[ensembl-dev] Atlas tracks - fail to add on Gramene genome browser, method not allowed

[Anne Lyle]

Hi

We’re aware of this issue, and recently pushed out a fix which sends a GET request instead of HEAD. Have you updated your ensembl-webcode repository in the past few days?

Cheers

Anne



> On 23 Mar 2015, at 17:37, Wei, Xuehong <weix at cshl.edu> wrote:
> 
> Hi, Ensembl Developers,
> 
> On Gramene genome browser which is build on top of ensemble web infrastructure, users cannot succeed in adding Atlas tracks by url. In the error log, we see error messages like
> 
> "Uncaught exception 'URLException' with message 'Could not get headers.'\n  Thrown by EnsEMBL::Web::File::Utils::URL::get_headers in module EnsEMBL::Web::File::Utils::URL at /usr/local/ensembl-live/ensembl-webcode/modules/EnsEMBL/Web/File/Utils/URL.pm on line 302…”
> 
> I further trace the source of the error to the following code in function get_header
> 
>    my $http = HTTP::Tiny->new(%params);
>    my $response = $http->request('HEAD', $url); ####FAILED
> 
> I wrote a test script to test this $http->request and found while ‘HEAD’ returned error, ‘GET’ would succeed (See below). Obviously ensemble genome browser has no problem using ‘HEAD’. So I am wondering whether this is a permission setting on wwwdev.ebi.ac.uk<http://wwwdev.ebi.ac.uk> that restricts the methods from outside request to ‘GET’. If it is, could you grant outside request ‘HEAD’ method too?
> 
> Thanks,
> 
> 
> #!/bin/env perl
> 
> use HTTP::Tiny;
> use Data::Dumper;
> 
> my $url='http://wwwdev.ebi.ac.uk/gxa/experiments/E-ATMX-20/tracks/E-ATMX-20.g1_g2.genes.log2foldchange.bedGraph';
> 
> 
> my $http = HTTP::Tiny->new;
> 
> my $response = $http->request('HEAD', $url);
> 
> warn (Dumper($response));
> 
> 
> perl test.pl
> 
> $VAR1 = {
>          'success' => '',
>          'protocol' => 'HTTP/1.1',
>          'headers' => {
>                         'content-type' => 'text/html;charset=UTF-8',
>                         'set-cookie' => 'JSESSIONID=C3301F4233490280BC8F2658EF225186; Path=/gxa/; HttpOnly',
>                         'transfer-encoding' => 'chunked',
>                         'date' => 'Sun, 22 Mar 2015 19:13:36 GMT',
>                         'vary' => 'Accept-Encoding',
>                         'allow' => 'GET',
>                         'server' => 'Apache-Coyote/1.1'
>                       },
>          'status' => '405',
>          'url' => 'http://wwwdev.ebi.ac.uk/gxa/experiments/E-ATMX-20/tracks/E-ATMX-20.g1_g2.genes.log2foldchange.bedGraph',
>          'reason' => 'Method Not Allowed'
>        };
> 
> Sharon
> 
> 
> 
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