Re: [galaxy-dev] can't create user on a new instance
Hey Folks,
When I used the kickstart, I hit this always:
TASK [galaxyprojectdotorg.galaxy-os : Update APT cache]
*
[WARNING]: sftp transfer mechanism failed on [localhost]. Use
ANSIBLE_DEBUG=1 to see detailed information
fatal: [localhost]: FAILED! => {"changed": false, "failed": true, "msg":
"Failed to update apt cache."}
Have you seen this before? If you do, please give me a hand. :)
Thanks,
Rui
On Fri, Oct 12, 2018 at 2:17 PM Rui Wang wrote:
> Hi Qiang,
>
> Let me try that. I think the postgres might be contaminated by the attempt
> to use kickstart. During that it modify the config of postgres permissions
> and it took me a while to clean those to get postgres working again(which
> may or may not really clean the change completely).
>
> I'll get back to you on this. Also I'll let you know my attempts on the
> kickstart. The problem was with the updater. :-(
>
> Thanks,
> Rui
>
> On Fri, Oct 12, 2018 at 12:23 PM Qiang Gu wrote:
>
>> Hi Rui,
>>
>> Galaxy will use the default sqlite if you comment out the db setting the
>> config file (`config/galaxy.yml`). You mean the sqlite works the same as
>> the postgresql, which doesn't allow you to create users?
>> If that's the case, try `git clone` a new galaxy repo, in the galaxy
>> folder, `git checkout remotes/original/release_18.05`, `git checkout -b
>> release_18.05`, `./run.sh`.
>> Basically, I would like to make the sqlite working first, then switch to
>> postgresql. The above-mentioned steps may help identify the hidden issue.
>>
>> Good luck!
>>
>> -Qiang
>>
>>
>> ------------------
>> *From:* Rui Wang [ruiwang...@gmail.com]
>> *Sent:* Friday, October 12, 2018 1:01 AM
>> *To:* Qiang Gu
>> *Cc:* galaxy-dev@lists.galaxyproject.org
>> *Subject:* Re: [galaxy-dev] can't create user on a new instance
>>
>> Hi Qiang,
>>
>> Thanks so much for the email. The default sqlite seems to be the same. I
>> spent some time with the kickstart. That would be fantastic if it
>> works...sadly it failed on me. :-( Let me make some more effort on that.
>> Btw, do you have a better version of the instructions for the kickstart?
>>
>> Cheers,
>> Rui
>>
>> On Wed, Oct 10, 2018 at 10:12 PM Qiang Gu wrote:
>>
>>> Hi Rui,
>>>
>>> Does the default database sqlite work for you? I guess there is certain
>>> mis-configuration in your
>>> postgresql settings or certain element in the config/galaxy.yml file is
>>> broken. Try to enter your postgresql database in terminal using the
>>> same login info and create a table to make sure you have proper privileges.
>>> Alternatively, using GalaxyKickStart (
>>> https://github.com/ARTbio/GalaxyKickStart) to deploy a server
>>> isn't that difficult and a postgresql database comes with it by default.
>>> Good luck!
>>>
>>> Thanks,
>>>
>>> -Qiang
>>>
>>> --
>>> *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on
>>> behalf of Rui Wang [ruiwang...@gmail.com]
>>> *Sent:* Wednesday, October 10, 2018 9:30 PM
>>> *To:* galaxy-dev@lists.galaxyproject.org
>>> *Subject:* Re: [galaxy-dev] can't create user on a new instance
>>>
>>> Hi Folks,
>>>
>>> I still could not create new user account with the same error message.
>>> Has anyone happened to see this before?
>>>
>>> Cheers,
>>> Rui
>>>
>>> On Tue, Oct 9, 2018 at 5:48 PM Rui Wang wrote:
>>>
>>>> Hey Folks,
>>>>
>>>> I just installed a new 18.05 instance with a new postgresql db created.
>>>> However, the UI doesn't allow me to create any user. After I provided all
>>>> input information, it says
>>>>
>>>> galaxy.web.framework.webapp WARNING 2018-10-09 17:28:35,735
>>>> [p:32925,w:1,m:0] [uWSGIWorker1Core2] Wrong session token found, denying
>>>> request
>>>>
>>>> in the server log. Btw, I enabled 'allow to create user' and admin user
>>>> list is empty.
>>>>
>>>> I looked into it, and it's a function in
>>>> lib/galaxy/web/framework/webapp.py:
>>>>
>>>> def check_csrf_token(self):
>>>> session_csrf_token =
>>>> self.request.params.get("session_csrf_token", None)
>>>> problem = False
>>>> if not session_csrf_token:
>>>> log.warning("No session_csrf_token set, denying request.")
>>>> problem = True
>>>> elif session_csrf_token != self.session_csrf_token:
>>>> log.warning("Wrong session token found, denying request.")
>>>> problem = True
>>>>
>>>> if problem:
>>>> return self.show_warn_message("Failed to authorize action.")
>>>>
>>>> Could someone give me a hand? :-)
>>>>
>>>> Cheers,
>>>> Rui
>>>>
>>>
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Re: [galaxy-dev] can't create user on a new instance
Hi Qiang,
I looked at the postgres, here is the ownership info:
bioinfoadmin=> \l
List of databases
Name |Owner | Encoding | Collate |Ctype|
Access privileges
--+--+--+-+-+---
bioinfoadmin | bioinfoadmin | UTF8 | en_US.UTF-8 | en_US.UTF-8 |
citation | bioinfoadmin | UTF8 | en_US.UTF-8 | en_US.UTF-8 |
postgres | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 |
template0| postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 |
=c/postgres +
| | | | |
postgres=CTc/postgres
template1| postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 |
=c/postgres +
| | | | |
postgres=CTc/postgres
(5 rows)
Does this look okay to you? the db bioinfoadmin is the one that is set in
the galaxy config, and it's owned by
the user bioinfoadmin which is used to start galaxy.
Thanks,
Rui
On Wed, Oct 10, 2018 at 10:12 PM Qiang Gu wrote:
> Hi Rui,
>
> Does the default database sqlite work for you? I guess there is certain
> mis-configuration in your
> postgresql settings or certain element in the config/galaxy.yml file is
> broken. Try to enter your postgresql database in terminal using the same
> login info and create a table to make sure you have proper privileges.
> Alternatively, using GalaxyKickStart (
> https://github.com/ARTbio/GalaxyKickStart) to deploy a server
> isn't that difficult and a postgresql database comes with it by default.
> Good luck!
>
> Thanks,
>
> -Qiang
>
> --
> *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf
> of Rui Wang [ruiwang...@gmail.com]
> *Sent:* Wednesday, October 10, 2018 9:30 PM
> *To:* galaxy-dev@lists.galaxyproject.org
> *Subject:* Re: [galaxy-dev] can't create user on a new instance
>
> Hi Folks,
>
> I still could not create new user account with the same error message. Has
> anyone happened to see this before?
>
> Cheers,
> Rui
>
> On Tue, Oct 9, 2018 at 5:48 PM Rui Wang wrote:
>
>> Hey Folks,
>>
>> I just installed a new 18.05 instance with a new postgresql db created.
>> However, the UI doesn't allow me to create any user. After I provided all
>> input information, it says
>>
>> galaxy.web.framework.webapp WARNING 2018-10-09 17:28:35,735
>> [p:32925,w:1,m:0] [uWSGIWorker1Core2] Wrong session token found, denying
>> request
>>
>> in the server log. Btw, I enabled 'allow to create user' and admin user
>> list is empty.
>>
>> I looked into it, and it's a function in
>> lib/galaxy/web/framework/webapp.py:
>>
>> def check_csrf_token(self):
>> session_csrf_token =
>> self.request.params.get("session_csrf_token", None)
>> problem = False
>> if not session_csrf_token:
>> log.warning("No session_csrf_token set, denying request.")
>> problem = True
>> elif session_csrf_token != self.session_csrf_token:
>> log.warning("Wrong session token found, denying request.")
>> problem = True
>>
>> if problem:
>> return self.show_warn_message("Failed to authorize action.")
>>
>> Could someone give me a hand? :-)
>>
>> Cheers,
>> Rui
>>
>
___
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Re: [galaxy-dev] can't create user on a new instance
Hi Marius,
Thanks for your suggestion! I tried it with a different browser that never
accessed galaxy, but it still gave me the same message. :-( Any thoughts?
Cheers,
Rui
On Wed, Oct 10, 2018 at 11:25 PM Marius van den Beek
wrote:
> Hi Rui,
>
> The session token is used to prevent certain kinds of attacks. Your
> browser may still have a session token for the old instance. You can delete
> the cookies for this address in your browser and you should be issued a new
> and valid token.
>
> Hope that helps,
> Marius
>
> On Thu, Oct 11, 2018, 7:12 AM Qiang Gu wrote:
>
>> Hi Rui,
>>
>> Does the default database sqlite work for you? I guess there is certain
>> mis-configuration in your
>> postgresql settings or certain element in the config/galaxy.yml file is
>> broken. Try to enter your postgresql database in terminal using the same
>> login info and create a table to make sure you have proper privileges.
>> Alternatively, using GalaxyKickStart (
>> https://github.com/ARTbio/GalaxyKickStart) to deploy a server
>> isn't that difficult and a postgresql database comes with it by default.
>> Good luck!
>>
>> Thanks,
>>
>> -Qiang
>>
>> --
>> *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on
>> behalf of Rui Wang [ruiwang...@gmail.com]
>> *Sent:* Wednesday, October 10, 2018 9:30 PM
>> *To:* galaxy-dev@lists.galaxyproject.org
>> *Subject:* Re: [galaxy-dev] can't create user on a new instance
>>
>> Hi Folks,
>>
>> I still could not create new user account with the same error message.
>> Has anyone happened to see this before?
>>
>> Cheers,
>> Rui
>>
>> On Tue, Oct 9, 2018 at 5:48 PM Rui Wang wrote:
>>
>>> Hey Folks,
>>>
>>> I just installed a new 18.05 instance with a new postgresql db created.
>>> However, the UI doesn't allow me to create any user. After I provided all
>>> input information, it says
>>>
>>> galaxy.web.framework.webapp WARNING 2018-10-09 17:28:35,735
>>> [p:32925,w:1,m:0] [uWSGIWorker1Core2] Wrong session token found, denying
>>> request
>>>
>>> in the server log. Btw, I enabled 'allow to create user' and admin user
>>> list is empty.
>>>
>>> I looked into it, and it's a function in
>>> lib/galaxy/web/framework/webapp.py:
>>>
>>> def check_csrf_token(self):
>>> session_csrf_token =
>>> self.request.params.get("session_csrf_token", None)
>>> problem = False
>>> if not session_csrf_token:
>>> log.warning("No session_csrf_token set, denying request.")
>>> problem = True
>>> elif session_csrf_token != self.session_csrf_token:
>>> log.warning("Wrong session token found, denying request.")
>>> problem = True
>>>
>>> if problem:
>>> return self.show_warn_message("Failed to authorize action.")
>>>
>>> Could someone give me a hand? :-)
>>>
>>> Cheers,
>>> Rui
>>>
>> ___
>> 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:
>> https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/
>
>
___
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] can't create user on a new instance
Hi Qiang,
Thanks so much for the email. The default sqlite seems to be the same. I
spent some time with the kickstart. That would be fantastic if it
works...sadly it failed on me. :-( Let me make some more effort on that.
Btw, do you have a better version of the instructions for the kickstart?
Cheers,
Rui
On Wed, Oct 10, 2018 at 10:12 PM Qiang Gu wrote:
> Hi Rui,
>
> Does the default database sqlite work for you? I guess there is certain
> mis-configuration in your
> postgresql settings or certain element in the config/galaxy.yml file is
> broken. Try to enter your postgresql database in terminal using the same
> login info and create a table to make sure you have proper privileges.
> Alternatively, using GalaxyKickStart (
> https://github.com/ARTbio/GalaxyKickStart) to deploy a server
> isn't that difficult and a postgresql database comes with it by default.
> Good luck!
>
> Thanks,
>
> -Qiang
>
> --
> *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf
> of Rui Wang [ruiwang...@gmail.com]
> *Sent:* Wednesday, October 10, 2018 9:30 PM
> *To:* galaxy-dev@lists.galaxyproject.org
> *Subject:* Re: [galaxy-dev] can't create user on a new instance
>
> Hi Folks,
>
> I still could not create new user account with the same error message. Has
> anyone happened to see this before?
>
> Cheers,
> Rui
>
> On Tue, Oct 9, 2018 at 5:48 PM Rui Wang wrote:
>
>> Hey Folks,
>>
>> I just installed a new 18.05 instance with a new postgresql db created.
>> However, the UI doesn't allow me to create any user. After I provided all
>> input information, it says
>>
>> galaxy.web.framework.webapp WARNING 2018-10-09 17:28:35,735
>> [p:32925,w:1,m:0] [uWSGIWorker1Core2] Wrong session token found, denying
>> request
>>
>> in the server log. Btw, I enabled 'allow to create user' and admin user
>> list is empty.
>>
>> I looked into it, and it's a function in
>> lib/galaxy/web/framework/webapp.py:
>>
>> def check_csrf_token(self):
>> session_csrf_token =
>> self.request.params.get("session_csrf_token", None)
>> problem = False
>> if not session_csrf_token:
>> log.warning("No session_csrf_token set, denying request.")
>> problem = True
>> elif session_csrf_token != self.session_csrf_token:
>> log.warning("Wrong session token found, denying request.")
>> problem = True
>>
>> if problem:
>> return self.show_warn_message("Failed to authorize action.")
>>
>> Could someone give me a hand? :-)
>>
>> Cheers,
>> Rui
>>
>
___
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] can't create user on a new instance
Hi Rui,
The session token is used to prevent certain kinds of attacks. Your browser
may still have a session token for the old instance. You can delete the
cookies for this address in your browser and you should be issued a new and
valid token.
Hope that helps,
Marius
On Thu, Oct 11, 2018, 7:12 AM Qiang Gu wrote:
> Hi Rui,
>
> Does the default database sqlite work for you? I guess there is certain
> mis-configuration in your
> postgresql settings or certain element in the config/galaxy.yml file is
> broken. Try to enter your postgresql database in terminal using the same
> login info and create a table to make sure you have proper privileges.
> Alternatively, using GalaxyKickStart (
> https://github.com/ARTbio/GalaxyKickStart) to deploy a server
> isn't that difficult and a postgresql database comes with it by default.
> Good luck!
>
> Thanks,
>
> -Qiang
>
> --
> *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf
> of Rui Wang [ruiwang...@gmail.com]
> *Sent:* Wednesday, October 10, 2018 9:30 PM
> *To:* galaxy-dev@lists.galaxyproject.org
> *Subject:* Re: [galaxy-dev] can't create user on a new instance
>
> Hi Folks,
>
> I still could not create new user account with the same error message. Has
> anyone happened to see this before?
>
> Cheers,
> Rui
>
> On Tue, Oct 9, 2018 at 5:48 PM Rui Wang wrote:
>
>> Hey Folks,
>>
>> I just installed a new 18.05 instance with a new postgresql db created.
>> However, the UI doesn't allow me to create any user. After I provided all
>> input information, it says
>>
>> galaxy.web.framework.webapp WARNING 2018-10-09 17:28:35,735
>> [p:32925,w:1,m:0] [uWSGIWorker1Core2] Wrong session token found, denying
>> request
>>
>> in the server log. Btw, I enabled 'allow to create user' and admin user
>> list is empty.
>>
>> I looked into it, and it's a function in
>> lib/galaxy/web/framework/webapp.py:
>>
>> def check_csrf_token(self):
>> session_csrf_token =
>> self.request.params.get("session_csrf_token", None)
>> problem = False
>> if not session_csrf_token:
>> log.warning("No session_csrf_token set, denying request.")
>> problem = True
>> elif session_csrf_token != self.session_csrf_token:
>> log.warning("Wrong session token found, denying request.")
>> problem = True
>>
>> if problem:
>> return self.show_warn_message("Failed to authorize action.")
>>
>> Could someone give me a hand? :-)
>>
>> Cheers,
>> Rui
>>
> ___
> 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:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/
___
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:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] can't create user on a new instance
Hi Rui,
Does the default database sqlite work for you? I guess there is certain
mis-configuration in your
postgresql settings or certain element in the config/galaxy.yml file is broken.
Try to enter your postgresql database in terminal using the same login info and
create a table to make sure you have proper privileges.
Alternatively, using GalaxyKickStart
(https://github.com/ARTbio/GalaxyKickStart) to deploy a server
isn't that difficult and a postgresql database comes with it by default. Good
luck!
Thanks,
-Qiang
From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of Rui
Wang [ruiwang...@gmail.com]
Sent: Wednesday, October 10, 2018 9:30 PM
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] can't create user on a new instance
Hi Folks,
I still could not create new user account with the same error message. Has
anyone happened to see this before?
Cheers,
Rui
On Tue, Oct 9, 2018 at 5:48 PM Rui Wang
mailto:ruiwang...@gmail.com>> wrote:
Hey Folks,
I just installed a new 18.05 instance with a new postgresql db created.
However, the UI doesn't allow me to create any user. After I provided all input
information, it says
galaxy.web.framework.webapp WARNING 2018-10-09 17:28:35,735 [p:32925,w:1,m:0]
[uWSGIWorker1Core2] Wrong session token found, denying request
in the server log. Btw, I enabled 'allow to create user' and admin user list is
empty.
I looked into it, and it's a function in lib/galaxy/web/framework/webapp.py:
def check_csrf_token(self):
session_csrf_token = self.request.params.get("session_csrf_token", None)
problem = False
if not session_csrf_token:
log.warning("No session_csrf_token set, denying request.")
problem = True
elif session_csrf_token != self.session_csrf_token:
log.warning("Wrong session token found, denying request.")
problem = True
if problem:
return self.show_warn_message("Failed to authorize action.")
Could someone give me a hand? :-)
Cheers,
Rui
___
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
Re: [galaxy-dev] can't create user on a new instance
Hi Folks,
I still could not create new user account with the same error message. Has
anyone happened to see this before?
Cheers,
Rui
On Tue, Oct 9, 2018 at 5:48 PM Rui Wang wrote:
> Hey Folks,
>
> I just installed a new 18.05 instance with a new postgresql db created.
> However, the UI doesn't allow me to create any user. After I provided all
> input information, it says
>
> galaxy.web.framework.webapp WARNING 2018-10-09 17:28:35,735
> [p:32925,w:1,m:0] [uWSGIWorker1Core2] Wrong session token found, denying
> request
>
> in the server log. Btw, I enabled 'allow to create user' and admin user
> list is empty.
>
> I looked into it, and it's a function in
> lib/galaxy/web/framework/webapp.py:
>
> def check_csrf_token(self):
> session_csrf_token = self.request.params.get("session_csrf_token",
> None)
> problem = False
> if not session_csrf_token:
> log.warning("No session_csrf_token set, denying request.")
> problem = True
> elif session_csrf_token != self.session_csrf_token:
> log.warning("Wrong session token found, denying request.")
> problem = True
>
> if problem:
> return self.show_warn_message("Failed to authorize action.")
>
> Could someone give me a hand? :-)
>
> Cheers,
> Rui
>
___
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
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[galaxy-dev] can't create user on a new instance
Hey Folks,
I just installed a new 18.05 instance with a new postgresql db created.
However, the UI doesn't allow me to create any user. After I provided all
input information, it says
galaxy.web.framework.webapp WARNING 2018-10-09 17:28:35,735
[p:32925,w:1,m:0] [uWSGIWorker1Core2] Wrong session token found, denying
request
in the server log. Btw, I enabled 'allow to create user' and admin user
list is empty.
I looked into it, and it's a function in lib/galaxy/web/framework/webapp.py:
def check_csrf_token(self):
session_csrf_token = self.request.params.get("session_csrf_token",
None)
problem = False
if not session_csrf_token:
log.warning("No session_csrf_token set, denying request.")
problem = True
elif session_csrf_token != self.session_csrf_token:
log.warning("Wrong session token found, denying request.")
problem = True
if problem:
return self.show_warn_message("Failed to authorize action.")
Could someone give me a hand? :-)
Cheers,
Rui
___
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
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