X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=datadb%2Fcompbio%2Fcassandra%2FJpredParserLocalFile.java;h=f48178c9f862bd961270425e3c248258335098ed;hb=0e1f92db0e4043bfa93417481274b6461cdb09cd;hp=27d4252c19d5e9594de6742f1dda011d7901e7d7;hpb=3887e427255a9ed5e9e43f4a52a377935331e5d3;p=proteocache.git

diff --git a/datadb/compbio/cassandra/JpredParserLocalFile.java b/datadb/compbio/cassandra/JpredParserLocalFile.java
index 27d4252..f48178c 100644
--- a/datadb/compbio/cassandra/JpredParserLocalFile.java
+++ b/datadb/compbio/cassandra/JpredParserLocalFile.java
@@ -15,19 +15,22 @@ import java.util.Calendar;
 import java.util.Date;
 import java.util.List;
 
+import compbio.data.sequence.FastaReader;
+import compbio.data.sequence.FastaSequence;
+
 public class JpredParserLocalFile implements JpredParser {
-	private CassandraNativeConnector cc = new CassandraNativeConnector();
+	private CassandraWriter cw = new CassandraWriter();
 	private String dirprefix;
 
 	public void setSource(String newsourceprefix) {
 		this.dirprefix = newsourceprefix;
 	}
 
-	JpredParserLocalFile() {
+	public JpredParserLocalFile() {
 		this.dirprefix = "/home/asherstnev/Projects/Java.projects/proteocache/data_stress_test/data.dat";
 	}
 
-	JpredParserLocalFile(String sourceurl) {
+	public JpredParserLocalFile(String sourceurl) {
 		this.dirprefix = sourceurl;
 	}
 
@@ -58,7 +61,7 @@ public class JpredParserLocalFile implements JpredParser {
 		System.out.println("Execution Time = " + execTime + " ms");
 	}
 
-	private int ParsingForDate(List<String> input, String date) {
+	private void ParsingForDate(List<String> input, String date) {
 		int totalcount = 0;
 		int countNoData = 0;
 		int countUnclearFASTAid = 0;
@@ -66,64 +69,51 @@ public class JpredParserLocalFile implements JpredParser {
 		int countinserted = 0;
 		int counAlignments = 0;
 		int countStrange = 0;
-		int njobs = 0;
 
 		System.out.println("Inserting jobs for " + date);
 		for (String in : input) {
-			if (in.matches(date + "(.*)jp_[^\\s]+")) {
+			if (in.matches(date + ":(.*)jp_[^\\s]+")) {
 				String[] table = in.split("\\s+");
 				String starttime = table[0];
 				String finishtime = table[1];
 				String ip = table[2];
 				String id = table[table.length - 1];
 				totalcount++;
-				//if (!cc.CheckID(id)) {
-					if (true) {
-					String confilename = dirprefix + "/" + id + "/" + id + ".concise";
-					File confile = new File(confilename);
-					if (confile.exists()) {
-						try {
-							final FastaReader fr = new FastaReader(confilename);
-							final List<FastaSequence> seqs = new ArrayList<FastaSequence>();
-							String newprotein = "";
-							while (fr.hasNext()) {
-								final FastaSequence fs = fr.next();
-								if (fs.getId().equals("QUERY") || fs.getId().equals(id))
-									newprotein = fs.getSequence().replaceAll("\n", "");
-								else if (fs.getId().equals("jnetpred") || fs.getId().equals("JNETPRED")) {
-									seqs.add(fs);
-								}
+				String confilename = dirprefix + "/" + id + "/" + id + ".concise";
+				File confile = new File(confilename);
+				if (confile.exists()) {
+					try {
+						final FastaReader fr = new FastaReader(confilename);
+						final List<FastaSequence> seqs = new ArrayList<FastaSequence>();
+						String newprotein = "";
+						while (fr.hasNext()) {
+							final FastaSequence fs = fr.next();
+							if (fs.getId().equals("QUERY") || fs.getId().equals(id))
+								newprotein = fs.getSequence().replaceAll("\n", "");
+							else if (fs.getId().equals("jnetpred") || fs.getId().equals("JNETPRED")) {
+								seqs.add(fs);
 							}
-							if (newprotein.equals("")) {
-								countUnclearFASTAid++;
-							} else {
-								SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
-								String dateInString1 = starttime.substring(0, starttime.indexOf(":"));
-								long dateWork1 = 0;
-								try {
-									Date dat = formatter.parse(dateInString1);
-									dateWork1 = dat.getTime();
-								} catch (ParseException e) {
-									e.printStackTrace();
-								}
-								cc.InsertData(dateWork1, starttime, finishtime, ip, id, "OK", "OK", newprotein, seqs);
-								++countinsertions;
-								++njobs;
-								// flush every 50 insertions
-								//if (0 == countinsertions % 50) {
-								//	cc.flushData();
-								//	njobs -= 50;
-								//}
+						}
+						if (newprotein.equals("")) {
+							countUnclearFASTAid++;
+						} else {
+							SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
+							String dateInString1 = starttime.substring(0, starttime.indexOf(":"));
+							long insertdate = 0;
+							try {
+								Date dat = formatter.parse(dateInString1);
+								insertdate = dat.getTime();
+							} catch (ParseException e) {
+								e.printStackTrace();
 							}
-							fr.close();
-						} catch (IOException e) {
-							e.printStackTrace();
+							//countinsertions += cw.FormQueryTables(insertdate, starttime, finishtime, ip, id, "OK", "OK", newprotein, seqs);
 						}
-					} else {
-						countNoData++;
+						fr.close();
+					} catch (IOException e) {
+						e.printStackTrace();
 					}
 				} else {
-					++countinserted;
+					countNoData++;
 				}
 			} else {
 				if (in.matches(date + "(.*)Sequence0/(.*)")) {
@@ -142,7 +132,6 @@ public class JpredParserLocalFile implements JpredParser {
 			System.out.println("   " + countUnclearFASTAid + " jobs with unclear FASTA protein id in *.concise.fasta");
 			System.out.println("   " + countinsertions + " new job insertions\n");
 		}
-		return njobs;
 	}
 
 }