Re: [galaxy-dev] workflow input param issue
This should be resolved in changeset 1ac27213bafb in galaxy-central. Thanks for pointing this out! -Dannon On Dec 3, 2012, at 11:37 AM, Marc Logghe wrote: > Hi, > The conf of the parameters in question looks like this: > > > > > > > > > > > > >Select 1 or more targets if you would like to restrict your data set > > > > The idea is that if a project is chosen from the project1 dropdown list, the > target1 parameter is updated. > This seems to work fine as a standalone tool. > As soon as the tool is wrapped into a workflow, this gets broken: if project1 > is chosen from the list, a server call is made but the response seems to > reset the form fields. Both project1 and target1. > > Thanks, > Marc > > > > From: galaxy-dev-boun...@lists.bx.psu.edu > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Marc Logghe > Sent: Monday, December 03, 2012 11:46 AM > To: galaxy-dev@lists.bx.psu.edu > Subject: [galaxy-dev] workflow input param issue > > Hi, > I have a workflow that basically needs a select parameter as input. 2 steps > in the workflow actually need the very same input. I don’t think there is a > (easy) way to let the user only input the parameter once and that it is > passed to both steps. > Anyhow, currently - as a workaround and not very user friendly - the user > needs to input the very same parameter twice, for each step where that > parameter is required. > The first issue however, is that as soon as the first parameter is set, the > second is set as well apparently (they have the same name, that could > explain) which is fine, but not to the chosen one, eg. both are kind of reset > to default. No errors or something, simply reset, which makes it impossible > to enter the parameter. > > > THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY > TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, > CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. > If the reader of this E-mail message is not the intended recipient, you are > hereby notified that any dissemination, distribution or copying of this > communication is strictly prohibited. If you have received this communication > in error, please notify us immediately at abl...@ablynx.com. Thank you for > your co-operation. > "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. > > ___ > 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: > > http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] workflow input param issue
Hi, The conf of the parameters in question looks like this: Select 1 or more targets if you would like to restrict your data set The idea is that if a project is chosen from the project1 dropdown list, the target1 parameter is updated. This seems to work fine as a standalone tool. As soon as the tool is wrapped into a workflow, this gets broken: if project1 is chosen from the list, a server call is made but the response seems to reset the form fields. Both project1 and target1. Thanks, Marc From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Marc Logghe Sent: Monday, December 03, 2012 11:46 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] workflow input param issue Hi, I have a workflow that basically needs a select parameter as input. 2 steps in the workflow actually need the very same input. I don't think there is a (easy) way to let the user only input the parameter once and that it is passed to both steps. Anyhow, currently - as a workaround and not very user friendly - the user needs to input the very same parameter twice, for each step where that parameter is required. The first issue however, is that as soon as the first parameter is set, the second is set as well apparently (they have the same name, that could explain) which is fine, but not to the chosen one, eg. both are kind of reset to default. No errors or something, simply reset, which makes it impossible to enter the parameter. THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] workflow input param issue
Hi John,
Your patch works indeed. Issues--
Thanks,
Marc
-Original Message-
From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton
Sent: Monday, December 03, 2012 2:58 PM
To: Marc Logghe
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] workflow input param issue
I am really very sorry about that. It seems this must be related to my pull
request "fixing" multiple input tool parameters. I have spent some time this
morning trying to reproduce your error, but I cannot.
That said I think I can fix it, this patch should work:
diff --git a/templates/workflow/run.mako b/templates/workflow/run.mako index
c7cd138..175f148 100644
--- a/templates/workflow/run.mako
+++ b/templates/workflow/run.mako
@@ -243,9 +243,12 @@ if wf_parms:
%if isinstance( param, DataToolParameter ):
%if ( prefix + param.name ) in step.input_connections_by_name:
<%
-conn = step.input_connections_by_name[ prefix
+ param.name ]
+conns = step.input_connections_by_name[
prefix + param.name ]
+if not isinstance(conns, list):
+conns = [conns]
+vals = ["Output dataset '%s' from step %d" %
(conn.output_name, int(conn.output_step.order_index)+1
%>
-Output dataset '${conn.output_name}' from step
${int(conn.output_step.order_index)+1}
+${",".join(vals)}
%else:
## FIXME: Initialize in the controller
<%
Can you apply the patch and tell me if it works? Probably a similar fix needs
to be applied to display.mako also, but I want to be able to recreate the
problem first or at least verify this fixes it.
-John
On Mon, Dec 3, 2012 at 4:45 AM, Marc Logghe wrote:
> Hi,
>
> I have a workflow that basically needs a select parameter as input. 2
> steps in the workflow actually need the very same input. I don't think
> there is a
> (easy) way to let the user only input the parameter once and that it
> is passed to both steps.
>
> Anyhow, currently - as a workaround and not very user friendly - the
> user needs to input the very same parameter twice, for each step where
> that parameter is required.
>
> The first issue however, is that as soon as the first parameter is
> set, the second is set as well apparently (they have the same name,
> that could
> explain) which is fine, but not to the chosen one, eg. both are kind
> of reset to default. No errors or something, simply reset, which makes
> it impossible to enter the parameter.
>
>
>
> Next, I hoped to solve the issue by upgrading galaxy to the most
> recent version. This was not the case since the workflow did not run
> at all anymore, which brings me to the second issue (see exception dump
> below).
>
> Any ideas anyone ?
>
> Thanks and regards,
>
> Marc
>
>
>
>
>
> Error - : 'list' object has no
> attribute 'output_name'
>
> URL: http://smith:8889/workflow/run?id=4b187121143038ff
>
> File
> '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/exceptions/err
> ormiddleware.py',
> line 143 in __call__
>
> app_iter = self.application(environ, start_response)
>
> File
> '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
> line 80 in __call__
>
> return self.application(environ, start_response)
>
> File
> '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions
> .py',
> line 632 in __call__
>
> return self.application(environ, start_response)
>
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/base.py', line
> 160 in __call__
>
> body = method( trans, **kwargs )
>
> File
> '/home/galaxy/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/workflo
> w.py',
> line 1523 in run
>
>
> enable_unique_defaults=trans.app.config.enable_unique_workflow_default
> s)
>
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py',
> line
> 836 in fill_template
>
> return self.fill_template_mako( filename, **kwargs )
>
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py',
> line
> 847 in fill_template_mako
>
> return template.render( **data )
>
> File
> '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
> line 296 in render
>
> return runtime._render(self, self.callable_, args, data)
>
> File
> '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
> line 660 in _render
>
> **_kwarg
Re: [galaxy-dev] workflow input param issue
I am really very sorry about that. It seems this must be related to my
pull request "fixing" multiple input tool parameters. I have spent
some time this morning trying to reproduce your error, but I cannot.
That said I think I can fix it, this patch should work:
diff --git a/templates/workflow/run.mako b/templates/workflow/run.mako
index c7cd138..175f148 100644
--- a/templates/workflow/run.mako
+++ b/templates/workflow/run.mako
@@ -243,9 +243,12 @@ if wf_parms:
%if isinstance( param, DataToolParameter ):
%if ( prefix + param.name ) in step.input_connections_by_name:
<%
-conn = step.input_connections_by_name[ prefix
+ param.name ]
+conns = step.input_connections_by_name[
prefix + param.name ]
+if not isinstance(conns, list):
+conns = [conns]
+vals = ["Output dataset '%s' from step %d" %
(conn.output_name, int(conn.output_step.order_index)+1
%>
-Output dataset '${conn.output_name}' from step
${int(conn.output_step.order_index)+1}
+${",".join(vals)}
%else:
## FIXME: Initialize in the controller
<%
Can you apply the patch and tell me if it works? Probably a similar
fix needs to be applied to display.mako also, but I want to be able to
recreate the problem first or at least verify this fixes it.
-John
On Mon, Dec 3, 2012 at 4:45 AM, Marc Logghe wrote:
> Hi,
>
> I have a workflow that basically needs a select parameter as input. 2 steps
> in the workflow actually need the very same input. I don’t think there is a
> (easy) way to let the user only input the parameter once and that it is
> passed to both steps.
>
> Anyhow, currently - as a workaround and not very user friendly - the user
> needs to input the very same parameter twice, for each step where that
> parameter is required.
>
> The first issue however, is that as soon as the first parameter is set, the
> second is set as well apparently (they have the same name, that could
> explain) which is fine, but not to the chosen one, eg. both are kind of
> reset to default. No errors or something, simply reset, which makes it
> impossible to enter the parameter.
>
>
>
> Next, I hoped to solve the issue by upgrading galaxy to the most recent
> version. This was not the case since the workflow did not run at all
> anymore, which brings me to the second issue (see exception dump below).
>
> Any ideas anyone ?
>
> Thanks and regards,
>
> Marc
>
>
>
>
>
> Error - : 'list' object has no attribute
> 'output_name'
>
> URL: http://smith:8889/workflow/run?id=4b187121143038ff
>
> File
> '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py',
> line 143 in __call__
>
> app_iter = self.application(environ, start_response)
>
> File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
> line 80 in __call__
>
> return self.application(environ, start_response)
>
> File
> '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py',
> line 632 in __call__
>
> return self.application(environ, start_response)
>
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in
> __call__
>
> body = method( trans, **kwargs )
>
> File
> '/home/galaxy/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/workflow.py',
> line 1523 in run
>
> enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults)
>
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line
> 836 in fill_template
>
> return self.fill_template_mako( filename, **kwargs )
>
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line
> 847 in fill_template_mako
>
> return template.render( **data )
>
> File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
> line 296 in render
>
> return runtime._render(self, self.callable_, args, data)
>
> File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
> line 660 in _render
>
> **_kwargs_for_callable(callable_, data))
>
> File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
> line 692 in _render_context
>
> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
>
> File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
> line 718 in _exec_template
>
> callable_(context, *args, **kwargs)
>
> File '/home/galaxy/galaxy-dev/database/compiled_templates/base.mako.py',
> line 42 in render_body
>
> __M_writer(unicode(next.body()))
>
> File
> '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py',
> line 171 in render_body
>
> __M_writer(unicode(do_inputs( tool.inputs, step.state.inputs, errors.get(
> step.id, dict() ), "", step, None, used_accumulator )))
>
> File
> '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py',
> line 4
[galaxy-dev] workflow input param issue
Hi, I have a workflow that basically needs a select parameter as input. 2 steps in the workflow actually need the very same input. I don't think there is a (easy) way to let the user only input the parameter once and that it is passed to both steps. Anyhow, currently - as a workaround and not very user friendly - the user needs to input the very same parameter twice, for each step where that parameter is required. The first issue however, is that as soon as the first parameter is set, the second is set as well apparently (they have the same name, that could explain) which is fine, but not to the chosen one, eg. both are kind of reset to default. No errors or something, simply reset, which makes it impossible to enter the parameter. Next, I hoped to solve the issue by upgrading galaxy to the most recent version. This was not the case since the workflow did not run at all anymore, which brings me to the second issue (see exception dump below). Any ideas anyone ? Thanks and regards, Marc Error - : 'list' object has no attribute 'output_name' URL: http://smith:8889/workflow/run?id=4b187121143038ff File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 1523 in run enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults) File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 836 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 847 in fill_template_mako return template.render( **data ) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy/galaxy-dev/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 171 in render_body __M_writer(unicode(do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator ))) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 40 in do_inputs return render_do_inputs(context.locals_(__M_locals),inputs,values,errors,prefix,step,other_values,already_used) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 435 in render_do_inputs __M_writer(unicode(row_for_param( input, values[ input.name ], other_values, errors, prefix, step, already_used ))) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 338 in row_for_param return render_row_for_param(context,param,value,other_values,error_dict,prefix,step,already_used) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 498 in render_row_for_param __M_writer(unicode(conn.output_name)) AttributeError: 'list' object has no attribute 'output_name' THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ___ 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: http://lists.bx.psu.edu/
