Use getfullargspec on python3

`getargspec` is marked for deprecation.

lib/galaxy/jobs/mapper.py

@@ -1,10 +1,10 @@
 import importlib
-import inspect
 import logging
 
 import galaxy.jobs.rules
 from galaxy.jobs import stock_rules
 from galaxy.jobs.dynamic_tool_destination import map_tool_to_destination
+from galaxy.util.getargspec import getfullargspec
 from galaxy.util.submodules import import_submodules
 from .rule_helper import RuleHelper
 
@@ -56,7 +56,7 @@ class JobRunnerMapper(object):
             self.rules_module = importlib.import_module(module_name)
 
     def __invoke_expand_function(self, expand_function, destination):
-        function_arg_names = inspect.getargspec(expand_function).args
+        function_arg_names = getfullargspec(expand_function).args
         app = self.job_wrapper.app
         possible_args = {
             "job_id": self.job_wrapper.job_id,

lib/galaxy/jobs/splitters/multi.py

@@ -1,9 +1,9 @@
-import inspect
 import logging
 import os
 import shutil
 
 from galaxy import model, util
+from galaxy.util.getargspec import getfullargspec
 
 
 log = logging.getLogger(__name__)
@@ -157,7 +157,7 @@ def do_merge(job_wrapper, task_wrappers):
                                   % (len(output_files), len(task_dirs), output_file_name))
                     # First two args to merge always output_files and path of dataset. More
                     # complicated merge methods may require more parameters. Set those up here.
-                    extra_merge_arg_names = inspect.getargspec(output_type.merge).args[2:]
+                    extra_merge_arg_names = getfullargspec(output_type.merge).args[2:]
                     extra_merge_args = {}
                     if "output_dataset" in extra_merge_arg_names:
                         extra_merge_args["output_dataset"] = output_dataset

lib/galaxy/tools/lint.py

@@ -4,6 +4,7 @@ from __future__ import print_function
 import inspect
 
 from galaxy.util import submodules
+from galaxy.util.getargspec import getfullargspec
 from .parser import get_tool_source
 
 
@@ -42,7 +43,7 @@ def lint_tool_source_with(lint_context, tool_source, extra_modules=[]):
                 # Look at the first argument to the linter to decide
                 # if we should lint the XML description or the abstract
                 # tool parser object.
-                first_arg = inspect.getargspec(value).args[0]
+                first_arg = getfullargspec(value).args[0]
                 if first_arg == "tool_xml":
                     if tool_xml is None:
                         # XML linter and non-XML tool, skip for now

lib/galaxy/tools/verify/asserts/__init__.py

@@ -1,8 +1,8 @@
-import inspect
 import logging
 import sys
 
 from galaxy.util import unicodify
+from galaxy.util.getargspec import getfullargspec
 
 log = logging.getLogger(__name__)
 
@@ -43,7 +43,7 @@ def verify_assertion(data, assertion_description):
         errmsg = "Unable to find test function associated with XML tag '%s'. Check your tool file syntax." % tag
         raise AssertionError(errmsg)
 
-    assert_function_args = inspect.getargspec(assert_function).args
+    assert_function_args = getfullargspec(assert_function).args
     args = {}
     for attribute, value in assertion_description["attributes"].items():
         if attribute in assert_function_args:

lib/galaxy/util/getargspec.py

@@ -0,0 +1,9 @@
+import inspect
+
+
+def getfullargspec(func):
+    try:
+        return inspect.getfullargspec(func)
+    except AttributeError:
+        # on python 2
+        return inspect.getargspec(func)

lib/galaxy/util/pastescript/loadwsgi.py

@@ -12,6 +12,7 @@ import pkg_resources
 from six import iteritems
 from six.moves.urllib.parse import unquote
 
+from galaxy.util.getargspec import getfullargspec
 from galaxy.util.properties import NicerConfigParser
 
 
@@ -58,11 +59,11 @@ def fix_type_error(exc_info, callable, varargs, kwargs):
     if exc_info is None:
         exc_info = sys.exc_info()
     if (exc_info[0] != TypeError or
-            str(exc_info[1]).find('arguments') == -1 or
+            str(exc_info[1]).find('argument') == -1 or
             getattr(exc_info[1], '_type_error_fixed', False)):
         return exc_info
     exc_info[1]._type_error_fixed = True
-    argspec = inspect.formatargspec(*inspect.getargspec(callable))
+    argspec = inspect.formatargspec(*getfullargspec(callable))
     args = ', '.join(map(_short_repr, varargs))
     if kwargs and args:
         args += ', '

lib/galaxy/web/framework/decorators.py

@@ -1,4 +1,3 @@
-import inspect
 import logging
 from functools import wraps
 from json import loads
@@ -12,6 +11,7 @@ from galaxy.util import (
     parse_non_hex_float,
     unicodify
 )
+from galaxy.util.getargspec import getfullargspec
 from galaxy.util.json import safe_dumps
 from galaxy.web.framework import url_for
 
@@ -176,7 +176,7 @@ def __extract_payload_from_request(trans, func, kwargs):
         # in the payload. Therefore, the decorated method's formal arguments are discovered through reflection and removed from
         # the payload dictionary. This helps to prevent duplicate argument conflicts in downstream methods.
         payload = kwargs.copy()
-        named_args, _, _, _ = inspect.getargspec(func)
+        named_args = getfullargspec(func).args
         for arg in named_args:
             payload.pop(arg, None)
         for k, v in payload.items():

test/unit/test_fix_type_error.py

@@ -0,0 +1,23 @@
+import six
+
+from galaxy.util.pastescript.loadwsgi import fix_type_error
+
+if six.PY2:
+    argtype = ' keyword'
+else:
+    argtype = ''
+EXP_STRING = "a_func() got multiple values for%s argument 'kwarg'; got (1, 2, kwarg=...), wanted (argone, kwarg=True)" % argtype
+
+
+def a_func(argone, kwarg=True):
+    pass
+
+
+def test_fix_type_error():
+    args = [1, 2]
+    kwargs = {'kwarg': False}
+    try:
+        a_func(*args, **kwargs)
+    except TypeError:
+        exc_info = fix_type_error(None, a_func, args, kwargs)
+    assert exc_info[1].args[0] == EXP_STRING