Merging postreleasefix/114 to main

* postreleasefix/114:
  Tweak handling of strain, Pan and subtree export (#1074)
  Load underlying slices iff needed for alignslice view (#1076)
  Update Apache access logs format: print request ips (#1077)

Author: ens_adm02

conf/httpd.conf

@@ -453,7 +453,7 @@ LogFormat ":%{X-Forwarded-For}i %v %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-
 <IfDefine !ec2>
 # this for live at Hinx
 LogFormat               "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\"" combined
-LogFormat               "[%P/%{ENSEMBL_CHILD_COUNT}e %{ENSEMBL_SCRIPT_TIME}e %{outstream}n/%{instream}n=%{ratio}n] %h/%{HTTP_X_FORWARDED_FOR}e %l/%{ENSEMBL_SESSION_ID}e %u/%{ENSEMBL_USER_ID}e %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\" \"%{HTTP_X_Requested_With}e\" %{ENSEMBL_SCRIPT_START}e/%{ENSEMBL_SCRIPT_END}e" ensembl_extended
+LogFormat               "[%P/%{ENSEMBL_CHILD_COUNT}e %{ENSEMBL_SCRIPT_TIME}e %{outstream}n/%{instream}n=%{ratio}n] %h/%{X-Cluster-Client-Ip}i %l/%{ENSEMBL_SESSION_ID}e %u/%{ENSEMBL_USER_ID}e %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\" \"%{HTTP_X_Requested_With}e\" %{ENSEMBL_SCRIPT_START}e/%{ENSEMBL_SCRIPT_END}e" ensembl_extended
 </IfDefine>
 #
 ####

modules/EnsEMBL/Web/Command/DataExport/Output.pm

@@ -157,7 +157,7 @@ sub process {
     $url_params->{'__clear'}        = 1;
     ## Pass parameters needed for Back button to work
     my @core_params = keys %{$hub->core_object('parameters')};
-    push @core_params, qw(export_action data_type data_action component align g1);
+    push @core_params, qw(export_action data_type data_action component align g1 node strain);
     push @core_params, $self->config_params; 
     foreach (@core_params) {
       my @values = $component->param($_);

modules/EnsEMBL/Web/Component/Location/Compara_AlignSliceBottom.pm

@@ -64,13 +64,15 @@ sub content {
     ));
   }
 
+  my $need_underlying_slices = !$self->has_image || $align_details->{'class'} eq 'GenomicAlignTree.ancestral_alignment';
   my $image_width     = $self->image_width;
   my $slice           = $object->slice;
   my %export_params   = $hub->param('data_type') ? ('data_type' => $hub->param('data_type'), 'component' => $hub->param('data_action'))
                                                  : ();
   my ($slices)        = $object->get_slices({
                                               'slice' => $slice, 
                                               'align' => $align_params, 
+                                              'image' => !$need_underlying_slices,
                                               'species' => $primary_species,
                                               %export_params
                         });
@@ -136,6 +138,7 @@ sub content {
                                 'species' => $prodname, 
                                 'cdb'     => $self->param('cdb') || 'compara',
                                 'ignore'  => 'ancestral_sequences',
+                                'image'   => !$need_underlying_slices,
                                 });
 
   return $alert_box if $error;

modules/EnsEMBL/Web/Constants.pm

@@ -199,6 +199,37 @@ sub GENE_JOIN_TYPES {
   }
 }
 
+sub GENE_TREE_CONSTANTS {
+### Compara lookup for various gene-tree views
+  my ($cdb, $strain, $clusterset_id) = @_;
+
+  my $GENE_TREE_CONSTANTS = {
+    compara_pan_ensembl => {
+      action => 'PanComparaTree',
+      component => 'PanComparaTree',
+    },
+    compara_strain => {
+      action => 'Strain_Compara_Tree',
+      component => 'ComparaTree',
+    },
+    compara => {
+      action => 'Compara_Tree',
+      component => 'ComparaTree',
+    },
+  };
+
+  my $gene_tree_view_key;
+  if ($cdb eq 'compara_pan_ensembl') {
+    $gene_tree_view_key = 'compara_pan_ensembl';
+  } elsif ($strain) {
+    $gene_tree_view_key = 'compara_strain';
+  } else {
+    $gene_tree_view_key = 'compara';
+  }
+
+  return $GENE_TREE_CONSTANTS->{$gene_tree_view_key};
+}
+
 sub ALIGNMENT_FORMATS {
 ### Metadata for alignment export formats
   return (

modules/EnsEMBL/Web/ZMenu/ComparaTreeNode.pm

@@ -26,14 +26,17 @@ use URI::Escape qw(uri_escape);
 use IO::String;
 use Bio::AlignIO;
 
+use EnsEMBL::Web::Constants;
+
 use base qw(EnsEMBL::Web::ZMenu);
 
 sub content {
   my $self   = shift;
   my $cdb    = shift || 'compara';
   my $hub    = $self->hub;
   my $object = $self->object;
-  my $strain_tree = $hub->species_defs->get_config($self->hub->species,'RELATED_TAXON') if $hub->param('strain');
+  my $is_strain   = $hub->param('strain');
+  my $strain_tree = $hub->species_defs->get_config($self->hub->species,'RELATED_TAXON') if $is_strain;
   my $tree   = $object->isa('EnsEMBL::Web::Object::GeneTree') ? $object->tree : $object->get_GeneTree($cdb, "", $strain_tree);
 
   die 'No tree for gene' unless $tree;
@@ -165,6 +168,7 @@ sub content {
 
   }
 
+  my $gene_tree_constants = EnsEMBL::Web::Constants::GENE_TREE_CONSTANTS($cdb, $is_strain, $tree->tree->clusterset_id);
   my $lookup = $hub->species_defs->prodnames_to_urls_lookup;
   if ($is_leaf and $is_supertree) {
 
@@ -177,9 +181,6 @@ sub content {
 
       my $link_gene = $node->{_sub_reference_gene};
 
-      ## Strain trees and other trees are very different!
-      my $action = $hub->param('strain') ? 'Strain_Compara_Tree' : 'Compara_Tree';
-
       my $that_subtree_link;
       if ($tree_stable_id) {
         $that_subtree_link = $hub->url({
@@ -193,27 +194,10 @@ sub content {
         my $link_gene = $node->{_sub_reference_gene};
         my $species = $lookup->{$link_gene->genome_db->name};
 
-        # This is not the most elegant approach, but it will change the $action
-        # only where gene-tree constants are available (e.g. Metazoa),
-        # and only for non-default protein trees that lack a stable ID.
-        require EnsEMBL::Web::Component::Gene::ComparaOrthologs;
-        if (defined $EnsEMBL::Web::Component::Gene::ComparaOrthologs::GENE_TREE_CONSTANTS) {
-          my $gene_tree_constants = $EnsEMBL::Web::Component::Gene::ComparaOrthologs::GENE_TREE_CONSTANTS;
-          if (defined $gene_tree_constants) {
-            my $clusterset_id = $tree->tree->clusterset_id;
-            if (exists $gene_tree_constants->{$clusterset_id}) {
-              my $clusterset_specific_action = $gene_tree_constants->{$clusterset_id}{url_part};
-              if (defined $clusterset_specific_action) {
-                $action = $clusterset_specific_action;
-              }
-            }
-          }
-        }
-
         $that_subtree_link = $hub->url({
           species  => $species,
           type     => 'Gene',
-          action   => $action,
+          action   => $gene_tree_constants->{action},
           __clear  => 1,
           g        => $link_gene->stable_id,
         });
@@ -387,11 +371,13 @@ sub content {
     my $params    = {
                       'type'      => 'DataExport',
                       'action'    => 'GeneTree',
+                      'cdb'       => $cdb,
                       'data_type' => 'Gene',
-                      'component' => 'ComparaTree',
+                      'component' => $gene_tree_constants->{component},
                       'gene_name' => $gene_name,
                       'align'     => 'tree',
                       'node'      => $node_id,
+                      'strain'    => $is_strain,
                     };
 
     $self->add_entry({