals("file")) {
+			// get irtifical data generated for the DB stress tests
+			System.out.println("Parsing local file data source......");
+			String datasrc = "/home/asherstnev/Projects/Java.projects/proteocache/data_stress_test/data.dat";
+			String prefix = "/home/asherstnev/Projects/Java.projects/proteocache/data_stress_test/Jpreddata";
+			JpredParserLocalFile parser = new JpredParserLocalFile(prefix);
+			parser.Parsing(datasrc, 365);
+			flushData();
+		} else {
+			System.out.println("Unknown data source......");
+		}
 	}
 
 	public void flushData() {
 		mutatorString.execute();
 		mutatorLong.execute();
 		mutatorLog.execute();
-		//System.out.println("Flush new data...");
+		// System.out.println("Flush new data...");
 	}
 
 	public void Closing() {
@@ -94,7 +114,9 @@ public class CassandraCreate {
 		System.out.println("Cassandra has been shut down");
 	}
 
-	// check whether the job id exists in the DB
+	/*
+	 * check whether the job id exists in the DB
+	 */
 	public boolean CheckID(String jobid) {
 		SliceQuery<String, String, String> sliceQuery = HFactory.createSliceQuery(ksp, ss, ss, ss);
 		sliceQuery.setColumnFamily("ProteinLog").setKey(jobid).setRange("", "", false, 100);
@@ -105,6 +127,9 @@ public class CassandraCreate {
 		return false;
 	}
 
+	/*
+	 * prepare data for insertion into the db
+	 */
 	public void InsertData(long dataWork, String dataBegin, String dataEnd, String ip, String id, String statusEx, String statusFinal,
 			String protein, List<FastaSequence> jnetpred) {
 		mutatorLog.addInsertion(id, "ProteinLog", HFactory.createColumn("ip", ip, ss, ss))