Re: [galaxy-dev] remote user CAS invalide session

[Laure QUINTRIC]

Thank you for your quick support.
Laure

Le 19/04/2016 19:05, Dannon Baker a écrit :
This turned out to be a problem with how the maildomain was handled 
after a recent fix to support API interactions bypassing remote user 
auth.


I'm working on a fix which you can follow and test here: 
https://github.com/galaxyproject/galaxy/pull/2195


Thanks again for the report!

On Tue, Apr 19, 2016 at 8:25 AM, Dannon Baker > wrote:


Thank you for the report!  I'm able to reproduce this here on my
local test install and will try to figure out what's going on and
let you know when I have a fix.

-Dannon

On Tue, Apr 19, 2016 at 3:07 AM, Laure QUINTRIC
mailto:laure.quint...@ifremer.fr>> wrote:

Hi galaxy users,

I just installed version 16.04 of galaxy. I can connect to
galaxy with remote user through CAS authentification but my
session is invalidated, I get this message in the history :
An error occurred while getting updates from the server.
Please contact a Galaxy administrator if the problem persists.
Details

In paster.log, I can see this :

galaxy.web.framework.webapp WARNING 2016-04-18 17:37:47,308
User logged in as 't...@company.fr '
externally, but has a cookie as 'toto' invalidating session

and just after I can see :

galaxy.web.framework.webapp WARNING 2016-04-18 17:37:48,018
User logged in as 'toto' externally, but has a cookie as
't...@company.fr ' invalidating session

It seems that variables remote_user_email and
galaxy_session.user.email ( in
galaxy/lib/web/framework/webapp.py) are set to
login@maildomain and then set to login only... so the user
login is not always the user email address.

In the config/galaxy.ini I set
remote_user_maildomain = company.fr 
remote_user_header = HTTP_CAS_UID

Can you tell me how to go through this ? I did not have this
problem in v16.01.

Best regards




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Re: [galaxy-dev] remote user CAS invalide session

[Dannon Baker]

This turned out to be a problem with how the maildomain was handled after a
recent fix to support API interactions bypassing remote user auth.

I'm working on a fix which you can follow and test here:
https://github.com/galaxyproject/galaxy/pull/2195

Thanks again for the report!

On Tue, Apr 19, 2016 at 8:25 AM, Dannon Baker 
wrote:

> Thank you for the report!  I'm able to reproduce this here on my local
> test install and will try to figure out what's going on and let you know
> when I have a fix.
>
> -Dannon
>
> On Tue, Apr 19, 2016 at 3:07 AM, Laure QUINTRIC  > wrote:
>
>> Hi galaxy users,
>>
>> I just installed version 16.04 of galaxy. I can connect to galaxy with
>> remote user through CAS authentification but my session is invalidated, I
>> get this message in the history :
>> An error occurred while getting updates from the server. Please contact a
>> Galaxy administrator if the problem persists. Details
>>
>> In paster.log, I can see this :
>>
>> galaxy.web.framework.webapp WARNING 2016-04-18 17:37:47,308 User logged
>> in as 't...@company.fr' externally, but has a cookie as 'toto'
>> invalidating session
>>
>> and just after I can see :
>>
>> galaxy.web.framework.webapp WARNING 2016-04-18 17:37:48,018 User logged
>> in as 'toto' externally, but has a cookie as 't...@company.fr'
>> invalidating session
>>
>> It seems that variables remote_user_email and galaxy_session.user.email (
>> in galaxy/lib/web/framework/webapp.py) are set to login@maildomain and
>> then set to login only... so the user login is not always the user email
>> address.
>>
>> In the config/galaxy.ini I set
>> remote_user_maildomain = company.fr
>> remote_user_header = HTTP_CAS_UID
>>
>> Can you tell me how to go through this ? I did not have this problem in
>> v16.01.
>>
>> Best regards
>>
>>
>>
>>
>> ___
>> 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/mailinglists/
>>
>
>
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Re: [galaxy-dev] Question: Cannot start local Galaxy after upgrade to v16.01

[Nicola Soranzo]

Hi Daniel,
by looking at your traceback, it seems you have a file 
/opt/galaxy/lib/pkg_resources.py which has been removed in Galaxy 16.01 .

To verify that you can execute

git status

which should print something like:

On branch release_16.01
Your branch is up-to-date with 'origin/release_16.01'.

Untracked files:
  (use "git add ..." to include in what will be committed)

lib/pkg_resources.py

If you see that, you can remove lib/pkg_resources.py and Galaxy should work.

Cheers,
Nicola


On 19/04/16 16:54, D K wrote:

Hi Galaxy Devs,

I posted this question on biostars but didn't get an answer so I'll 
try here:


I just tried upgrading my local instance of Galaxy from 15.10 to 
16.01. When I start it up I get an error. Does anyone have any 
suggestions?


|galaxy@galaxy galaxy$ sh run.sh Activating virtualenv at .venv 
DEPRECATION: Python 2.6 is no longer supported by the Python core 
team, please upgrade your Python. A future version of pip will drop 
support for Python 2.6 Ignoring indexes: 
https://pypi.python.org/simple 
/opt/galaxy/.venv/lib/python2.6/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315 
: 
SNIMissingWarning: An HTTPS request has been made, but the SNI 
(Subject Name Indication) extension to TLS is not available on this 
platform. This may cause the server to present an incorrect TLS 
certificate, which can cause validation failures. For more 
information, see 
https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. 
SNIMissingWarning 
/opt/galaxy/.venv/lib/python2.6/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: 
InsecurePlatformWarning: A true SSLContext object is not available. 
This prevents urllib3 from configuring SSL appropriately and may cause 
certain SSL connections to fail. For more information, see 
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. 
InsecurePlatformWarning Requirement already up-to-date: pip==8.0.2+gx2 
in ./.venv/lib/python2.6/site-packages DEPRECATION: Python 2.6 is no 
longer supported by the Python core team, please upgrade your Python. 
A future version of pip will drop support for Python 2.6 Requirement 
already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in 
./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 
2)) Requirement already satisfied (use --upgrade to upgrade): 
MarkupSafe==0.23 in ./.venv/lib/python2.6/site-packages (from -r 
requirements.txt (line 3)) Requirement already satisfied (use 
--upgrade to upgrade): PyYAML==3.11 in 
./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 
4)) Requirement already satisfied (use --upgrade to upgrade): 
SQLAlchemy==1.0.8 in ./.venv/lib/python2.6/site-packages (from -r 
requirements.txt (line 5)) Requirement already satisfied (use 
--upgrade to upgrade): mercurial==3.4.2 in 
./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 
7)) Requirement already satisfied (use --upgrade to upgrade): 
numpy==1.9.2 in ./.venv/lib/python2.6/site-packages (from -r 
requirements.txt (line 8)) Requirement already satisfied (use 
--upgrade to upgrade): pycrypto==2.6.1 in 
./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 
9)) Requirement already satisfied (use --upgrade to upgrade): 
Paste==2.0.2 in ./.venv/lib/python2.6/site-packages (from -r 
requirements.txt (line 16)) Requirement already satisfied (use 
--upgrade to upgrade): PasteDeploy==1.5.2 in 
./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 
17)) Requirement already satisfied (use --upgrade to upgrade): 
docutils==0.12 in ./.venv/lib/python2.6/site-packages (from -r 
requirements.txt (line 18)) Requirement already satisfied (use 
--upgrade to upgrade): wchartype==0.1 in 
./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 
19)) Requirement already satisfied (use --upgrade to upgrade): 
repoze.lru==0.6 in ./.venv/lib/python2.6/site-packages (from -r 
requirements.txt (line 20)) Requirement already satisfied (use 
--upgrade to upgrade): Routes==2.2 in 
./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 
21)) Requirement already satisfied (use --upgrade to upgrade): 
WebOb==1.4.1 in ./.venv/lib/python2.6/site-packages (from -r 
requirements.txt (line 22)) Requirement already satisfied (use 
--upgrade to upgrade): WebHelpers==1.3 in 
./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 
23)) Requirement already satisfied (use --upgrade to upgrade): 
Mako==1.0.2 in ./.venv/lib/python2.6/site-packages (from -r 
requirements.txt (line 24)) Requirement already satisfied (use 
--upgrade to upgrade): pytz==2015.4 in 
./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 
25)) Requirement already satisfied (use --upgrade to upgrade): 
Babel==2.0 in ./.venv/lib/python2.6/site-packages (fro

Re: [galaxy-dev] Question: Cannot start local Galaxy after upgrade to v16.01

[Scott Szakonyi]

Hi Daniel,

I'm a relative novice at Galaxy administration, but at first blush it looks
like you're missing (or the Galaxy user doesn't have permissions on) the
paste process. You can try a GIT status or diff to see if something just
didn't download right. Otherwise, check to make sure that your entire
galaxy install directory is owned by the Galaxy user and the group that the
Galaxy user belongs to.

Hope this helps!

pkg_resources.DistributionNotFound: Paste


-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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[galaxy-dev] Question: Cannot start local Galaxy after upgrade to v16.01

[D K]

Hi Galaxy Devs,

I posted this question on biostars but didn't get an answer so I'll try
here:

I just tried upgrading my local instance of Galaxy from 15.10 to 16.01.
When I start it up I get an error. Does anyone have any suggestions?

galaxy@galaxy galaxy$ sh run.sh
Activating virtualenv at .venv
DEPRECATION: Python 2.6 is no longer supported by the Python core
team, please upgrade your Python. A future version of pip will drop
support for Python 2.6
Ignoring indexes: https://pypi.python.org/simple
/opt/galaxy/.venv/lib/python2.6/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315:
SNIMissingWarning: An HTTPS request has been made, but the SNI
(Subject Name Indication) extension to TLS is not available on this
platform. This may cause the server to present an incorrect TLS
certificate, which can cause validation failures. For more
information, see
https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
  SNIMissingWarning
/opt/galaxy/.venv/lib/python2.6/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120:
InsecurePlatformWarning: A true SSLContext object is not available.
This prevents urllib3 from configuring SSL appropriately and may cause
certain SSL connections to fail. For more information, see
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
Requirement already up-to-date: pip==8.0.2+gx2 in
./.venv/lib/python2.6/site-packages
DEPRECATION: Python 2.6 is no longer supported by the Python core
team, please upgrade your Python. A future version of pip will drop
support for Python 2.6
Requirement already satisfied (use --upgrade to upgrade):
bx-python==0.7.3 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 2))
Requirement already satisfied (use --upgrade to upgrade):
MarkupSafe==0.23 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 3))
Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
4))
Requirement already satisfied (use --upgrade to upgrade):
SQLAlchemy==1.0.8 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 5))
Requirement already satisfied (use --upgrade to upgrade):
mercurial==3.4.2 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 7))
Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
8))
Requirement already satisfied (use --upgrade to upgrade):
pycrypto==2.6.1 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 9))
Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
16))
Requirement already satisfied (use --upgrade to upgrade):
PasteDeploy==1.5.2 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 17))
Requirement already satisfied (use --upgrade to upgrade):
docutils==0.12 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 18))
Requirement already satisfied (use --upgrade to upgrade):
wchartype==0.1 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 19))
Requirement already satisfied (use --upgrade to upgrade):
repoze.lru==0.6 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 20))
Requirement already satisfied (use --upgrade to upgrade): Routes==2.2
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
21))
Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
22))
Requirement already satisfied (use --upgrade to upgrade):
WebHelpers==1.3 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 23))
Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
24))
Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
25))
Requirement already satisfied (use --upgrade to upgrade): Babel==2.0
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
26))
Requirement already satisfied (use --upgrade to upgrade):
Beaker==1.7.0 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 27))
Requirement already satisfied (use --upgrade to upgrade):
Cheetah==2.4.4 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 30))
Requirement already satisfied (use --upgrade to upgrade):
Markdown==2.6.3 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 31))
Requirement already satisfied (use --upgrade to upgrade):
bioblend==0.6.1 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 34))
Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0
in ./.venv/lib/python2.6/site-packa

Re: [galaxy-dev] novice galaxy user needs help retrieving MIA history

[Jennifer Hillman-Jackson]

Hello Ryan,

Try finding it this way as a first step:

https://wiki.galaxyproject.org/Support#Example:_My_History_is_missing.21

Thanks,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Mon, Apr 18, 2016 at 7:20 PM, ryan stueve  wrote:

> Greetings,
>  I am a novice Galaxy user. I was getting along perfectly this
> morning (made some mistakes, deleted some steps) and got to alignment steps
> in my RNAseq analysis. Went to some afternoon meetings, returned & logged
> back in- MY HISTORY WAS EMPTY!
>
> can you advise?
>
> Instance: MAIN/public
> Username/email: jnkacc...@outlook.com
> History name: something like "LUAD RNA-seq"; definitely had "LUAD" in title
>
> also, here is one of the steps/filenames that should be in history (I
> downloaded before meeting):
> "Galaxy240-[H1648_TopHat_on_data_164_and_data_163__accepted_hits].bam"
>
>
> any help sincerely appreciated
>
> ___
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>
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[galaxy-dev] novice galaxy user needs help retrieving MIA history

[ryan stueve]

Greetings,  I am a novice Galaxy user. I was getting along perfectly 
this morning (made some mistakes, deleted some steps) and got to alignment 
steps in my RNAseq analysis. Went to some afternoon meetings, returned & logged 
back in- MY HISTORY WAS EMPTY!
can you advise?
Instance: MAIN/publicUsername/email: jnkaccnt1@outlook.comHistory name: 
something like "LUAD RNA-seq"; definitely had "LUAD" in title
also, here is one of the steps/filenames that should be in history (I 
downloaded before 
meeting):"Galaxy240-[H1648_TopHat_on_data_164_and_data_163__accepted_hits].bam"

any help sincerely appreciated___
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Re: [galaxy-dev] remote user CAS invalide session

[Dannon Baker]

Thank you for the report!  I'm able to reproduce this here on my local test
install and will try to figure out what's going on and let you know when I
have a fix.

-Dannon

On Tue, Apr 19, 2016 at 3:07 AM, Laure QUINTRIC 
wrote:

> Hi galaxy users,
>
> I just installed version 16.04 of galaxy. I can connect to galaxy with
> remote user through CAS authentification but my session is invalidated, I
> get this message in the history :
> An error occurred while getting updates from the server. Please contact a
> Galaxy administrator if the problem persists. Details
>
> In paster.log, I can see this :
>
> galaxy.web.framework.webapp WARNING 2016-04-18 17:37:47,308 User logged in
> as 't...@company.fr' externally, but has a cookie as 'toto' invalidating
> session
>
> and just after I can see :
>
> galaxy.web.framework.webapp WARNING 2016-04-18 17:37:48,018 User logged in
> as 'toto' externally, but has a cookie as 't...@company.fr' invalidating
> session
>
> It seems that variables remote_user_email and galaxy_session.user.email (
> in galaxy/lib/web/framework/webapp.py) are set to login@maildomain and
> then set to login only... so the user login is not always the user email
> address.
>
> In the config/galaxy.ini I set
> remote_user_maildomain = company.fr
> remote_user_header = HTTP_CAS_UID
>
> Can you tell me how to go through this ? I did not have this problem in
> v16.01.
>
> Best regards
>
>
>
>
> ___
> 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/mailinglists/
>
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[galaxy-dev] remote user CAS invalide session

[Laure QUINTRIC]

Hi galaxy users,

I just installed version 16.04 of galaxy. I can connect to galaxy with 
remote user through CAS authentification but my session is invalidated, 
I get this message in the history :
An error occurred while getting updates from the server. Please contact 
a Galaxy administrator if the problem persists. Details 


In paster.log, I can see this :

galaxy.web.framework.webapp WARNING 2016-04-18 17:37:47,308 User logged 
in as 't...@company.fr' externally, but has a cookie as 'toto' 
invalidating session


and just after I can see :

galaxy.web.framework.webapp WARNING 2016-04-18 17:37:48,018 User logged 
in as 'toto' externally, but has a cookie as 't...@company.fr' 
invalidating session


It seems that variables remote_user_email and galaxy_session.user.email 
( in galaxy/lib/web/framework/webapp.py) are set to login@maildomain and 
then set to login only... so the user login is not always the user email 
address.


In the config/galaxy.ini I set
remote_user_maildomain = company.fr
remote_user_header = HTTP_CAS_UID

Can you tell me how to go through this ? I did not have this problem in 
v16.01.


Best regards



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