Dear Developers,

I would like to use bioblend to export the result of a galaxy workflow.

To do that, we want to use an implemented tool called export_data; which enables the copy of a result file from galaxy arborescence to a local directory which belong to the user making the analysis and the export.

We tried to launch this tool using the run_tool function but it doesn't work.


giOlivia.tools.run_tool(history_id='xxxxxxxxxxx',tool_id='yyyyyyyy/export_data/export/2.2',tool_inputs={'input':'id_data','name':"data"})

I get an error message which is very long and attached to this email.

Please help me on that it is the final step of several ones using bioblend.

Have a nice day,

--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur

Traceback (most recent call last):
  File "script_testBioblend_distant.py", line 6, in <module>
    
giOlivia.tools.run_tool(history_id='729031331e2ffdfc',tool_id='galaxy.web.pasteur.fr/toolshed-pasteur/repos/fmareuil/export_data/export/2.2',tool_inputs=tool_inputs)
  File 
"/usr/local/lib/python2.7/dist-packages/bioblend-0.4.2_dev-py2.7.egg/bioblend/galaxy/tools/__init__.py",
 line 25, in run_tool
    return Client._post(self, payload)
  File 
"/usr/local/lib/python2.7/dist-packages/bioblend-0.4.2_dev-py2.7.egg/bioblend/galaxy/client.py",
 line 71, in _post
    r = self.gi.make_post_request(url, payload=payload, 
files_attached=files_attached)
  File 
"/usr/local/lib/python2.7/dist-packages/bioblend-0.4.2_dev-py2.7.egg/bioblend/galaxyclient.py",
 line 94, in make_post_request
    r.status_code, body=r.text)     # @see self.body for HTTP response body
bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy: 500: 
    <!DOCTYPE HTML>
    <html>
    <head>
    <style type="text/css">
    body { color: #303030; background: #dfe5f9; font-family:"Lucida 
Grande",verdana,arial,helvetica,sans-serif; font-size:12px; line-height:16px; }
    .content { max-width: 720px; margin: auto; margin-top: 50px; }
    </style>
    <title>Internal Server Error</title>
    
<style type="text/css">
body {
  font-family: Helvetica, sans-serif;
}

table {
  width: 100%;
}

tr.header {
  background-color: #006;
  color: #fff;
}

tr.even {
  background-color: #ddd;
}

table.variables td {
  vertical-align: top;
  overflow: auto;
}

a.button {
  background-color: #ccc;
  border: 2px outset #aaa;
  color: #000;
  text-decoration: none;
}

a.button:hover {
  background-color: #ddd;
}

code.source {
  color: #006;
}

a.switch_source {
  color: #090;
  text-decoration: none;
}

a.switch_source:hover {
  background-color: #ddd;
}

.source-highlight {
  background-color: #ff9;
}

</style>

<script type="text/javascript">
function hide_display(id) {
    var el = document.getElementById(id);
    if (el.className == "hidden-data") {
        el.className = "";
        return true;
    } else {
        el.className = "hidden-data";
        return false;
    }
}
document.write('<style type="text/css">\n');
document.write('.hidden-data {display: none}\n');
document.write('</style>\n');
function show_button(toggle_id, name) {
    document.write('<a href="#' + toggle_id
        + '" onclick="javascript:hide_display(\'' + toggle_id
        + '\')" class="button">' + name + '</a><br>');
}

function switch_source(el, hide_type) {
    while (el) {
        if (el.getAttribute &&
            el.getAttribute('source-type') == hide_type) {
            break;
        }
        el = el.parentNode;
    }
    if (! el) {
        return false;
    }
    el.style.display = 'none';
    if (hide_type == 'long') {
        while (el) {
            if (el.getAttribute &&
                el.getAttribute('source-type') == 'short') {
                break;
            }
            el = el.nextSibling;
        }
    } else {
        while (el) {
            if (el.getAttribute &&
                el.getAttribute('source-type') == 'long') {
                break;
            }
            el = el.previousSibling;
        }
    }
    if (el) {
        el.style.display = '';
    }
    return false;
}

</script>
    </head>
    <body>
    <div class="content">
    <h1>Internal Server Error</h1>

    <h2>Galaxy was unable to successfully complete your request</h2>

    <p>
    URL: <a 
href="http://galaxy.web.pasteur.fr/api/tools?key=c23d8cb98671911813305051710d4ae1";>http://galaxy.web.pasteur.fr/api/tools?key=c23d8cb98671911813305051710d4ae1</a><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py">galaxy.web.framework.middleware.error</span>:<b>149</b>
 in <code>__call__</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; 
</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
__traceback_supplement__ = Supplement, self, environ<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 sr_checker = ResponseStartChecker(start_response)<br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 app_iter = self.application(environ, sr_checker)</span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 return self.make_catching_iter(app_iter, environ, sr_checker)<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
except:</code><code class="source" source-type="short"><a onclick="return 
switch_source(this, 'short')" class="switch_source" href="#">&gt;&gt;&nbsp; 
</a><font color="#333333">app_iter</font> <b>=</b> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">application</font><b>(</b><font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">sr_checker</font><b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py">paste.recursive</span>:<b>84</b>
 in <code>__call__</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; </a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#333333">environ</font><b>[</b><font 
color="#600080">'paste.recursive.script_name'</font><b>]</b> <b>=</b> <font 
color="#333333">my_script_name</font><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>try</b></font><b>:</b><br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">application</font><b>(</b><font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font><b>)</b></span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>except</b></font> <font 
color="#333333">ForwardRequestException</font><b>,</b> <font 
color="#333333">e</font><b>:</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#333333">middleware</font> <b>=</b> <font 
color="#333333">CheckForRecursionMiddleware</font><b>(</b></code><code 
class="source" source-type="short"><a onclick="return switch_source(this, 
'short')" class="switch_source" href="#">&gt;&gt;&nbsp; </a><font 
color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">application</font><b>(</b><font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font><b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py">galaxy.web.framework.middleware.remoteuser</span>:<b>96</b>
 in <code>__call__</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; 
</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
#self.error( start_response, &quot;Access to PASTEUR GALAXY is denied&quot;, 
&quot;GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA&quot;)&nbsp; #MAREUIL<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 # The API handles its own authentication via keys<br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 return self.app( environ, start_response )</span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else:<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 title = &quot;Access to Galaxy is denied&quot;</code><code class="source" 
source-type="short"><a onclick="return switch_source(this, 'short')" 
class="switch_source" href="#">&gt;&gt;&nbsp; </a><font 
color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font color="#333333">app</font><b>(</b> 
<font color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font> <b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py">paste.httpexceptions</span>:<b>633</b>
 in <code>__call__</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; 
</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <b>[</b><b>]</b><b>)</b><b>.</b><font 
color="#333333">append</font><b>(</b><font 
color="#333333">HTTPException</font><b>)</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>try</b></font><b>:</b><br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">application</font><b>(</b><font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font><b>)</b></span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>except</b></font> <font 
color="#333333">HTTPException</font><b>,</b> <font 
color="#333333">exc</font><b>:</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#0000AF"><b>return</b></font> <font 
color="#333333">exc</font><b>(</b><font color="#333333">environ</font><b>,</b> 
<font color="#333333">start_response</font><b>)</b></code><code class="source" 
source-type="short"><a onclick="return switch_source(this, 'short')" 
class="switch_source" href="#">&gt;&gt;&nbsp; </a><font 
color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">application</font><b>(</b><font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font><b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py">galaxy.web.framework.base</span>:<b>132</b>
 in <code>__call__</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; </a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#333333">self</font><b>.</b><font color="#333333">trace</font><b>(</b> 
<font color="#333333">message</font><b>=</b><font color="#A0008A">"Starting 
request"</font> <b>)</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>try</b></font><b>:</b><br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">handle_request</font><b>(</b> <font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font> <b>)</b></span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>finally</b></font><b>:</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#333333">self</font><b>.</b><font 
color="#333333">trace</font><b>(</b> <font 
color="#333333">message</font><b>=</b><font color="#A0008A">"Handle request 
finished"</font> <b>)</b></code><code class="source" source-type="short"><a 
onclick="return switch_source(this, 'short')" class="switch_source" 
href="#">&gt;&gt;&nbsp; </a><font color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">handle_request</font><b>(</b> <font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font> <b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py">galaxy.web.framework.base</span>:<b>190</b>
 in <code>handle_request</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; </a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#333333">kwargs</font><b>.</b><font color="#333333">pop</font><b>(</b> 
<font color="#600080">'_'</font><b>,</b> <font color="#333333">None</font> 
<b>)</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>try</b></font><b>:</b><br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#333333">body</font> <b>=</b> <font 
color="#333333">method</font><b>(</b> <font 
color="#333333">trans</font><b>,</b> <b>**</b><font 
color="#333333">kwargs</font> <b>)</b></span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>except</b></font> <font 
color="#333333">Exception</font><b>,</b> <font 
color="#333333">e</font><b>:</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#333333">body</font> <b>=</b> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">handle_controller_exception</font><b>(</b> <font 
color="#333333">e</font><b>,</b> <font color="#333333">trans</font><b>,</b> 
<b>**</b><font color="#333333">kwargs</font> <b>)</b></code><code 
class="source" source-type="short"><a onclick="return switch_source(this, 
'short')" class="switch_source" href="#">&gt;&gt;&nbsp; </a><font 
color="#333333">body</font> <b>=</b> <font 
color="#333333">method</font><b>(</b> <font 
color="#333333">trans</font><b>,</b> <b>**</b><font 
color="#333333">kwargs</font> <b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py">galaxy.web.framework</span>:<b>201</b>
 in <code>decorator</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; 
</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; raise # 
handled<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; except 
Exception, err:<br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 log.exception( 'Uncaught exception in exposed API method:'+ 
str(err),exc_info=True)</span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 raise paste.httpexceptions.HTTPServerError()</code><code class="source" 
source-type="short"><a onclick="return switch_source(this, 'short')" 
class="switch_source" href="#">&gt;&gt;&nbsp; </a><font 
color="#333333">log</font><b>.</b><font 
color="#333333">exception</font><b>(</b> <font color="#600080">'Uncaught 
exception in exposed API method:'</font><b>+</b> <font 
color="#333333">str</font><b>(</b><font 
color="#333333">err</font><b>)</b><b>,</b><font 
color="#333333">exc_info</font><b>=</b><font 
color="#333333">True</font><b>)</b></code><br>
<b>TypeError: exception() got an unexpected keyword argument 'exc_info'</b><br>
<script type="text/javascript">
show_button('extra_data', 'extra data');
</script>
<div id="extra_data" class="hidden-data">
<br>
<table class="variables">
<tr class="header"><th colspan="2">CGI Variables</th></tr>
<tr class="odd"><td>CONTENT_LENGTH</td>
<td><tt>'192'</tt></td></tr>
<tr class="even"><td>CONTENT_TYPE</td>
<td><tt>'application/json'</tt></td></tr>
<tr class="odd"><td>HTTP_ACCEPT</td>
<td><tt>'*/*'</tt></td></tr>
<tr class="even"><td>HTTP_ACCEPT_ENCODING</td>
<td><tt>'gzip, deflate, compress'</tt></td></tr>
<tr class="odd"><td>HTTP_CONNECTION</td>
<td><tt>'Keep-Alive'</tt></td></tr>
<tr class="even"><td>HTTP_HOST</td>
<td><tt>'galaxy.web.pasteur.fr'</tt></td></tr>
<tr class="odd"><td>HTTP_USER_AGENT</td>
<td><tt>'python-requests/2.0.1 CPython/2.7.5+ 
Linux/3.11.0-15-generic'</tt></td></tr>
<tr class="even"><td>HTTP_X_FORWARDED_FOR</td>
<td><tt>'87.231.42.131'</tt></td></tr>
<tr class="odd"><td>HTTP_X_FORWARDED_HOST</td>
<td><tt>'galaxy.web.pasteur.fr'</tt></td></tr>
<tr class="even"><td>HTTP_X_FORWARDED_SERVER</td>
<td><tt>'galaxy.web.pasteur.fr'</tt></td></tr>
<tr class="odd"><td>ORGINAL_HTTP_HOST</td>
<td><tt>'localhost:18085'</tt></td></tr>
<tr class="even"><td>ORGINAL_REMOTE_ADDR</td>
<td><tt>'127.0.0.1'</tt></td></tr>
<tr class="odd"><td>PATH_INFO</td>
<td><tt>'/api/tools'</tt></td></tr>
<tr class="even"><td>QUERY_STRING</td>
<td><tt>'key=c23d8cb98671911813305051710d4ae1'</tt></td></tr>
<tr class="odd"><td>REMOTE_ADDR</td>
<td><tt>'87.231.42.131'</tt></td></tr>
<tr class="even"><td>REQUEST_METHOD</td>
<td><tt>'POST'</tt></td></tr>
<tr class="odd"><td>SERVER_NAME</td>
<td><tt>'127.0.0.1'</tt></td></tr>
<tr class="even"><td>SERVER_PORT</td>
<td><tt>'18085'</tt></td></tr>
<tr class="odd"><td>SERVER_PROTOCOL</td>
<td><tt>'HTTP/1.1'</tt></td></tr>
</table><br>
<table class="variables">
<tr class="header"><th colspan="2">WSGI Variables</th></tr>
<tr class="odd"><td>application</td>
<td><tt>&lt;paste.recursive.RecursiveMiddleware object at 
0x9814050&gt;</tt></td></tr>
<tr class="even"><td>is_api_request</td>
<td><tt>True</tt></td></tr>
<tr class="odd"><td>paste.cookies</td>
<td><tt>(&lt;SimpleCookie: &gt;, '')</tt></td></tr>
<tr class="even"><td>paste.expected_exceptions</td>
<td><tt>[&lt;class 'paste.httpexceptions.HTTPException'&gt;]</tt></td></tr>
<tr class="odd"><td>paste.httpexceptions</td>
<td><tt>&lt;paste.httpexceptions.HTTPExceptionHandler object at 
0x97eef90&gt;</tt></td></tr>
<tr class="even"><td>paste.httpserver.thread_pool</td>
<td><tt>&lt;paste.httpserver.ThreadPool object at 0x9b0c210&gt;</tt></td></tr>
<tr class="odd"><td>paste.parsed_querystring</td>
<td><tt>([('key', 'c23d8cb98671911813305051710d4ae1')], 
'key=c23d8cb98671911813305051710d4ae1')</tt></td></tr>
<tr class="even"><td>paste.recursive.forward</td>
<td><tt>&lt;paste.recursive.Forwarder from /&gt;</tt></td></tr>
<tr class="odd"><td>paste.recursive.include</td>
<td><tt>&lt;paste.recursive.Includer from /&gt;</tt></td></tr>
<tr class="even"><td>paste.recursive.include_app_iter</td>
<td><tt>&lt;paste.recursive.IncluderAppIter from /&gt;</tt></td></tr>
<tr class="odd"><td>paste.recursive.script_name</td>
<td><tt>''</tt></td></tr>
<tr class="even"><td>paste.throw_errors</td>
<td><tt>True</tt></td></tr>
<tr class="odd"><td>request_id</td>
<td><tt>'50dfed809adc11e3aebd003048f24604'</tt></td></tr>
<tr class="even"><td>webob._parsed_query_vars</td>
<td><tt>(MultiDict([('key', 'c23d8cb98671911813305051710d4ae1')]), 
'key=c23d8cb98671911813305051710d4ae1')</tt></td></tr>
<tr class="odd"><td>wsgi process</td>
<td><tt>'Multithreaded'</tt></td></tr>
</table><br>
</div>
    <br>
    <script type="text/javascript">
    show_button('full_traceback', 'full traceback')
    </script>
    <div id="full_traceback" class="hidden-data">
    URL: <a 
href="http://galaxy.web.pasteur.fr/api/tools?key=c23d8cb98671911813305051710d4ae1";>http://galaxy.web.pasteur.fr/api/tools?key=c23d8cb98671911813305051710d4ae1</a><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py">galaxy.web.framework.middleware.error</span>:<b>149</b>
 in <code>__call__</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; 
</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
__traceback_supplement__ = Supplement, self, environ<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 sr_checker = ResponseStartChecker(start_response)<br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 app_iter = self.application(environ, sr_checker)</span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 return self.make_catching_iter(app_iter, environ, sr_checker)<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
except:</code><code class="source" source-type="short"><a onclick="return 
switch_source(this, 'short')" class="switch_source" href="#">&gt;&gt;&nbsp; 
</a><font color="#333333">app_iter</font> <b>=</b> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">application</font><b>(</b><font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">sr_checker</font><b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py">paste.recursive</span>:<b>84</b>
 in <code>__call__</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; </a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#333333">environ</font><b>[</b><font 
color="#600080">'paste.recursive.script_name'</font><b>]</b> <b>=</b> <font 
color="#333333">my_script_name</font><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>try</b></font><b>:</b><br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">application</font><b>(</b><font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font><b>)</b></span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>except</b></font> <font 
color="#333333">ForwardRequestException</font><b>,</b> <font 
color="#333333">e</font><b>:</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#333333">middleware</font> <b>=</b> <font 
color="#333333">CheckForRecursionMiddleware</font><b>(</b></code><code 
class="source" source-type="short"><a onclick="return switch_source(this, 
'short')" class="switch_source" href="#">&gt;&gt;&nbsp; </a><font 
color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">application</font><b>(</b><font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font><b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py">galaxy.web.framework.middleware.remoteuser</span>:<b>96</b>
 in <code>__call__</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; 
</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
#self.error( start_response, &quot;Access to PASTEUR GALAXY is denied&quot;, 
&quot;GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA&quot;)&nbsp; #MAREUIL<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 # The API handles its own authentication via keys<br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 return self.app( environ, start_response )</span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else:<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 title = &quot;Access to Galaxy is denied&quot;</code><code class="source" 
source-type="short"><a onclick="return switch_source(this, 'short')" 
class="switch_source" href="#">&gt;&gt;&nbsp; </a><font 
color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font color="#333333">app</font><b>(</b> 
<font color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font> <b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py">paste.httpexceptions</span>:<b>633</b>
 in <code>__call__</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; 
</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <b>[</b><b>]</b><b>)</b><b>.</b><font 
color="#333333">append</font><b>(</b><font 
color="#333333">HTTPException</font><b>)</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>try</b></font><b>:</b><br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">application</font><b>(</b><font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font><b>)</b></span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>except</b></font> <font 
color="#333333">HTTPException</font><b>,</b> <font 
color="#333333">exc</font><b>:</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#0000AF"><b>return</b></font> <font 
color="#333333">exc</font><b>(</b><font color="#333333">environ</font><b>,</b> 
<font color="#333333">start_response</font><b>)</b></code><code class="source" 
source-type="short"><a onclick="return switch_source(this, 'short')" 
class="switch_source" href="#">&gt;&gt;&nbsp; </a><font 
color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">application</font><b>(</b><font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font><b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py">galaxy.web.framework.base</span>:<b>132</b>
 in <code>__call__</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; </a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#333333">self</font><b>.</b><font color="#333333">trace</font><b>(</b> 
<font color="#333333">message</font><b>=</b><font color="#A0008A">"Starting 
request"</font> <b>)</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>try</b></font><b>:</b><br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">handle_request</font><b>(</b> <font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font> <b>)</b></span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>finally</b></font><b>:</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#333333">self</font><b>.</b><font 
color="#333333">trace</font><b>(</b> <font 
color="#333333">message</font><b>=</b><font color="#A0008A">"Handle request 
finished"</font> <b>)</b></code><code class="source" source-type="short"><a 
onclick="return switch_source(this, 'short')" class="switch_source" 
href="#">&gt;&gt;&nbsp; </a><font color="#0000AF"><b>return</b></font> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">handle_request</font><b>(</b> <font 
color="#333333">environ</font><b>,</b> <font 
color="#333333">start_response</font> <b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py">galaxy.web.framework.base</span>:<b>190</b>
 in <code>handle_request</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; </a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#333333">kwargs</font><b>.</b><font color="#333333">pop</font><b>(</b> 
<font color="#600080">'_'</font><b>,</b> <font color="#333333">None</font> 
<b>)</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>try</b></font><b>:</b><br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#333333">body</font> <b>=</b> <font 
color="#333333">method</font><b>(</b> <font 
color="#333333">trans</font><b>,</b> <b>**</b><font 
color="#333333">kwargs</font> <b>)</b></span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font 
color="#0000AF"><b>except</b></font> <font 
color="#333333">Exception</font><b>,</b> <font 
color="#333333">e</font><b>:</b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <font color="#333333">body</font> <b>=</b> <font 
color="#333333">self</font><b>.</b><font 
color="#333333">handle_controller_exception</font><b>(</b> <font 
color="#333333">e</font><b>,</b> <font color="#333333">trans</font><b>,</b> 
<b>**</b><font color="#333333">kwargs</font> <b>)</b></code><code 
class="source" source-type="short"><a onclick="return switch_source(this, 
'short')" class="switch_source" href="#">&gt;&gt;&nbsp; </a><font 
color="#333333">body</font> <b>=</b> <font 
color="#333333">method</font><b>(</b> <font 
color="#333333">trans</font><b>,</b> <b>**</b><font 
color="#333333">kwargs</font> <b>)</b></code><br>
Module <span class="module" 
title="/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py">galaxy.web.framework</span>:<b>201</b>
 in <code>decorator</code><br>
<code style="display: none" class="source" source-type="long"><a 
class="switch_source" onclick="return switch_source(this, 'long')" 
href="#">&lt;&lt;&nbsp; 
</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; raise # 
handled<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; except 
Exception, err:<br>
<span 
class="source-highlight">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 log.exception( 'Uncaught exception in exposed API method:'+ 
str(err),exc_info=True)</span><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 raise paste.httpexceptions.HTTPServerError()</code><code class="source" 
source-type="short"><a onclick="return switch_source(this, 'short')" 
class="switch_source" href="#">&gt;&gt;&nbsp; </a><font 
color="#333333">log</font><b>.</b><font 
color="#333333">exception</font><b>(</b> <font color="#600080">'Uncaught 
exception in exposed API method:'</font><b>+</b> <font 
color="#333333">str</font><b>(</b><font 
color="#333333">err</font><b>)</b><b>,</b><font 
color="#333333">exc_info</font><b>=</b><font 
color="#333333">True</font><b>)</b></code><br>
<b>TypeError: exception() got an unexpected keyword argument 'exc_info'</b>
    </div>
    <br>
    <script type="text/javascript">
    show_button('text_version', 'text version')
    </script>
    <div id="text_version" class="hidden-data">
    <textarea style="width: 100%" rows=10 cols=60>URL: 
http://galaxy.web.pasteur.fr/api/tools?key=c23d8cb98671911813305051710d4ae1
File 
'/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
 line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File 
'/pasteur/projets/common/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
 line 84 in __call__
  return self.application(environ, start_response)
File 
'/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
 line 96 in __call__
  return self.app( environ, start_response )
File 
'/pasteur/projets/common/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
 line 633 in __call__
  return self.application(environ, start_response)
File 
'/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', 
line 132 in __call__
  return self.handle_request( environ, start_response )
File 
'/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', 
line 190 in handle_request
  body = method( trans, **kwargs )
File 
'/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
 line 201 in decorator
  log.exception( 'Uncaught exception in exposed API method:'+ 
str(err),exc_info=True)
TypeError: exception() got an unexpected keyword argument 'exc_info'</textarea>
    </div>
    </p>

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