Hey Greg, Unfortunately after pulling your changeset I got a new error related to '1_field_name'. Here is the error traceback: URL: http://localhost:8080/requests_common/add_samples?cntrller=requests&id=f2db41e1fa331b3e File '/home/jcruz/galaxy-central/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/jcruz/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/jcruz/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/jcruz/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/jcruz/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/jcruz/galaxy-central/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/jcruz/galaxy-central/lib/galaxy/web/framework/__init__.py', line 84 in decorator return func( self, trans, *args, **kwargs ) File '/home/jcruz/galaxy-central/lib/galaxy/web/controllers/requests_common.py', line 831 in add_samples return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, workflows, **kwd ) File '/home/jcruz/galaxy-central/lib/galaxy/web/controllers/requests_common.py', line 1163 in __import_samples sample_copy_select_field=sample_copy_select_field ) File '/home/jcruz/galaxy-central/lib/galaxy/web/framework/__init__.py', line 661 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/jcruz/galaxy-central/lib/galaxy/web/framework/__init__.py', line 672 in fill_template_mako return template.render( **data ) File '/home/jcruz/galaxy-central/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/home/jcruz/galaxy-central/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/home/jcruz/galaxy-central/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/jcruz/galaxy-central/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/home/jcruz/galaxy-central/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/home/jcruz/galaxy-central/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in <lambda> return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/home/jcruz/galaxy-central/database/compiled_templates/requests/common/ add_samples.mako.py', line 176 in render_body __M_writer(unicode(render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, show_saved_samples_read_only=True ))) File '/home/jcruz/galaxy-central/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in <lambda> return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/home/jcruz/galaxy-central/database/compiled_templates/requests/common/ common.mako.py', line 120 in render_render_request_type_sample_form_grids __M_writer(unicode(render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict, display_only ))) File '/home/jcruz/galaxy-central/database/compiled_templates/requests/common/ common.mako.py', line 73 in render_sample_form return render_render_sample_form(context,index,sample_name,sample_values,fields_dict,display_only) File '/home/jcruz/galaxy-central/database/compiled_templates/requests/common/ common.mako.py', line 186 in render_render_sample_form field_value = sample_values[ field_name ] KeyError: '1_field_name' Let me know if you need anything else. Thanks again! joe On Wed, Jun 8, 2011 at 2:49 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Joe,
Thanks very much for the example csv file. I've fixed this issue in change set 5668:81a5c317d909, which should be available in the distribution within the next few weeks. If you don't want to wait, you can update from our development repo at https://bitbucket.org/galaxy/galaxy-central/wiki/Home.
Greg Von Kuster
On Jun 7, 2011, at 6:21 PM, Joe Cruz wrote:
For my sample forms I have fields for Sample type, concentration, run type, and read length.
I greatly appreciate your help Greg. If you have any other questions let me know.
Thanks,
Joe
On Tue, Jun 7, 2011 at 2:56 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Joe,
Can you send me your csv file?
Thanks!
On Jun 7, 2011, at 10:45 AM, Joe Cruz wrote:
Hello Everyone,
I wanted to ask if anyone has experience successfully importing sample information through a csv file.
I know there is an issue already created for csv file import, which I left a comment earlier:
https://bitbucket.org/galaxy/galaxy-central/issue/398/csv-import-of-sample-i... \
but my bug doesn't seem to deal with an 'Invalid Request ID' as the issue above states.
This is the error I get:
URL: http://localhost/requests_common/add_samples?cntrller=requests&id=a65cf3ca8eb85be3 File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 84 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/controllers/requests_common.py', line 829 in add_samples return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/controllers/requests_common.py', line 1109 in __import_samples sample_copy_select_field=sample_copy_select_field ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy1/galaxy-dist/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in <lambda> return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/home/galaxy1/galaxy-dist/database/compiled_templates/requests/common/ add_samples.mako.py', line 164 in render_body __M_writer(unicode(render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', adding_new_samples=True, encoded_selected_sample_ids=[], render_buttons=False, grid_header=grid_header ))) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in <lambda> return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/home/galaxy1/galaxy-dist/database/compiled_templates/requests/common/ common.mako.py', line 749 in render_render_samples_grid sample_widget_history = sample_widget[ 'history' ] KeyError: 'history'
I greatly appreciate your help and patience.
Thanks,
joe ___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
<importSample.csv>
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu