Re: [galaxy-dev] email activation setting failed

[Dannon Baker]

Per the error message 'Temporary failure in name resolution', it sounds
like your server was unable to locate smtp.gmail.com.  Can you verify the
server does have the ability to connect to this machine and send email?

This may help:
https://stackoverflow.com/questions/11988454/how-to-check-if-smtp-is-working-from-commandline-linux

If it's working, then just retry sending the activation email.

On Mon, Nov 9, 2015 at 5:06 AM Jun Fan  wrote:

> Hi all,
>
>
>
>  I am using smtp.gmail.com as the smtp server with gmail account. It
> worked perfectly fine in the past. Just this morning, I received an email
> reporting the issue of failing to receive the activation email. The error
> message from Galaxy is “This account has not been activated yet but we are
> unable to send the activation link. “ Similarly in the error report
> function, there is also an expected error: “An error occurred sending the
> report by email: [Errno-3] temporary failure in name resolution”. Any ideas
> of how to solve the issue?
>
>
>
> Best regards!
>
> Jun
> ___
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Re: [galaxy-dev] login problem (redirection to the login page)

[Dannon Baker]

Hi Floreline,

This sounds a lot like your cookie_path specified in galaxy.ini might be
incorrect.  Are you using a proxy (and the proxy_prefix) in galaxy?  Can
you share the following lines and settings from your galaxy.ini, including
any comments (#) on the lines?  They should be near the beginning of the
file.

# Define the proxy-prefix filter.

[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy

filter-with = proxy-prefix
cookie_path = /galaxy



On Mon, Nov 9, 2015 at 5:59 AM Floreline TOUCHARD <
floreline.touch...@gmail.com> wrote:

> Hi,
>
> I'm still stuck with my login issue. Here is some additional information :
> - when I log in, it seems the authentication works because I get no error
> in the log but I'm redirected to the login page.
> - I saw some detailed http exchanges during the authentication phase.
> Between the login and redirection the session cookie changes. I don't know
> why.
> - I try to log in without Apache with the same result.
> - one of my colleagues advised me to watch the third part cookie loss
> problems with iframe. But I use Firefox which enables third part cookie.
> - My problem seems to lie on the server side. Is there other cache than
> Firefox I should clear ?
>
> Thank,
> F.T
> Le 5 nov. 2015 18:16, "Floreline TOUCHARD" 
> a écrit :
>
>> Hi,
>>
>> I come back to you with some news of my login problem.
>> I delete my browser cache and cookies with no result.
>> I restart all my services (Apache, PostgreSQL, Galaxy) with no more
>> result.
>> I try to start fresh with my PostgreSQL database cluster (to clear all
>> the user information). But it didn't solve the problem. When I register
>> with a user name, I get :
>>
>> - on the browser side:
>> "Now logged in as @example.com.
>> Verification email has been sent to your email address. Please verify it
>> by clicking the activation link in the email.
>> Please check your spam/trash folder in case you cannot find the message.
>> Return to the home page."
>>
>> - on the server side :
>> "galaxy.util ERROR 2015-11-05 17:21:25,394 Mail is not configured for
>> this Galaxy instance.
>> galaxy.util INFO 2015-11-05 17:21:25,394 From nobody Thu Nov  5 17:21:25
>> 2015
>> Content-Type: text/plain; charset="us-ascii"
>> MIME-Version: 1.0
>> Content-Transfer-Encoding: 7bit
>> To: @example.com
>> From:
>> Subject: Galaxy Account Activation
>> Hello ,
>> In order to complete the activation process for @example.com
>> begun on 11/05/15 at ip:port, please click on the following link to verify
>> your account:
>> http://ip:port/activate?email=%40example.com
>> _token=3285151b21c8f85590db0f0c1089110d934f2400
>> By clicking on the above link and opening a Galaxy account you are also
>> confirming that you have read and agreed to Galaxy's Terms and Conditions
>> for use of this service (None). This includes a quota limit of one account
>> per user. Attempts to subvert this limit by creating multiple accounts or
>> through any other method may result in termination of all associated
>> accounts and data.
>> Please contact us if you need help with your account at: None. You can
>> also browse resources available at: None.
>> More about the Galaxy Project can be found at galaxyproject.org
>> Your Galaxy Team"
>>
>>
>> I get a new entry in the galaxy_user table (PostgreSQl table) with "f" in
>> the activate field. which I find logical.
>> If I activate the account with the link, the value becomes "t". Still
>> logical.
>>
>> But I'm redirected to the welcome page after the login and there's only
>> the "login" and "register" options under the user tab.
>> I have no error on the server log.
>> For each connection attempt I can see this line :
>> "galaxy.auth.providers.localdb DEBUG 2015-11-05 17:31:04,681 User:
>> @example.com, LOCALDB: True
>> 10.80.6.195 - - [05/Nov/2015:17:31:04 +0200] "POST
>> /user/login?use_panels=False HTTP/1.1" 200 - "http://ip:port/user/login;
>> "Mozilla/5.0 (Windows NT 6.1; rv:39.0) Gecko/20100101 Firefox/39.0"
>> 10.80.6.195 - - [05/Nov/2015:17:31:04 +0200] "GET /root HTTP/1.1" 200 -
>> "http://ip:port/user/login?use_panels=False; "Mozilla/5.0 (Windows NT
>> 6.1; rv:39.0) Gecko/20100101 Firefox/39.0"
>> 10.80.6.195 - - [05/Nov/2015:17:31:05 +0200] "GET /root/welcome HTTP/1.1"
>> 302 - "http://ip:port/root; "Mozilla/5.0 (Windows NT 6.1; rv:39.0)
>> Gecko/20100101 Firefox/39.0"
>> "
>> Is it normal ?
>>
>> My postgreSQl database seems to work fine.
>> It doesn't come from a browser cache issue (I clear mine and I try to
>> login to Galaxy with another computer on the same network).
>> Or are there other caches I should be aware of ?
>> Is there another way to get an operational application ? And where did
>> this issue come from ? I'm only testing the application but it surprises me
>> since I had a working instance for few months.
>>
>> Thanks in advance,
>> F.T
>>
>> 2015-11-04 16:44 GMT+01:00 Floreline TOUCHARD <
>> floreline.touch...@gmail.com>:
>>
>>> Update :
>>> 

Re: [galaxy-dev] feature request

[Ryan G]

Thanks.

On Mon, Nov 9, 2015 at 4:40 PM, Martin Čech  wrote:

> Created it for you here:
> https://github.com/galaxyproject/galaxy/issues/1045
>
>
> On Mon, Nov 9, 2015 at 4:39 PM Ryan G  wrote:
>
>> Yes, I'll do it there.
>>
>> On Mon, Nov 9, 2015 at 4:38 PM, Björn Grüning 
>> wrote:
>>
>>> Hi Ryan,
>>>
>>> can you create a github issue with this suggestion :)
>>>
>>> Thanks,
>>> Bjoern
>>>
>>> Am 09.11.2015 um 22:37 schrieb Ryan G:
>>> > I'd put this into Trello, but Trello is blocked from my place of
>>> business...
>>> >
>>> > I have a data library with over 200 files in it.  Half of them are
>>> > "clipped" and the other half are not.  I'd like to be able to search
>>> and
>>> > display a subset of files in the data library.  This will make
>>> selecting
>>> > the files I want to import into my history much easier.
>>> >
>>> >
>>> >
>>> > ___
>>> > 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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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
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>>   http://galaxyproject.org/search/mailinglists/
>
>
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[galaxy-dev] feature request

[Ryan G]

I'd put this into Trello, but Trello is blocked from my place of business...

I have a data library with over 200 files in it.  Half of them are
"clipped" and the other half are not.  I'd like to be able to search and
display a subset of files in the data library.  This will make selecting
the files I want to import into my history much easier.
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Re: [galaxy-dev] feature request

[Ryan G]

Yes, I'll do it there.

On Mon, Nov 9, 2015 at 4:38 PM, Björn Grüning 
wrote:

> Hi Ryan,
>
> can you create a github issue with this suggestion :)
>
> Thanks,
> Bjoern
>
> Am 09.11.2015 um 22:37 schrieb Ryan G:
> > I'd put this into Trello, but Trello is blocked from my place of
> business...
> >
> > I have a data library with over 200 files in it.  Half of them are
> > "clipped" and the other half are not.  I'd like to be able to search and
> > display a subset of files in the data library.  This will make selecting
> > the files I want to import into my history much easier.
> >
> >
> >
> > ___
> > 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] feature request

[Martin Čech]

Created it for you here: https://github.com/galaxyproject/galaxy/issues/1045

On Mon, Nov 9, 2015 at 4:39 PM Ryan G  wrote:

> Yes, I'll do it there.
>
> On Mon, Nov 9, 2015 at 4:38 PM, Björn Grüning 
> wrote:
>
>> Hi Ryan,
>>
>> can you create a github issue with this suggestion :)
>>
>> Thanks,
>> Bjoern
>>
>> Am 09.11.2015 um 22:37 schrieb Ryan G:
>> > I'd put this into Trello, but Trello is blocked from my place of
>> business...
>> >
>> > I have a data library with over 200 files in it.  Half of them are
>> > "clipped" and the other half are not.  I'd like to be able to search and
>> > display a subset of files in the data library.  This will make selecting
>> > the files I want to import into my history much easier.
>> >
>> >
>> >
>> > ___
>> > 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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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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[galaxy-dev] python_mysqldb caused zip_safe flag not set

[Mic]

Hello,
I tried to install CEAS from testtoolshed, but I have recieved the below
error from python_mysqldb
(tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f)

The installation directory for this tool dependency had contents but the
database had no record. The installation log may show this tool dependency
to be correctly installed, but due to the missing database record it is now
being set to Error.

I installed MariaDB 10.1 on Ubuntu 14.04 in the following way:

apt-key adv --recv-keys --keyserver hkp://keyserver.ubuntu.com:80
0xcbcb082a1bb943db
add-apt-repository 'deb [arch=amd64,i386]
http://mirror.aarnet.edu.au/pub/MariaDB/repo/10.1/ubuntu trusty main'
apt-get update
apt-get install mariadb-server libmariadbclient-dev

The INSTALLATION.log shows the following information:
...
byte-compiling build/bdist.linux-x86_64/egg/MySQLdb/cursors.py to
cursors.pyc
creating stub loader for _mysql.so
byte-compiling build/bdist.linux-x86_64/egg/_mysql.py to _mysql.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying MySQL_python.egg-info/SOURCES.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying MySQL_python.egg-info/dependency_links.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying MySQL_python.egg-info/top_level.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
creating dist
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Creating
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python/site.py
Processing MySQL_python-1.2.5-py2.7-linux-x86_64.egg
Copying MySQL_python-1.2.5-py2.7-linux-x86_64.egg to
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python
Adding MySQL-python 1.2.5 to easy-install.pth file

Installed
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python/MySQL_python-1.2.5-py2.7-linux-x86_64.egg
Processing dependencies for MySQL-python==1.2.5
Finished processing dependencies for MySQL-python==1.2.5
#

#

 export
PYTHONPATH=$PYTHONPATH:/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python
&&
 python setup.py install --install-lib
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python
--install-scripts
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/bin

STDERR
zip_safe flag not set; analyzing archive contents...

What did I miss?

Thank you in advance.

Mic
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Re: [galaxy-dev] login problem (redirection to the login page)

[Floreline TOUCHARD]

Hi,

I'm still stuck with my login issue. Here is some additional information :
- when I log in, it seems the authentication works because I get no error
in the log but I'm redirected to the login page.
- I saw some detailed http exchanges during the authentication phase.
Between the login and redirection the session cookie changes. I don't know
why.
- I try to log in without Apache with the same result.
- one of my colleagues advised me to watch the third part cookie loss
problems with iframe. But I use Firefox which enables third part cookie.
- My problem seems to lie on the server side. Is there other cache than
Firefox I should clear ?

Thank,
F.T
Le 5 nov. 2015 18:16, "Floreline TOUCHARD"  a
écrit :

> Hi,
>
> I come back to you with some news of my login problem.
> I delete my browser cache and cookies with no result.
> I restart all my services (Apache, PostgreSQL, Galaxy) with no more result.
> I try to start fresh with my PostgreSQL database cluster (to clear all the
> user information). But it didn't solve the problem. When I register with a
> user name, I get :
>
> - on the browser side:
> "Now logged in as @example.com.
> Verification email has been sent to your email address. Please verify it
> by clicking the activation link in the email.
> Please check your spam/trash folder in case you cannot find the message.
> Return to the home page."
>
> - on the server side :
> "galaxy.util ERROR 2015-11-05 17:21:25,394 Mail is not configured for this
> Galaxy instance.
> galaxy.util INFO 2015-11-05 17:21:25,394 From nobody Thu Nov  5 17:21:25
> 2015
> Content-Type: text/plain; charset="us-ascii"
> MIME-Version: 1.0
> Content-Transfer-Encoding: 7bit
> To: @example.com
> From:
> Subject: Galaxy Account Activation
> Hello ,
> In order to complete the activation process for @example.com
> begun on 11/05/15 at ip:port, please click on the following link to verify
> your account:
> http://ip:port/activate?email=%40example.com
> _token=3285151b21c8f85590db0f0c1089110d934f2400
> By clicking on the above link and opening a Galaxy account you are also
> confirming that you have read and agreed to Galaxy's Terms and Conditions
> for use of this service (None). This includes a quota limit of one account
> per user. Attempts to subvert this limit by creating multiple accounts or
> through any other method may result in termination of all associated
> accounts and data.
> Please contact us if you need help with your account at: None. You can
> also browse resources available at: None.
> More about the Galaxy Project can be found at galaxyproject.org
> Your Galaxy Team"
>
>
> I get a new entry in the galaxy_user table (PostgreSQl table) with "f" in
> the activate field. which I find logical.
> If I activate the account with the link, the value becomes "t". Still
> logical.
>
> But I'm redirected to the welcome page after the login and there's only
> the "login" and "register" options under the user tab.
> I have no error on the server log.
> For each connection attempt I can see this line :
> "galaxy.auth.providers.localdb DEBUG 2015-11-05 17:31:04,681 User:
> @example.com, LOCALDB: True
> 10.80.6.195 - - [05/Nov/2015:17:31:04 +0200] "POST
> /user/login?use_panels=False HTTP/1.1" 200 - "http://ip:port/user/login;
> "Mozilla/5.0 (Windows NT 6.1; rv:39.0) Gecko/20100101 Firefox/39.0"
> 10.80.6.195 - - [05/Nov/2015:17:31:04 +0200] "GET /root HTTP/1.1" 200 -
> "http://ip:port/user/login?use_panels=False; "Mozilla/5.0 (Windows NT
> 6.1; rv:39.0) Gecko/20100101 Firefox/39.0"
> 10.80.6.195 - - [05/Nov/2015:17:31:05 +0200] "GET /root/welcome HTTP/1.1"
> 302 - "http://ip:port/root; "Mozilla/5.0 (Windows NT 6.1; rv:39.0)
> Gecko/20100101 Firefox/39.0"
> "
> Is it normal ?
>
> My postgreSQl database seems to work fine.
> It doesn't come from a browser cache issue (I clear mine and I try to
> login to Galaxy with another computer on the same network).
> Or are there other caches I should be aware of ?
> Is there another way to get an operational application ? And where did
> this issue come from ? I'm only testing the application but it surprises me
> since I had a working instance for few months.
>
> Thanks in advance,
> F.T
>
> 2015-11-04 16:44 GMT+01:00 Floreline TOUCHARD <
> floreline.touch...@gmail.com>:
>
>> Update :
>> When I clic several time on the galaxy name, I got this on the log :
>>
>> Exception happened during processing of request from ('127.0.0.1', 45055)
>> Traceback (most recent call last):
>>   File
>> path/to/galaxy-master/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
>> line 1068, in process_request_in_thread
>> self.finish_request(request, client_address)
>>   File "/usr/lib64/python2.6/SocketServer.py", line 332, in finish_request
>> self.RequestHandlerClass(request, client_address, self)
>>   File "/usr/lib64/python2.6/SocketServer.py", line 628, in __init__
>> self.finish()
>>   File "/usr/lib64/python2.6/SocketServer.py", line 671, in finish
>>