example_watch_folder.py : URL did not return JSON data
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
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
___________________________________________________________ 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:
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 <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.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
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
example, 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:
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.leclerc@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
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.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
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
example, 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:
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.baker@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.leclerc@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.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
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
example, 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:
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/81991b32733a4f... 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.leclerc@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.baker@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.leclerc@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.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
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
example, lines)
4. I extracted a workflow from the history and recorded the workflow
(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
id 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:
participants (2)
-
Dannon Baker -
Rob Leclerc