Merge branch 'servlets'

[proteocache.git] / datadb / compbio / cassandra / JpredParserLocalFile.java

diff --git a/datadb/compbio/cassandra/JpredParserLocalFile.java b/datadb/compbio/cassandra/JpredParserLocalFile.java
index 27d4252..a379d4e 100644 (file)
--- a/datadb/compbio/cassandra/JpredParserLocalFile.java
+++ b/datadb/compbio/cassandra/JpredParserLocalFile.java
@@ -16,18 +16,18 @@ import java.util.Date;
 import java.util.List;
 
 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 +58,7 @@ 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 +66,51 @@ 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 +129,6 @@ 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;
        }
 
 }