Hey Greg,

Sorry for not being clear.  I'm trying to create a sample information form
where users can import csv files which would contain DIFFERENT values for
each field.  So, while one sample may have value 'agctac'  for the last
field, another sample will have a different value, say '123.  So, these
can't be hardcoded in the sample form definition. Since these are form
fields, of course the field NAMES should remain standard and field VALUES
should will keep changing.  From what I understand, the sample form
definition will have the field NAMES and the csv file will have different
field VALUES. Galaxy should map the field VALUES to the field NAMES.

My form has the following field names:  (change this accordingly)

SampleName
LibraryName
LibraryFolder
History
Workflow
Barcode

A user may submit a csv file such as:

Sample1,Library1,Folder1,History1,Workflow1,BarcodeAC
Sample10,Library10,Folder10,History10,Workflow10,BarcodeDE

Galaxy should take this csv file, parse it, create two samples (Sample1 and
Sample10) and assign the rest of the values to the corresponding fields for
each sample.


Thanks,
joe

On Thu, Jun 9, 2011 at 8:50 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:

> Joe,
>
> Try editing your Sample Form Definition, changing the "Field name" value
> from the default of "1_field_name" to be your desired "agctac".  Then, your
> csv file with the line
>
> Sample1,Library1,Lib1Folder1,History,Workflow,agctac
>
> should work.
>
> Greg
>
>
> On Jun 9, 2011, at 6:03 PM, Joe Cruz wrote:
>
> Hey Greg,
>
> I got it to work by filling the field names with their default names, but I
> thought you could fill out the entire sample forms, including the field
> names, with the csv file.  For example:
>
> Sample1,Library1,Lib1Folder1,History,Workflow,1_field_name
>
> The above works when imported, filling out the sample name, library,
> folder, history, and workflow fields but leaving 1_field_name (barcode field
> in this case) empty.
>
> We wish this next example to work,which I currently get the '1_field_name'
>  error:
>
> Sample1,Library1,Lib1Folder1,History,Workflow,agctac
>
> Currently we have clients fill out a spreadsheet for the samples they
> intend to submit, since many submit multiple samples and most of the time
> have the same parameters for all of them.  We wish to convert their
> completed spreadsheet into a csv file and then import it into galaxy so they
> dont' have to fill out all the fields repetitively.
>
> joe
>
> On Thu, Jun 9, 2011 at 3:20 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>
>> Hello Joe,
>>
>> Sorry you've bumped into problems - we know we're lacking on documentation
>> for the sample tracking stuff currently.   I believe this new issue is due
>> to a field named differently in your Sample FormDefinition vs your csf file.
>>  In looking at this, I found a slightly incorrect description of the csv
>> file layout on our Add Samples page, which I've corrected.
>>
>> In the Sample FormDefinition, the default name for a field is
>> 1_field_name, 2_field_name, etc.  Below is a screen capture that show this.
>>  However, the csv file you sent me previously includes the following:
>>
>>
>> SampleName1,library1,library1_folder1,history1,workflow1,sampleType1,conc,runType,readLength
>>
>> The csv layout is as follows ( I've correct the incorrect FieldValue1, etc
>> to be Field1Name, etc.
>>
>> The csv file must be in the following format:
>>
>> SampleName,DataLibraryName,DataLibraryFolderName,HistoryName,WorkflowName,Field1Name,Field2name..
>>
>> The Field1Name, Field2Name values in your csv file must match the value in
>> the Field name form field in the screen shot below.
>>
>> After making this change, let me know if you bump into any other problems.
>>
>> Thanks for you patience on this,
>>
>> Greg
>>
>> <sample_form.tiff>
>> On Jun 9, 2011, at 12:32 PM, Joe Cruz wrote:
>>
>> 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 <g...@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 <g...@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-information-is-broken#comment-510683
>>>> \
>>>>
>>>> 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:
>>>>
>>>>  http://lists.bx.psu.edu/
>>>>
>>>>
>>>>  Greg Von Kuster
>>>> Galaxy Development Team
>>>> g...@bx.psu.edu
>>>>
>>>>
>>>>
>>>>
>>> <importSample.csv>
>>>
>>>
>>>  Greg Von Kuster
>>> Galaxy Development Team
>>> g...@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/
>>
>>
>> Greg Von Kuster
>> Galaxy Development Team
>> g...@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/
>
>
> Greg Von Kuster
> Galaxy Development Team
> g...@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/

Reply via email to