[Solved]
Hi,
You were right. It was because, I had to use the port 80 :P
Thanks
Gildas
Le 16/09/2014 22:45, John Chilton a écrit :
Is there some small difference between your test and production
instance? It seems like you client is trying to connect to port 8080
in production? Is this acc
Is there some small difference between your test and production
instance? It seems like you client is trying to connect to port 8080
in production? Is this accessible? The error makes me think this is
not a Galaxy problem but a firewall or proxy issue. Is your production
instance served out on port
Hi,
Just a little up ! I promise, it's the first and the last one :P
But I really need a clue.
This script is included in an automatic process to create account (LDAP)
on our network, create directories (some for Galaxy, some for backup)
and create galaxy libraries.
The part of my script, wh
Hi,
I wrote a script which need to retrieve a list of all users on our
production instance.
It seems that we have too many users (325) :P
bioblend.galaxy.client.ConnectionError:
HTTPConnectionPool(host='galaxy.sb-roscoff.fr', port=8080): Max retries
exceeded with url: /api/users?key=fd420ze
Hello Neil,
The newer uploader targets the tool's API with in browser JavaScript
- so bioblend say targets the same API with its tool client
(https://github.com/afgane/bioblend/blob/master/bioblend/galaxy/tools/__init__.py#L104).
I imagine you could get a similar degree of parallelism by splitti
Hi,
I really like the multi-file upload tool in the latest version of Galaxy.
Is there an API for it so we can send files via a script rather than using the
user interface? If so are there any examples?
Thanks
Neil
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On Fri, Jul 18, 2014 at 5:14 PM, Dave Bouvier wrote:
> John, Peter,
>
> The buildbot builders are already using the api interactor for both
> functional tests and the install and test framework.
>
> --Dave B.
Great news.
When did that happen? Did it cause any regressions (and
can/did you flag
John, Peter,
The buildbot builders are already using the api interactor for both
functional tests and the install and test framework.
--Dave B.
On Fri 18 Jul 2014 11:34:01 AM EDT, John Chilton wrote:
I think the confusion over two different test methods has reached a
high level and Dave an
I think the confusion over two different test methods has reached a
high level and Dave and I agreed previously that we should try to make
the API driven version the default during this release cycle - but it
is not our call :).
Greg - is there anything else you feel that needs to happen to at
lea
On Wed, Jul 16, 2014 at 7:44 PM, Saket Choudhary wrote:
> Thanks Peter, I guess I should then rely on API based tests.
>
If it is just the order, make sure the order of the output files in the
is consistent with that in the and it make be OK with Twill...
I wonder if I filed a Trello card on th
Thanks Peter, I guess I should then rely on API based tests.
On 15 July 2014 14:18, Peter Cock wrote:
> Hi Saket,
>
> From memory the Twill tests are fragile with the output file order in the
> XML.
>
> John was discussing switching the default from the Twill to API backend,
> not sure when tha
Hi Saket,
>From memory the Twill tests are fragile with the output file order in the XML.
John was discussing switching the default from the Twill to API backend,
not sure when that is happening though...
Peter
On Tue, Jul 15, 2014 at 9:31 AM, Saket Choudhary wrote:
> I recently updated tests
I recently updated tests for one of my wrappers and came across this
strange behaviour:
The twill based testing reports a failure:
https://travis-ci.org/saketkc/galaxy_tools/jobs/29956682#L1463
whereas, the API based testing shows success:
https://travis-ci.org/saketkc/galaxy_tools/jobs/29956683
Hi!
What do we want :
Using the API (bioblend 0.4.3, Galaxy-dist ( 22 jan 2014 ) ): upload files
from user's FTP directory to Galaxy and launch workflow
How we do it :
1. Determine the user's *libraryID* and *historyID*
2. Upload files : *gi.libraries.upload_file_from_server (libraryID,
server_dir
Hello to all,
I'm trying to use the script import_library_dataset_to_history.py in
order to upload a file from a dataset in a history.
I get an error, but I'm not sure that I use it the right way.
The command line I use is:
python import_library_dataset_to_history.py
cd065330048989af4ae266cf94
OK, I would like to see that happen too :-)
I have been thinking about possible 'elegant' solutions to enable this
exporting. I am very enthousiastic about Bittorrent Sync, which could
perhaps be an efficient and secure way to export the histories
(http://labs.bittorrent.com/experiments/sync.h
> Is it currently possible to export histories via the API?
Not possible yet but is definitely something we'd like to implement and/or see
from a community contribution.
Best,
J.
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Hi all,
Is it currently possible to export histories via the API? I have one
user who want to download and store her data. Total sizes of all her
histories combined is about ~700GB.
I think this is a typical API job: to list all her histories, start
'exporting to file' all of them, and final
Take a look at the item_tags API controller; you can manage (add/delete/show)
history, dataset, and workflow tags using it. There's not much documentation
for it yet, but it should be pretty straight-forward. Let us know if you have
questions.
Best,
J.
On Jun 20, 2013, at 9:59 AM, Philip Mabon
Hey,
I was curious if it was possible to allow the API to change tags associated
with a history? At the moment in the galaxy code it's forbidden.
Having the ability to add tags using the API would be helpful of
associating multiple histories to a particular project. So later, it would
be easier t
Hello, all
Thanks to you both for reporting this.
John, in the steps to reproduce you mention, is step 4 going through the
browser?
If using curl/wget with an api key, they should of course, allow you to
retrieve all histories (logged in or not).
If through the browser, where you able to retrieve
Hi John,
Thanks! I restarted the server, regenerated the API key, and can confirm
that it's now working. As you mentioned, it's possible that I was missing a
value on the end of the API key and was caught by the bug which allowed me
to check find histories when I was logged out.
Cheers!
Rob
On
I'm trying to use the blend4j to access the Galaxy API, but I'm getting a
403 error, however when I pass the same request string through my browser I
get a json response (Status 200).
//Here is the URL string being passed in both cases:
http://localhost:8080/api/histories?key=c5954f0e726e52da297cd
Hi,I have a very bizarre problem with Galaxy.I have to run a workflow through the API, since Galaxy cannot deal with many pair-end FASTQ files...In the past I had no issues with this and it always run as expected.But in the last few days when I select 2 FASTQ files to be run in with the API, invari
Hi All,
We have just released the first beta version of a Galaxy API extension,
that greatly simplifies some of the typical jobs that are performed by
external jobs, that uses the Galaxy API.
Please note that this API extension project is *NOT a part of the Galaxy
project*. The Galaxy develo
Hi L-A,
This exists. See your universe_wsgi for the following lines:
# Optional list of email addresses of API users who can make calls on behalf of
# other users
#api_allow_run_as = None
And then with any api call from a user in the allow list above you can add an
extra parameter to the reque
Hello everyone!
I just wanted to know if the user impersonation will be available
through the API someday :) It could be veeery useful for triggering
automatic QA on the data without having to share the resulting histories
afterwards.
Best regards,
L-A
___
For those of you who've been keeping up with recent posts concerning
confusion over the value of IDs returned by the API, the most recent
commit to galaxy-central (5994:435e3f628e7d) addresses this issue.
Here's the commit message:
Do away with the encoding of 'file.' and 'folder.' in the
Le 31/08/2011 19:34, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Hello everyone,
I'm currently trying to automate data loading and pre-processing
through Galaxy's API, and I will need to delete and share histories
at some point. I know the API is still very new but is there a way
to do t
Louise-Amélie Schmitt wrote:
> Hello everyone,
>
> I'm currently trying to automate data loading and pre-processing
> through Galaxy's API, and I will need to delete and share histories
> at some point. I know the API is still very new but is there a way
> to do that by any chance?
Hi L-A,
As of
Le 30/08/2011 18:00, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Le 30/08/2011 16:51, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
I just changed it and ran into an error, so I modified the line and
it now works fine:
$__app__.security.encode_id( '%s' % $input1.id )
What was the '
Louise-Amélie Schmitt wrote:
> Le 30/08/2011 16:51, Nate Coraor a écrit :
> >Louise-Amélie Schmitt wrote:
> >>I just changed it and ran into an error, so I modified the line and
> >>it now works fine:
> >>$__app__.security.encode_id( '%s' % $input1.id )
> >>What was the 'file.' originally for?
> >O
Le 30/08/2011 16:51, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
I just changed it and ran into an error, so I modified the line and
it now works fine:
$__app__.security.encode_id( '%s' % $input1.id )
What was the 'file.' originally for?
On the API side, a library or history's "contents"
Louise-Amélie Schmitt wrote:
> I just changed it and ran into an error, so I modified the line and
> it now works fine:
> $__app__.security.encode_id( '%s' % $input1.id )
> What was the 'file.' originally for?
On the API side, a library or history's "contents" are all identified by
ID, so:
ht
I just changed it and ran into an error, so I modified the line and it
now works fine:
$__app__.security.encode_id( '%s' % $input1.id )
What was the 'file.' originally for?
Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit :
Thanks a lot!
I found another way to do it but it is awfully more
Le 29/08/2011 18:54, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Le 29/08/2011 15:52, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Hello everyone,
These questions are a bit silly but I'm really ignorant when it
comes to security. Sorry about that.
Why use API keys instead of us
Louise-Amélie Schmitt wrote:
> Le 29/08/2011 15:52, Nate Coraor a écrit :
> >Louise-Amélie Schmitt wrote:
> >>Hello everyone,
> >>
> >>These questions are a bit silly but I'm really ignorant when it
> >>comes to security. Sorry about that.
> >>
> >>Why use API keys instead of user names? Is it to
Le 29/08/2011 15:52, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Hello everyone,
These questions are a bit silly but I'm really ignorant when it
comes to security. Sorry about that.
Why use API keys instead of user names? Is it to to prevent anyone
from figuring out who is behind an UR
Louise-Amélie Schmitt wrote:
> Hi,
>
> I ran into a little something that is a bit annoying for debug when
> trying to upload files through the API with
> library_upload_from_import_dir.py. When the specified folder is
> wrong, python tries to process the error tuple like a dict, so the
> original
Louise-Amélie Schmitt wrote:
> Hello everyone,
>
> These questions are a bit silly but I'm really ignorant when it
> comes to security. Sorry about that.
>
> Why use API keys instead of user names? Is it to to prevent anyone
> from figuring out who is behind an URL? Or did I miss the point?
Hi
Hello everyone,
These questions are a bit silly but I'm really ignorant when it comes to
security. Sorry about that.
Why use API keys instead of user names? Is it to to prevent anyone from
figuring out who is behind an URL? Or did I miss the point?
Also, why encrypt the dataset/library/fol
Thanks a lot!
I found another way to do it but it is awfully more complicated so I'll
change as soon as I have some time.
Best,
L-A
Le 23/08/2011 19:49, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Hi,
I would need to make a tool that can get the API dataset id out of
the input data
Louise-Amélie Schmitt wrote:
> Hi,
>
> I would need to make a tool that can get the API dataset id out of
> the input dataset of the tool, how can I do that?
Hi L-A,
Pass in as an argument:
$__app__.security.encode_id( 'file.%s' % $input1.id )
Where 'input1' is the param name of your input
Hello L-A,
On 8/9/11 12:06 AM, Louise-Amélie Schmitt wrote:
Hi Jen,
Hum.. what is a bitbucket ticket? How do you get there?
http://bitbucket.org/galaxy/galaxy-central/src
Tickets are created the same place that the galaxy-central source
repository is located. Click on the "Issues" tag to se
Hi Jen,
Hum.. what is a bitbucket ticket? How do you get there?
There's no real hurry anyway, as far as I'm concerned. I made
API-versions of the tools I need where the python wrapper gets the
needed parameters from a database. But yeah, I'm still very interested
in how the API evolves.
By
Hi L-A,
Should we make a bitbucket ticket to keep track of this enhancement request?
If you would like to make one, that would be great since you could put
in all the details, or just write back and I can create a simple ticket.
Thanks!
Jen
Galaxy team
On 8/5/11 6:59 AM, Louise-Amélie Schmi
Hi,
I would need to make a tool that can get the API dataset id out of the
input dataset of the tool, how can I do that?
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Hello,
Just a quick message to ask if you had the time to work on passing
parameters to workflows through the API. Just to know, since I'm using
workflows with the API.
Best,
L-A
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s way.
Nevertheless, the actions are properly triggered in Galaxy, surprisingly.
Here is an example:
When I launch a workflow, I get the following traceback even though
the workflow is properly executed:
http://localhost/galaxy-dev/api/workflows?key=273c7b4e3aaffd3884ef715aaf780d9a
tions are properly triggered in Galaxy, surprisingly.
Here is an example:
When I launch a workflow, I get the following traceback even though the
workflow is properly executed:
http://localhost/galaxy-dev/api/workflows?key=273c7b4e3aaffd3884ef715aaf780d9a
File "automated_preprocessing.py
Hello everyone,
I'm currently trying to automate data loading and pre-processing through
Galaxy's API, and I will need to delete and share histories at some
point. I know the API is still very new but is there a way to do that by
any chance?
Thanks,
L-A
__
Hello,
I have been working on running a workflow programmatically on my local
galaxy instance using library datasets.
It took me a few hours to figure out the problem I was having so I thought I
would document it here in case it helps anyone. Also, I have a question
regarding 'ldda' IDs (see below
Hi,
I ran into a little something that is a bit annoying for debug when
trying to upload files through the API with
library_upload_from_import_dir.py. When the specified folder is wrong,
python tries to process the error tuple like a dict, so the original
error is hard to find.
I modified a
Frederick,
The API is distributed along with galaxy. To enable it, set the following in
your universe_wsgi.ini:
enable_api = True
Once that's enabled, each user can create an API key using the "API Keys"
option in the user menu of the main masthead. For additional information, see
/scripts/
Anyone know where i can get the galaxy API?
Regards
Fred
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: Paszkiewicz, Konrad
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] API connection error
Paszkiewicz, Konrad wrote:
> Dear all,
>
> I'm getting the following error when trying to follow the instructions in the
> API README file. Universe_wsgi.ini is pasted below.
>
&
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] API connection error
>
> Paszkiewicz, Konrad wrote:
> > Dear all,
> >
> > I'm getting the following error when trying to follow the instructions in
> > the API README file. Universe_wsgi.i
Paszkiewicz, Konrad wrote:
> Dear all,
>
> I'm getting the following error when trying to follow the instructions in the
> API README file. Universe_wsgi.ini is pasted below.
>
>
> [galaxy@zeus api]$ ./display.py c43c7605ba60633a2ed60f46c12f354e
> http://zeus.ex.ac.uk:4000/api/libraries
>
Hi
Dear all,
I'm getting the following error when trying to follow the instructions in the
API README file. Universe_wsgi.ini is pasted below.
[galaxy@zeus api]$ ./display.py c43c7605ba60633a2ed60f46c12f354e
http://zeus.ex.ac.uk:4000/api/libraries
Any suggestions would be very welcome.
All the
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