Improved configuration options for shed-tools tool test functionality, fixes.

Author: jmchilton

ephemeris/shed_tools.py

@@ -293,15 +293,16 @@ def _parser():
         install_resolver_dependencies=False,
         force_latest_revision=False,
         test=False,
+        test_user_api_key=None,
+        test_user="ephemeris@galaxyproject.org",
         test_json="tool_test_output.json",
         test_existing=False,
     )
     install_command_parser = subparsers.add_parser(
         "install",
         help="This installs tools in Galaxy from the Tool Shed."
              "Use shed-tools install --help for more information",
-        parents=[common_arguments],
-        )
+        parents=[common_arguments])
     update_command_parser = subparsers.add_parser(
         "update",
         help="This updates all tools in Galaxy to the latest revision. "
@@ -312,7 +313,7 @@ def _parser():
         "test",
         help="This tests the supplied list of tools in Galaxy. "
              "Use shed-tools test --help for more information",
-    )
+        parents=[common_arguments])
 
     for command_parser in [install_command_parser, test_command_parser]:
         command_parser.add_argument(
@@ -399,6 +400,22 @@ def _parser():
             help="If testing tools, record tool test output to specified file. "
                  "This file can be turned into reports with ``planemo test_reports <output.json>``."
         )
+        command_parser.add_argument(
+            "--test_user_api_key",
+            dest="test_json",
+            help="If testing tools, a user is needed to execute the tests. "
+                 "This can be different the --api_key which is assumed to be an admin key. "
+                 "If --api_key is a valid user (e.g. it is not a master API key) this does "
+                 "not need to be specified and --api_key will be reused."
+        )
+        command_parser.add_argument(
+            "--test_user",
+            dest="test_json",
+            help="If testing tools, a user is needed to execute the tests. "
+                 "If --api_key is a master api key (i.e. not tied to a real user) and "
+                 "--test_user_api_key isn't specified, this user email will be used. This "
+                 "user will be created if needed."
+        )
 
     # Same test_json as above but language modified for test instead of install/update.
     test_command_parser.add_argument(
@@ -408,6 +425,23 @@ def _parser():
              "This file can be turned into reports with ``planemo test_reports <output.json>``."
     )
 
+    test_command_parser.add_argument(
+        "--test_user_api_key",
+        dest="test_user_api_key",
+        help="A user is needed to execute the tests. "
+             "This can be different the --api_key which is assumed to be an admin key. "
+             "If --api_key is a valid user (e.g. it is not a master API key) this does "
+             "not need to be specified and --api_key will be reused."
+    )
+    test_command_parser.add_argument(
+        "--test_user",
+        dest="test_user",
+        help="A user is needed to execute the tests. "
+             "If --api_key is a master api key (i.e. not tied to a real user) and "
+             "--test_user_api_key isn't specified, this user email will be used. This "
+             "user will be created if needed."
+    )
+
     update_command_parser.set_defaults(
         action="update",
     )
@@ -577,6 +611,8 @@ def get_install_repository_manager(options):
                               default_install_resolver_dependencies=install_resolver_dependencies,
                               force_latest_revision=force_latest_revision,
                               test=options.test,
+                              test_user=options.test_user,
+                              test_user_api_key=options.test_user_api_key,
                               test_existing=options.test_existing,
                               test_json=options.test_json,
                               )
@@ -593,6 +629,8 @@ def __init__(self,
                  require_tool_panel_info=True,
                  force_latest_revision=False,
                  test=False,
+                 test_user_api_key=None,
+                 test_user="ephemeris@galaxyproject.org",
                  test_existing=False,
                  test_json="tool_test_output.json"):
         self.repositories = repositories
@@ -609,6 +647,8 @@ def __init__(self,
         self.test = test
         self.test_existing = test_existing
         self.test_json = test_json
+        self.test_user_api_key = test_user_api_key
+        self.test_user = test_user
         self.tests_passed = []
         self.test_exceptions = []
 
@@ -756,17 +796,24 @@ def test_repositories(self, target_repositories=None):
         )
         log.info("Failed tool tests ({0}): {1}".format(
             len(self.test_exceptions),
-            [t[0] for t in self.errored_repositories])
+            [t[0] for t in self.test_exceptions])
         )
         log.info("Total tool test time: {0}".format(dt.datetime.now() - tool_test_start))
 
     def _test_tool(self, tool):
+        test_user_api_key = self.test_user_api_key
+        if test_user_api_key is None:
+            whoami = self.gi.make_get_request(self.gi.url + "/whoami").json()
+            if whoami is not None:
+                test_user_api_key = self.gi.key
         galaxy_interactor_kwds = {
             "galaxy_url": re.sub('/api', '', self.gi.url),
             "master_api_key": self.gi.key,
             "api_key": None,  # TODO
             "keep_outputs_dir": '',
         }
+        if test_user_api_key is None:
+            galaxy_interactor_kwds["test_user"] = self.test_user
         galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
         tool_id = tool["id"]
         tool_version = tool["version"]