From: Sasha Sherstnev <sherstnv@gmail.com>
Date: Fri, 1 Aug 2014 08:07:38 +0000 (+0100)
Subject: fix html errors
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5e76924c64903dd27013651144b1b7e2fcfc7c27;p=proteocache.git

fix html errors
---

diff --git a/.swp b/.swp
new file mode 100644
index 0000000..873b61d
Binary files /dev/null and b/.swp differ
diff --git a/conf/Proteocache.properties b/conf/Proteocache.properties
index 2b2a2fd..5502dc3 100644
--- a/conf/Proteocache.properties
+++ b/conf/Proteocache.properties
@@ -1,8 +1,8 @@
 #################################################################################
 # Cassandra host or IP
 # test server is 10.0.115.190
-#cassandra.host=localhost
-cassandra.host=Main-laptop2.dyn.lifesci.dundee.ac.uk
+cassandra.host=localhost
+#cassandra.host=Main-laptop2.dyn.lifesci.dundee.ac.uk
 #cassandra.host=gjb-www-1.cluster.lifesci.dundee.ac.uk
 #cassandra.host=c6100-1.cluster.lifesci.dundee.ac.uk
 
@@ -34,6 +34,7 @@ cassandra.jpred.local.period=300
 #################################################################################
 # archive features
 archive.enable=true
-archive.path = /home/asherstnev/Projects/Java.projects/proteocache/archive
+#archive.path = /home/asherstnev/Projects/Java.projects/proteocache/archive
+archive.path = /drives/c/Users/as373024/Java_dev/archive/
 #archive.path = /homes/www-jws2/ProteoCacheArchive
 archive.web.dir=results
diff --git a/datadb/compbio/cassandra/CassandraNewTableWriter.java b/datadb/compbio/cassandra/CassandraNewTableWriter.java
index db0e70c..c82cd63 100644
--- a/datadb/compbio/cassandra/CassandraNewTableWriter.java
+++ b/datadb/compbio/cassandra/CassandraNewTableWriter.java
@@ -102,4 +102,6 @@ public class CassandraNewTableWriter {
 		Date gaga = new Date(newearliestday);
 		System.out.println("New EarliestJobDate is " + gaga.toString());
 	}
+	public void FillNewTable() {
+	}
 }
diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index c6db457..42df7cc 100644
--- a/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@ -5,8 +5,10 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.net.Authenticator;
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
+import java.net.PasswordAuthentication;
 import java.net.URL;
 import java.net.URLConnection;
 import java.text.ParseException;
@@ -41,10 +43,29 @@ public class JpredParserHTTP implements JpredParser {
 
 	public JpredParserHTTP() {
 		dirprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
+		launchAuthenticator();
 	}
 
+	public void launchAuthenticator() {
+		final String authUser = "as373024";
+	    final String authPassword = "Zx1--L12";
+	    final String authHost = "gskproxy.gsk.com";
+	    final String authPort = "800";
+	      Authenticator.setDefault(new Authenticator() {
+	         public PasswordAuthentication getPasswordAuthentication() {
+	            return new PasswordAuthentication(authUser, authPassword.toCharArray());
+	         }
+	      });
+	      System.setProperty("proxySet", "true");
+	      System.setProperty("http.proxyUser", authUser);
+	      System.setProperty("http.proxyPassword", authPassword);
+	      System.setProperty("http.proxyHost", authHost);
+	      System.setProperty("http.proxyPort", authPort);
+	}
+	
 	public JpredParserHTTP(String sourceurl) {
-		dirprefix = sourceurl;
+	      dirprefix = sourceurl;
+	      launchAuthenticator();
 	}
 
 	public void setSource(String newsourceprefix) {
diff --git a/server/compbio/ws/jpred/JpredClient.java b/server/compbio/ws/jpred/JpredClient.java
index 6fe8f84..ea62bde 100644
--- a/server/compbio/ws/jpred/JpredClient.java
+++ b/server/compbio/ws/jpred/JpredClient.java
@@ -15,9 +15,9 @@ public class JpredClient {
 		URL url = new URL("http://localhost:8080/proteocache-1.0/ProteoCacheWS");
 		Service service = Service.create(url, qname);
 		Jpred sequense = service.getPort(Jpred.class);
-		String result = sequense.findSequence("EQCGRQAGGKLCPNNLCCSQWGWCGSTDEYCS", "Jpred", "3.0.1");
+		int result = sequense.findSequence("EQCGRQAGGKLCPNNLCCSQWGWCGSTDEYCS", "Jpred", "3.0.1");
 
-		System.out.println("Result : " + result);
+		System.out.println("Result : " + result + " jobs found");
 	}
 
 }
diff --git a/webapp/resources/datatables-1.9.4/docs/DataTable.defaults.html b/webapp/resources/datatables-1.9.4/docs/DataTable.defaults.html
index d86664a..2349749 100644
--- a/webapp/resources/datatables-1.9.4/docs/DataTable.defaults.html
+++ b/webapp/resources/datatables-1.9.4/docs/DataTable.defaults.html
@@ -257,7 +257,7 @@ aid styling. The follow syntax is used:
   <ul>
     <li>The following options are allowed: <br />
       <ul>
-        <li>'l' - Length changing</li
+        <li>'l' - Length changing</li>
         <li>'f' - Filtering input</li>
         <li>'t' - The table!</li>
         <li>'i' - Information</li>
@@ -1620,7 +1620,7 @@ aid styling. The follow syntax is used:
   <ul>
     <li>The following options are allowed: <br />
       <ul>
-        <li>'l' - Length changing</li
+        <li>'l' - Length changing</li>
         <li>'f' - Filtering input</li>
         <li>'t' - The table!</li>
         <li>'i' - Information</li>