Merge pull request #4927 from solgenomics/topic/genefamilies

Add a genefamily overview table

lib/SGN/Controller/AJAX/Genefamily.pm

@@ -0,0 +1,26 @@
+
+package SGN::Controller::AJAX::Genefamily;
+
+use Moose;
+use SGN::Genefamily;
+
+BEGIN { extends 'Catalyst::Controller::REST'; }
+
+sub browse_families_table :Path('/ajax/tools/genefamily/table') Args(0) {
+    my $self = shift;
+    my $c = shift;
+
+    my $build = $c->req->param("build");
+
+    my $genefamily_dir = $c->config->{genefamily_dir};
+    my $genefamily_format = $c->config->{genefamily_format};
+
+    my $gf = SGN::Genefamily->new( { files_dir => $genefamily_dir, genefamily_format => $genefamily_format, build => $build });
+
+    my $data_ref = $gf -> table();
+
+    $c->stash->{rest} = { data => $data_ref };
+
+}
+
+1;

lib/SGN/Controller/Genefamily.pm

@@ -0,0 +1,187 @@
+
+package SGN::Controller::Genefamily;
+
+use Moose;
+
+use Data::Dumper;
+
+BEGIN { extends 'Catalyst::Controller'; }
+
+sub genefamily_index :Path('/tools/genefamily') Args(0) {
+    my $self = shift;
+    my $c = shift;
+
+    $c->stash->{template} = '/tools/genefamily/index.mas';
+}
+
+
+sub search : Path('/tools/genefamily/search') Args(0) {
+    my $self = shift;
+    my $c = shift;
+
+#    if ($c->user()) { 
+#	if (grep(/curator|genefamily_editor/, $c->user->get_object()->get_roles() )) { 
+
+	    $c->stash->{genefamily_id} = $c->req->param("genefamily_id") || '';
+	    $c->stash->{build} = $c->req->param("build") || '';
+	    $c->stash->{member_id} = $c->req->param("member_id") || '';
+	    $c->stash->{action} = $c->req->param("action") || '';
+
+	    $c->stash->{template} = '/tools/genefamily/search.mas';
+#	}
+#	else {
+#	    $c->stash->{message} = "You do not have the necessary privileges to access this page.";
+#	    $c->stash->{template} = "/generic_message.mas";
+#	}
+
+ #   }
+  #  else {
+#	$c->stash->{message} = "You need to be logged in to access this page.";
+#	$c->stash->{template} = "/generic_message.mas";
+ #   }
+
+}
+
+sub sequence_details :Path('/tools/genefamily/seq') Args(3) {
+    my $self = shift;
+    my $c = shift;
+    my $build = shift;
+    my $family = shift;
+    my $sequence = shift;
+
+    my $gf = SGN::Genefamily->new(
+	name      => $family,
+        build   => $build,
+        files_dir => $c->config()->{genefamily_dir},
+	);
+
+    print STDERR "Trying to locate sequence $sequence\n";
+
+    my $seq_info  = $gf->get_sequence($sequence);
+
+    my ($seq_id, $desc, $seq) = @$seq_info;
+    $c->stash->{build} = $build;
+    $c->stash->{family} = $family;
+    $c->stash->{seq_id} = $seq_id;
+    $c->stash->{desc} = $desc || "[ no description provided ]";
+    $c->stash->{seq} = $seq;
+
+    $c->stash->{template} = '/tools/genefamily/sequence.mas';
+
+
+}
+
+sub get_family_fasta :Path('/tools/genefamily/fasta/') Args(2) {
+    my $self = shift;
+    my $c = shift;
+    my $build = shift;
+    my $family = shift;
+
+    my $gf = SGN::Genefamily->new(
+	name      => $family,
+        build   => $build,
+        files_dir => $c->config()->{genefamily_dir},
+	);
+
+    my $fasta_seq = $gf -> get_fasta();
+
+    $c->stash->{build} = $build;
+    $c->stash->{family} = $family;
+    $c->stash->{fasta} = $fasta_seq;
+
+    $c->stash->{template} = '/tools/genefamily/fasta.mas';
+}
+
+sub genefamily_details :Path('/tools/genefamily/details') Args(2) {
+    my $self = shift;
+    my $c = shift;
+    my $build = shift;
+    my $family = shift;
+
+    my $gf = SGN::Genefamily->new(
+        name      => $family,
+        build   => $build,
+        files_dir => $c->config()->{genefamily_dir},
+	);
+
+    my $seq_data ="";
+    my $fasta_data = "";
+    my $tree_data = "";
+    my $annot_data = "";
+    my $exp_data = "";
+
+    my $align_link_disabled = "";
+    my $fasta_link_disabled = "";
+    my $tree_link_disabled = "";
+    my $exp_link_disabled = "";
+
+    my $errors = "";
+    my $big_errors = 0;
+
+    if (!$family) {
+	$c->stash->{template} = '/generic_message.mas';
+	$c->stash->{message} = 'Need a family to display!';
+	return;
+    }
+
+    $c->stash->{genefamily_id} = $family;
+
+    my $members = $gf->get_members($family);
+
+    print STDERR "Members: ".Dumper($members);
+
+    $c->stash->{member_count} = scalar(@$members);
+    $c->stash->{members} = join(", ", @$members);
+
+
+    eval {
+      $c->stash->{seq_data} = $gf->get_alignment();
+    };
+
+    if ($@) {
+      $errors .= "Alignment data not available. ";
+      $big_errors++;
+      $align_link_disabled="disabled";
+    }
+
+    eval {
+      $c->stash->{fasta_data} = $gf->get_fasta();
+
+    };
+
+    if ($@) {
+      $errors .= "Sequence data not available. ";
+      $big_errors++;
+      $fasta_link_disabled = "disabled";
+    }
+    eval {
+      $c->stash->{tree_data} = $gf->get_tree();
+    };
+    if ($@) {
+      $errors .= "Tree data not available. ";
+      $c->stash->{tree_link_disabled} = "disabled"
+    }
+    eval {
+      $c->stash->{annot_data} = $gf->get_annotation();
+    };
+    if ($@) {
+      $errors .= "Annotation data not available. ";
+      $c->stash->{annot_data} = "(No annotation data available)";
+    }
+    eval {
+      $errors .= "Expression data not available. ";
+      $c->stash->{exp_data} = $gf->get_expression();
+    };
+    if ($@) {
+      $c->stash->{exp_link_disabled} = "disabled";
+    }
+
+    if ($big_errors > 0) { 
+      $errors = "This family does not seem to exist!\n";
+    }
+
+    $c->stash->{template} = '/tools/genefamily/details.mas';
+
+}
+
+1;