From 39e14393f6bd36b2d0a9c50f05befdd732445ea5 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 3 Feb 2014 17:07:41 +0000
Subject: [PATCH] Replace the old EBI server for quering protein IDs

---
 jpred/lib/Jpred.pm       |   50 +++++++++++-----------------------------------
 websoft/bin/concise2html |    8 ++++----
 2 files changed, 16 insertions(+), 42 deletions(-)

diff --git a/jpred/lib/Jpred.pm b/jpred/lib/Jpred.pm
index 7119d28..e53f0fa 100755
--- a/jpred/lib/Jpred.pm
+++ b/jpred/lib/Jpred.pm
@@ -12,38 +12,8 @@ use strict;
 BEGIN {
   use Exporter;
   our @ISA = ('Exporter');
-  our @EXPORT = qw(
-    $WEBSERVER
-    $WEBSERVERCGI
-    $SERVERROOT
-    $SRSSERVER
-    $CHKLOG
-    $RESULTS
-    $PDBLNK
-    $CSS
-    $IMAGES
-    $JNET
-    $TIMEOUT
-    $BATCHLIM
-    $DUNDEE
-    $JPREDUSER
-    $JPREDEMAIL
-    $MAILHOST
-    $JPREDROOT
-    $BINDIR
-    $LIBDIR
-    $JOBDIR
-    $PREFIX
-    $RESOURCE
-    $BLASTDB
-    $SWALL
-    $SWALLFILT
-    $PDB
-    $PDB_DAT
-    $JPREDHEAD
-    $JPREDFOOT
-    &xsystem
-  );
+  our @EXPORT =
+    qw($WEBSERVER $WEBSERVERCGI $SERVERROOT $SRSSERVER $CHKLOG $RESULTS $PDBLNK $CSS $IMAGES $JNET $TIMEOUT $BATCHLIM $DUNDEE $JPREDUSER $JPREDEMAIL $MAILHOST $JPREDROOT $BINDIR $LIBDIR $JOBDIR $PREFIX $RESOURCE $BLASTDB $SWALL $SWALLFILT $PDB $PDB_DAT $JPREDHEAD $JPREDFOOT &xsystem);
   our @EXPORT_OK = @EXPORT;
 }
 
@@ -51,15 +21,20 @@ BEGIN {
 # for some reason doesn't work if in PERL5LIB
 use lib '/sw/lib/perl5.10.1/lib/perl5';
 
+############################################################################
 # URIs
-our $WEBSERVER = 'http://www.compbio.dundee.ac.uk/www-jpred';
+#production server
+#our $WEBSERVER = 'http://www.compbio.dundee.ac.uk/www-jpred';
+#development server
+our $WEBSERVER    = 'http://gjb-www-1.cluster.lifesci.dundee.ac.uk:3209';
+############################################################################
 
-#our $WEBSERVER    = 'http://webserv1.cluster.lifesci.dundee.ac.uk:3209';
 our $WEBSERVERCGI = "$WEBSERVER/cgi-bin";
 
 #$SERVERROOT = "$WEBSERVER/~www-jpred";
 our $SERVERROOT = "$WEBSERVER";
-our $SRSSERVER  = 'http://srs.ebi.ac.uk/srs6bin/cgi-bin';
+#our $SRSSERVER  = 'http://srs.ebi.ac.uk/srs6bin/cgi-bin';
+our $SRSSERVER  = 'http://www.ebi.ac.uk/ebisearch/search.ebi';
 our $CHKLOG     = "$WEBSERVERCGI/chklog?";
 our $RESULTS    = "$SERVERROOT/results";
 our $PDBLNK     = "http://www.ebi.ac.uk/pdbsum/";
@@ -79,9 +54,8 @@ our $JPREDEMAIL = 'www-jpred@compbio.dundee.ac.uk';
 our $MAILHOST   = 'smtp.lifesci.dundee.ac.uk';        # CC 19/05/06 - updated to current smtp host from weevil
 
 # Server paths
-our $JPREDROOT = '/homes/www-jpred/live';
-
-#our $JPREDROOT = '/homes/www-jpred/devel';
+#our $JPREDROOT = '/homes/www-jpred/live';
+our $JPREDROOT = '/homes/www-jpred/devel';
 
 # Directory for binaries either on the cluster or on the www server
 our $BINDIR = "$JPREDROOT/bin";
diff --git a/websoft/bin/concise2html b/websoft/bin/concise2html
index 105501b..bd123dd 100755
--- a/websoft/bin/concise2html
+++ b/websoft/bin/concise2html
@@ -282,9 +282,9 @@ foreach (0..$#align) {
 	      ## differentiate between Uniprot and Uniparc (UniRef90_UNI\w+) IDs as they require
 	      ## different SRS query strings
 	      if ($align[$_] =~ /UniRef90_(UPI\w+)/) {
-	         print HTML "<a href=$SRSSERVER/wgetz?-e+[uniparc-AccNumber:$1]>$align[$_]</a>";
+	         print HTML "<a href=$SRSSERVER?db=allebi&query=$1>$align[$_]</a>";
 	      } else {
-	         print HTML "<a href=$SRSSERVER/wgetz?-e+[UNIREF90-acc:$align[$_]]>$align[$_]</a>";
+	         print HTML "<a href=$SRSSERVER?db=allebi&query=$align[$_]>$align[$_]</a>";
 	      }
 	   } else {
 	      print HTML "$align[$_]";
@@ -306,9 +306,9 @@ foreach (0..$#align) {
               ## differentiate between Uniprot and Uniparc IDs as they require
               ## different SRS query strings
               if ($align[$_] =~ /UniRef90_(UPI\w+)/) {
-                 print HTML " : <a href=$SRSSERVER/wgetz?-e+[uniparc-AccNumber:$1]>$align[$_]</a>\n";
+                 print HTML " : <a href=$SRSSERVER?db=allebi&query=$1>$align[$_]</a>\n";
               } else {
-                 print HTML " : <a href=$SRSSERVER/wgetz?-e+[UNIREF90-acc:$align[$_]]>$align[$_]</a>\n";
+                 print HTML " : <a href=$SRSSERVER?db=allebi&query=$align[$_]>$align[$_]</a>\n";
               }
 	   } else {
 	      print HTML " : $align[$_]\n";
-- 
1.7.10.2