Improvements for mirror availability (#1125)

- Remove pause:300 from the biomart request limiting. This will prevent
  an Apache worker from doing any work
- Remove Gnomad URL that is no longer valid
- Fix URL used in Psychic
- Use v4 address for Apache
- Use shorter global read timeout (30s instead of 300) for Apache

Author: EbiArnie

conf/httpd.conf

@@ -94,7 +94,7 @@ SecDataDir /tmp
   SecRule REQUEST_METHOD !^POST$ allow,nolog,id:1
   SecAction initcol:ip=%{REQUEST_HEADERS.X-Cluster-Client-Ip},pass,nolog,id:2
   SecAction "phase:5,deprecatevar:ip.biomartcounter=1/1,pass,nolog,id:3"
-  SecRule IP:BIOMARTCOUNTER "@gt 100" "phase:2,pause:300,deny,status:509,setenv:RATELIMITED,skip:1,nolog,id:4"
+  SecRule IP:BIOMARTCOUNTER "@gt 100" "phase:2,deny,status:509,setenv:RATELIMITED,skip:1,log,id:4"
   SecAction "phase:2,pass,setvar:ip.biomartcounter=+1,nolog,id:5"
   Header always set Retry-After "10" env=RATELIMITED
 </LocationMatch>
@@ -223,7 +223,7 @@ $MaxSpareServers = $SiteDefs::ENSEMBL_MAX_SPARE_SERVERS;
 $MaxRequestsPerChild = 1000;
 $StartServers    = $SiteDefs::ENSEMBL_START_SERVERS;
 
-@Listen          = ($SiteDefs::ENSEMBL_PORT);
+@Listen          = ("127.0.0.1:" . $SiteDefs::ENSEMBL_PORT);
 
 $ServerAdmin     = $SiteDefs::ENSEMBL_SERVERADMIN;
 $ServerName      = $SiteDefs::ENSEMBL_SERVERNAME;
@@ -399,7 +399,7 @@ fix_lvalues("EnsEMBL::",\%EnsEMBL::);
 # Apache-style Config
 #######################
 ServerTokens            prod
-Timeout                 300
+Timeout                 30
 <IfDefine PERLDB>
 KeepAlive               Off
 MaxClients              1

conf/ini-files/DEFAULTS.ini

@@ -387,7 +387,6 @@ GEM_J_POP                   = https://togovar.biosciencedbc.jp/doc/datasets/gem_
 GEM_J_POP_USE               = https://togovar.biosciencedbc.jp/doc/datasets/gem_j_wga#terms
 GENE3D                      = https://www.ebi.ac.uk/interpro/entry/cathgene3d/###ID###
 GIANT                       = http://www.broadinstitute.org/collaboration/giant/index.php/Main_Page
-GNOMAD_SV                   = https://gnomad.broadinstitute.org/variant/###ID###?dataset=gnomad_sv_r4
 HAPMAP                      = http://www.hapmap.org/cgi-perl/secure/gbrowse/snp_details/hapmap?class=SNP;name=###ID###
 HBVAR                       = http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=###ID### 
 HGMD-PUBLIC                 = http://www.hgmd.cf.ac.uk/ac/index.php

modules/EnsEMBL/Web/Controller/Psychic.pm

@@ -88,7 +88,7 @@ sub _psychic {
 
   return "//www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$query"  if $dest_site eq 'ebi';
   return "//www.sanger.ac.uk/search?db=allsanger&t=$query"              if $dest_site eq 'sanger';
-  return "//www.ensemblgenomes.org/search/?query=$query"                if $dest_site eq 'ensembl_genomes';
+  return "//www.ensemblgenomes.org/search/eg/$query"                    if $dest_site eq 'ensembl_genomes';
 
   my $extra = '';
   if(@extra) {