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

[Wei, Xuehong]

Hi Anne,

Thanks for the information. I just updated ensembl-webcode to the release/79. The problem is still there. And I take a look at the master code at https://github.com/Ensembl/ensembl-webcode/blob/release/79/modules/EnsEMBL/Web/File/Utils/URL.pm

The function get_headers still use my $response = $http->request('HEAD', $url);

sub get_headers {
        ### Get one or all headers from a remote file
        ### @param url - URL of file
        ### @param Args Hashref
        ### header (optional) String - name of header
        ### hub EnsEMBL::Web::Hub
        ### nice (optional) Boolean - see introduction
        ### compression String (optional) - compression type
        ### @return Hashref containing results (single header or hashref of headers) or errors (ArrayRef)
        my ($file, $args) = @_;
        my $url = ref($file) ? $file->absolute_read_path : $file;
        my ($all_headers, $result, $error);

        if ($url =~ /^ftp/) {
        ## TODO - support FTP properly!
        return {'Content-Type' => 1};
        }
        else {
        my %params = ('timeout' => 10);
        if ($args->{'hub'}->species_defs->ENSEMBL_WWW_PROXY) {
        $params{'http_proxy'} = $args->{'hub'}->species_defs->ENSEMBL_WWW_PROXY;
        $params{'https_proxy'} = $args->{'hub'}->species_defs->ENSEMBL_WWW_PROXY;
        }
        my $http = HTTP::Tiny->new(%params);

        my $response = $http->request('HEAD', $url);
        if ($response->{'success'}) {
        $all_headers = $response->{'headers'};
        }
        else {
        $error = _get_http_tiny_error($response);
        }
        }

        $result = $args->{'header'} ? $all_headers->{$args->{'header'}} : $all_headers;

        if ($args->{'nice'}) {
        return $error ? {'error' => [$error]} : {'headers' => $result};
        }
        else {
        if ($error) {
        throw exception('URLException', "Could not get headers.") unless $args->{'no_exception'};
        return 0;
        }
        else {
        return $result;
        }
        }
        }



Sharon


On Mar 24, 2015, at 5:14 AM, Anne Lyle <annelyle at ebi.ac.uk<mailto:annelyle at ebi.ac.uk>> wrote:

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<mailto: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><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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