Refactor API helpers for re-use in rest of test framework.

- Move api.helpers to base.populators.
- Refactor helper subclasses adapted to use bioblend instead of test framework stuff into base.populators for greater visibility.
- Refactor workflow format 2 testing stuff for reuse by Selenium.

test/api/test_dataset_collections.py

@@ -1,8 +1,7 @@
 import json
 
 from base import api
-
-from .helpers import DatasetCollectionPopulator, DatasetPopulator
+from base.populators import DatasetCollectionPopulator, DatasetPopulator
 
 
 class DatasetCollectionApiTestCase( api.ApiTestCase ):

test/api/test_datasets.py

@@ -3,8 +3,7 @@ from __future__ import print_function
 import textwrap
 
 from base import api
-
-from .helpers import TestsDatasets
+from base.populators import TestsDatasets
 
 
 class DatasetsApiTestCase( api.ApiTestCase, TestsDatasets ):

test/api/test_histories.py

@@ -8,7 +8,7 @@ from requests import (
 
 from base import api
 
-from .helpers import DatasetPopulator, wait_on
+from base.populators import DatasetPopulator, wait_on
 
 
 class HistoriesApiTestCase( api.ApiTestCase ):

test/api/test_history_contents.py

@@ -5,8 +5,7 @@ import json
 from requests import delete, put
 
 from base import api
-
-from .helpers import DatasetCollectionPopulator, LibraryPopulator, TestsDatasets
+from base.populators import DatasetCollectionPopulator, LibraryPopulator, TestsDatasets
 
 
 # TODO: Test anonymous access.

test/api/test_history_contents_provenance.py

@@ -1,6 +1,5 @@
 from base import api
-
-from .helpers import DatasetPopulator
+from base.populators import DatasetPopulator
 
 
 class TestProvenance( api.ApiTestCase ):

test/api/test_jobs.py

@@ -4,8 +4,7 @@ import time
 from operator import itemgetter
 
 from base import api
-
-from .helpers import TestsDatasets
+from base.populators import TestsDatasets
 
 
 class JobsApiTestCase( api.ApiTestCase, TestsDatasets ):

test/api/test_libraries.py

@@ -1,6 +1,5 @@
 from base import api
-
-from .helpers import (
+from base.populators import (
     LibraryPopulator,
     TestsDatasets,
     wait_on_state

test/api/test_search.py

@@ -1,8 +1,7 @@
 from base import api
+from base.populators import WorkflowPopulator
 from requests import delete
 
-from .helpers import WorkflowPopulator
-
 
 class SearchApiTestCase( api.ApiTestCase ):
 

test/api/test_tools.py

@@ -2,11 +2,14 @@
 import json
 
 from base import api
+from base.populators import (
+    DatasetCollectionPopulator,
+    DatasetPopulator,
+    LibraryPopulator,
+    skip_without_tool
+)
 from galaxy.tools.verify.test_data import TestDataResolver
 
-from .helpers import (DatasetCollectionPopulator, DatasetPopulator,
-    LibraryPopulator, skip_without_tool)
-
 
 class ToolsTestCase( api.ApiTestCase ):
 

test/api/test_workflow_extraction.py

@@ -5,7 +5,8 @@ import operator
 from collections import namedtuple
 from json import dumps, loads
 
-from .helpers import skip_without_tool
+from base.populators import skip_without_tool
+
 from .test_workflows import BaseWorkflowsApiTestCase
 
 

test/api/test_workflows.py

@@ -9,12 +9,16 @@ import yaml
 from requests import delete, put
 
 from base import api
+from base.populators import (
+    DatasetCollectionPopulator,
+    DatasetPopulator,
+    skip_without_tool,
+    WorkflowPopulator
+)
 from galaxy.exceptions import error_codes
 from galaxy.tools.verify.test_data import TestDataResolver
 
-from .helpers import (DatasetCollectionPopulator, DatasetPopulator,
-    skip_without_tool, WorkflowPopulator)
-from .workflows_format_2 import (
+from base.workflows_format_2 import (
     convert_and_import_workflow,
     ImporterGalaxyInterface,
 )
@@ -1216,11 +1220,9 @@ test_data:
     def test_workflow_stability( self ):
         # Run this index stability test with following command:
         #   ./run_tests.sh test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_stability
-        from pkg_resources import resource_string
         num_tests = 1
-        for workflow_file in [ "test_workflow_topoambigouity.ga", "test_workflow_topoambigouity_auto_laidout.ga" ]:
-            workflow_str = resource_string( __name__, workflow_file )
-            workflow = self.workflow_populator.load_workflow( "test1", content=workflow_str )
+        for workflow_file in [ "test_workflow_topoambigouity", "test_workflow_topoambigouity_auto_laidout" ]:
+            workflow = self.workflow_populator.load_workflow_from_resource( workflow_file )
             last_step_map = self._step_map( workflow )
             for i in range(num_tests):
                 uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )

test/base/populators.py

@@ -1,17 +1,20 @@
 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__, "test_workflow_1.ga" )
+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__, "test_workflow_2.ga" )
+workflow_random_x2_str = resource_string( __name__, "data/test_workflow_2.ga" )
 
 
 DEFAULT_TIMEOUT = 15  # Secs to wait for state to turn ok
@@ -229,7 +232,7 @@ class BaseWorkflowPopulator( object ):
 
     def load_workflow_from_resource( self, name, filename=None ):
         if filename is None:
-            filename = "%s.ga" % name
+            filename = "data/%s.ga" % name
         content = resource_string( __name__, filename )
         return self.load_workflow( name, content=content )
 
@@ -476,6 +479,54 @@ def wait_on_state( state_func, assert_ok=False, timeout=DEFAULT_TIMEOUT ):
     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

test/manual/workflows_scaling.py

@@ -14,13 +14,16 @@ from argparse import ArgumentParser
 from threading import Thread
 from uuid import uuid4
 
-import requests
 from bioblend import galaxy
 
 galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir))
 sys.path[1:1] = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ]
 
-from api import helpers
+from base.populators import (
+    GiDatasetCollectionPopulator,
+    GiDatasetPopulator,
+    GiWorkflowPopulator,
+)
 from api.workflows_format_2.converter import python_to_workflow
 
 LONG_TIMEOUT = 1000000000
@@ -109,51 +112,6 @@ def _run(args, gi, workflow_id, uuid):
         )
 
 
-class GiPostGetMixin:
-    """Mixin for adapting Galaxy API testing 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(helpers.BaseDatasetPopulator, GiPostGetMixin):
-    """Utility class for dealing with datasets and histories."""
-
-    def __init__(self, gi):
-        """Construct a dataset populator from a bioblend GalaxyInstance."""
-        self._gi = gi
-
-
-class GiDatasetCollectionPopulator(helpers.BaseDatasetCollectionPopulator, GiPostGetMixin):
-    """Utility class for dealing with dataset collections."""
-
-    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(helpers.BaseWorkflowPopulator, GiPostGetMixin):
-    """Utility class for dealing with workflows."""
-
-    def __init__(self, gi):
-        """Construct a workflow populator from a bioblend GalaxyInstance."""
-        self._gi = gi
-        self.dataset_populator = GiDatasetPopulator(gi)
-
-
 def _workflow_struct(args, input_uuid):
     if args.two_outputs:
         return _workflow_struct_two_outputs(args, input_uuid)