Re: [galaxy-dev] History seems to load forever
Hi Carrie Was the history which is causing troubles created before you switched to external authentication? Or has the user a slightly different e-mail address now? eg different use of capital letters, like 'foo.bar@home' and 'Foo.Bar@home' - we had such problems, when we switched to external authentication. I had to dig into our MySQL database and fix the galaxy_user table. In your case, I recommend looking at the galaxy_user table and check whether the user has more than one entry. Take the id (ie the number) and search the history table using the id as 'user_id'. I would guess you can fix your problem by changing the 'user_id' in the history table for the history which is causing troubles. BUT, BE VERY CAREFUL! you can do a lot of damage to the database. Switch off the galaxy server first, and MAKE a back up the database before you change anything. Regards, Hans-Rudolf On 03/11/2014 11:58 PM, Ganote, Carrie L wrote: Hi List, I just pulled and merged from galaxy-dist (I think it's dc067a95261d), updated my database, and migrated my tools. The issues I am able to see are minor, but I have a user who can no longer access a particular history. It apparently just hangs. If they delete the history, Galaxy responds, but it will hang again when they try to add back any datasets. Unfortunately, I don't see any errors in the paster logs about this. I fear that their dataset entries in the Postgresql db have been corrupted during the update, or perhaps the files themselves were purged. I cannot reproduce their issues with my own histories - I'm able to bring up saved histories and upload etc. I don't know if they can share a history if it can't be loaded. How should I troubleshoot this? I'm set up to authenticate through apache, which makes it harder to get in as the user and see what's up. Is there an easy way to find out what histories belong to what users? I can search the database? Any advice would be greatly appreciated! -Carrie ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] History seems to load forever
Hi Hans,
Thanks for the advice! Sadly, I think our situations might not be the same.
We've been using external auth for a long time, so it's definitely not a new
change, and the user in question created their account after this was in place.
We log our users in with just their IU username, and tack the @indiana.edu
onto it with Apache to create the email address after authenticating the
username through IU. I checked the galaxy_user table, and there doesn't seem to
be any accidental duplicates or funny business with the user name.
User is active, external, not deleted, not purged, and we don't enforce any
disk quotas.
I pulled the histories associated with the user id:
select * from history where user_id = '95' ;
id |create_time |update_time | user_id |
name| hid_counter | deleted | purged | genome_build | importable |
slug | published | importing
--+++-++-+-++--++--+---+---
1665 | 2014-02-23 18:42:23.497483 | 2014-03-11 19:04:55.614609 | 95 |
Unnamed history| 5 | t | f | dm3 | f
| | f | f
1722 | 2014-02-28 20:46:50.292015 | 2014-03-11 19:06:47.498152 | 95 |
RNAseq | 7 | f | f | ?| f
| | f | f
1811 | 2014-03-11 19:04:55.910381 | 2014-03-11 19:13:06.82213 | 95 |
Unnamed history| 2 | f | f | ?| f
| | f | f
(3 rows)
I took a look at RNAseq:
select * from history_dataset_association where history_id = '1722';
id: 10027
history_id: 1722
dataset_id: 7258
create_time: 2014-02-28 20:51:32.369667
update_time: 2014-03-06 15:37:27.033951
copied_from_history_dataset_association_id: 9778
hid: 4
name :
https://usegalaxy.org/datasets/bbd44e69cb8906b52e29eb7a7c6c4900/display?to_ext=
peek:@HWI-B5-690_0086_FC:2:1:2711:936#CN/1 ... (this checks out with the
datafile)
extension: txt
metadata: {data_lines: 145087556, dbkey: dm3}
deleted: f
visible: t
purged: f
extended_metadata_id: uploaded txt file
I found this file in the dataset_files and there doesn't appear to be anything
wrong about it. It appears that the datasets in question were downloaded from
Galaxy main (by the looks of the upload URL).
I'm at a loss. I'll ask the user to clear all their browser information just in
case this is something simple like that. I'll ask them to re-upload those
files. In the meantime, any other sleuthing suggestions would be greatly
appreciated.
Sincerely,
Carrie Ganote
From: Hans-Rudolf Hotz [h...@fmi.ch]
Sent: Wednesday, March 12, 2014 5:07 AM
To: Ganote, Carrie L
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] History seems to load forever
Hi Carrie
Was the history which is causing troubles created before you switched to
external authentication? Or has the user a slightly different e-mail
address now? eg different use of capital letters, like 'foo.bar@home'
and 'Foo.Bar@home' - we had such problems, when we switched to external
authentication.
I had to dig into our MySQL database and fix the galaxy_user table. In
your case, I recommend looking at the galaxy_user table and check
whether the user has more than one entry. Take the id (ie the number)
and search the history table using the id as 'user_id'. I would guess
you can fix your problem by changing the 'user_id' in the history
table for the history which is causing troubles.
BUT, BE VERY CAREFUL! you can do a lot of damage to the database. Switch
off the galaxy server first, and MAKE a back up the database before you
change anything.
Regards, Hans-Rudolf
On 03/11/2014 11:58 PM, Ganote, Carrie L wrote:
Hi List,
I just pulled and merged from galaxy-dist (I think it's dc067a95261d),
updated my database, and migrated my tools. The issues I am able to see
are minor, but I have a user who can no longer access a particular
history. It apparently just hangs. If they delete the history, Galaxy
responds, but it will hang again when they try to add back any datasets.
Unfortunately, I don't see any errors in the paster logs about this. I
fear that their dataset entries in the Postgresql db have been corrupted
during the update, or perhaps the files themselves were purged. I cannot
reproduce their issues with my own histories - I'm able to bring up
saved histories and upload etc. I don't know if they can share a history
if it can't be loaded. How should I troubleshoot this?
I'm set up to authenticate through apache, which makes it harder to get
in as the user and see what's up. Is there an easy way to find out what
histories belong to what users? I can search the database?
Any advice would be greatly appreciated
Re: [galaxy-dev] History seems to load forever
Hi, Carrie
Can you (or the other user) open the javascript console and try to load the
history again in order to reproduce the problem?
You can open the console:
- by going to the menu command: Tools-Web Developer-Web Console in
Firefox.
- going to: the 'control menu' (the three horizontal bar button on the top
right)-Tools-Javascript Console in Chrome.
- by enabling the developer tools and going to Develop-Show Error Console
in Safari. Enable the developer menu by going to
preferences-advanced-Show develop menu in menu bar.
It may be there's an error on the client side involved and having this open
will show that error. Additionally, if an API call is returning a 400 range
http error - you won't see it in the server logs.
Thanks for the help and let me know what you find,
Carl
On Wed, Mar 12, 2014 at 10:22 AM, Ganote, Carrie L cgan...@iu.edu wrote:
Hi Hans,
Thanks for the advice! Sadly, I think our situations might not be the
same. We've been using external auth for a long time, so it's definitely
not a new change, and the user in question created their account after this
was in place. We log our users in with just their IU username, and tack the
@indiana.edu onto it with Apache to create the email address after
authenticating the username through IU. I checked the galaxy_user table,
and there doesn't seem to be any accidental duplicates or funny business
with the user name.
User is active, external, not deleted, not purged, and we don't enforce
any disk quotas.
I pulled the histories associated with the user id:
select * from history where user_id = '95' ;
id |create_time |update_time | user_id
|name| hid_counter | deleted | purged | genome_build |
importable | slug | published | importing
--+++-++-+-++--++--+---+---
1665 | 2014-02-23 18:42:23.497483 | 2014-03-11 19:04:55.614609 | 95
| Unnamed history| 5 | t | f | dm3 | f
| | f | f
1722 | 2014-02-28 20:46:50.292015 | 2014-03-11 19:06:47.498152 | 95
| RNAseq | 7 | f | f | ?|
f | | f | f
1811 | 2014-03-11 19:04:55.910381 | 2014-03-11 19:13:06.82213 | 95
| Unnamed history| 2 | f | f | ?| f
| | f | f
(3 rows)
I took a look at RNAseq:
select * from history_dataset_association where history_id = '1722';
id: 10027
history_id: 1722
dataset_id: 7258
create_time: 2014-02-28 20:51:32.369667
update_time: 2014-03-06 15:37:27.033951
copied_from_history_dataset_association_id: 9778
hid: 4
name :
https://usegalaxy.org/datasets/bbd44e69cb8906b52e29eb7a7c6c4900/display?to_ext=
peek:@HWI-B5-690_0086_FC:2:1:2711:936#CN/1 ... (this checks out with
the datafile)
extension: txt
metadata: {data_lines: 145087556, dbkey: dm3}
deleted: f
visible: t
purged: f
extended_metadata_id: uploaded txt file
I found this file in the dataset_files and there doesn't appear to be
anything wrong about it. It appears that the datasets in question were
downloaded from Galaxy main (by the looks of the upload URL).
I'm at a loss. I'll ask the user to clear all their browser information
just in case this is something simple like that. I'll ask them to re-upload
those files. In the meantime, any other sleuthing suggestions would be
greatly appreciated.
Sincerely,
Carrie Ganote
From: Hans-Rudolf Hotz [h...@fmi.ch]
Sent: Wednesday, March 12, 2014 5:07 AM
To: Ganote, Carrie L
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] History seems to load forever
Hi Carrie
Was the history which is causing troubles created before you switched to
external authentication? Or has the user a slightly different e-mail
address now? eg different use of capital letters, like 'foo.bar@home'
and 'Foo.Bar@home' - we had such problems, when we switched to external
authentication.
I had to dig into our MySQL database and fix the galaxy_user table. In
your case, I recommend looking at the galaxy_user table and check
whether the user has more than one entry. Take the id (ie the number)
and search the history table using the id as 'user_id'. I would guess
you can fix your problem by changing the 'user_id' in the history
table for the history which is causing troubles.
BUT, BE VERY CAREFUL! you can do a lot of damage to the database. Switch
off the galaxy server first, and MAKE a back up the database before you
change anything.
Regards, Hans-Rudolf
On 03/11/2014 11:58 PM, Ganote, Carrie L wrote:
Hi List,
I just pulled and merged from galaxy-dist (I think it's dc067a95261d),
updated my database, and migrated my tools. The issues I am able to see
are minor, but I
[galaxy-dev] History seems to load forever
Hi List, I just pulled and merged from galaxy-dist (I think it's dc067a95261d), updated my database, and migrated my tools. The issues I am able to see are minor, but I have a user who can no longer access a particular history. It apparently just hangs. If they delete the history, Galaxy responds, but it will hang again when they try to add back any datasets. Unfortunately, I don't see any errors in the paster logs about this. I fear that their dataset entries in the Postgresql db have been corrupted during the update, or perhaps the files themselves were purged. I cannot reproduce their issues with my own histories - I'm able to bring up saved histories and upload etc. I don't know if they can share a history if it can't be loaded. How should I troubleshoot this? I'm set up to authenticate through apache, which makes it harder to get in as the user and see what's up. Is there an easy way to find out what histories belong to what users? I can search the database? Any advice would be greatly appreciated! -Carrie ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] History will not load
Hello, I have been having trouble with Galaxy since yesterday. I have been trying to run cuffdiff which has been waiting to run since Friday afternoon and now my history will not even load (red error message shows up). Any incite would be much appreciated. Maria ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
