From de163a599fc19e931fbd1905444e952f8f8330c1 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Tue, 1 Oct 2013 11:19:06 +0000
Subject: [PATCH] [ENSCORESW-680]. Adding a max allowed time limit to optimise
a tree in for web.
The optimise tree step can take a very long time and cause web timeouts. We have
added a time limit expressed in floting-point seconds. If an optimisation is
taking longer than the specified time we will abort any more attempts.
---
.../Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm | 16 +++++++++++-----
1 file changed, 11 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
index 9434161e19..48817ec201 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
@@ -802,12 +802,18 @@ sub fetch_successors_by_archive_id {
=head2 fetch_history_tree_by_stable_id
- Arg[1] : String $stable_id - the stable ID to fetch the history tree for
- Arg[2] : (optional) Int $num_high_scorers
+ Arg [1] : String $stable_id - the stable ID to fetch the history tree for
+ Arg [2] : (optional) Int $num_high_scorers
number of mappings per stable ID allowed when filtering
- Arg[3] : (optional) Int $max_rows
+ Arg [3] : (optional) Int $max_rows
maximum number of stable IDs in history tree (used for
filtering)
+ Arg [4] : (optional) Float $time_limit
+ Optimise tree normally runs until it hits a minimised state
+ but this can take a very long time. Therefore you can
+ opt to bail out of the optimisation early. Specify the
+ time in seconds. Floating point values are supported should you
+ require sub-second limits
Example : my $history = $archive_adaptor->fetch_history_tree_by_stable_id(
'ENSG00023747897');
Description : Returns the history tree for a given stable ID. This will
@@ -825,7 +831,7 @@ sub fetch_successors_by_archive_id {
=cut
sub fetch_history_tree_by_stable_id {
- my ($self, $stable_id, $num_high_scorers, $max_rows) = @_;
+ my ($self, $stable_id, $num_high_scorers, $max_rows, $time_limit) = @_;
throw("Expecting a stable ID argument.") unless $stable_id;
@@ -981,7 +987,7 @@ sub fetch_history_tree_by_stable_id {
# calculate grid coordinates for the sorted tree; this will also try to
# untangle the tree
- $history->calculate_coords;
+ $history->calculate_coords($time_limit);
return $history;
}
--
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