LDAP Auto register - "username is None"
by Martin Vickers
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Hi All,
I've been trying to get the new LDAP module to work. It works fine for
existing users but I can't get auto-register to work. In the logs I can
see the successful logins look like this;
galaxy.webapps.galaxy.controllers.user DEBUG 2015-09-02 13:35:06,130
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:35:06,131 LDAP
authenticate: email is mjv08(a)aber.ac.uk
galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:35:06,131 LDAP
authenticate: username is mjv08
....
galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:35:06,235 LDAP
authentication successful
and those that are unsuccessful have a username as None, which is why
the search filter isn't working;
galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:47:13,951 LDAP
authenticate: email is unreguser(a)aber.ac.uk
galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:47:13,951 LDAP
authenticate: username is None
....
galaxy.auth.providers.ldap_ad WARNING 2015-09-02 13:47:14,110 LDAP
authenticate: search returned no results
My auth_config.xml openldap authenticator looks like this (edited to
remove openldap server details);
<authenticator>
<type>ldap</type>
<filter>'{email}'.endswith('@example.com')</filter>
<options>
<auto-register>True</auto-register>
<allow-register>Challenge</allow-register>
<server>ldaps://dc1.example.com</server>
<search-base>ou=People,dc=dc1,dc=example,dc=com</search-base>
<search-user>cn=searchuser,ou=People,dc=dc1,dc=example,dc=com</search-user>
<search-password>searchuserpassword</search-password>
<search-fields>cn,mail</search-fields>
<search-filter>(&(cn={username})(mail={email}))</search-filter>
<bind-user>{dn}</bind-user>
<bind-password>{password}</bind-password>
<auto-register-username>{cn}</auto-register-username>
<auto-register-email>{mail}</auto-register-email>
</options>
</authenticator>
Are there any settings in galaxy.ini that are required to enable this to
work?
Many thanks
Martin
- --
- --
Dr. Martin Vickers
Data Manager/HPC Systems Administrator
Institute of Biological, Environmental and Rural Sciences
IBERS New Building
Aberystwyth University
w: http://www.martin-vickers.co.uk/
e: mjv08(a)aber.ac.uk
t: 01970 62 2807
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7 years, 2 months
ActiveDirectory issues with auto register functionality
by Yves Gagnon
Hello everybody!
I try to configure Active Directory authentication on our local instance. So far, I got the authentication to work using direct binding. I have these options in the auth_conf.xml :
<allow-register>No</allow-register>
<auto-register>Yes</auto-register>
<server>ldap:/REDACTED /</server>
<bind-user>{username}@REDACTED</bind-user>
<bind-password>{password}</bind-password>
<continue-on-failure>False</continue-on-failure>
<auto-register-username>{sAMAccountName}</auto-register-username>
<login-use-username>True</login-use-username>
<auto-register-email>{mail}</auto-register-email>
Paster.log:
galaxy.auth.providers.ldap_ad DEBUG 2015-09-03 11:26:20,158 LDAP authenticate: whoami is u:REDACTED\GagnonY
galaxy.auth.providers.ldap_ad DEBUG 2015-09-03 11:26:20,159 LDAP authentication successful
However, the authentication module does not seem to be able to fetch information from LDAP to auto register
With these settings, I get the debug message in galaxy when I try to log in :
URL: http://localhost:8080/user/login?use_panels=False
File '/home/galaxy/galaxy_app/galaxy/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond
app_iter = self.application(environ, detect_start_response)
File '/home/galaxy/galaxy_app/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy_app/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/web/framework/base.py', line 133 in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/web/framework/base.py', line 191 in handle_request
body = method( trans, **kwargs )
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/webapps/galaxy/controllers/user.py', line 482 in login
message, status, user, success = self.__validate_login( trans, **kwd )
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/webapps/galaxy/controllers/user.py', line 524 in __validate_login
autoreg = trans.app.auth_manager.check_auto_registration(trans, login, password)
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/auth/__init__.py', line 100 in check_auto_registration
auth_result, auto_email, auto_username = provider.authenticate(email, username, password, options)
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/auth/providers/ldap_ad.py', line 177 in authenticate
_get_subs(options, 'auto-register-email', params),
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/auth/providers/ldap_ad.py', line 19 in _get_subs
return str(d[k]).format(**params)
KeyError: 'mail'
So for some reason, the module cannot fetch the mail field from AD. If I try to bypass this by putting a harcoded email, same issue occurs with sAMAccountName field. Did anybody encounter this before?
Thanks in advance for the help.
Yves Gagnon
7 years, 2 months
discover_datasets
by Sabrina Legoueix Rodriguez
Hi,
I am developing a tool with unknown output dataset number;
so, I am trying to use discover_datasets tag.
I have tested the following code as explained in the galaxy project
documentation:
<tool id="sr_discover1" name="Discover">
<command>
echo "Hello" > $report;
mkdir subdir1;
echo "This" > subdir1/this.txt;
echo "That" > subdir1/that.txt;
mkdir subdir2;
echo "1" > subdir2/CUSTOM_1.txt;
echo "2" > subdir2/CUSTOM_2.tabular;
echo "3" > subdir2/CUSTOM_3.txt;
mkdir subdir3;
echo "Foo" > subdir3/Foo;
echo "mapped reads" > split_bam_.MAPPED.bam;
echo "unmapped reads" > split_bam_.UNMAPPED.bam;
echo "1" > sample1.report.tsv;
echo "2" > sample2.report.tsv;
echo "3" > sample3.report.tsv;
</command>
<inputs>
<param name="num_param" type="integer" value="7" />
<param name="input" type="data" />
</inputs>
<outputs>
<data format="txt" name="report">
<discover_datasets pattern="__designation_and_ext__"
directory="subdir1" visible="true" />
<discover_datasets
pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)"
directory="subdir2" visible="true" />
<discover_datasets pattern="__designation__" directory="subdir3"
ext="input" visible="true" />
<discover_datasets
pattern="split_bam_\.(?P<designation>([A-Z-])\w+)\.bam" ext="txt"
visible="true" />
<discover_datasets
pattern="(?P<designation>.+)\.report\.tsv" ext="tabular"
visible="true" />
</data>
</outputs>
</tool>
But, when I look at he result, I only obtain a single dataset
corresponding to the "report" and the following information:
Job Command-Line: echo "Hello" >
/path/database/job_working_directory/002/2227/galaxy_dataset_5307.dat;
mkdir subdir1; echo "This" > subdir1/this.txt; echo "That" >
subdir1/that.txt; mkdir subdir2; echo "1" > subdir2/CUSTOM_1.txt; echo
"2" > subdir2/CUSTOM_2.tabular; echo "3" > subdir2/CUSTOM_3.txt; mkdir
subdir3; echo "Foo" > subdir3/Foo; echo "mapped reads" >
split_bam_.MAPPED.bam; echo "unmapped reads" > split_bam_.UNMAPPED.bam;
echo "1" > sample1.report.tsv; echo "2" > sample2.report.tsv; echo "3" >
sample3.report.tsv;
and when I check in the job_working_directory, no "subdir(1,2 and 3)"
folders have been created and no datasets displayed on galaxy as results.
Can someone help me understand how discover_datasets work and why all
the supposed multi datasets are not displayed in the galaxy interface?
Thanks in advance.
Best regards,
--
Signature e-mail TWB
Sabrina
**Sabrina LEGOUEIX RODRIGUEZ**
Responsable Plateau Bioinformatique
Tél. : +33 (0) 5 61 28 57 92
sabrina.legoueix(a)toulouse.inra.fr <mailto:[MAIL]>
www.toulouse-white-biotechnology.com
<http://www.toulouse-white-biotechnology.com/>
LinkedIn <https://www.linkedin.com/company/2757525h> Twitter
<https://twitter.com/TWB_Biotech>
TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue
Ariane • 31520 Ramonville Saint-Agne
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7 years, 3 months
ProFTPd in CloudMan
by Alexander Vowinkel
Hi,
I get the error "Could not read from socket: ECONNRESET - Connection reset
by peer" when connecting with FileZilla to the Cloud Instance.
Using launch.usegalaxy.org
FileZilla Log: http://pastebin.com/zfACC6wH
ProFTP Log: http://pastebin.com/T9JxKVCb
With console FTP in linux I can connect, get a listing and upload files.
I tried to find out what the reason is, but no solution found.
bareFTP is also not able to connect.
The ports for PassivePorts are open (checked in AWS)
Any idea on this?
Thanks,
Alexander
7 years, 3 months
about galaxy
by Dong Liu
Dear Galaxy
I am a new user on Galaxy online service. When I uploaded my data file in fastq form, the utility of Galaxy such as NGS:QC and manipulation, FastQC and Trim sequences can not be availabe. I dont why. can you tell me how to use Galaxy using my data?
Dong Liu
visiting scholar at the University of Georgia,GA, USA
7 years, 3 months
PBS Torque 15007: No permission
by Ben Archuleta
Hello All,
I have Galaxy running on the latest version of Biolinux configured to
work with PBS/Torque version Version: 4.2.8, all jobs are being
submitted as Debian-galaxy (This is a global user in the cluster and a
local user on the Biolinux box).
Whenever we submit a job we get the error below:
galaxy.jobs.runners.pbs ERROR 2015-08-28 11:52:42,608 Connection to PBS
server for submit failed: 15007: No permission
We are using:
/usr/lib/galaxy-server/eggs/pbs_python-4.4.0-py2.7-linux-x86_64-ucs4.egg
to interact with the PBS.
Below is how the two identical accounts are configured:
Debian-galaxy:x:2136:100::/var/lib/galaxy-server/database:/bin/fasle
Debian-galaxy:XXXXXXX:2136:100:Debian-galaxy:/var/lib/galaxy-server/database:/bin/bash
Is this a PBS Python error or could this be directly related to the PBS?
I can submit jobs on that node by hand through Bash but not through
Biolinux.
Thank You!
Ben
7 years, 3 months
PBS Torque 15007: No permission
by Ben Archuleta
Hello All,
I have Galaxy running on the latest version of Biolinux configured to
work with PBS/Torque version Version: 4.2.8, all jobs are being
submitted as Debian-galaxy (This is a global user in the cluster and a
local user on the Biolinux box).
Whenever we submit a job we get the error below:
galaxy.jobs.runners.pbs ERROR 2015-08-28 11:52:42,608 Connection to PBS
server for submit failed: 15007: No permission
We are using:
/usr/lib/galaxy-server/eggs/pbs_python-4.4.0-py2.7-linux-x86_64-ucs4.egg
to interact with the PBS.
Below is how the two identical accounts are configured:
Debian-galaxy:x:2136:100::/var/lib/galaxy-server/database:/bin/fasle
Debian-galaxy:XXXXXXX:2136:100:Debian-galaxy:/var/lib/galaxy-server/database:/bin/bash
Is this a PBS Python error or could this be directly related to the PBS?
I can submit jobs on that node by hand through Bash but not through
Biolinux.
Thank You!
Ben
7 years, 3 months
