From 1cf6c980f2877f2709b6c525ce1debdcdaebb015 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 8 Nov 2020 08:23:51 -0500
Subject: [PATCH] More fixes for tool test script.

---
 lib/galaxy/tool_util/verify/script.py     | 17 +++++++++++------
 test/unit/tool_util/test_verify_script.py | 20 ++++++++++++++++++++
 2 files changed, 31 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tool_util/verify/script.py b/lib/galaxy/tool_util/verify/script.py
index 3c58d81b1a2..688608c990c 100644
--- a/lib/galaxy/tool_util/verify/script.py
+++ b/lib/galaxy/tool_util/verify/script.py
@@ -18,7 +18,7 @@ from galaxy.tool_util.verify.interactor import (
 
 DESCRIPTION = """Script to quickly run a tool test against a running Galaxy instance."""
 DEFAULT_SUITE_NAME = "Galaxy Tool Tests"
-ALL_TESTS = "*"
+ALL_TESTS = -1
 ALL_TOOLS = "*"
 ALL_VERSION = "*"
 LATEST_VERSION = None
@@ -213,7 +213,6 @@ def _test_tool(
         def register(job_data_):
             nonlocal job_data
             job_data = job_data_
-            job_data['id'] = test_id
 
         try:
             while run_retries >= 0:
@@ -236,7 +235,11 @@ def _test_tool(
                     run_retries -= 1
         finally:
             if job_data is not None:
-                results.register_result(job_data)
+                results.register_result({
+                    "id": test_id,
+                    "has_data": True,
+                    "data": job_data,
+                })
             if job_exception is not None:
                 was_recorded = job_data is not None
                 test_exception = TestException(tool_id, job_exception, was_recorded)
@@ -309,7 +312,7 @@ def main(argv=None):
     verify_kwds = dict(
         client_test_config=tools_client_test_config,
         force_path_paste=args.force_path_paste,
-        skip_with_reference_data=args.skip_with_reference_data,
+        skip_with_reference_data=not args.with_reference_data,
         quiet=not verbose,
     )
     test_tools(
@@ -339,8 +342,10 @@ def _arg_parser():
     parser.add_argument('--verbose', default=False, action="store_true", help="Verbose logging.")
     parser.add_argument('-c', '--client-test-config', default=None, help="Test config YAML to help with client testing")
     parser.add_argument('--suite-name', default=DEFAULT_SUITE_NAME, help="Suite name for tool test output")
-    parser.add_argument('--skip-with-reference-data', default=False, action="store_true", help="Skip tests the Galaxy server believes use data tables or loc files.")
-    parser.add_argument('--history-per-test-case', default=False, action="store_true", help="Create new history per test case.")
+    parser.add_argument('--with-reference-data', dest="with_reference_data", default=False, action="store_true")
+    parser.add_argument('--skip-with-reference-data', dest="with_reference_data", action="store_false", help="Skip tests the Galaxy server believes use data tables or loc files.")
+    parser.add_argument('--history-per-suite', dest="history_per_test_case", default=False, action="store_false", help="Create new history per test suite (all tests in same history).")
+    parser.add_argument('--history-per-test-case', dest="history_per_test_case", action="store_true", help="Create new history per test case.")
     parser.add_argument('--no-history-cleanup', default=False, action="store_true", help="Perserve histories created for testing.")
     parser.add_argument('--retries', default=0, type=int, help="Retry failed tests.")
     return parser
diff --git a/test/unit/tool_util/test_verify_script.py b/test/unit/tool_util/test_verify_script.py
index 58f52ade7b7..357964a9ff1 100644
--- a/test/unit/tool_util/test_verify_script.py
+++ b/test/unit/tool_util/test_verify_script.py
@@ -4,6 +4,7 @@ from tempfile import NamedTemporaryFile
 from unittest import mock
 
 from galaxy.tool_util.verify.script import (
+    _arg_parser,
     build_case_references,
     Results,
     test_tools as run,
@@ -14,6 +15,25 @@ VT_PATH = 'galaxy.tool_util.verify.script.verify_tool'
 NEW_HISTORY = object()
 
 
+def test_arg_parse():
+    parser = _arg_parser()
+
+    # defaults
+    args = parser.parse_args([])
+    assert not args.with_reference_data
+    assert not args.history_per_test_case
+
+    # skip flags
+    args = parser.parse_args(["--skip-with-reference-data", "--history-per-test-case"])
+    assert not args.with_reference_data
+    assert args.history_per_test_case
+
+    # enable flags
+    args = parser.parse_args(["--with-reference-data", "--history-per-suite"])
+    assert args.with_reference_data
+    assert not args.history_per_test_case
+
+
 def test_test_tools():
     interactor = MockGalaxyInteractor()
     f = NamedTemporaryFile()