X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FJpredParserHTTP.java;h=d03ac7999384cc0fec99f299625d266602a7fc1c;hb=87b9ef699282c308e5f259fb576b08eb25a1a25f;hp=e308a253a0ad2aba5cc582f29e46a903eef71818;hpb=2260ca3b3c0382ef6bfeea7341a692508058a2a6;p=proteocache.git

diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index e308a25..d03ac79 100644
--- a/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@ -1,6 +1,7 @@
 package compbio.cassandra;
 
 import java.io.BufferedReader;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.net.HttpURLConnection;
@@ -17,7 +18,7 @@ import java.util.List;
 import compbio.cassandra.JpredParser;
 
 public class JpredParserHTTP implements JpredParser {
-	private CassandraCreate cc = new CassandraCreate();
+	private CassandraNativeConnector cc = new CassandraNativeConnector();
 	private String dirprefix;
 
 	JpredParserHTTP() {
@@ -32,7 +33,7 @@ public class JpredParserHTTP implements JpredParser {
 		dirprefix = newsourceprefix;
 	}
 
-	public void Parsing(String source, int nDays) {
+	public void Parsing(String source, int nDays) throws IOException {
 		Calendar cal = Calendar.getInstance();
 		cal.add(Calendar.DATE, -nDays);
 		for (int i = 0; i < nDays; ++i) {
@@ -45,7 +46,7 @@ public class JpredParserHTTP implements JpredParser {
 		}
 	}
 
-	private void ParsingForDate(String input, String date) {
+	private int ParsingForDate(String input, String date) {
 		int totalcount = 0;
 		int countNoData = 0;
 		int countUnclearFASTAid = 0;
@@ -53,6 +54,7 @@ public class JpredParserHTTP implements JpredParser {
 		int countinserted = 0;
 		int counAlignments = 0;
 		int countStrange = 0;
+		int njobs = 0;
 
 		System.out.println("Inserting jobs for " + date);
 		try {
@@ -83,8 +85,9 @@ public class JpredParserHTTP implements JpredParser {
 									final FastaSequence fs = fr.next();
 									if (fs.getId().equals("QUERY") || fs.getId().equals(id))
 										newprotein = fs.getSequence().replaceAll("\n", "");
-									else
+									else if (fs.getId().equals("jnetpred") || fs.getId().equals("JNETPRED")) {
 										seqs.add(fs);
+									}
 								}
 								if (newprotein.equals("")) {
 									countUnclearFASTAid++;
@@ -100,10 +103,12 @@ public class JpredParserHTTP implements JpredParser {
 									}
 									cc.InsertData(dateWork1, table[0], table[1], table[2], id, "OK", "OK", newprotein, seqs);
 									++countinsertions;
-									// flush every 100 insertions
-									if (0 == countinsertions % 100) {
-										cc.flushData();
-									}
+									++njobs;
+									// flush every 50 insertions
+									//if (0 == countinsertions % 50) {
+									//	cc.flushData();
+									//	njobs -= 50;
+									//}
 								}
 							} catch (IOException e) {
 								e.printStackTrace();
@@ -135,5 +140,6 @@ public class JpredParserHTTP implements JpredParser {
 		} catch (IOException e) {
 			e.printStackTrace();
 		}
+		return njobs;
 	}
 }