internlm/SWE-Fixer-Train-110K huggingface dataset:
Repository: certbot/certbot

Issue:
StandaloneAuthenticator tests fail when port 443 is taken
```
test_can_perform (letsencrypt.client.plugins.standalone.tests.authenticator_test.PerformTest)
What happens if start_listener() returns True. ... 
-------------------------------------------------------------------------------
The program apache2 (process ID 25204) is already listening on TCP port 443.
This will prevent us from binding to that port. Please stop the apache2 program
temporarily and then try again.
-------------------------------------------------------------------------------
Press Enter to Continue
FAIL
test_cannot_perform (letsencrypt.client.plugins.standalone.tests.authenticator_test.PerformTest)
What happens if start_listener() returns False. ... 
-------------------------------------------------------------------------------
The program apache2 (process ID 25204) is already listening on TCP port 443.
This will prevent us from binding to that port. Please stop the apache2 program
temporarily and then try again.
-------------------------------------------------------------------------------
Press Enter to Continue
FAIL

```



Discussion:
Probably mistakenly missing a mock....

#463 changes the default port to `5001` but this should be mocked out anyway


Resolving patch:
diff --git a/letsencrypt/plugins/standalone/authenticator.py b/letsencrypt/plugins/standalone/authenticator.py
--- a/letsencrypt/plugins/standalone/authenticator.py
+++ b/letsencrypt/plugins/standalone/authenticator.py
@@ -152,7 +152,6 @@ def do_parent_process(self, port, delay_amount=5):
         :rtype: bool
 
         """
-
         display = zope.component.getUtility(interfaces.IDisplay)
 
         start_time = time.time()


Test patch:
diff --git a/letsencrypt/plugins/standalone/tests/authenticator_test.py b/letsencrypt/plugins/standalone/tests/authenticator_test.py
--- a/letsencrypt/plugins/standalone/tests/authenticator_test.py
+++ b/letsencrypt/plugins/standalone/tests/authenticator_test.py
@@ -317,6 +317,7 @@ def test_can_perform(self):
         """What happens if start_listener() returns True."""
         self.authenticator.start_listener = mock.Mock()
         self.authenticator.start_listener.return_value = True
+        self.authenticator.already_listening = mock.Mock(return_value=False)
         result = self.authenticator.perform(self.achalls)
         self.assertEqual(len(self.authenticator.tasks), 2)
         self.assertTrue(
@@ -335,6 +336,7 @@ def test_cannot_perform(self):
         """What happens if start_listener() returns False."""
         self.authenticator.start_listener = mock.Mock()
         self.authenticator.start_listener.return_value = False
+        self.authenticator.already_listening = mock.Mock(return_value=False)
         result = self.authenticator.perform(self.achalls)
         self.assertEqual(len(self.authenticator.tasks), 2)
         self.assertTrue(
Repository: certbot/certbot

Issue:
nginx plugin destroys config
I have a config file called webp.conf in /etc/nginx/conf.d/ which works great.
After running letsencrypt -d example.org run the webp.conf is broken because it's missing a closing }
https://pastebin.mozilla.org/8837365
Line 18 gets removed.



Discussion:
Seems the parse has an issue with the indentation.

Minimum testcase:

```
if ($http_accept ~* "webp") { set $webp "true"; }
```

A non-extensive test shows it can be fixed by a small change:

``` patch
diff --git a/letsencrypt-nginx/letsencrypt_nginx/nginxparser.py b/letsencrypt-nginx/letsencrypt_nginx/nginxparser.py
index 749c009..2df26fe 100644
--- a/letsencrypt-nginx/letsencrypt_nginx/nginxparser.py
+++ b/letsencrypt-nginx/letsencrypt_nginx/nginxparser.py
@@ -37,7 +37,7 @@ class RawNginxParser(object):
         + Group(ZeroOrMore(Group(assignment) | block))
         + right_bracket)

-    script = OneOrMore(Group(assignment) | block) + stringEnd
+    script = OneOrMore(Group(assignment) ^ block) + stringEnd
```

Reversing the order of `block` and `Group(assignment)` while preserving `|` also fixes it.

After https://github.com/letsencrypt/letsencrypt/pull/602 lands I'll do a full test


Resolving patch:
diff --git a/letsencrypt-nginx/letsencrypt_nginx/nginxparser.py b/letsencrypt-nginx/letsencrypt_nginx/nginxparser.py
--- a/letsencrypt-nginx/letsencrypt_nginx/nginxparser.py
+++ b/letsencrypt-nginx/letsencrypt_nginx/nginxparser.py
@@ -37,7 +37,7 @@ class RawNginxParser(object):
         + Group(ZeroOrMore(Group(comment | assignment) | block))
         + right_bracket)
 
-    script = OneOrMore(Group(comment | assignment) | block) + stringEnd
+    script = OneOrMore(Group(comment | assignment) ^ block) + stringEnd
 
     def __init__(self, source):
         self.source = source


Test patch:
diff --git a/letsencrypt-nginx/letsencrypt_nginx/tests/nginxparser_test.py b/letsencrypt-nginx/letsencrypt_nginx/tests/nginxparser_test.py
--- a/letsencrypt-nginx/letsencrypt_nginx/tests/nginxparser_test.py
+++ b/letsencrypt-nginx/letsencrypt_nginx/tests/nginxparser_test.py
@@ -5,7 +5,7 @@
 from pyparsing import ParseException
 
 from letsencrypt_nginx.nginxparser import (
-    RawNginxParser, load, dumps, dump)
+    RawNginxParser, loads, load, dumps, dump)
 from letsencrypt_nginx.tests import util
 
 
@@ -160,6 +160,13 @@ def test_comments(self):
               ['#', ' listen 80;']]],
         ])
 
+    def test_issue_518(self):
+        parsed = loads('if ($http_accept ~* "webp") { set $webp "true"; }')
+
+        self.assertEqual(parsed, [
+            [['if', '($http_accept ~* "webp")'],
+             [['set', '$webp "true"']]]
+        ])
 
 if __name__ == '__main__':
     unittest.main()  # pragma: no cover
Repository: certbot/certbot

Issue:
Make manpages for installed binaries
Currently, the client produces three binaries - /usr/bin/letsencrypt, /usr/bin/letsencrypt-renewer, and /usr/bin/jws.  However, the sphinx build of documentation only includes a single manpage - letsencrypt.1.

Please create manpages for the other installed binaries, if they are needed.  If they're not needed, let me know, and I will prune them from the Debian packaging.



Discussion:

Resolving patch:
diff --git a/docs/conf.py b/docs/conf.py
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -54,6 +54,7 @@
     'sphinx.ext.coverage',
     'sphinx.ext.viewcode',
     'repoze.sphinx.autointerface',
+    'sphinxcontrib.programoutput',
 ]
 
 autodoc_member_order = 'bysource'
@@ -283,7 +284,12 @@
 # (source start file, name, description, authors, manual section).
 man_pages = [
     ('index', 'letsencrypt', u'Let\'s Encrypt Documentation',
-     [u'Let\'s Encrypt Project'], 1)
+     [project], 7),
+    ('man/letsencrypt', 'letsencrypt', u'letsencrypt script documentation',
+     [project], 1),
+    ('man/letsencrypt-renewer', 'letsencrypt-renewer',
+     u'letsencrypt-renewer script documentation', [project], 1),
+    ('man/jws', 'jws', u'jws script documentation', [project], 1),
 ]
 
 # If true, show URL addresses after external links.
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -60,6 +60,7 @@ def read_file(filename, encoding='utf8'):
     'repoze.sphinx.autointerface',
     'Sphinx>=1.0',  # autodoc_member_order = 'bysource', autodoc_default_flags
     'sphinx_rtd_theme',
+    'sphinxcontrib-programoutput',
 ]
 
 testing_extras = [


Test patch:
Repository: certbot/certbot

Issue:
Storage.version returns unnecessarily long path
/tmp/tmpWbM0gL/live/example.org/../../archive/example.org/cert8.pem



Discussion:

Resolving patch:
diff --git a/letsencrypt/storage.py b/letsencrypt/storage.py
--- a/letsencrypt/storage.py
+++ b/letsencrypt/storage.py
@@ -223,7 +223,7 @@ def current_target(self, kind):
         target = os.readlink(link)
         if not os.path.isabs(target):
             target = os.path.join(os.path.dirname(link), target)
-        return target
+        return os.path.abspath(target)
 
     def current_version(self, kind):
         """Returns numerical version of the specified item.


Test patch:
Repository: certbot/certbot

Issue:
rename /etc/letsencrypt/configs to /etc/letsencrypt/renewal
Since it doesn't contain anything except renewal configuration files, people will probably find the current name confusing.



Discussion:
Duplicate of #731?


Resolving patch:
diff --git a/letsencrypt/constants.py b/letsencrypt/constants.py
--- a/letsencrypt/constants.py
+++ b/letsencrypt/constants.py
@@ -88,7 +88,7 @@
 TEMP_CHECKPOINT_DIR = "temp_checkpoint"
 """Temporary checkpoint directory (relative to `IConfig.work_dir`)."""
 
-RENEWAL_CONFIGS_DIR = "configs"
+RENEWAL_CONFIGS_DIR = "renewal"
 """Renewal configs directory, relative to `IConfig.config_dir`."""
 
 RENEWER_CONFIG_FILENAME = "renewer.conf"


Test patch:
diff --git a/letsencrypt-compatibility-test/letsencrypt_compatibility_test/util.py b/letsencrypt-compatibility-test/letsencrypt_compatibility_test/util.py
--- a/letsencrypt-compatibility-test/letsencrypt_compatibility_test/util.py
+++ b/letsencrypt-compatibility-test/letsencrypt_compatibility_test/util.py
@@ -39,7 +39,7 @@ def create_le_config(parent_dir):
 
 def extract_configs(configs, parent_dir):
     """Extracts configs to a new dir under parent_dir and returns it"""
-    config_dir = os.path.join(parent_dir, "configs")
+    config_dir = os.path.join(parent_dir, "renewal")
 
     if os.path.isdir(configs):
         shutil.copytree(configs, config_dir, symlinks=True)
diff --git a/letsencrypt/tests/renewer_test.py b/letsencrypt/tests/renewer_test.py
--- a/letsencrypt/tests/renewer_test.py
+++ b/letsencrypt/tests/renewer_test.py
@@ -43,13 +43,13 @@ def setUp(self):
         # TODO: maybe provide RenewerConfiguration.make_dirs?
         os.makedirs(os.path.join(self.tempdir, "live", "example.org"))
         os.makedirs(os.path.join(self.tempdir, "archive", "example.org"))
-        os.makedirs(os.path.join(self.tempdir, "configs"))
+        os.makedirs(os.path.join(self.tempdir, "renewal"))
 
         config = configobj.ConfigObj()
         for kind in ALL_FOUR:
             config[kind] = os.path.join(self.tempdir, "live", "example.org",
                                         kind + ".pem")
-        config.filename = os.path.join(self.tempdir, "configs",
+        config.filename = os.path.join(self.tempdir, "renewal",
                                        "example.org.conf")
         self.config = config
Repository: certbot/certbot

Issue:
Don't hide real permissions errors from the user
Since we landed #778 yesterday, we now completely hide permissions errors.

```
ubuntu@ip-172-31-3-78:~/letsencrypt$ venv/bin/letsencrypt
An unexpected error occurred. Please see the logfile 'letsencrypt.log' for more details.
ubuntu@ip-172-31-3-78:~/letsencrypt$ cat ./letsencrypt.log
Traceback (most recent call last):
  File "venv/bin/letsencrypt", line 9, in <module>
    load_entry_point('letsencrypt==0.1', 'console_scripts', 'letsencrypt')()
  File "/home/ubuntu/letsencrypt/venv/local/lib/python2.7/site-packages/letsencrypt/cli.py", line 882, in main
    _setup_logging(args)
  File "/home/ubuntu/letsencrypt/venv/local/lib/python2.7/site-packages/letsencrypt/cli.py", line 801, in _setup_logging
    log_file_name, maxBytes=2 ** 20, backupCount=10)
  File "/usr/lib/python2.7/logging/handlers.py", line 117, in __init__
    BaseRotatingHandler.__init__(self, filename, mode, encoding, delay)
  File "/usr/lib/python2.7/logging/handlers.py", line 64, in __init__
    logging.FileHandler.__init__(self, filename, mode, encoding, delay)
  File "/usr/lib/python2.7/logging/__init__.py", line 903, in __init__
    StreamHandler.__init__(self, self._open())
  File "/usr/lib/python2.7/logging/__init__.py", line 928, in _open
    stream = open(self.baseFilename, self.mode)
IOError: [Errno 13] Permission denied: '/var/log/letsencrypt/letsencrypt.log'
```



Discussion:
Kuba suggests catching the error and re-subclassing it from Error.Error.  Another solution, which I might prefer, is to handle `IOError` or at least the Permission denied subcase specifically in @bmw's error handling code.  Or going further in that direction, to essentially include the full final error message for the user, while continuing to hide the full traceback.


Resolving patch:
diff --git a/letsencrypt/cli.py b/letsencrypt/cli.py
--- a/letsencrypt/cli.py
+++ b/letsencrypt/cli.py
@@ -845,14 +845,17 @@ def _handle_exception(exc_type, exc_value, trace, args):
 
         if issubclass(exc_type, errors.Error):
             sys.exit(exc_value)
-        elif args is None:
-            sys.exit(
-                "An unexpected error occurred. Please see the logfile '{0}' "
-                "for more details.".format(logfile))
         else:
-            sys.exit(
-                "An unexpected error occurred. Please see the logfiles in {0} "
-                "for more details.".format(args.logs_dir))
+            # Tell the user a bit about what happened, without overwhelming
+            # them with a full traceback
+            msg = ("An unexpected error occurred.\n" +
+                   traceback.format_exception_only(exc_type, exc_value)[0] +
+                   "Please see the ")
+            if args is None:
+                msg += "logfile '{0}' for more details.".format(logfile)
+            else:
+                msg += "logfiles in {0} for more details.".format(args.logs_dir)
+            sys.exit(msg)
     else:
         sys.exit("".join(
             traceback.format_exception(exc_type, exc_value, trace)))


Test patch:
Repository: certbot/certbot

Issue:
Apache support is marked "alpha," but Nginx is not
Steps to reproduce:

`letsencrypt`

Follow prompts, when selecting which web server to use, Apache has "- alpha" after it, but Nginx does not. Nginx support is far less mature than Apache. I've heard about from two other people (and experienced myself) a failure to complete an issuance flow. I think we should probably remove the alpha tag from Apache and add it to Nginx. Or perhaps temporarily disable Nginx support, since it seems to be broken for a number of people?



Discussion:

Resolving patch:
diff --git a/letsencrypt-nginx/letsencrypt_nginx/configurator.py b/letsencrypt-nginx/letsencrypt_nginx/configurator.py
--- a/letsencrypt-nginx/letsencrypt_nginx/configurator.py
+++ b/letsencrypt-nginx/letsencrypt_nginx/configurator.py
@@ -56,7 +56,7 @@ class NginxConfigurator(common.Plugin):
     zope.interface.implements(interfaces.IAuthenticator, interfaces.IInstaller)
     zope.interface.classProvides(interfaces.IPluginFactory)
 
-    description = "Nginx Web Server"
+    description = "Nginx Web Server - Alpha"
 
     @classmethod
     def add_parser_arguments(cls, add):


Test patch:
Repository: certbot/certbot

Issue:
Read The Docs build errors
- https://readthedocs.org/projects/letsencrypt/builds/3376545/ (0f85a74dcd1147109b192e52f5604cf0c238feed)
- https://readthedocs.org/projects/letsencrypt/builds/3376579/ (22d756992b94f4da9882d1c74ff8f8c04c00e79a)
- https://readthedocs.org/projects/letsencrypt/builds/3376631/ (88def4854b05d3634a5cbc2b92d559d5a5c696b4)

```
Running Sphinx v1.3.1
making output directory...

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/letsencrypt/envs/latest/local/lib/python2.7/site-packages/sphinx/cmdline.py", line 244, in main
    opts.warningiserror, opts.tags, opts.verbosity, opts.jobs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/letsencrypt/envs/latest/local/lib/python2.7/site-packages/sphinx/application.py", line 126, in __init__
    confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/letsencrypt/envs/latest/local/lib/python2.7/site-packages/sphinx/config.py", line 277, in __init__
    execfile_(filename, config)
  File "/home/docs/checkouts/readthedocs.org/user_builds/letsencrypt/envs/latest/local/lib/python2.7/site-packages/sphinx/util/pycompat.py", line 128, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/letsencrypt/envs/latest/local/lib/python2.7/site-packages/six.py", line 672, in exec_
    exec("""exec _code_ in _globs_, _locs_""")
  File "<string>", line 1, in <module>
  File "conf.py", line 84, in <module>
    version = '.'.join(meta['version'].split('.')[:2])
KeyError: 'version'

Exception occurred:
  File "conf.py", line 84, in <module>
    version = '.'.join(meta['version'].split('.')[:2])
KeyError: 'version'
The full traceback has been saved in /tmp/sphinx-err-FzHqPN.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
```



Discussion:

Resolving patch:
diff --git a/docs/conf.py b/docs/conf.py
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -30,7 +30,7 @@
 # read version number (and other metadata) from package init
 init_fn = os.path.join(here, '..', 'letsencrypt', '__init__.py')
 with codecs.open(init_fn, encoding='utf8') as fd:
-    meta = dict(re.findall(r"""__([a-z]+)__ = "([^"]+)""", fd.read()))
+    meta = dict(re.findall(r"""__([a-z]+)__ = '([^']+)""", fd.read()))
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the


Test patch:
Repository: certbot/certbot

Issue:
renewer: fails to create directories
```
$ letsencrypt-renewer --config-dir /tmp/le/conf --work-dir /tmp/le/logs --logs-dir /tmp/le/logs
Traceback (most recent call last):
  File "/home/jakub/dev/letsencrypt/letsencrypt/venv/bin/letsencrypt-renewer", line 9, in <module>
    load_entry_point('letsencrypt==0.1', 'console_scripts', 'letsencrypt-renewer')()
  File "/home/jakub/dev/letsencrypt/letsencrypt/letsencrypt/renewer.py", line 149, in main
    for i in os.listdir(cli_config.renewal_configs_dir):
OSError: [Errno 2] No such file or directory: '/tmp/le/conf/renewal'
```



Discussion:

Resolving patch:
diff --git a/letsencrypt/renewer.py b/letsencrypt/renewer.py
--- a/letsencrypt/renewer.py
+++ b/letsencrypt/renewer.py
@@ -18,6 +18,7 @@
 
 from letsencrypt import account
 from letsencrypt import configuration
+from letsencrypt import constants
 from letsencrypt import colored_logging
 from letsencrypt import cli
 from letsencrypt import client
@@ -152,7 +153,8 @@ def main(config=None, cli_args=sys.argv[1:]):
 
     args = _create_parser().parse_args(cli_args)
 
-    le_util.make_or_verify_dir(args.logs_dir, 0o700, os.geteuid())
+    uid = os.geteuid()
+    le_util.make_or_verify_dir(args.logs_dir, 0o700, uid)
     cli.setup_logging(args, _cli_log_handler, logfile='renewer.log')
 
     cli_config = configuration.RenewerConfiguration(args)
@@ -166,6 +168,9 @@ def main(config=None, cli_args=sys.argv[1:]):
     # specify a config file on the command line, which, if provided, should
     # take precedence over this one.
     config.merge(configobj.ConfigObj(cli_config.renewer_config_file))
+    # Ensure that all of the needed folders have been created before continuing
+    le_util.make_or_verify_dir(
+            cli_config.work_dir, constants.CONFIG_DIRS_MODE, uid)
 
     for i in os.listdir(cli_config.renewal_configs_dir):
         print "Processing", i


Test patch:
Repository: certbot/certbot

Issue:
email address issues
1.) There is no explanation what the email is for. You should say something like "Please enter a valid email address for recovery purposes and notifications. We will not add it to your certificate nor will we share it. You can also leave this field empty, but that makes recovery harder."
1. ) Right now when an invalid email address is given, the error message says 'an unexpected error occured, please check the logfile'. This should be changed to something along the lines of "You gave an invalid email address. Please enter a valid email address for recovery purposes and notifications, or leave the field empty to give no email address".



Discussion:
Related to #414.


Resolving patch:
diff --git a/letsencrypt/display/ops.py b/letsencrypt/display/ops.py
--- a/letsencrypt/display/ops.py
+++ b/letsencrypt/display/ops.py
@@ -124,7 +124,7 @@ def get_email():
     """
     while True:
         code, email = zope.component.getUtility(interfaces.IDisplay).input(
-            "Enter email address")
+            "Enter email address (used for urgent notices and lost key recovery)")
 
         if code == display_util.OK:
             if le_util.safe_email(email):


Test patch:
Repository: certbot/certbot

Issue:
Possibility of infinite loop?
It seems unlikely to be a problem, but this [comment](https://github.com/letsencrypt/letsencrypt/blob/master/letsencrypt/auth_handler.py#L156) suggests the possibility of an infinite loop while solving challenges. I haven't had the time to look into the issue personally, but if this is true, it should be fixed.



Discussion:

Resolving patch:
diff --git a/letsencrypt/auth_handler.py b/letsencrypt/auth_handler.py
--- a/letsencrypt/auth_handler.py
+++ b/letsencrypt/auth_handler.py
@@ -153,10 +153,8 @@ def _send_responses(self, achalls, resps, chall_update):
         """
         active_achalls = []
         for achall, resp in itertools.izip(achalls, resps):
-            # XXX: make sure that all achalls, including those
-            # corresponding to None or False returned from
-            # Authenticator are removed from the queue and thus avoid
-            # infinite loop
+            # This line needs to be outside of the if block below to
+            # ensure failed challenges are cleaned up correctly
             active_achalls.append(achall)
 
             # Don't send challenges for None and False authenticator responses
diff --git a/letsencrypt/client.py b/letsencrypt/client.py
--- a/letsencrypt/client.py
+++ b/letsencrypt/client.py
@@ -329,8 +329,6 @@ def deploy_certificate(self, domains, privkey_path,
 
         with error_handler.ErrorHandler(self.installer.recovery_routine):
             for dom in domains:
-                # TODO: Provide a fullchain reference for installers like
-                #       nginx that want it
                 self.installer.deploy_cert(
                     domain=dom, cert_path=os.path.abspath(cert_path),
                     key_path=os.path.abspath(privkey_path),
diff --git a/letsencrypt/renewer.py b/letsencrypt/renewer.py
--- a/letsencrypt/renewer.py
+++ b/letsencrypt/renewer.py
@@ -95,7 +95,7 @@ def renew(cert, old_version):
         sans = crypto_util.get_sans_from_cert(f.read())
     new_certr, new_chain, new_key, _ = le_client.obtain_certificate(sans)
     if new_chain:
-        # XXX: Assumes that there was no key change.  We need logic
+        # XXX: Assumes that there was a key change.  We need logic
         #      for figuring out whether there was or not.  Probably
         #      best is to have obtain_certificate return None for
         #      new_key if the old key is to be used (since save_successor
@@ -180,7 +180,6 @@ def main(config=None, cli_args=sys.argv[1:]):
         rc_config = configobj.ConfigObj(cli_config.renewer_config_file)
         rc_config.merge(configobj.ConfigObj(
             os.path.join(cli_config.renewal_configs_dir, i)))
-        # TODO: this is a dirty hack!
         rc_config.filename = os.path.join(cli_config.renewal_configs_dir, i)
         try:
             # TODO: Before trying to initialize the RenewableCert object,


Test patch: