Hi Christian,

I'd suggest creating a virtualenv and starting Galaxy from that.

--nate

On Wed, Aug 12, 2015 at 8:24 AM, Christian Schudoma (TSL) <
christian.schud...@sainsbury-laboratory.ac.uk> wrote:

> Hi Guys,
>
> I started pulling in the patches named below. After applying patch 345
> (curl ... | patch -p1), all new job submissions and finishing jobs fail
> with
>
> /tsl/services/galaxy/dist/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: 
> Module simplejson was already imported from 
> /tsl/services/galaxy/dist/lib/python2.6/site-packages/simplejson-3.6.5-py2.6-linux-x86_64.egg/simplejson/__init__.pyc,
>  but 
> /tsl/services/galaxy/dist/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg
>  is being added to sys.path self.check_version_conflict()
>
>
> Any ideas?
>
>
> Thanks
> Christian
>
>
>
> On 16/07/15 19:36, Poole, Richard wrote:
>
> Hi Nate,
>
> Problem solved (with one small exception) with much help from Marius. I
> followed his instructions to apply the three patches via mercurial:
>
> You can get the diff of a pull request by adding .diff, like so:
>
>
> https://patch-diff.githubusercontent.com/raw/galaxyproject/galaxy/pull/345.diff
>
> https://patch-diff.githubusercontent.com/raw/galaxyproject/galaxy/pull/416.diff
>
> https://patch-diff.githubusercontent.com/raw/galaxyproject/galaxy/pull/466.diff
>
> These should be the 3 pull requests for the issue you referenced.
> So you should be able to do curl
> https://patch-diff.githubusercontent.com/raw/galaxyproject/galaxy/pull/345.diff
>  |patch
> -p1
>
> and then the other 2.
> It's probably a good idea to do another branch for testing this,
> e.g.
> hg branch fix_metadata
> hg commit -m "branch to test metadatafix"
>
> I had to manually resolve one of the patches in
> lib/galaxy/tools/actions/metadata
>
>
> I also had to manually resolve that one as the patch for that file didn’t
> apply properly.
>
> I was then able to reset all metadata for the BAMs listed following the
> SQL search and hey presto history display back to normal speed :)
>
> The one issue I still have is that 9 of the offending BAMs are actually in
> a history that I deleted permanently by accident during the UI
> slow-response. So they are still listed in the SQL search. This doesn’t
> seem to be adversely affecting the speed but obviously I can’t reset their
> metadata now. Is this a problem?
>
> Thanks for the help,
> Rich
>
>
> On 16 Jul 2015, at 11:45, Poole, Richard <r.po...@ucl.ac.uk> wrote:
>
> Hi Nate,
>
> I have managed to update to the latest version of the default branch but I
> do not see the ‘max_metadate_value_size’ in my universe_wsgi.ini (this file
> was not changed during the update). Same thing if I use hg pull && hg
> update stable or hg pull && hg update release_15.05.
>
> Does this mean this change is not yet on mercurial and if so how can I
> pull this specific change (using curl?) to generate my own branch specific
> for the patch?
>
> Thanks,
> Richard
>
> On 15 Jul 2015, at 20:59, Richard Poole <ucga...@live.ucl.ac.uk> wrote:
>
> Just a little update - executed the SQL query and luckily only returned 20
> BAM files - the most recently generated ones of course. Now makes sense
> this could well be the cause of the UI problem as my account became more
> and more unresponsive the more of these 20 BAM files I generated over the
> last week………..
>
> Rich
>
> On 15 Jul 2015, at 20:38, Richard Poole <ucga...@live.ucl.ac.uk> wrote:
>
> Hi Nate,
>
> Ok - I can try this but I’m not an SQL database expert - far from it in
> fact. That query will just list ‘problematic’ datasets? I have a lot of
> histories with BAM files ;)
>
> Resetting the metadata needs to be done before this fix works? I ask
> because my history is so slow now as to be unusable…….or setting the cutoff
> allows Galaxy to be usable but it wipes out the metadata (which then needs
> resetting).
>
> I am still using universe_wsgi.ini not galaxy.ini and I don’t see the
> 'max_metadata_value_size’ in any section of my universe_wsgi_ini file - I
> guess because I’m not on latest update. I am actually not sure what version
> I am on as to fix an earlier issue with shared datasets (that wasn’t yet on
> mercurial) on the advice of a few folks I generated a branch specific for
> the patch using:
>
> hg branch fix_history_sharing
>
> curl
> https://github.com/galaxyproject/galaxy/commit/62772bc86e2504982f207a982542cbcc3faf0c65.diff|patch
>  -p1
>
> Also not being a huge mecurial expert I am a little unsure now how to
> switch back to stable branch correctly and pull the latest updates. Could
> you advise (sorry to be a noob)?
>
> Rich
>
>
>
> On 15 Jul 2015, at 20:22, Nate Coraor <n...@bx.psu.edu> wrote:
>
> Hi Richard,
>
> Unfortunately, you will need to reset metadata for any problematic
> datasets once you have updated to the latest version of 15.05 and set a
> cutoff value. You can find the datasets with the following SQL query in
> your database:
>
> select hda.id, u.email, h.name, hda.hid, hda.name, length(hda.metadata)
> from history_dataset_association hda
> join history h on hda.history_id=h.id
> join galaxy_user u on h.user_id=u.id
> where length(hda.metadata) > 1048576 order by length(hda.metadata) desc;
>
> And you can reset metadata by clicking on the dataset's pencil icon in
> your history and clicking "auto-detect".
>
> --nate
>
> On Wed, Jul 15, 2015 at 3:16 PM, Poole, Richard <r.po...@ucl.ac.uk> wrote:
>
>> Hi Nate,
>>
>> I am indeed using later than 15.05………so I will try this fix next time I
>> can restart the server and let you know.
>>
>> Richard
>>
>> On 15 Jul 2015, at 19:32, Nate Coraor <n...@bx.psu.edu> wrote:
>>
>> Hi Richard,
>>
>> By any chance, are you running Galaxy 15.05 or later? 15.05 includes new
>> metadata for bam files that can cause UI performance problems with certain
>> types of bam files. This can be limited with the new
>> `max_metadata_value_size` in galaxy.ini (on usegalaxy.org we've set it
>> to 1000000).
>>
>> I've also created a pull request to make this limiting the default:
>> https://github.com/galaxyproject/galaxy/pull/466
>>
>> However, if you are using an older version of Galaxy, this issue is not
>> related to the problem you're experiencing.
>>
>> --nate
>>
>> On Wed, Jul 15, 2015 at 2:16 PM, Poole, Richard <r.po...@ucl.ac.uk>
>> wrote:
>>
>>> Hi Christian and Carl,
>>>
>>> Thanks both for the replies.
>>>
>>> To answer your questions in reverse order. I have about XX histories in
>>> my account each with an average of about XX datasets. Total data in my
>>> account is about 1TB.
>>>
>>> It is indeed an admin account and other users with close to 1TB of data
>>> do not have a similar slow down. Although their data is spread over far
>>> fewer histories. Is there a way then to prevent the file_name attribute
>>> being requested for admin accounts so I can see if this speeds things back
>>> up again?
>>>
>>> Although the Galaxy server is running on my iMac the data is stored
>>> external on a large directly attached NAS. I think I first noticed this
>>> slow down after deleting and purging a bunch of older histories to free
>>> space on the NAS. I have tried running some of the cleanup_datasets scripts
>>> but they are actually returning errors and not running right now (can give
>>> you the error messages if necessary).
>>>
>>> The slowdown is actually getting worse now and it is even slow to
>>> display tool pages, as well as often getting this error if it is really
>>> slow:
>>> Proxy Error
>>>
>>> The proxy server received an invalid response from an upstream server.
>>> The proxy server could not handle the request *GET /history/list
>>> <http://iworm.anat.ucl.ac.uk:8080/history/list>*.
>>>
>>> Reason: *Error reading from remote server*
>>> I am running through an apache proxy - perhaps the apache settings need
>>> tweaking too? (I forget right now where I set these up!).
>>>
>>> As for the database itself, I am running PostgreSQL 9.3 and I tweaked
>>> the settings in my universe_wsgi.ini as per the instructions on
>>> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Advanced_configuration
>>>
>>> So my settings are:
>>>
>>> # -- Database
>>>
>>> # By default, Galaxy uses a SQLite database at
>>> 'database/universe.sqlite'.  You
>>> # may use a SQLAlchemy connection string to specify an external database
>>> # instead.  This string takes many options which are explained in detail
>>> in the
>>> # config file documentation.
>>> database_connection =
>>> postgresql://*******:*******@localhost:5432/galaxy_prod
>>>
>>> # If the server logs errors about not having enough database pool
>>> connections,
>>> # you will want to increase these values, or consider running more Galaxy
>>> # processes.
>>> database_engine_option_pool_size = 10
>>> database_engine_option_max_overflow = 20
>>>
>>> # If using MySQL and the server logs the error "MySQL server has gone
>>> away",
>>> # you will want to set this to some positive value (7200 should work).
>>> #database_engine_option_pool_recycle = -1
>>>
>>> # If large database query results are causing memory or response time
>>> issues in
>>> # the Galaxy process, leave the result on the server instead.  This
>>> option is
>>> # only available for PostgreSQL and is highly recommended.
>>> database_engine_option_server_side_cursors = True
>>>
>>> # Create only one connection to the database per thread, to reduce the
>>> # connection overhead.  Recommended when not using SQLite:
>>> database_engine_option_strategy = threadlocal
>>>
>>> # Log all database transactions, can be useful for debugging and
>>> performance
>>> # profiling.  Logging is done via Python's 'logging' module under the
>>> qualname
>>> # 'galaxy.model.orm.logging_connection_proxy'
>>> database_query_profiling_proxy = False
>>>
>>> # -- Files and directories
>>>
>>> Let me know if you think these settings are appropriate or need further
>>> tweaks.
>>>
>>> Thanks again for your responses so far,
>>>
>>> Richard
>>>
>>>
>>>
>>> On 13 Jul 2015, at 16:31, Carl Eberhard <carlfeberh...@gmail.com> wrote:
>>>
>>> Hi, Richard
>>>
>>> How many histories are on your account? How many datasets (roughly)?
>>>
>>> Are you using an Admin account to view the histories and does the slow
>>> down still occur for regular users with large amounts of data?
>>>
>>> One of the exposed attributes of datasets (for admins - not other users
>>> generally) is the file_name. I've noticed that retrieving this attribute
>>> from the file system can be slow.
>>>
>>> Christian also provides good advice.
>>>
>>> On Thu, Jul 9, 2015 at 4:12 AM, Christian Brenninkmeijer <
>>> christian.brenninkmei...@manchester.ac.uk> wrote:
>>>
>>>> Hi Richard,
>>>>
>>>> I am relatively new to galaxy so if you get a different response from
>>>> one of the core team ignore this.
>>>>
>>>> One thing I would check is the underlying database.
>>>> What do you have set for "database_connection" in your galaxy.ini file.
>>>>
>>>> Especially if you are using the default sqlite this could be the issue.
>>>> As that is store in a single file on disk.
>>>>
>>>> Whichever database you have make sure it has enough resources to handle
>>>> what will now be a large size.
>>>>
>>>> Christian
>>>> ------------------------------
>>>> *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on
>>>> behalf of Poole, Richard [r.po...@ucl.ac.uk]
>>>> *Sent:* Wednesday, July 08, 2015 9:04 PM
>>>> *To:* galaxy-dev@lists.galaxyproject.org
>>>> *Subject:* [galaxy-dev] Slow repsonses viewing histories
>>>>
>>>> Hi all,
>>>>
>>>> I am having trouble right now with my own personal account on my
>>>> production server. Grid refreshes are taking a huge amount of time (e.g.
>>>> when viewing ‘saved histories’ or even generating the dataset list for a
>>>> single history). My account is very full of data (1TB), could it be this?
>>>>
>>>> There are no obvious messages in the logs though so I am a bit stumped
>>>> as to why.I do not have the same trouble when impersonating other users
>>>> with fairly full accounts. Perhaps a database issue (I do not know how to
>>>> ‘cleanup’ the database or indeed Galaxy user accounts). Any thoughts?
>>>>
>>>> Thanks,
>>>> Richard
>>>>
>>>> *Richard J Poole PhD*
>>>> Wellcome Trust Fellow
>>>> Department of Cell and Developmental Biology
>>>> University College London
>>>> 21 University Street, London WC1E 6DE
>>>> Office (518 Rockefeller): +44 20 7679 6577 (int. 46577)
>>>> Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)
>>>>
>>>>
>>>> ___________________________________________________________
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>>>>
>>>
>>>
>>>
>>> ___________________________________________________________
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>>>
>>
>>
>>
>
>
>
>
>
>
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