Uncaught exception in exposed API method when creating data library (new interface)

Question: Uncaught exception in exposed API method when creating data library (new interface)

3.0 years ago by

Belgium

Hi,

I have a freshly installed local Galaxy server, and I'm trying to create a new data library through the (new) interface. Everything seems in order, but when I click the "create" button I get the following popup:

"Uncaught exception in exposed API method"

In the logs, I get the following error:

galaxy.web.framework.decorators ERROR 2015-12-14 11:48:53,435 Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "lib/galaxy/web/framework/decorators.py", line 260, in decorator
    rval = func( self, trans, *args, **kwargs)
  File "lib/galaxy/webapps/galaxy/api/libraries.py", line 112, in create
    library_dict = self.library_manager.get_library_dict( trans, library )
  File "lib/galaxy/managers/libraries.py", line 189, in get_library_dict
    library_dict[ 'create_time_pretty'] = pretty_print_time_interval( library_dict[ 'create_time' ], precise=True )
  File "lib/galaxy/util/__init__.py", line 355, in pretty_print_time_interval
    time = datetime.strptime( time, "%Y-%m-%dT%H:%M:%S.%f" )
  File "/usr/lib/python2.7/_strptime.py", line 325, in _strptime
    (data_string, format))
ValueError: time data '2015-12-14T11:48:53' does not match format '%Y-%m-%dT%H:%M:%S.%f'

It seems like the python interpreter doesn't parse the datetime output correctly..

Any help?

Thanks!

galaxy api data libraries galaxy 15.10 • 1.9k views

ADD COMMENT • link •

modified 3.0 years ago • written 3.0 years ago by matthias.desmet • 150

What version of Galaxy are you using? Is it any of the releases or dev branch? What version of Python does the machine use?

ADD REPLY • link written 3.0 years ago by Martin Čech ♦♦ 4.9k

Hi Martin,

I'm using the latest version Galaxy (15.10) and the latest version of python 2.7 (2.7.11), so nothing exotic going on.

ADD REPLY • link written 3.0 years ago by matthias.desmet • 150

3.0 years ago by

matthias.desmet • 150

Belgium

matthias.desmet • 150 wrote:

Fixed by @dannon in https://github.com/galaxyproject/galaxy/pull/1339

Much thanks to everyone who helped!

ADD COMMENT • link written 3.0 years ago by matthias.desmet • 150

3.0 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

I have tried to reproduce this on release_15.10 branch but with no luck. Please make sure you are up to date with the branch and if you are there is something specific about your installation. What operating system are you using? Are you using virtualenv?

ADD COMMENT • link modified 3.0 years ago • written 3.0 years ago by Martin Čech ♦♦ 4.9k

3.0 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k wrote:

This seems an awful lot like a locale problem. Galaxy is expecting a date with microseconds but the create_time attribute of the library dict (which I believe should just be the value of the create_time column in the database) is missing the microseconds.

Two things to check:

1. What are your locale settings in the shell where run.sh works (e.g. the output of `locale`)?

2. What is the encoding of the database? `\l` in psql will show you this.

ADD COMMENT • link written 3.0 years ago by Nate Coraor ♦ 3.2k

3.0 years ago by

matthias.desmet • 150

Belgium

matthias.desmet • 150 wrote:

SUCCESS!

I modified the function "pretty_print_time_interval" at galaxy/lib/galaxy/util/__init__.py in the source code. I removed the requirement for milliseconds (so instead of

time = datetime.strptime( time, "%Y-%m-%dT%H:%M:%S.%f" )

it is now

time = datetime.strptime( time, "%Y-%m-%dT%H:%M:%S" )

which seems to fixed the issue here.
Does this seem like a viable fix for you guys? Or is this just something quick and dirty?

Matthias

ADD COMMENT • link written 3.0 years ago by matthias.desmet • 150

3.0 years ago by

matthias.desmet • 150

Belgium

matthias.desmet • 150 wrote:

I installed galaxy through the ansible roles found in de galaxy repository, so yeah, everything is in a virtualenv.

I'll try doing a fresh checkout and tomorrow and see how it goes, but I don't suppose much has changed since last friday. Maybe I can try pulling the master branch instead.

Thanks for the help!

ADD COMMENT • link written 3.0 years ago by matthias.desmet • 150

Could you please link me to what roles you used to install Galaxy? thanks.

ADD REPLY • link written 3.0 years ago by Martin Čech ♦♦ 4.9k

3.0 years ago by

matthias.desmet • 150

Belgium

matthias.desmet • 150 wrote:

https://github.com/galaxyproject/ansible-galaxy

https://github.com/galaxyproject/ansible-galaxy-extras

ADD COMMENT • link written 3.0 years ago by matthias.desmet • 150

please try running Galaxy without ansible (just git clone https://github.com/galaxyproject/galaxy and then `sh run.sh`) to validate whetehr it is ansible related

ADD REPLY • link written 3.0 years ago by Martin Čech ♦♦ 4.9k

Hi Martin,

Bad news (well, for me anyway). The issue does indeed seem to be related to the ansible deployment scripts, a local checkout of v15.10 works fine here.

Damn.., I'll try to find what the issue is.

ADD REPLY • link written 3.0 years ago by matthias.desmet • 150

I tried to reinstall the whole thing, but no luck, seems to be something funky going with the dataTime output I'm getting from my Python interpreter, altough the output seems to be allright..

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by matthias.desmet • 150

I will point the Galaxy ansible creator here. Sorry for the inconvenience :/

ADD REPLY • link written 3.0 years ago by Martin Čech ♦♦ 4.9k

what locale does the system use (and what system is it?)?

ADD REPLY • link written 3.0 years ago by Martin Čech ♦♦ 4.9k

3.0 years ago by

matthias.desmet • 150

Belgium

matthias.desmet • 150 wrote:

Hi Nate,

Sorry to drag you into this, I don't want to point any fingers and the ansible roles work great.

I'm working on a Ubuntu 14.04.03 LTS system,

Output of 'locale' is:

LANG=en_US.UTF-8
LANGUAGE=
LC_CTYPE="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=

As database, we're using a MariaDB backed MySQL database, locale of the db is set to en_US.

Could it be some kind of error in the mysql version of the query? The database can output timestamps with milliseconds.
I'll check out the source code and see what I can come up with.

Thanks for the time you're putting into this!

M

ADD COMMENT • link written 3.0 years ago by matthias.desmet • 150

3.0 years ago by

matthias.desmet • 150

Belgium

matthias.desmet • 150 wrote:

For future reference, discussion moved to GitHub

https://github.com/galaxyproject/galaxy/pull/1335

ADD COMMENT • link written 3.0 years ago by matthias.desmet • 150

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