Hi Dannon. Thanks! I had been experimenting with BioBlend and forgot to add the /api/ on the url.

./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f http://localhost:8080/api/ /Users/Rob/Documents/galaxy-db/input/ /Users/Rob/Documents/galaxy-db/output/ "API Imports" 2a56795cad3c7db3

However, I am now running into a new error when it tries to create the API Imports folder

Traceback (most recent call last):
File "./example_watch_folder.py", line 87, in <module>
main(api_key, api_url, in_folder, out_folder, data_library, workflow )

File "./example_watch_folder.py", line 30, in main
library_id = library[0]['id']
KeyError: 0

(This is coming from the section that creates 'API Imports' library if it doesn't already exist)

24: for library in libs:

25:      if library['name'] == data_library:

26:         library_id = library['id']

27:  if not library_id:

28:        lib_create_data = {'name':data_library}

29:        library = submit(api_key, api_url + 'libraries', lib_create_data, return_formatted=False)

30:        library_id = library[0]['id']

As I mentioned, I'm not familiar with python, but I can't see where 'library[0]['id']' is set or is in scope, since this seems to be the item in the iterator above this section.

Cheers,

Rob

Rob Leclerc, PhD

P: (US) +1-(917)-873-3037

P: (Shanghai) +86-1-(861)-612-5469

Personal Email: rob.leclerc@aya.yale.edu

On Tue, Mar 12, 2013 at 6:14 PM, Dannon Baker <dannon.baker@gmail.com> wrote:

The second argument there should point to the url of Galaxy's API --
in this case http://localhost:8080/api, I'm guessing.

-Dannon

On Tue, Mar 12, 2013 at 6:11 PM, Rob Leclerc <robert.leclerc@gmail.com> wrote:
>
> I'm trying to get the example_watch_folder.py to work with a simple example,
> but I am running into an error (Caveat, python is not my native language)
>
> I call the following script, but get the subsequent error:
>
> $ ./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f
> http://localhost:8080/ /Users/Rob/Documents/galaxy-db/input/
> /Users/Rob/Documents/galaxy-db/output/ "API Imports" 2a56795cad3c7db3
>
>
> URL did not return JSON data
>
>
> The preconditions I have in place are:
>
> 1. I copied my api_key: 8c25bc83f6f9e4001dd21eb7b64f063f
>
>
> 2. I created a new history on http://localhost:8080
>
> 3. I downloaded the the exons from hg19/chr22 from UCSC
>
> 3. On the dataset I performed a Text Manipulation > Select first (20 lines)
>
> 4. I extracted a workflow from the history and recorded the workflow id
> (2a56795cad3c7db3).
>
> 5. I created directories:
>
> /Users/Rob/Documents/galaxy-db/input/
> /Users/Rob/Documents/galaxy-db/output/
>
>
> My args may be malformed. Can someone provide me an example of a theirs?
>
> Cheers,
> Rob
>
>
>

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