Re: [galaxy-dev] AD Intergration

[Chen, John (IT)]

Jelle,

After messing around a few time with the config file.. I have it working 
already.   I am able to authenticate against AD now.. 

Matthias,
I saw that posting, but that wasn’t the issue, but thanks anyway.



John Chen
Tel: 646-524-0080

Cell: 347-587-9655
https://nyumc.webex.com/join/chenj29

Email: john.ch...@nyumc.org

On 6/16/17, 12:30 PM, "galaxy-dev on behalf of Matthias Bernt" 
 wrote:

Hi Jelle,

I just (in this very moment) solved the "option error" issue for our 
galaxy installation.

see my comment on the first issue mentioned by john:


https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_galaxyproject_galaxy_issues_3178-23issuecomment-2D306538866=DQIGaQ=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE=bOqvdGabzr80lh6GA_AnYh1-lz5wZ9iCLk4PxBK4Z3M=N2VIuDVupElUxyy8Q_CJmDB_VsT9Ck4MTnE5Fpqep3o=s0_hB56pHAp1xLeW2_kGub14aZ7Ci_JANFHwVRT93sg=
 

Maybe you do not need to compile everything from source (as I needed to).

Best,
Matthias

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Re: [galaxy-dev] AD Intergration

[Matthias Bernt]

Hi Jelle,

I just (in this very moment) solved the "option error" issue for our 
galaxy installation.


see my comment on the first issue mentioned by john:

https://github.com/galaxyproject/galaxy/issues/3178#issuecomment-306538866

Maybe you do not need to compile everything from source (as I needed to).

Best,
Matthias

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Re: [galaxy-dev] AD Intergration

[Jelle Scholtalbers]

Hi John,

this error looks familiar:
https://github.com/galaxyproject/galaxy/issues/3178
https://github.com/galaxyproject/galaxy/issues/4153
https://github.com/galaxyproject/starforge/issues/130

To remedy the 'option' error:

source /home/galaxy/galaxy/.venv/bin/activate
pip install --upgrade python-ldap


Hope this brings you a step further.

- Jelle

On Wed, Jun 14, 2017 at 6:09 PM, John Chen <jchen...@yahoo.com> wrote:

> Jelle
>
> I did all that and it looks correct.. it is retrieving the correct field.
> This is the error i am still getting..  I am using pretty much the same
> option in other apps..
>
>
>
> galaxy.webapps.galaxy.controllers.user DEBUG 2017-06-14 12:04:40,648
> trans.app.config.auth_config_file: ./config/auth_conf.xml
> galaxy.auth.providers.ldap_ad DEBUG 2017-06-14 12:04:40,648 LDAP
> authenticate: email is johnu...@example.org
> galaxy.auth.providers.ldap_ad DEBUG 2017-06-14 12:04:40,648 LDAP
> authenticate: username is None
> galaxy.auth.providers.ldap_ad DEBUG 2017-06-14 12:04:40,648 LDAP
> authenticate: options are {'bind-user': '{dn}', 'search-fields':
> 'uid,mail', 'login-use-username': 'False', 'allow-register': 'True',
> 'ldap-options': 'OPT_X_TLS_REQUIRE_CERT=OPT_X_TLS_ALLOW',
> 'auto-register-email': '{email}', 'server': 'ldap://ldap.nyumc.org',
> 'auto-register': 'True', 'search-base': 'DC=example,DC=org',
> 'search-filter': '(mail={email})', 'continue-on-failure': 'True',
> 'auto-register-username': '{sAMAccountName', 'bind-password': '{password}',
> 'allow-password-change': 'False'}
> galaxy.auth.providers.ldap_ad DEBUG 2017-06-14 12:04:40,648 LDAP
> authenticate: Valid LDAP option pair OPT_X_TLS_REQUIRE_CERT=OPT_X_TLS_ALLOW
> -> 24582=3
> galaxy.auth.providers.ldap_ad ERROR 2017-06-14 12:04:40,648 LDAP
> authenticate: search exception
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy/lib/galaxy/auth/providers/ldap_ad.py", line
> 118, in authenticate
> ldap.set_option(*opt)
>   File 
> "/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/ldap/functions.py",
> line 135, in set_option
> return _ldap_function_call(None,_ldap.set_option,option,invalue)
>   File 
> "/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/ldap/functions.py",
> line 66, in _ldap_function_call
> result = func(*args,**kwargs)
> ValueError: option error
>
>
> Are you running MS AD ?   if so, could i take a look at your config file?
>
> Thanks
> John
>
>
> --
> *From:* Jelle Scholtalbers <j.scholtalb...@gmail.com>
> *To:* Hans-Rudolf Hotz <h...@fmi.ch>
> *Cc:* John Chen <jchen...@yahoo.com>; Galaxy Dev List <galaxy-dev@lists.
> galaxyproject.org>
> *Sent:* Monday, June 12, 2017 3:16 AM
> *Subject:* Re: [galaxy-dev] AD Intergration
>
> Hi John,
>
> as a tip, you can use the tool "ldapsearch", from e.g. the package
> "openldap-client", to figure out with which attributes you search and which
> attributes you can retrieve.
>
> Examples:
> $ ldapsearch -vv -x -H ldap://dc1.example.com -b
> cn=Users,dc=exampke,dc=org" # retrieve all AD/ldap entries
> $ ldapsearch -vv -x -H ldap://dc1.example.com -b
> cn=Users,dc=exampke,dc=org "uid=a_username"  # retrieve all attributes for
> user with uid "a_username"
> $ ldapsearch -vv -x -H ldap://dc1.example.com -b
> cn=Users,dc=exampke,dc=org "sAMAccountName=a_username" mail # only
> retrieve the mail attribute by searching for the sAMAccountName
>
>
> In addition, if you get it working, you might want to switch to the more
> secure ldap*s* if that is supported by your IT.
>
> Cheers,
> Jelle
>
>
>
> On Mon, Jun 12, 2017 at 8:32 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>
>
>
> On 06/09/2017 03:29 PM, John Chen wrote:
>
> Hans-Rudolf,
>
> That got me past the error, but I i am now having issue authenticating
> with against AD, as if its not able to search for the users.  Do I need
> a binding service account to search AD object?  Does the bottow 5 lines
> look correct?
>
>
> They look right, but I can't say whether they are correct. You need to
> discuss this with the person who has set up your Active Directory
>
>
> Hans-Rudolf
>
>
>
>
> cn=galaxy,ou=Secu rity,ou=somegroup,dc=example,
> dc=org
>
> ((objectCl ass=user)(sAMAccountName={
> username}))
>  ADsearchAccount< /search-user>
>  AD_Search_Pa sswrd
>  {sAMAccountName}
>
> The logs show that it found the userID and email, but gets an invalid
> password on the webportal
>
> galaxy.webapps.galaxy.controll ers.user DEBUG 2017-06-09 09:26:34,5

Re: [galaxy-dev] AD Intergration

[Youssef GHORBAL]

Hello,

>From my experience, By default, Active Directory does not allow bind operation 
>over plain LDAP, you need LDAPS for that to happen.
My 2 cents.

Youssef Ghorbal

On 9 Jun 2017, at 15:29, John Chen 
<jchen...@yahoo.com<mailto:jchen...@yahoo.com>> wrote:

Hans-Rudolf,

That got me past the error, but I i am now having issue authenticating with 
against AD, as if its not able to search for the users.  Do I need a binding 
service account to search AD object?  Does the bottow 5 lines look correct?

   
cn=galaxy,ou=Security,ou=somegroup,dc=example,dc=org

((objectClass=user)(sAMAccountName={username}))
ADsearchAccount
AD_Search_Passwrd
{sAMAccountName}

The logs show that it found the userID and email, but gets an invalid password 
on the webportal

galaxy.webapps.galaxy.controllers.user DEBUG 2017-06-09 09:26:34,592 
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP authenticate: 
email is testuser.n...@example.org<mailto:testuser.n...@example.org>
galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP authenticate: 
username is testUser
galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP authenticate: 
options are {'bind-user': '{sAMAccountName}', 'search-fields': 
'sAMAccountName,mail', 'login-use-username': 'True', 'allow-register': 'False', 
'auto-register-email': '{mail}', 'server': 'ldap://xxx.xxx.xx', 
'auto-register': 'True', 'search-base': 'cn=xxx-xx,ou=Security,ou=x 
xxx,dc=xxx,dc=xx', 'search-filter': 
'(&(objectClass=user)(sAMAccountName={username}))', 'auto-register-username': 
'{sAMAccountName}', 'search-password': '', 'search-user': '', 
'bind-password': '{password}'}
galaxy.auth.providers.ldap_ad WARNING 2017-06-09 09:26:34,596 LDAP 
authenticate: search returned no results
10.127.220.227 - - [09/Jun/2017:09:26:34 -0400] "POST 
/user/login?use_panels=False HTTP/1.1" 200 - 
"http://glxlcdcpvm01.nyumc.org:8080/user/login?use_panels=False; "Mozilla/5.0 
(Windows NT 10.0; WOW64; rv:53.0) Gecko/20100101 Firefox/53.0"



From: Hans-Rudolf Hotz <h...@fmi.ch<mailto:h...@fmi.ch>>
To: John Chen <jchen...@yahoo.com<mailto:jchen...@yahoo.com>>; Galaxy Dev List 
<galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>>
Sent: Friday, June 9, 2017 3:34 AM
Subject: Re: [galaxy-dev] AD Intergration

always keep the mailing list in the loop! in order for others to help or
learn



On 06/08/2017 07:27 PM, John Chen wrote:
> Hans-Rudolf
>
> This is the error I get when I start the Galaxy server.
>
...
> xml.etree.ElementTree.ParseError: mismatched tag: line 8, column 105
>

This is very informative. Looking at line 8 in your file:


ldap://ldap.xxx.xx;>ldap://ldap.xxx.xx


The element "a" is not  terminated


What happens, if you try just

ldap://ldap.xxx.xx





Regards, Hans-Rudolf


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Re: [galaxy-dev] AD Intergration

[Jelle Scholtalbers]

Hi John,

as a tip, you can use the tool "ldapsearch", from e.g. the package
"openldap-client", to figure out with which attributes you search and which
attributes you can retrieve.

Examples:
$ ldapsearch -vv -x -H ldap://dc1.example.com -b cn=Users,dc=exampke,dc=org"
# retrieve all AD/ldap entries
$ ldapsearch -vv -x -H ldap://dc1.example.com -b cn=Users,dc=exampke,dc=org
"uid=a_username"  # retrieve all attributes for user with uid "a_username"
$ ldapsearch -vv -x -H ldap://dc1.example.com -b cn=Users,dc=exampke,dc=org
"sAMAccountName=a_username" mail # only retrieve the mail attribute by
searching for the sAMAccountName


In addition, if you get it working, you might want to switch to the more
secure ldap*s* if that is supported by your IT.

Cheers,
Jelle



On Mon, Jun 12, 2017 at 8:32 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:

>
>
> On 06/09/2017 03:29 PM, John Chen wrote:
>
>> Hans-Rudolf,
>>
>> That got me past the error, but I i am now having issue authenticating
>> with against AD, as if its not able to search for the users.  Do I need
>> a binding service account to search AD object?  Does the bottow 5 lines
>> look correct?
>>
>
> They look right, but I can't say whether they are correct. You need to
> discuss this with the person who has set up your Active Directory
>
>
> Hans-Rudolf
>
>
>
>
>> cn=galaxy,ou=Security,ou=somegroup,dc=example,
>> dc=org
>>
>> ((objectClass=user)(sAMAccountName={
>> username}))
>>  ADsearchAccount
>>  AD_Search_Passwrd
>>  {sAMAccountName}
>>
>> The logs show that it found the userID and email, but gets an invalid
>> password on the webportal
>>
>> galaxy.webapps.galaxy.controllers.user DEBUG 2017-06-09 09:26:34,592
>> trans.app.config.auth_config_file: ./config/auth_conf.xml
>> galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
>> authenticate: email is testuser.n...@example.org
>> galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
>> authenticate: username is testUser
>> galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
>> authenticate: options are {'bind-user': '{sAMAccountName}',
>> 'search-fields': 'sAMAccountName,mail', 'login-use-username': 'True',
>> 'allow-register': 'False', 'auto-register-email': '{mail}', 'server':
>> 'ldap://xxx.xxx.xx', 'auto-register': 'True', 'search-base':
>> 'cn=xxx-xx,ou=Security,ou=x xxx,dc=xxx,dc=xx', 'search-filter':
>> '(&(objectClass=user)(sAMAccountName={username}))',
>> 'auto-register-username': '{sAMAccountName}', 'search-password': '',
>> 'search-user': '', 'bind-password': '{password}'}
>> galaxy.auth.providers.ldap_ad WARNING 2017-06-09 09:26:34,596 LDAP
>> authenticate: search returned no results
>> 10.127.220.227 - - [09/Jun/2017:09:26:34 -0400] "POST
>> /user/login?use_panels=False HTTP/1.1" 200 -
>> "http://glxlcdcpvm01.nyumc.org:8080/user/login?use_panels=False;
>> "Mozilla/5.0 (Windows NT 10.0; WOW64; rv:53.0) Gecko/20100101
>> Firefox/53.0"
>>
>>
>> 
>> *From:* Hans-Rudolf Hotz <h...@fmi.ch>
>> *To:* John Chen <jchen...@yahoo.com>; Galaxy Dev List
>> <galaxy-dev@lists.galaxyproject.org>
>> *Sent:* Friday, June 9, 2017 3:34 AM
>> *Subject:* Re: [galaxy-dev] AD Intergration
>>
>> always keep the mailing list in the loop! in order for others to help or
>> learn
>>
>>
>>
>> On 06/08/2017 07:27 PM, John Chen wrote:
>>  > Hans-Rudolf
>>  >
>>  > This is the error I get when I start the Galaxy server.
>>  >
>> ...
>>  > xml.etree.ElementTree.ParseError: mismatched tag: line 8, column 105
>>  >
>>
>> This is very informative. Looking at line 8 in your file:
>>
>>
>> > href="ldap://ldap.xxx.xx;>ldap://ldap.xxx.xx
>>
>>
>> The element "a" is not  terminated
>>
>>
>> What happens, if you try just
>>
>> ldap://ldap.xxx.xx
>>
>>
>>
>>
>>
>> Regards, Hans-Rudolf
>>
>>
>> ___
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Re: [galaxy-dev] AD Intergration

[Hans-Rudolf Hotz]

On 06/09/2017 03:29 PM, John Chen wrote:

Hans-Rudolf,

That got me past the error, but I i am now having issue authenticating
with against AD, as if its not able to search for the users.  Do I need
a binding service account to search AD object?  Does the bottow 5 lines
look correct?


They look right, but I can't say whether they are correct. You need to 
discuss this with the person who has set up your Active Directory



Hans-Rudolf





cn=galaxy,ou=Security,ou=somegroup,dc=example,dc=org

((objectClass=user)(sAMAccountName={username}))
 ADsearchAccount
 AD_Search_Passwrd
 {sAMAccountName}

The logs show that it found the userID and email, but gets an invalid
password on the webportal

galaxy.webapps.galaxy.controllers.user DEBUG 2017-06-09 09:26:34,592
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
authenticate: email is testuser.n...@example.org
galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
authenticate: username is testUser
galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
authenticate: options are {'bind-user': '{sAMAccountName}',
'search-fields': 'sAMAccountName,mail', 'login-use-username': 'True',
'allow-register': 'False', 'auto-register-email': '{mail}', 'server':
'ldap://xxx.xxx.xx', 'auto-register': 'True', 'search-base':
'cn=xxx-xx,ou=Security,ou=x xxx,dc=xxx,dc=xx', 'search-filter':
'(&(objectClass=user)(sAMAccountName={username}))',
'auto-register-username': '{sAMAccountName}', 'search-password': '',
'search-user': '', 'bind-password': '{password}'}
galaxy.auth.providers.ldap_ad WARNING 2017-06-09 09:26:34,596 LDAP
authenticate: search returned no results
10.127.220.227 - - [09/Jun/2017:09:26:34 -0400] "POST
/user/login?use_panels=False HTTP/1.1" 200 -
"http://glxlcdcpvm01.nyumc.org:8080/user/login?use_panels=False;
"Mozilla/5.0 (Windows NT 10.0; WOW64; rv:53.0) Gecko/20100101 Firefox/53.0"



*From:* Hans-Rudolf Hotz <h...@fmi.ch>
*To:* John Chen <jchen...@yahoo.com>; Galaxy Dev List
<galaxy-dev@lists.galaxyproject.org>
*Sent:* Friday, June 9, 2017 3:34 AM
*Subject:* Re: [galaxy-dev] AD Intergration

always keep the mailing list in the loop! in order for others to help or
learn



On 06/08/2017 07:27 PM, John Chen wrote:
 > Hans-Rudolf
 >
 > This is the error I get when I start the Galaxy server.
 >
...
 > xml.etree.ElementTree.ParseError: mismatched tag: line 8, column 105
 >

This is very informative. Looking at line 8 in your file:


ldap://ldap.xxx.xx;>ldap://ldap.xxx.xx


The element "a" is not  terminated


What happens, if you try just

ldap://ldap.xxx.xx





Regards, Hans-Rudolf



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Re: [galaxy-dev] AD Intergration

[Hans-Rudolf Hotz]

always keep the mailing list in the loop! in order for others to help or 
learn




On 06/08/2017 07:27 PM, John Chen wrote:

Hans-Rudolf

This is the error I get when I start the Galaxy server.


...

xml.etree.ElementTree.ParseError: mismatched tag: line 8, column 105



This is very informative. Looking at line 8 in your file:


href="ldap://ldap.xxx.xx;>ldap://ldap.xxx.xx



The element "a" is not  terminated


What happens, if you try just

ldap://ldap.xxx.xx




Regards, Hans-Rudolf
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Re: [galaxy-dev] AD Intergration

[Nicola Soranzo]

On 08/06/17 16:36, Hans-Rudolf Hotz wrote:

Hi John



I am trying to integrate AD with Galaxy. My auth_config.xml  look like
the below, but galaxy won't start with those setting.


what error do you get in the log?




activedirectory


This should be "ldap", shouldn't-it?




Actually activedirectory here is fine, it's just an alias for ldap.

Cheers,
Nicola
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Re: [galaxy-dev] AD Intergration

[Hans-Rudolf Hotz]

Hi John



I am trying to integrate AD with Galaxy. My auth_config.xml  look like
the below, but galaxy won't start with those setting.


what error do you get in the log?




 activedirectory


This should be "ldap", shlouldn't-it?



Regards, Hans-Rudolf



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