/
populators.py
548 lines (426 loc) · 20.8 KB
/
populators.py
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import json
import time
from operator import itemgetter
import requests
from pkg_resources import resource_string
from six import StringIO
from base import api_asserts
# Simple workflow that takes an input and call cat wrapper on it.
workflow_str = resource_string( __name__, "data/test_workflow_1.ga" )
# Simple workflow that takes an input and filters with random lines twice in a
# row - first grabbing 8 lines at random and then 6.
workflow_random_x2_str = resource_string( __name__, "data/test_workflow_2.ga" )
DEFAULT_TIMEOUT = 60 # Secs to wait for state to turn ok
def skip_without_tool( tool_id ):
""" Decorate an API test method as requiring a specific tool,
have nose skip the test case is the tool is unavailable.
"""
def method_wrapper( method ):
def get_tool_ids( api_test_case ):
index = api_test_case.galaxy_interactor.get( "tools", data=dict(in_panel=False) )
tools = index.json()
# In panels by default, so flatten out sections...
tool_ids = [itemgetter( "id" )(_) for _ in tools]
return tool_ids
def wrapped_method( api_test_case, *args, **kwargs ):
if tool_id not in get_tool_ids( api_test_case ):
from nose.plugins.skip import SkipTest
raise SkipTest( )
return method( api_test_case, *args, **kwargs )
# Must preserve method name so nose can detect and report tests by
# name.
wrapped_method.__name__ = method.__name__
return wrapped_method
return method_wrapper
# Deprecated mixin, use dataset populator instead.
# TODO: Rework existing tests to target DatasetPopulator in a setup method instead.
class TestsDatasets:
def _new_dataset( self, history_id, content='TestData123', **kwds ):
return DatasetPopulator( self.galaxy_interactor ).new_dataset( history_id, content=content, **kwds)
def _wait_for_history( self, history_id, assert_ok=False ):
return DatasetPopulator( self.galaxy_interactor ).wait_for_history( history_id, assert_ok=assert_ok )
def _new_history( self, **kwds ):
return DatasetPopulator( self.galaxy_interactor ).new_history( **kwds )
def _upload_payload( self, history_id, content, **kwds ):
return DatasetPopulator( self.galaxy_interactor ).upload_payload( history_id, content, **kwds )
def _run_tool_payload( self, tool_id, inputs, history_id, **kwds ):
return DatasetPopulator( self.galaxy_interactor ).run_tool_payload( tool_id, inputs, history_id, **kwds )
class BaseDatasetPopulator( object ):
""" Abstract description of API operations optimized for testing
Galaxy - implementations must implement _get and _post.
"""
def new_dataset( self, history_id, content='TestData123', wait=False, **kwds ):
payload = self.upload_payload( history_id, content, **kwds )
run_response = self._post( "tools", data=payload ).json()
if wait:
job = run_response["jobs"][0]
self.wait_for_job(job["id"])
self.wait_for_history(history_id, assert_ok=True)
return run_response["outputs"][0]
def wait_for_history( self, history_id, assert_ok=False, timeout=DEFAULT_TIMEOUT ):
try:
return wait_on_state( lambda: self._get( "histories/%s" % history_id ), assert_ok=assert_ok, timeout=timeout )
except AssertionError:
self._summarize_history_errors( history_id )
raise
def wait_for_job( self, job_id, assert_ok=False, timeout=DEFAULT_TIMEOUT ):
return wait_on_state( lambda: self.get_job_details( job_id ), assert_ok=assert_ok, timeout=timeout )
def get_job_details( self, job_id, full=False ):
return self._get( "jobs/%s?full=%s" % (job_id, full) )
def _summarize_history_errors( self, history_id ):
pass
def new_history( self, **kwds ):
name = kwds.get( "name", "API Test History" )
create_history_response = self._post( "histories", data=dict( name=name ) )
history_id = create_history_response.json()[ "id" ]
return history_id
def upload_payload( self, history_id, content, **kwds ):
name = kwds.get( "name", "Test Dataset" )
dbkey = kwds.get( "dbkey", "?" )
file_type = kwds.get( "file_type", 'txt' )
upload_params = {
'files_0|NAME': name,
'dbkey': dbkey,
'file_type': file_type,
}
if hasattr(content, 'read'):
upload_params[ "files_0|file_data"] = content
else:
upload_params[ 'files_0|url_paste' ] = content
if "to_posix_lines" in kwds:
upload_params[ "files_0|to_posix_lines"] = kwds[ "to_posix_lines" ]
if "space_to_tab" in kwds:
upload_params[ "files_0|space_to_tab" ] = kwds[ "space_to_tab" ]
return self.run_tool_payload(
tool_id='upload1',
inputs=upload_params,
history_id=history_id,
upload_type='upload_dataset'
)
def run_tool_payload( self, tool_id, inputs, history_id, **kwds ):
if "files_0|file_data" in inputs:
kwds[ "__files" ] = { "files_0|file_data": inputs[ "files_0|file_data" ] }
del inputs[ "files_0|file_data" ]
return dict(
tool_id=tool_id,
inputs=json.dumps(inputs),
history_id=history_id,
**kwds
)
def run_tool( self, tool_id, inputs, history_id, **kwds ):
payload = self.run_tool_payload( tool_id, inputs, history_id, **kwds )
tool_response = self._post( "tools", data=payload )
api_asserts.assert_status_code_is( tool_response, 200 )
return tool_response.json()
def get_history_dataset_content( self, history_id, wait=True, **kwds ):
dataset_id = self.__history_content_id( history_id, wait=wait, **kwds )
display_response = self.__get_contents_request( history_id, "/%s/display" % dataset_id )
assert display_response.status_code == 200, display_response.content
return display_response.content
def get_history_dataset_details( self, history_id, **kwds ):
dataset_id = self.__history_content_id( history_id, **kwds )
details_response = self.__get_contents_request( history_id, "/datasets/%s" % dataset_id )
assert details_response.status_code == 200
return details_response.json()
def get_history_collection_details( self, history_id, **kwds ):
hdca_id = self.__history_content_id( history_id, **kwds )
details_response = self.__get_contents_request( history_id, "/dataset_collections/%s" % hdca_id )
assert details_response.status_code == 200, details_response.content
return details_response.json()
def __history_content_id( self, history_id, wait=True, **kwds ):
if wait:
assert_ok = kwds.get( "assert_ok", True )
self.wait_for_history( history_id, assert_ok=assert_ok )
# kwds should contain a 'dataset' object response, a 'dataset_id' or
# the last dataset in the history will be fetched.
if "dataset_id" in kwds:
history_content_id = kwds[ "dataset_id" ]
elif "dataset" in kwds:
history_content_id = kwds[ "dataset" ][ "id" ]
else:
hid = kwds.get( "hid", None ) # If not hid, just grab last dataset
history_contents = self.__get_contents_request( history_id ).json()
if hid:
history_content_id = None
for history_item in history_contents:
if history_item["hid"] == hid:
history_content_id = history_item["id"]
if history_content_id is None:
raise Exception("Could not find content with HID [%s] in [%s]" % (hid, history_contents))
else:
# No hid specified - just grab most recent element.
history_content_id = history_contents[-1]["id"]
return history_content_id
def __get_contents_request( self, history_id, suffix=""):
url = "histories/%s/contents" % history_id
if suffix:
url = "%s%s" % ( url, suffix )
return self._get( url )
class DatasetPopulator( BaseDatasetPopulator ):
def __init__( self, galaxy_interactor ):
self.galaxy_interactor = galaxy_interactor
def _post( self, route, data={}, files=None ):
files = data.get( "__files", None )
if files is not None:
del data[ "__files" ]
return self.galaxy_interactor.post( route, data, files=files )
def _get( self, route ):
return self.galaxy_interactor.get( route )
def _summarize_history_errors( self, history_id ):
self.galaxy_interactor._summarize_history_errors( history_id )
class BaseWorkflowPopulator( object ):
def load_workflow( self, name, content=workflow_str, add_pja=False ):
workflow = json.loads( content )
workflow[ "name" ] = name
if add_pja:
tool_step = workflow[ "steps" ][ "2" ]
tool_step[ "post_job_actions" ][ "RenameDatasetActionout_file1" ] = dict(
action_type="RenameDatasetAction",
output_name="out_file1",
action_arguments=dict( newname="foo ${replaceme}" ),
)
return workflow
def load_random_x2_workflow( self, name ):
return self.load_workflow( name, content=workflow_random_x2_str )
def load_workflow_from_resource( self, name, filename=None ):
if filename is None:
filename = "data/%s.ga" % name
content = resource_string( __name__, filename )
return self.load_workflow( name, content=content )
def simple_workflow( self, name, **create_kwds ):
workflow = self.load_workflow( name )
return self.create_workflow( workflow, **create_kwds )
def create_workflow( self, workflow, **create_kwds ):
upload_response = self.create_workflow_response( workflow, **create_kwds )
uploaded_workflow_id = upload_response.json()[ "id" ]
return uploaded_workflow_id
def create_workflow_response( self, workflow, **create_kwds ):
data = dict(
workflow=json.dumps( workflow ),
**create_kwds
)
upload_response = self._post( "workflows/upload", data=data )
return upload_response
def wait_for_invocation( self, workflow_id, invocation_id, timeout=DEFAULT_TIMEOUT ):
url = "workflows/%s/usage/%s" % ( workflow_id, invocation_id )
return wait_on_state( lambda: self._get( url ), timeout=timeout )
def wait_for_workflow( self, workflow_id, invocation_id, history_id, assert_ok=True, timeout=DEFAULT_TIMEOUT ):
""" Wait for a workflow invocation to completely schedule and then history
to be complete. """
self.wait_for_invocation( workflow_id, invocation_id, timeout=timeout )
self.dataset_populator.wait_for_history( history_id, assert_ok=assert_ok, timeout=timeout )
class WorkflowPopulator( BaseWorkflowPopulator ):
def __init__( self, galaxy_interactor ):
self.galaxy_interactor = galaxy_interactor
self.dataset_populator = DatasetPopulator( galaxy_interactor )
def _post( self, route, data={} ):
return self.galaxy_interactor.post( route, data )
def _get( self, route ):
return self.galaxy_interactor.get( route )
class LibraryPopulator( object ):
def __init__( self, api_test_case ):
self.api_test_case = api_test_case
self.galaxy_interactor = api_test_case.galaxy_interactor
def new_private_library( self, name ):
library = self.new_library( name )
library_id = library[ "id" ]
role_id = self.user_private_role_id()
self.set_permissions( library_id, role_id )
return library
def new_library( self, name ):
data = dict( name=name )
create_response = self.galaxy_interactor.post( "libraries", data=data, admin=True )
return create_response.json()
def set_permissions( self, library_id, role_id=None ):
if role_id:
perm_list = json.dumps( role_id )
else:
perm_list = json.dumps( [] )
permissions = dict(
LIBRARY_ACCESS_in=perm_list,
LIBRARY_MODIFY_in=perm_list,
LIBRARY_ADD_in=perm_list,
LIBRARY_MANAGE_in=perm_list,
)
self.galaxy_interactor.post( "libraries/%s/permissions" % library_id, data=permissions, admin=True )
def user_email( self ):
users_response = self.galaxy_interactor.get( "users" )
users = users_response.json()
assert len( users ) == 1
return users[ 0 ][ "email" ]
def user_private_role_id( self ):
user_email = self.user_email()
roles_response = self.api_test_case.galaxy_interactor.get( "roles", admin=True )
users_roles = [ r for r in roles_response.json() if r[ "name" ] == user_email ]
assert len( users_roles ) == 1
return users_roles[ 0 ][ "id" ]
def create_dataset_request( self, library, **kwds ):
create_data = {
"folder_id": kwds.get( "folder_id", library[ "root_folder_id" ] ),
"create_type": "file",
"files_0|NAME": kwds.get( "name", "NewFile" ),
"upload_option": kwds.get( "upload_option", "upload_file" ),
"file_type": kwds.get( "file_type", "auto" ),
"db_key": kwds.get( "db_key", "?" ),
}
files = {
"files_0|file_data": kwds.get( "file", StringIO( kwds.get( "contents", "TestData" ) ) ),
}
return create_data, files
def new_library_dataset( self, name, **create_dataset_kwds ):
library = self.new_private_library( name )
payload, files = self.create_dataset_request( library, **create_dataset_kwds )
url_rel = "libraries/%s/contents" % ( library[ "id" ] )
dataset = self.api_test_case.galaxy_interactor.post( url_rel, payload, files=files ).json()[0]
def show():
return self.api_test_case.galaxy_interactor.get( "libraries/%s/contents/%s" % ( library[ "id" ], dataset[ "id" ] ) )
wait_on_state(show, timeout=DEFAULT_TIMEOUT)
return show().json()
class BaseDatasetCollectionPopulator( object ):
def create_list_from_pairs( self, history_id, pairs, name="Dataset Collection from pairs" ):
element_identifiers = []
for i, pair in enumerate( pairs ):
element_identifiers.append( dict(
name="test%d" % i,
src="hdca",
id=pair
) )
payload = dict(
instance_type="history",
history_id=history_id,
element_identifiers=json.dumps(element_identifiers),
collection_type="list:paired",
name=name,
)
return self.__create( payload )
def create_list_of_pairs_in_history( self, history_id, **kwds ):
pair1 = self.create_pair_in_history( history_id, **kwds ).json()["id"]
return self.create_list_from_pairs( history_id, [ pair1 ] )
def create_pair_in_history( self, history_id, **kwds ):
payload = self.create_pair_payload(
history_id,
instance_type="history",
**kwds
)
return self.__create( payload )
def create_list_in_history( self, history_id, **kwds ):
payload = self.create_list_payload(
history_id,
instance_type="history",
**kwds
)
return self.__create( payload )
def create_list_payload( self, history_id, **kwds ):
return self.__create_payload( history_id, identifiers_func=self.list_identifiers, collection_type="list", **kwds )
def create_pair_payload( self, history_id, **kwds ):
return self.__create_payload( history_id, identifiers_func=self.pair_identifiers, collection_type="paired", **kwds )
def __create_payload( self, history_id, identifiers_func, collection_type, **kwds ):
contents = None
if "contents" in kwds:
contents = kwds[ "contents" ]
del kwds[ "contents" ]
if "element_identifiers" not in kwds:
kwds[ "element_identifiers" ] = json.dumps( identifiers_func( history_id, contents=contents ) )
if "name" not in kwds:
kwds["name"] = "Test Dataset Collection"
payload = dict(
history_id=history_id,
collection_type=collection_type,
**kwds
)
return payload
def pair_identifiers( self, history_id, contents=None ):
hda1, hda2 = self.__datasets( history_id, count=2, contents=contents )
element_identifiers = [
dict( name="forward", src="hda", id=hda1[ "id" ] ),
dict( name="reverse", src="hda", id=hda2[ "id" ] ),
]
return element_identifiers
def list_identifiers( self, history_id, contents=None ):
count = 3 if not contents else len( contents )
# Contents can be a list of strings (with name auto-assigned here) or a list of
# 2-tuples of form (name, dataset_content).
if contents and isinstance(contents[0], tuple):
hdas = self.__datasets( history_id, count=count, contents=[c[1] for c in contents] )
def hda_to_identifier(i, hda):
return dict(name=contents[i][0], src="hda", id=hda["id"])
else:
hdas = self.__datasets( history_id, count=count, contents=contents )
def hda_to_identifier(i, hda):
return dict(name="data%d" % (i + 1), src="hda", id=hda["id"])
element_identifiers = [hda_to_identifier(i, hda) for (i, hda) in enumerate(hdas)]
return element_identifiers
def __create( self, payload ):
return self._create_collection( payload )
def __datasets( self, history_id, count, contents=None ):
datasets = []
for i in range( count ):
new_kwds = {}
if contents:
new_kwds[ "content" ] = contents[ i ]
datasets.append( self.dataset_populator.new_dataset( history_id, **new_kwds ) )
return datasets
class DatasetCollectionPopulator( BaseDatasetCollectionPopulator ):
def __init__( self, galaxy_interactor ):
self.galaxy_interactor = galaxy_interactor
self.dataset_populator = DatasetPopulator( galaxy_interactor )
def _create_collection( self, payload ):
create_response = self.galaxy_interactor.post( "dataset_collections", data=payload )
return create_response
def wait_on_state( state_func, assert_ok=False, timeout=DEFAULT_TIMEOUT ):
def get_state( ):
response = state_func()
assert response.status_code == 200, "Failed to fetch state update while waiting."
state = response.json()[ "state" ]
if state not in [ "running", "queued", "new", "ready" ]:
if assert_ok:
assert state == "ok", "Final state - %s - not okay." % state
return state
else:
return None
return wait_on( get_state, desc="state", timeout=timeout)
class GiPostGetMixin:
"""Mixin for adapting Galaxy testing populators helpers to bioblend."""
def _get(self, route):
return self._gi.make_get_request(self.__url(route))
def _post(self, route, data={}):
data = data.copy()
data['key'] = self._gi.key
return requests.post(self.__url(route), data=data)
def __url(self, route):
return self._gi.url + "/" + route
class GiDatasetPopulator(BaseDatasetPopulator, GiPostGetMixin):
"""Implementation of BaseDatasetPopulator backed by bioblend."""
def __init__(self, gi):
"""Construct a dataset populator from a bioblend GalaxyInstance."""
self._gi = gi
class GiDatasetCollectionPopulator(BaseDatasetCollectionPopulator, GiPostGetMixin):
"""Implementation of BaseDatasetCollectionPopulator backed by bioblend."""
def __init__(self, gi):
"""Construct a dataset collection populator from a bioblend GalaxyInstance."""
self._gi = gi
self.dataset_populator = GiDatasetPopulator(gi)
def _create_collection(self, payload):
create_response = self._post( "dataset_collections", data=payload )
return create_response
class GiWorkflowPopulator(BaseWorkflowPopulator, GiPostGetMixin):
"""Implementation of BaseWorkflowPopulator backed by bioblend."""
def __init__(self, gi):
"""Construct a workflow populator from a bioblend GalaxyInstance."""
self._gi = gi
self.dataset_populator = GiDatasetPopulator(gi)
def wait_on( function, desc, timeout=DEFAULT_TIMEOUT ):
delta = .25
iteration = 0
while True:
total_wait = delta * iteration
if total_wait > timeout:
timeout_message = "Timed out after %s seconds waiting on %s." % (
total_wait, desc
)
assert False, timeout_message
iteration += 1
value = function()
if value is not None:
return value
time.sleep( delta )