I was able to get the script to work. I've written down some notes for a
quickstart for anyone else who might be following in my footsteps.
1. Create input and output directores where you will drop and emit files.
In my example I used:
/Users/Rob/Documents/galaxy-drop/input
/Users/Rob/Documents/galaxy-drop/output
2. Edit the galaxy-dist configuration script (universe_wsgi.ini) and set:
allow_library_path_paste = true
3. In example_watch_folder.py, comment out line 30 and replace it with:
#library_id = library[0]['id] This causes a "key error : 0"
library_id = library['id']
4. CREATE A SAMPLE Workflow & Dataset:
1. Start Galaxy
2. Go to USCS and upload the Exons from chr22 to your clean history file
3. Use the Text Manipulation tool to select the first 5 lines of the
gene exon file
4. Extract the workflow
5. *RESTART Galaxy* (You'll get a 500 Internal Server Error if you try
to run this without restarting)
6. Download the exons file to local
5. In your browser go to: http://localhost:8080/api/workflows and identify
the id of the workflow you've just created. Let's assume it is
(4b187121143038ff) and that your api_key for admin is
(8c25bc83f6f9e4001dd21eb7b64f063f)
6. Run the script:
./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f
http://localhost:8080/api/ /Users/Rob/Documents/galaxy-drop/input
/Users/Rob/Documents/galaxy-drop/output "My API Import" 4b187121143038ff
7. Copy the exons file to /Users/Rob/Documents/galaxy-drop/input when the
process is complete the file will be placed in
/Users/Rob/Documents/galaxy-drop/output
8. In your browser go to: http://localhost:8080/api/histories locate the
recently created history and then navigate to:
http://localhost:8080/api/histories/<history_id>/contents
where <history_id> is the id of the history that was created when you ran
the dataset on the last workflow.
This is my result. The second file is the output file.
[
{
"id": "0d16186aaff7cbfd",
"name": "Galaxy1-[Exons_chr22].bed",
"type": "file",
"url": "/api/histories/2d9035b3fc152403/contents/0d16186aaff7cbfd"
},
{
"id": "81991b32733a4fc4",
"name": "top200",
"type": "file",
"url": "/api/histories/2d9035b3fc152403/contents/81991b32733a4fc4"
]
9. You can navigate to the JSON description of the file in your browser:
http://localhost:8080/api/histories/2d9035b3fc152403/contents/81991b32733a4fc4
and the output file can be downloaded here:
http:localhost:8080/datasets/81991b32733a4fc4/display?to_ext=data
Cheers!
Rob
On Wed, Mar 13, 2013 at 12:15 PM, Rob Leclerc <robert.lecl...@gmail.com>wrote:
> Hi Dannon,
>
> Thanks. I've moved to a full size monitor, apparently my eyes are going!
>
> They *key error: 0* seems to be the result of a bug in the code.
>
> print(library)
>
>
> results in:
>
> {'url': '/api/libraries/4b187121143038ff', 'id': '4b187121143038ff',
> 'name': 'API Import11'}
>
>
> So library[0]['id'] doesn't point to anything, resulting in the key error.
> I changed the code on line 30
>
> library_id = library['id']
>
>
> This seems to fix the issue. I've now got to the section of code where I
> am watching the in_folder, but there doesn't seem to be any subsequent
> activity. I'll post my findings or questions as I make progress or lack
> thereof.
>
> Cheers,
> Rob
>
>
>
> On Wed, Mar 13, 2013 at 7:35 AM, Dannon Baker <dannon.ba...@gmail.com>wrote:
>
>> It should be set on line 29 as the result of that submit function. Can
>> you add (between 29 and 30) a 'print library' to see what that call
>> actually results in?
>>
>> Off the top of my head, this might be happening if your user account
>> (that the API key is associated with) isn't an admin account -- only admins
>> can create Data Libraries.
>>
>>
>> On Tue, Mar 12, 2013 at 6:35 PM, Rob Leclerc <robert.lecl...@gmail.com>wrote:
>>
>>> 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
>>>
>>>
>>>
>>>
>>> On Tue, Mar 12, 2013 at 6:14 PM, Dannon Baker <dannon.ba...@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.lecl...@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
>>>> >
>>>> >
>>>> >
>>>> > ___________________________________________________________
>>>> > 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/
>>>>
>>>
>>>
>>
>
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