Others might have responded to this, and I can't remember the very latest
approach, but I used the approach below... Its not easy though since api
is read via <code> script [BTW, topically, I still need <code> on a
regular basis!], but is passed over to command line app securely via a
<configfile>. For error situation messaging back to user I was using a
dynamic box radio drill_down input. All this code is in toolshed under
"versioned_data". Teasing out what you need might require some work
though - the code also has a chunk of stuff for maintaining use of an
administrator's api key as well as the user's since the app needed to do
admin level api work on behalf of a user.
>------------------------------
>
>Message: 11
>Date: Wed, 27 Jan 2016 12:42:17 +0000
>From: Matthias De Smet <matthias.des...@ugent.be>
>...
>Hi again
>
>I’m trying to create a tool that interacts with galaxy through the API.
>For this, I need to get the users API key (or equivalent) en the domain
>name of the Galaxy host.
>
>The purpose of this tool is to get data and put it in a data library, so
>I suppose I need to use the API. Or is there another way to do this with
>a tool?
>
>Thanks!
>Matthias
<command interpreter="python">
#assert $__user__, Exception( 'You must be logged in to use this tool.' )
versioned_data.py
...
-O "$__app__.security.encode_id($log.id)"
--api_info_path "$api_info_path" ##Actually a file path to configfile
that holds api key
</command>
<inputs>
...
<param name="api_info" display="radio" type="drill_down" label="For user
with Galaxy API Key" dynamic_options="vdb_init_tool_user(__trans__)" />
</inputs>
<configfiles>
<configfile name="api_info_path">${__user__.api_keys[0].key}
$api_info
</configfile>
</configfiles>
<code file="versioned_data_form.py" />
And over in versioned_data_form.py ( there's a reference to "set_trans()"
which feeds through to set_user_api() below...
import vdb_retrieval
def vdb_init_tool_user(trans):
"""
Retrieves a user's api key if they have one, otherwise lets them know
they need one
This function is automatically called from versioned_data.xml form on
presentation to user
Note that this is how self.api_url gets back into form, for passage back
to 2nd call via versioned_data.py
self.api_key is passed via secure <configfile> construct.
ALSO: squeezing history_id in this way since no other way to pass it.
"trans" is provided only by tool form presentation via <code file="...">
BUT NOW SEE John Chilton's:
https://gist.github.com/jmchilton/27c5bb05e155a611294d
See galaxy source code at
https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/web/framework
.html,
See
http://dev.list.galaxyproject.org/error-using-get-user-id-in-xml-file-in-ne
w-Galaxy-td4665274.html
See
http://dev.list.galaxyproject.org/hg-galaxy-2780-Real-Job-tm-support-for-th
e-library-upload-to-td4133384.html
master api key, set in galaxy config: #self.master_api_key =
trans.app.config.master_api_key
"""
global retrieval_obj
api_url = trans.request.application_url + '/api'
history_id = str(trans.security.encode_id(trans.history.id))
user_api_key = None
if trans.user:
user_name = trans.user.username
if trans.user.api_keys and len(trans.user.api_keys) > 0:
user_api_key = trans.user.api_keys[0].key #First key is
always the
active one?
items = [ { 'name': user_name, 'value': api_url + '-' +
history_id,
'options':[], 'selected': True } ]
else:
items = [ { 'name': user_name + ' - Note: you need a
key (see "User"
menu)!', 'value': '0', 'options':[], 'selected': False } ]
else:
items = [ { 'name': 'You need to be logged in to use this
tool!',
'value': '1', 'options':[], 'selected': False } ]
retrieval_obj = vdb_retrieval.VDBRetrieval()
retrieval_obj.set_trans(api_url, history_id, user_api_key)
return items
And over in tool xml's target code (versioned_data.py) it includes
vdb_retrieval.py BUT THIS HAS A LOT OF STUFF YOU PROBABLY DON'T NEED!
Sorry!:
from bioblend.galaxy import GalaxyInstance
class VDBRetrieval(object):
def __init__(self, api_key=None, api_url=None):
"""
This gets either trans.x.y from <code file="..."> call in
versioned_data.xml,
or it gets a call with api_key and api_url from
versioned_data.py
@param api_key_path string File path to temporary file
containing user's
galaxy api_key
@param api_url string contains http://[ip]:[port] for handling
galaxy
api calls.
"""
# Initialized constants during the life of a request:
self.global_retrieval_date = None
self.library_id = None
self.history_id = None
self.data_stores = []
# Entire json library structure. item.url, type=file|folder,
id, name
(library path)
# Note: changes to library during a request aren't reflected
here.
self.library = None
self.user_api_key = None
self.user_api = None
self.admin_api_key = None
self.admin_api = None
self.api_url = None
def set_trans(self, api_url, history_id, user_api_key=None):
#master_api_key=None,
"""
Used only on initial presentation of versioned_data.xml form.
Doesn't
need admin_api
"""
self.history_id = history_id
self.api_url = api_url
self.user_api_key = user_api_key
self.set_user_api()
self.set_admin_api()
self.set_datastores()
...
def set_user_api(self):
"""
Note: error message tacked on to self.data_stores for display
back to
user.
"""
self.user_api = GalaxyInstance(url=self.api_url,
key=self.user_api_key)
if not self.user_api:
self.data_stores.append({'name':'Error: user Galaxy API
connection was
not set up correctly. Try getting another user API key.', 'id':'none'})
return
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