1:12 a.m.
Hi,
I am getting an error page when I try to open the bowtie2 tool page (after
selecting older version 0.2 a54de7e658f7 from drop down on version 0.3
c1ec08cb34f9 page).
URL: http://....../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/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
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'params'
I can't see anything that gives me a clue where to investigate further,
hopefully someone here knows?
I have tried updating to latest changeset, and have restarted a few times,
but still the same error.
Thanks in advance for help
Anna
1:29 p.m.
Hi again,
I have just updated Picard, and am getting a similar error with some tools
from that repository when I switch to older version from tool page.
I also noticed that some tools from the Picard repo appear as multiple
entries for different in the tool panel rather than selecting the different
versions from the drop down.
These errors are all on tools with version dropdowns, however I don't get
these errors on all of the version dropdowns, for instance I can switch to
an older version of fastqc no problem.
So are the new versions of tools breaking old versions, or is there a
problem with the tool panel?
Any help appreciated!!
SamToFastq:
URL: http://....../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/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
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'single_paired_end_type'
ReorderSam:
URL: http://....../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/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
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'source'
FastqToSam:
URL: http://...../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/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
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'param_type'
On 18 December 2014 at 01:12, Anna Terry <iseeglass(a)googlemail.com> wrote:
Hi,
I am getting an error page when I try to open the bowtie2 tool page (after
selecting older version 0.2 a54de7e658f7 from drop down on version 0.3
c1ec08cb34f9 page).
URL: http://....../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/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
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'params'
I can't see anything that gives me a clue where to investigate further,
hopefully someone here knows?
I have tried updating to latest changeset, and have restarted a few times,
but still the same error.
Thanks in advance for help
Anna
1:55 p.m.
Deleting the newer 0.3 version of Bowtie fixes the problem with version 0.2.
On 18 December 2014 at 13:29, Anna Terry <iseeglass(a)googlemail.com> wrote:
Hi again,
I have just updated Picard, and am getting a similar error with some tools
from that repository when I switch to older version from tool page.
I also noticed that some tools from the Picard repo appear as multiple
entries for different in the tool panel rather than selecting the different
versions from the drop down.
These errors are all on tools with version dropdowns, however I don't get
these errors on all of the version dropdowns, for instance I can switch to
an older version of fastqc no problem.
So are the new versions of tools breaking old versions, or is there a
problem with the tool panel?
Any help appreciated!!
SamToFastq:
URL: http://....../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/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
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'single_paired_end_type'
ReorderSam:
URL: http://....../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/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
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'source'
FastqToSam:
URL: http://...../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/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
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'param_type'
On 18 December 2014 at 01:12, Anna Terry <iseeglass(a)googlemail.com> wrote:
>
> Hi,
> I am getting an error page when I try to open the bowtie2 tool page
> (after selecting older version 0.2 a54de7e658f7 from drop down on version
> 0.3 c1ec08cb34f9 page).
>
> URL: http://....../tool_runner/index
> File
>
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
> line 364 in respond
> app_iter = self.application(environ, detect_start_response)
> File
> '/home/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
>
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
> line 107 in __call__
> return self.app( environ, start_response )
> File
>
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
> 132 in __call__
> return self.handle_request( environ, start_response )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
> 190 in handle_request
> body = method( trans, **kwargs )
> File
>
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
> line 90 in index
> template, vars = tool.handle_input( trans, params.__dict__ )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136
> in handle_input
> errors, params = self.__check_param_values( trans, expanded_incoming,
> expanded_state, old_errors, process_state, history=history, source=source )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251
> in __check_param_values
> errors = self.update_state( trans, inputs, state.inputs, incoming,
> old_errors=old_errors or {}, source=source )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514
> in update_state
> group_state = state[input.name]
> KeyError: 'params'
>
> I can't see anything that gives me a clue where to investigate further,
> hopefully someone here knows?
> I have tried updating to latest changeset, and have restarted a few
> times, but still the same error.
>
> Thanks in advance for help
> Anna
>
>
2:27 p.m.
Hello Anna,
Yeah - this is readily reproducible. I will work on this problem today
- sorry about that.
-John
On Thu, Dec 18, 2014 at 8:55 AM, Anna Terry <iseeglass(a)googlemail.com> wrote:
Deleting the newer 0.3 version of Bowtie fixes the problem with
version 0.2.
On 18 December 2014 at 13:29, Anna Terry <iseeglass(a)googlemail.com> wrote:
>
> Hi again,
> I have just updated Picard, and am getting a similar error with some tools
> from that repository when I switch to older version from tool page.
> I also noticed that some tools from the Picard repo appear as multiple
> entries for different in the tool panel rather than selecting the different
> versions from the drop down.
> These errors are all on tools with version dropdowns, however I don't get
> these errors on all of the version dropdowns, for instance I can switch to
> an older version of fastqc no problem.
> So are the new versions of tools breaking old versions, or is there a
> problem with the tool panel?
>
> Any help appreciated!!
>
>
> SamToFastq:
> URL: http://....../tool_runner/index
> File
>
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
> line 364 in respond
> app_iter = self.application(environ, detect_start_response)
> File
> '/home/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
>
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
> line 107 in __call__
> return self.app( environ, start_response )
> File
>
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
> in __call__
> return self.handle_request( environ, start_response )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
> in handle_request
> body = method( trans, **kwargs )
> File
>
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
> line 90 in index
> template, vars = tool.handle_input( trans, params.__dict__ )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
> handle_input
> errors, params = self.__check_param_values( trans, expanded_incoming,
> expanded_state, old_errors, process_state, history=history, source=source )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
> __check_param_values
> errors = self.update_state( trans, inputs, state.inputs, incoming,
> old_errors=old_errors or {}, source=source )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
> update_state
> group_state = state[input.name]
> KeyError: 'single_paired_end_type'
>
>
> ReorderSam:
> URL: http://....../tool_runner/index
> File
>
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
> line 364 in respond
> app_iter = self.application(environ, detect_start_response)
> File
> '/home/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
>
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
> line 107 in __call__
> return self.app( environ, start_response )
> File
>
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
> in __call__
> return self.handle_request( environ, start_response )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
> in handle_request
> body = method( trans, **kwargs )
> File
>
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
> line 90 in index
> template, vars = tool.handle_input( trans, params.__dict__ )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
> handle_input
> errors, params = self.__check_param_values( trans, expanded_incoming,
> expanded_state, old_errors, process_state, history=history, source=source )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
> __check_param_values
> errors = self.update_state( trans, inputs, state.inputs, incoming,
> old_errors=old_errors or {}, source=source )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
> update_state
> group_state = state[input.name]
> KeyError: 'source'
>
> FastqToSam:
> URL: http://...../tool_runner/index
> File
>
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
> line 364 in respond
> app_iter = self.application(environ, detect_start_response)
> File
> '/home/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
>
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
> line 107 in __call__
> return self.app( environ, start_response )
> File
>
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
> in __call__
> return self.handle_request( environ, start_response )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
> in handle_request
> body = method( trans, **kwargs )
> File
>
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
> line 90 in index
> template, vars = tool.handle_input( trans, params.__dict__ )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
> handle_input
> errors, params = self.__check_param_values( trans, expanded_incoming,
> expanded_state, old_errors, process_state, history=history, source=source )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
> __check_param_values
> errors = self.update_state( trans, inputs, state.inputs, incoming,
> old_errors=old_errors or {}, source=source )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
> update_state
> group_state = state[input.name]
> KeyError: 'param_type'
>
>
>
>
> On 18 December 2014 at 01:12, Anna Terry <iseeglass(a)googlemail.com> wrote:
>>
>> Hi,
>> I am getting an error page when I try to open the bowtie2 tool page
>> (after selecting older version 0.2 a54de7e658f7 from drop down on version
>> 0.3 c1ec08cb34f9 page).
>>
>> URL: http://....../tool_runner/index
>> File
>>
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
>> line 364 in respond
>> app_iter = self.application(environ, detect_start_response)
>> File
>>
'/home/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
>>
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
>> line 107 in __call__
>> return self.app( environ, start_response )
>> File
>>
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
>> 132 in __call__
>> return self.handle_request( environ, start_response )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
>> 190 in handle_request
>> body = method( trans, **kwargs )
>> File
>>
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
>> line 90 in index
>> template, vars = tool.handle_input( trans, params.__dict__ )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136
>> in handle_input
>> errors, params = self.__check_param_values( trans, expanded_incoming,
>> expanded_state, old_errors, process_state, history=history, source=source )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251
>> in __check_param_values
>> errors = self.update_state( trans, inputs, state.inputs, incoming,
>> old_errors=old_errors or {}, source=source )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514
>> in update_state
>> group_state = state[input.name]
>> KeyError: 'params'
>>
>> I can't see anything that gives me a clue where to investigate further,
>> hopefully someone here knows?
>> I have tried updating to latest changeset, and have restarted a few
>> times, but still the same error.
>>
>> Thanks in advance for help
>> Anna
>>
___________________________________________________________
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3:50 p.m.
Okay - so there are a bunch of issues here. To me the highest priority
is not being able to even load and run the old versions of the tool. I
have opened a pull request with a fix for that here
(https://bitbucket.org/galaxy/galaxy-central/pull-request/620/stable-dont-...).
I would expect within a couple days it is back-ported to the
latest_2014.10.06 tag of galaxy-dist.
There is also the problem of the duplicated tools. For me that goes
away after one restarts Galaxy (unless the tools aren't in a tool
section). Can you verify that restarting Galaxy fixes the problem or
that you have installed them outside a tool section (like they aren't
is a Picard section on the side or something like that). The
non-grouping of non-sectioned parameters is a known issue being
tracked here -
https://trello.com/c/l9bjV0vT/1973-tool-grouping-doesn-t-work-outside-of-...
- I don't think it has seen much movement because we generally install
tools into sections on usegalaxy.org.
The issue with some of the picard tools appearing twice is a problem
but we don't really have a way to resolve it. The fully qualified id
changed as part of a big update to the picard wrappers - some tools
have new "owners" in the tool shed. I don't think we will change the
id again - so hopefully it is not a problem going forward (and we will
try to limit this problem from happening again if we can). If you
don't want to uninstall the older versions that are by themselves -
one fix would be to open your shed_tool_conf.xml file and add a
hidden="true" tag to each - this should allow workflows and tool
re-running to still work without actually causing the tool to appear
in the tool panel. This is how we are planning to resolve the problem
on our servers. This is less than ideal - there is more about this
topic here https://github.com/galaxyproject/tools-devteam/pull/34 if
you are curious.
I am very sorry about all of these problems - certainly these are all
still very active development priorities (how to display multiple
versions, dealing with tool lineages, etc...) and I am confident there
will be improvements to all of this over the next year.
Let me know if I missed something or if there are still outstanding problems.
-John
On Thu, Dec 18, 2014 at 8:29 AM, Anna Terry <iseeglass(a)googlemail.com> wrote:
Hi again,
I have just updated Picard, and am getting a similar error with some tools
from that repository when I switch to older version from tool page.
I also noticed that some tools from the Picard repo appear as multiple
entries for different in the tool panel rather than selecting the different
versions from the drop down.
These errors are all on tools with version dropdowns, however I don't get
these errors on all of the version dropdowns, for instance I can switch to
an older version of fastqc no problem.
So are the new versions of tools breaking old versions, or is there a
problem with the tool panel?
Any help appreciated!!
SamToFastq:
URL: http://....../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/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
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'single_paired_end_type'
ReorderSam:
URL: http://....../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/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
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'source'
FastqToSam:
URL: http://...../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/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
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'param_type'
On 18 December 2014 at 01:12, Anna Terry <iseeglass(a)googlemail.com> wrote:
>
> Hi,
> I am getting an error page when I try to open the bowtie2 tool page (after
> selecting older version 0.2 a54de7e658f7 from drop down on version 0.3
> c1ec08cb34f9 page).
>
> URL: http://....../tool_runner/index
> File
>
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
> line 364 in respond
> app_iter = self.application(environ, detect_start_response)
> File
> '/home/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
>
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
> line 107 in __call__
> return self.app( environ, start_response )
> File
>
'/home/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 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
> in __call__
> return self.handle_request( environ, start_response )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
> in handle_request
> body = method( trans, **kwargs )
> File
>
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
> line 90 in index
> template, vars = tool.handle_input( trans, params.__dict__ )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
> handle_input
> errors, params = self.__check_param_values( trans, expanded_incoming,
> expanded_state, old_errors, process_state, history=history, source=source )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
> __check_param_values
> errors = self.update_state( trans, inputs, state.inputs, incoming,
> old_errors=old_errors or {}, source=source )
> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
> update_state
> group_state = state[input.name]
> KeyError: 'params'
>
> I can't see anything that gives me a clue where to investigate further,
> hopefully someone here knows?
> I have tried updating to latest changeset, and have restarted a few times,
> but still the same error.
>
> Thanks in advance for help
> Anna
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
2752
days inactive
2752
days old
galaxy-dev@lists.galaxyproject.org
4 comments
2 participants
participants (2)
-
Anna Terry -
John Chilton