Re: [galaxy-dev] Manage API keys in admin panel

5 Mar 2013

      Hello,
For people interested in this API management through galaxy GUI, I created
a simple wrapper to use display.py :
hg clone http://remy-d1@testtoolshed.g2.bx.psu.edu/repos/remy-d1/api_tools
I think it should be better to use display.py API in a controller/template
way, like I did before for key management, because $__app__.config would be
depracated soon.
To add the previous templates to admin panel, just change the controller
like this :
cat lib/galaxy/webapps/galaxy/controllers/userskeys.py
"""
Contains the user interface in the Universe class
"""
import glob
import logging
import os
import socket
import string
import random
import pprint
from galaxy import web
from galaxy import util, model
from galaxy.model.orm import and_
from galaxy.security.validate_user_input import validate_email,
validate_publicname, validate_password, transform_publicname
from galaxy.util.json import from_json_string, to_json_string
from galaxy.web import url_for
from galaxy.web.base.controller import BaseUIController,
UsesFormDefinitionsMixin
from galaxy.web.form_builder import CheckboxField, build_select_field
from galaxy.web.framework.helpers import time_ago, grids
from inspect import getmembers
log = logging.getLogger( __name__ )
require_login_template = """
<p>
    This %s has been configured such that only users who are logged in may
use it.%s
</p>
<p/>
"""
class UserOpenIDGrid( grids.Grid ):
    use_panels = False
    title = "OpenIDs linked to your account"
    model_class = model.UserOpenID
    template = '/user/openid_manage.mako'
    default_filter = { "openid" : "All" }
    default_sort_key = "-create_time"
    columns = [
        grids.TextColumn( "OpenID URL", key="openid", link=( lambda x:
dict( action='openid_auth', login_button="Login", openid_url=x.openid if
not x.provider else '', openid_provider=x.provider, auto_associate=True ) )
),
        grids.GridColumn( "Created", key="create_time", format=time_ago ),
    ]
    operations = [
        grids.GridOperation( "Delete", async_compatible=True ),
    ]
    def build_initial_query( self, trans, **kwd ):
        return trans.sa_session.query( self.model_class ).filter(
self.model_class.user_id == trans.user.id )
class User( BaseUIController, UsesFormDefinitionsMixin ):
    user_openid_grid = UserOpenIDGrid()
    installed_len_files = None
@web.expose
    @web.require_login()
    @web.require_admin
    def index( self, trans, cntrller, **kwd ):
        return trans.fill_template( 'webapps/galaxy/user/list_users.mako',
action='all_users', cntrller=cntrller )
@web.expose
    @web.require_login()
    @web.require_admin
    def api_keys( self, trans, cntrller, uid, **kwd ):
        params = util.Params( kwd )
        message = util.restore_text( params.get( 'message', ''  ) )
        status = params.get( 'status', 'done' )
        uid = params.get('uid', uid)
        pprint.pprint(uid)
        if params.get( 'new_api_key_button', False ):
            new_key = trans.app.model.APIKeys()
            new_key.user_id = uid
            new_key.key = trans.app.security.get_new_guid()
            trans.sa_session.add( new_key )
            trans.sa_session.flush()
            message = "Generated a new web API key"
            status = "done"
        return trans.fill_template(
'webapps/galaxy/user/ok_admin_api_keys.mako',
                                    cntrller=cntrller,
                                    message=message,
                                    status=status )
@web.expose
    @web.require_login()
    @web.require_admin
    def all_users( self, trans, cntrller="userskeys", **kwd ):
        params = util.Params( kwd )
        message = util.restore_text( params.get( 'message', ''  ) )
        status = params.get( 'status', 'done' )
        users = []
        for user in trans.sa_session.query( trans.app.model.User ) \
                                    .filter(
trans.app.model.User.table.c.deleted==False ) \
                                    .order_by(
trans.app.model.User.table.c.email ):
                uid = int(user.id)
                userkey = ""
                for api_user in
trans.sa_session.query(trans.app.model.APIKeys) \
                                      .filter(
trans.app.model.APIKeys.user_id == uid):
                    userkey = api_user.key
                users.append({'uid':uid, 'email':user.email, 'key':userkey})
        return trans.fill_template( 'webapps/galaxy/user/list_users.mako',
                                    cntrller=cntrller,
                                    users=users,
                                    message=message,
                                    status=status )
Then, add an entry in templates/webapps/galaxy/admin/index.mako :
nl templates/webapps/galaxy/admin/index.mako |grep userskeys
    39                        <div class="toolTitle"><a href="${h.url_for(
controller='userskeys', action='all_users' )}" target="galaxy_main">Manage
users API keys</a></div>
(39 is the line number retrieve by "nl" command).
I think that more tools for API available through GUI could be usefull.
Regards,
Remy
2013/2/28 Rémy Dernat remy.d1@gmail.com
...
Ok, so I answer to myself. I created 2 template and 1 controller.
You need tu put the controller in
[galaxy_install_dir]/lib/galaxy/webapps/galaxy/controllers/userskeys.py
"""
Contains the user interface in the Universe class
"""
import glob
import logging
import os
import socket
import string
import random
import pprint
from galaxy import web
from galaxy import util, model
from galaxy.model.orm import and_
from galaxy.security.validate_user_input import validate_email,
validate_publicname, validate_password, transform_publicname
from galaxy.util.json import from_json_string, to_json_string
from galaxy.web import url_for
from galaxy.web.base.controller import BaseUIController,
UsesFormDefinitionsMixin
from galaxy.web.form_builder import CheckboxField, build_select_field
from galaxy.web.framework.helpers import time_ago, grids
from inspect import getmembers
log = logging.getLogger( __name__ )
require_login_template = """
<p>
    This %s has been configured such that only users who are logged in may
use it.%s
</p>
<p/>
"""
class UserOpenIDGrid( grids.Grid ):
    use_panels = False
    title = "OpenIDs linked to your account"
    model_class = model.UserOpenID
    template = '/user/openid_manage.mako'
    default_filter = { "openid" : "All" }
    default_sort_key = "-create_time"
    columns = [
        grids.TextColumn( "OpenID URL", key="openid", link=( lambda x:
dict( action='openid_auth', login_button="Login", openid_url=x.openid if
not x.provider else '', openid_provider=x.provider, auto_associate=True ) )
),
        grids.GridColumn( "Created", key="create_time", format=time_ago ),
    ]
    operations = [
        grids.GridOperation( "Delete", async_compatible=True ),
    ]
    def build_initial_query( self, trans, **kwd ):
        return trans.sa_session.query( self.model_class ).filter(
self.model_class.user_id == trans.user.id )
class User( BaseUIController, UsesFormDefinitionsMixin ):
    user_openid_grid = UserOpenIDGrid()
    installed_len_files = None
@web.expose
@web.require_login()
def api_keys( self, trans, cntrller, uid, **kwd ):
    params = util.Params( kwd )
    message = util.restore_text( params.get( 'message', ''  ) )
    status = params.get( 'status', 'done' )
    uid = params.get('uid', uid)
    pprint.pprint(uid)
    if params.get( 'new_api_key_button', False ):
        new_key = trans.app.model.APIKeys()
        new_key.user_id = uid
        new_key.key = trans.app.security.get_new_guid()
        trans.sa_session.add( new_key )
        trans.sa_session.flush()
        message = "Generated a new web API key"
        status = "done"
    return trans.fill_template(

'webapps/galaxy/user/ok_admin_api_keys.mako',
                                    cntrller=cntrller,
                                    message=message,
                                    status=status )
@web.expose
@web.require_login()
def all_users( self, trans, cntrller, **kwd ):
    params = util.Params( kwd )
    message = util.restore_text( params.get( 'message', ''  ) )
    status = params.get( 'status', 'done' )
    users = []
    for user in trans.sa_session.query( trans.app.model.User ) \
                                .filter(

trans.app.model.User.table.c.deleted==False ) \
                                    .order_by(
trans.app.model.User.table.c.email ):
                uid = int(user.id)
                userkey = ""
                for api_user in
trans.sa_session.query(trans.app.model.APIKeys) \
                                      .filter(
trans.app.model.APIKeys.user_id == uid):
                    userkey = api_user.key
                users.append({'uid':uid, 'email':user.email,
'key':userkey})
        return trans.fill_template( 'webapps/galaxy/user/list_users.mako',
                                    cntrller=cntrller,
                                    users=users,
                                    message=message,
                                    status=status )
Then the 2 templates [galaxy_install_dir]/templates/webapps/galaxy/user/
The first one listing all the users with their keys
cat templates/webapps/galaxy/user/list_users.mako
<%inherit file="/base.mako"/>
%if message:
    ${render_msg( message, status )}
%endif
%if users:
    <div class="toolForm">
            <div class="toolFormTitle">Users informations</div>
            <table>
                <thead><th>UID</th><th>email</th></thead>
                <tbody>
                %for user in users:
                     <tr>
                        <td>${user['uid']}</td>
                        <td>${user['email']}</td>
                        <td>${user['key']}</td>
                        <td>
                          <form action="${h.url_for(
controller='userskeys', action='api_keys', cntrller=cntrller )}"
method="POST">
                          <input type="hidden" name="uid"
value=${user['uid']} />
                          <input type="submit" name="new_api_key_button"
value="Generate a new key now" />
                          </form>
                        </td>
                     </tr>
                %endfor
                </tbody>
                </table>
            <div style="clear: both"></div>
    </div>
%else:
 <div>No informations available</div>
%endif
<p/>
The second one is just an information template :
cat templates/webapps/galaxy/user/ok_admin_api_keys.mako
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<br/><br/>
<ul class="manage-table-actions">
    <li>
        <a class="action-button"  href="${h.url_for(
controller='userskeys', action='all_users', cntrller=cntrller )}">List
users API keys</a>
    </li>
</ul>
%if message:
    ${render_msg( message, status )}
%endif
        <div>
            <div style="clear: both;">
SUCCESS. A new API key has been generated.
            </div>

            <div style="clear: both;">
                An API key will allow you to access Galaxy via its web
                API (documentation forthcoming).  Please note that
                <strong>this key acts as an alternate means to access
                your account, and should be treated with the same care
                as your login password</strong>.
            </div>
        </div>

Then, you can go to http://
[galaxy_address]/userskeys/all_users?cntrller=userskeys
I think it needs some control to check if you are an admin.
Hope this help.
Regards,
Remy
2013/2/25 Rémy Dernat remy.d1@gmail.com
...
Hi,
I would like to create a tool or a template that could list and
(re)generate key for the user you want if you are login as an admin.
I found the api_keys function in the user controller but I don't know how
to use it. It seems that the decorators before the function checked if you
are login as the good user...
I also found the mako template that used this api_keys function but it is
still unclear for me.
Here is my sql function (FULL OUTER JOIN compatibility for MySQL) that
list every keys even if they are empty :
SELECT `galaxy_user`.`id`, `api_keys`.`user_id`, `api_keys`.`key`,
`galaxy_user`.`email`, `galaxy_user`.`username`
FROM `galaxy_user`
LEFT JOIN `api_keys` on `api_keys`.`user_id` = `galaxy_user`.`id`
UNION
SELECT `galaxy_user`.`id`, `api_keys`.`user_id`, `api_keys`.`key`,
`galaxy_user`.`email`, `galaxy_user`.`username`
FROM `galaxy_user`
RIGHT JOIN `api_keys` on `api_keys`.`user_id` = `galaxy_user`.`id`
I know how to do that in PHP but it won't use python framework sqlalchemy
(= only for mysql or pgsql...) !
Morevoer I don't know how do you generate your api_keys. Is it a md5 sum
based on username / password ? Or is it just a random key with fix length ?
Any help would be gracefull,
Regards,
Remy

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Re: [galaxy-dev] Manage API keys in admin panel