Question: Cannot copy datasets from one history to another on local Galaxy
0
gravatar for mipsandc
6 days ago by
mipsandc0
mipsandc0 wrote:

Hi all,

We have a local instance of Galaxy installed but it is not able to be copy files from one history to another via the "copy datasets" option on the right tool bar. Is there a setting that has to be set so that this can occur, I have not found anything in the galaxy.ini file, but I could have missed it.

The log file prints has this stack trace, I am not sure what to make of it.

----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 45606)
Traceback (most recent call last):
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib64/python2.7/SocketServer.py", line 334, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib64/python2.7/SocketServer.py", line 649, in __init__
    self.handle()
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 459, in handle
    BaseHTTPRequestHandler.handle(self)
  File "/usr/lib64/python2.7/BaseHTTPServer.py", line 340, in handle
    self.handle_one_request()
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 454, in handle_one_request
    self.wsgi_execute()
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 304, in wsgi_execute
    self.wsgi_start_response)
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/deploy/config.py", line 291, in __call__
    return self.app(environ, start_response)
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/urlmap.py", line 216, in __call__
    return app(environ, start_response)
  File "/localdata1/galaxy/lib/galaxy/web/framework/middleware/batch.py", line 75, in __call__
    return self.application( environ, start_response )
  File "/localdata1/galaxy/lib/galaxy/web/framework/middleware/request_id.py", line 14, in __call__
    return self.app( environ, start_response )
  File "/localdata1/galaxy/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 22, in __call__
    return self.app( environ, start_response )
  File "/localdata1/galaxy/lib/galaxy/web/framework/middleware/translogger.py", line 71, in __call__
    return self.application(environ, replacement_start_response)
  File "/localdata1/galaxy/lib/galaxy/web/framework/middleware/error.py", line 164, in __call__
    exc_info)
  File "/localdata1/galaxy/lib/galaxy/web/framework/middleware/translogger.py", line 70, in replacement_start_response
    return start_response( status, headers, exc_info )
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 173, in wsgi_start_response
    six.reraise(exc_info[0], exc_info[1], exc_info[2])
  File "/localdata1/galaxy/lib/galaxy/web/framework/middleware/error.py", line 154, in __call__
    app_iter = self.application(environ, sr_checker)
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "/localdata1/galaxy/lib/galaxy/web/framework/base.py", line 134, in __call__
    return self.handle_request( environ, start_response )
  File "/localdata1/galaxy/lib/galaxy/web/framework/base.py", line 199, in handle_request
    return body_renderer( trans, body, environ, start_response )
  File "/localdata1/galaxy/lib/galaxy/web/framework/base.py", line 206, in _render_body
    return body( environ, start_response )
  File "/localdata1/galaxy/lib/galaxy/web/framework/webapp.py", line 918, in render
    template.render_context( context )
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/mako/template.py", line 468, in render_context
    **kwargs)
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/mako/runtime.py", line 864, in _render_context
    _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
  File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/mako/runtime.py", line 890, in _exec_template
    callable_(context, *args, **kwargs)
  File "/localdata1/galaxy/database/compiled_templates/base/base_panels.mako.py", line 125, in render_body
    __M_writer(unicode(self.center_panel()))
  File "/localdata1/galaxy/database/compiled_templates/display_base.mako.py", line 180, in render_center_panel
    __M_writer(unicode(self.render_content()))
  File "/localdata1/galaxy/database/compiled_templates/display_base.mako.py", line 144, in render_render_content
    __M_writer(unicode(self.render_item( item, item_data )))
  File "/localdata1/galaxy/database/compiled_templates/history/display.mako.py", line 79, in render_render_item
    __M_writer(unicode(h.dumps( content_dicts )))
  File "/localdata1/galaxy/lib/galaxy/util/json.py", line 64, in safe_dumps
    dumped = json.dumps( *args, allow_nan=False, **kwargs )
  File "/usr/lib64/python2.7/json/__init__.py", line 250, in dumps
    sort_keys=sort_keys, **kw).encode(obj)
  File "/usr/lib64/python2.7/json/encoder.py", line 207, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/usr/lib64/python2.7/json/encoder.py", line 270, in iterencode
    return _iterencode(o, 0)
  File "/usr/lib64/python2.7/json/encoder.py", line 184, in default
    raise TypeError(repr(o) + " is not JSON serializable")
TypeError: <mako.runtime.Undefined object="" at="" 0x3786a50=""> is not JSON serializable
----------------------------------------

If anyone could offer any insights, it would be much appreciated. Thanks!

galaxy • 32 views
ADD COMMENTlink written 6 days ago by mipsandc0
0
gravatar for mipsandc
3 days ago by
mipsandc0
mipsandc0 wrote:

This issue has resolved itself. Not sure how, as there was no restart or any changed made recently on our end.

ADD COMMENTlink written 3 days ago by mipsandc0
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