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Rajeev Vikram
@darkrid_twitter
Hi, I am trying to sun a set of jobs since yesterday on galaxy main, but nothings moving
*run and not sun
And when I try to log out, I get a "Failed to authorize Action" Msg
Dannon
@dannon
@darkrid_twitter "failed to authorize action" is the exact message? Where does that appear?
Ahh, found it in the codebase. It has to do with the new CSRF protection.
Dannon
@dannon
@darkrid_twitter: If you do happen to pop back in and see this, try clearing your cache for the page and reloading, and then I'm guessing logout will work fine.
Nicola Soranzo
@nsoranzo
test_fetch_ftp_directory test in test/integration/test_upload_configuration_options.py fails for me locally because the order of the elements in the created dataset collection is not the alphabetical order of the files in the subdir. Is the test wrong in this assumption or is there a bug somewhere?
moveisi
@moveisi
Hello
John Chilton
@jmchilton
Sounds like a bug - the ftp directory should be sorted on the server before creating a collection I think
moveisi
@moveisi
I am having trouble installing Galaxy with PostgreSQL on an Ubuntu 18.04 system.
Galaxy runs using SQLite with no problems. However, when I try to connect to PostgreSQL instead I get errors from "psycopg2". It says:
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/psycopg2/init.py", line 50, in <module>
from psycopg2._psycopg import BINARY, NUMBER, STRING, DATETIME, ROWID
ImportError: /home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/psycopg2/.libs/./libresolv-2-c4c53def.5.so: symbol __res_maybe_init version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
galaxybot
@galaxybot
[nekrut] @jmchilton: can you point me to your hierarchical collection upload PR. I cannot find it for some reason
moveisi
@moveisi
@jmchilton: sorry, if you are asking me, I am not sure which collection you mean.
John Chilton
@jmchilton
@moveisi I was responding to @nsoranzo - sorry about that
galaxybot
@galaxybot
[nekrut] @dave_b @nate: https://github.com/usegalaxy-eu/usegalaxy-eu-tools
[mrscribe] Title: GitHub - usegalaxy-eu/usegalaxy-eu-tools: List of tools included in (at github.com)
John Chilton
@jmchilton
@nekrut Frontend : galaxyproject/galaxy#5365 , backend : galaxyproject/galaxy#5220 , training : galaxyproject/training-material#676
galaxybot
@galaxybot
[mrscribe] Title: Rule-based Uploader / Builder by jmchilton · Pull Request #5365 · galaxyproject/galaxy · GitHub (at github.com)
[nekrut] TX!
John Chilton
@jmchilton
@moveisi I really don't know about your issue, this is just a stab in the dark but it might be worth trying: ./.venv/bin/pip uninstall psycopg2 && ./.venv/bin/pip install --no-cache-dir --no-binary psycopg2
In case the wheel we distribute with Galaxy for that dependency doesn't work - I think this variant should try to build one from source from PyPI. I'm not sure thouhg
moveisi
@moveisi
@jmchilton: that is great :smile: I will try it and get back to you ...
Dave B.
@davebx
seconding @jmchilton, I sometimes encounter that issue and that's how I resolve it
Rajeev Vikram
@darkrid_twitter
@dannon yeah checked it Thanks.
Dannon
@dannon
That fixed it?
Rajeev Vikram
@darkrid_twitter
Haven't yet cleaned out
Dannon
@dannon
Ahh, k, let me know if that doesn't fix it and we can try to debug more.
Rajeev Vikram
@darkrid_twitter

Yeah. still the same error.

https://usegalaxy.org/user/logout?session_csrf_token=null

galaxybot
@galaxybot
[mrscribe] Title: Galaxy | (at usegalaxy.org)
Dannon
@dannon
Ah-ha! How is that session_csrf_token null...
Rajeev Vikram
@darkrid_twitter
yep. its the null ....lol
Rajeev Vikram
@darkrid_twitter
Seems Fixed :clap:
Dannon
@dannon
Awesome. Cache clean and reload did it?
Rajeev Vikram
@darkrid_twitter
I suppose so.
Dannon
@dannon
Great, glad it's working again, especially since I wasn't having any great ideas other than the cache being out of date regarding that null, heh.
Rajeev Vikram
@darkrid_twitter
Now, only if galaxy server starts to run my jobs, the lag is extreme and I have some single cell RNA analysis going on. haha
Thanks.
Dannon
@dannon
Sure! Someone said there was a backup yesterday after the server updates, may just take a few to get moving.
moveisi
@moveisi

@jmchilton and @davebx thanks a lot for your help!
I could install psycopg2 with --no-cache-dir --no-binary as you recommended.
However, when I ./run.sh Galaxy again, it uninstalled my freshly installed psycopg2, and download and installed the binary version again! Any suggestions?

...
Collecting psycopg2==2.6.1 (from -r /dev/stdin (line 1))
Downloading https://wheels.galaxyproject.org/packages/psycopg2-2.6.1-cp27-cp27mu-manylinux1_x86_64.whl (2.0MB)
100% |████████████████████████████████| 2.0MB 553kB/s
Installing collected packages: psycopg2
Found existing installation: psycopg2 2.7.4
Uninstalling psycopg2-2.7.4:
Successfully uninstalled psycopg2-2.7.4
Successfully installed psycopg2-2.6.1
...

Dave B.
@davebx
@moveisi oh yeah, you'll want to add psycopg2==2.6.1 to the end of the pip install command
moveisi
@moveisi
@davebx sure I'll try :smile:
moveisi
@moveisi

@davebx Is it possible to get Galaxy work with PostgreSQL 10?
I am running Ubuntu 18.04 (with PostgreSQL 10 as the default verion). When I try

./.venv/bin/pip install --no-cache-dir --no-binary psycopg2 psycopg2==2.6.1

it says:

Error: could not determine PostgreSQL version from '10.2'

Dave B.
@davebx
that is a good question, I've only tried with postgres 9.x
Dannon
@dannon
Is 10.x the default in 18.04?
Actually, I was tinkering with an 18.04 VM here, let me see if I'm having the same problem there.
moveisi
@moveisi
Yes, apt install postgresql gives you version 10
@dannon I appreciate it!
Nicola Soranzo
@nsoranzo
Time to update our requirement and wheel?
Dave B.
@davebx
@dannon looks like yes
Dannon
@dannon
Yeah, might be if this is going to be a problem for all 18.04.
moveisi
@moveisi
so do I downgrade my postgresql to 9?