Unverified Commit 2ff26d40 authored by Dannon's avatar Dannon Committed by GitHub
Browse files

Merge pull request #9640 from nsoranzo/release_19.09_OSError_not_subscriptable 

[19.09] Fix `TypeError: OSError object is not subscriptable` under Python 3
parents 7adb2a38 dc5791c5

lib/galaxy/util/pastescript/serve.py

+7 −10
Original line number Diff line number Diff line
@@ -21,11 +21,15 @@ from __future__ import print_function 


import atexit

import errno

import grp

import logging

import optparse

import os

import pwd

import re

import resource

import signal

import socket

import subprocess

import sys

import textwrap
@@ -662,7 +666,6 @@ class ServeCommand(Command): 
            except AttributeError as e:

                # Capturing bad error response from paste

                if str(e) == "'WSGIThreadPoolServer' object has no attribute 'thread_pool'":

                    import socket

                    raise socket.error(98, 'Address already in use')

                else:

                    raise AttributeError(e)
@@ -699,7 +702,6 @@ class ServeCommand(Command): 


        # @@: Should we set the umask and cwd now?



        import resource  # Resource usage information.

        maxfd = resource.getrlimit(resource.RLIMIT_NOFILE)[1]

        if maxfd == resource.RLIM_INFINITY:

            maxfd = MAXFD
@@ -746,7 +748,7 @@ class ServeCommand(Command): 
                print("Could not delete: %s" % e)

                return 2

            return 1

        for j in range(10):

        for _i in range(10):

            if not live_pidfile(pid_file):

                break

            os.kill(pid, signal.SIGTERM)
@@ -820,15 +822,12 @@ class ServeCommand(Command): 
    def change_user_group(self, user, group):

        if not user and not group:

            return

        import pwd

        import grp

        uid = gid = None

        if group:

            try:

                gid = int(group)

                group = grp.getgrgid(gid).gr_name

            except ValueError:

                import grp

                try:

                    entry = grp.getgrnam(group)

                except KeyError:
@@ -983,15 +982,13 @@ def ensure_port_cleanup(bound_addresses, maxtries=30, sleeptime=2): 


def _cleanup_ports(bound_addresses, maxtries=30, sleeptime=2):

    # Wait for the server to bind to the port.

    import socket

    import errno

    for bound_address in bound_addresses:

        for attempt in range(maxtries):

        for _i in range(maxtries):

            sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)

            try:

                sock.connect(bound_address)

            except socket.error as e:

                if e.args[0] != errno.ECONNREFUSED:

                if e.errno != errno.ECONNREFUSED:

                    raise

                break

            else:

test/base/driver_util.py

+10 −6
Original line number Diff line number Diff line
@@ -310,13 +310,15 @@ def _tool_data_table_config_path(default_tool_data_table_config_path=None): 
    return tool_data_table_config_path





def nose_config_and_run(argv=None, env=None, ignore_files=[], plugins=None):

def nose_config_and_run(argv=None, env=None, ignore_files=None, plugins=None):

    """Setup a nose context and run tests.



    Tests are specified by argv (defaulting to sys.argv).

    """

    if env is None:

        env = os.environ

    if ignore_files is None:

        ignore_files = []

    if plugins is None:

        plugins = nose.plugins.manager.DefaultPluginManager()

    if argv is None:
@@ -472,7 +474,7 @@ def get_webapp_global_conf(): 
def wait_for_http_server(host, port, sleep_amount=0.1, sleep_tries=150):

    """Wait for an HTTP server to boot up."""

    # Test if the server is up

    for i in range(sleep_tries):

    for _ in range(sleep_tries):

        # directly test the app, not the proxy

        conn = http_client.HTTPConnection(host, port)

        try:
@@ -497,7 +499,7 @@ def attempt_ports(port): 
        raise Exception("An existing process seems bound to specified test server port [%s]" % port)

    else:

        random.seed()

        for i in range(0, 9):

        for _ in range(0, 9):

            port = str(random.randint(8000, 10000))

            yield port
@@ -515,7 +517,7 @@ def serve_webapp(webapp, port=None, host=None): 
            server = httpserver.serve(webapp, host=host, port=port, start_loop=False)

            break

        except socket.error as e:

            if e[0] == 98:

            if e.errno == 98:

                continue

            raise
@@ -947,7 +949,7 @@ class GalaxyTestDriver(TestDriver): 
                # one - other just read the properties above and use the default

                # implementation from this file.

                galaxy_config = getattr(config_object, "galaxy_config", None)

                if hasattr(galaxy_config, '__call__'):

                if callable(galaxy_config):

                    galaxy_config = galaxy_config()

                if galaxy_config is None:

                    setup_galaxy_config_kwds = dict(
@@ -1038,7 +1040,9 @@ class GalaxyTestDriver(TestDriver): 
            return test_classes

        return functional.test_toolbox



    def run_tool_test(self, tool_id, index=0, resource_parameters={}):

    def run_tool_test(self, tool_id, index=0, resource_parameters=None):

        if resource_parameters is None:

            resource_parameters = {}

        host, port, url = target_url_parts()

        galaxy_interactor_kwds = {

            "galaxy_url": url,