Yep, that example filesystem_paths you suggest should work fine.  The
sleep() bit was a complete hack from the start, for simplicity in
demonstrating a very basic pipeline, but what you probably want to do for a
real implementation is query the dataset in question via the API, verify
that the datatype/etc have been set, and only after that execute the
workflow; instead of relying on sleep.


On Mon, Apr 29, 2013 at 9:24 AM, Rob Leclerc <robert.lecl...@gmail.com>wrote:

> Hi Dannon,
>
> Thanks for the response. Sorry to be pedantic, but just to make sure that
> I understand the interpretation of this field on the other side of the API,
> I would need to have something like the following:
>
> data['filesystem_paths'] = "/home/me/file1.vcf \n /home/me/file2.vcf /n
> /home/me/file3.vcf"
>
> I assume I should also increase the time.sleep() to reflect the uploading
> of extra files?
>
> Cheers,
>
> Rob
>
> Rob Leclerc, PhD
> <http://www.linkedin.com/in/robleclerc><https://twitter.com/#!/robleclerc>
> P: (US) +1-(917)-873-3037
> P: (Shanghai) +86-1-(861)-612-5469
> Personal Email: rob.lecl...@aya.yale.edu
>
>
> On Mon, Apr 29, 2013 at 9:15 AM, Dannon Baker <dannon.ba...@gmail.com>wrote:
>
>> Hey Rob,
>>
>> That example_watch_folder.py does just submit exactly one at a time,
>> executes the workflow, and then does the next all in separate transactions.
>>  If you wanted to upload multiple filepaths at once, you'd just append more
>> to the ''filesystem_paths' field (newline separated paths).
>>
>> -Dannon
>>
>>
>> On Fri, Apr 26, 2013 at 11:54 PM, Rob Leclerc 
>> <robert.lecl...@gmail.com>wrote:
>>
>>> I'm looking at example_watch_folder.py and it's not clear from the
>>> example how you submit multiple datasets to a library. In the example, the
>>> first submit returns a libset [] with only a single entry and then proceeds
>>> to iterate through each dataset in the libset in the following section:
>>>
>>> data = {}
>>>
>>>    data['folder_id'] = library_folder_id
>>>
>>>    data['file_type'] = 'auto'
>>>
>>>    data['dbkey'] = ''
>>>
>>>    data['upload_option'] = 'upload_paths'
>>>
>>>
>>>
>>> *data['filesystem_paths'] = fullpath*
>>>
>>>    data['create_type'] = 'file'
>>>
>>>    libset = submit(api_key, api_url + "libraries/%s/contents" %
>>> library_id, data, return_formatted = False)
>>>
>>>    time.sleep(5)
>>>
>>>    for ds in libset:
>>>
>>>        if 'id' in ds:
>>>
>>>                         wf_data = {}
>>>
>>>                         wf_data['workflow_id'] = workflow['id']
>>>
>>>                         wf_data['history'] = "%s - %s" % (fname,
>>> workflow['name'])
>>>
>>>                         wf_data['ds_map'] = {}
>>>
>>>                         for step_id, ds_in in workflow['inputs'
>>> ].iteritems():
>>>
>>>                             wf_data['ds_map'][step_id] = {'src':'ld',
>>> 'id':ds['id']}
>>>
>>>                         res = submit( api_key, api_url + 'workflows',
>>> wf_data, return_formatted=False)
>>>
>>>
>>>
>>> Rob Leclerc, PhD
>>> <http://www.linkedin.com/in/robleclerc><https://twitter.com/#!/robleclerc>
>>> P: (US) +1-(917)-873-3037
>>> P: (Shanghai) +86-1-(861)-612-5469
>>> Personal Email: rob.lecl...@aya.yale.edu
>>>
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>>
>>
>
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