Shared Data, Data Libraries - Uncaught exception in exposed API method

[gad83]

Hello,

When I click on Shared Data --> Data Libraries a message appears: "Uncaught exception in exposed API method" (ref. picture attached).

Here is the logs:
192.168.0.1 - - [29/Jan/2016:13:13:18 -0400] "GET /galaxy-prod/library/list HTTP/1.1" 200 - "http://my.galaxy.my.network.com:8081/galaxy-prod/library/list" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/48.0.2564.97 Safari/537.36" 192.168.0.1 - - [29/Jan/2016:13:13:19 -0400] "GET /galaxy-prod/api/datatypes?extension_only=False& HTTP/1.1" 200 - "http://my.galaxy.my.network.com:8081/galaxy-prod/library/list" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/48.0.2564.97 Safari/537.36" 192.168.0.1 - - [29/Jan/2016:13:13:19 -0400] "GET /galaxy-prod/api/genomes HTTP/1.1" 200 - "http://my.galaxy.my.network.com:8081/galaxy-prod/library/list" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/48.0.2564.97 Safari/537.36" galaxy.web.framework.decorators ERROR 2016-01-29 13:13:19,311 Uncaught exception in exposed API method: Traceback (most recent call last): File "/home/galaxy/galaxy-prod/lib/galaxy/web/framework/decorators.py", line 260, in decorator rval = func( self, trans, *args, **kwargs) File "/home/galaxy/galaxy-prod/lib/galaxy/webapps/galaxy/api/libraries.py", line 43, in index libraries.append( self.library_manager.get_library_dict( trans, library ) ) File "/home/galaxy/galaxy-prod/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 "/home/galaxy/galaxy-prod/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/lib64/python2.6/_strptime.py", line 325, in _strptime (data_string, format)) ValueError: time data '2015-01-30T13:37:07' does not match format '%Y-%m-%dT%H:%M:%S.%f' 192.168.0.1 - - [29/Jan/2016:13:13:19 -0400] "GET /galaxy-prod/api/libraries HTTP/1.1" 500 - "http://my.galaxy.my.network.com:8081/galaxy-prod/library/list" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/48.0.2564.97 Safari/537.36"

I believe it's a simple typo (because the T is next to the %)

[gad83]

If you look at the following code:
pretty_print_time_interval time = datetime.strptime( time, "%Y-%m-%dT%H:%M:%S.%f" )
you will notice an extra 'T' where it shouldn't belong.

[martenson]

@gad83 I think this depends on locale because it works on our instances and in all my tests :/
I will look more into this.

[nsoranzo]

@gad83 The problem is not the T, but the final .%f. What database are you using? Not PostgreSQL, I guess.

[gad83]

thanks guys for the reply!
database mysql @nsoranzo

[nsoranzo]

@gad83 What MySQL version? https://bugs.mysql.com/bug.php?id=8523 should be fixed in 5.6.4

[nsoranzo]

@gad83 Can you try the following patch:

index d7cea71..6be669b 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -361,7 +361,11 @@ def pretty_print_time_interval( time=False, precise=False ):
     elif isinstance( time, datetime ):
         diff = now - time
     elif isinstance( time, string_types ):
-        time = datetime.strptime( time, "%Y-%m-%dT%H:%M:%S.%f" )
+        try:
+            time = datetime.strptime( time, "%Y-%m-%dT%H:%M:%S.%f" )
+        except ValueError:
+            # MySQL may not support microseconds precision
+            time = datetime.strptime( time, "%Y-%m-%dT%H:%M:%S" )
         diff = now - time
     else:
         diff = now - now

[martenson]

@nsoranzo very defensive, very nice

[nsoranzo]

@gad83 If you can confirm that the above patch works for you, I can open a pull request. What version of Galaxy are you using?

[gad83]

Hello @nsoranzo

Sorry but I have another uncaught exceptions:

galaxy.web.framework.decorators ERROR 2016-02-18 14:17:43,524 Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "/home/galaxy/galaxy/lib/galaxy/web/framework/decorators.py", line 260, in decorator
    rval = func( self, trans, *args, **kwargs)
  File "/home/galaxy/galaxy/lib/galaxy/webapps/galaxy/api/libraries.py", line 43, in index
    libraries.append( self.library_manager.get_library_dict( trans, library ) )
  File "/home/galaxy/galaxy/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 "/home/galaxy/galaxy/lib/galaxy/util/__init__.py", line 355, in pretty_print_time_interval
    try:
  File "/usr/lib64/python2.6/_strptime.py", line 325, in _strptime
    (data_string, format))
ValueError: time data '2015-01-30T13:37:07' does not match format '%Y-%m-%dT%H:%M:%S.%f'

[nsoranzo]

@gad83 Did you restart the Galaxy instance?

[gad83]

oops!
fix confirmed!
it works!

[nsoranzo]

@gad83 Thanks for testing!

What version of Galaxy are you using? I want to be sure I'm fixing the release you are on.

[gad83]

release_15.10

[nsoranzo]

@gad83 See pull request #1761.

[martenson]

fixed, thanks @nsoranzo