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

Issue:
Nginx plugin selection
We want to slowly roll out the Nginx plugin to make sure it's working for people. To do this we should:
- Mark the nginx plugin as hidden (we did this for the manual plugin)
- Disable automatic selection if it's the only available configurator (if not already the case, we should disable automatic selection of hidden plugins).
- Make sure the description of the Nginx plugin is sane (it used to say it was broken).



Discussion:

Resolving patch:
diff --git a/certbot-nginx/certbot_nginx/configurator.py b/certbot-nginx/certbot_nginx/configurator.py
--- a/certbot-nginx/certbot_nginx/configurator.py
+++ b/certbot-nginx/certbot_nginx/configurator.py
@@ -55,7 +55,9 @@ class NginxConfigurator(common.Plugin):
 
     """
 
-    description = "Nginx Web Server - currently doesn't work"
+    description = "Nginx Web Server plugin - Alpha"
+
+    hidden = True
 
     @classmethod
     def add_parser_arguments(cls, add):


Test patch:
Repository: certbot/certbot

Issue:
"No installers present" message is confusing.
```
No installers seem to be present and working on your system; fix that or try running certbot with the "certonly" command
```

This is one of the most common messages, received when running certbot on an Nginx installation, but it is confusing to a new user. What's an installer? Is it my mistake or certbot's that there are no installers? What does "certonly" do?

Instead how about:

```
Certbot doesn't know how to automatically configure the web server on this system. However, it can still get a certificate for you. Please run "certbot[-auto] certonly" to do so. You'll need to manually configure your web server to use the resulting certificate.
```



Discussion:
This won't be a usefull comment but just to let know that I ended up on this page and it helped me.
So it may indeed be a good idea to change the message.

We also had #1576 which is the same issue and was supposedly fixed by #3250, however, the only clarification made to installers is to add change it to "installer plugins".

We've had conversations in the past whether we should try to explain to our users what terminology like [installer](https://certbot.eff.org/docs/contributing.html#installer) means in the context of Certbot or hide such jargon entirely. Probably some combination of the two is the best approach.

@bmw: What do you think of my proposed verbiage above?

Oh, @Mathsoum thanks for mentioning that this was useful to you, that is in fact helpful to know!

I think it's good. It doesn't hint at the possibility that you're just missing a plugin in order to get automatic installation, but that might be a lot to fit into one error message.


Resolving patch:
diff --git a/certbot/plugins/selection.py b/certbot/plugins/selection.py
--- a/certbot/plugins/selection.py
+++ b/certbot/plugins/selection.py
@@ -261,9 +261,12 @@ def diagnose_configurator_problem(cfg_type, requested, plugins):
                    "your existing configuration.\nThe error was: {1!r}"
                    .format(requested, plugins[requested].problem))
     elif cfg_type == "installer":
-        msg = ('No installer plugins seem to be present and working on your system; '
-               'fix that or try running certbot with the "certonly" command to obtain'
-               ' a certificate you can install manually')
+        from certbot.cli import cli_command
+        msg = ('Certbot doesn\'t know how to automatically configure the web '
+          'server on this system. However, it can still get a certificate for '
+          'you. Please run "{0} certonly" to do so. You\'ll need to '
+          'manually configure your web server to use the resulting '
+          'certificate.').format(cli_command)
     else:
         msg = "{0} could not be determined or is not installed".format(cfg_type)
     raise errors.PluginSelectionError(msg)


Test patch:
Repository: certbot/certbot

Issue:
Remove get_all_keys_certs() from interfaces.py
We don't use it and we have no plans to immediately do so. Let's simply the plugin interface.


Discussion:

Resolving patch:
diff --git a/certbot/interfaces.py b/certbot/interfaces.py
--- a/certbot/interfaces.py
+++ b/certbot/interfaces.py
@@ -300,19 +300,6 @@ def supported_enhancements():
 
         """
 
-    def get_all_certs_keys():
-        """Retrieve all certs and keys set in configuration.
-
-        :returns: tuples with form `[(cert, key, path)]`, where:
-
-            - `cert` - str path to certificate file
-            - `key` - str path to associated key file
-            - `path` - file path to configuration file
-
-        :rtype: list
-
-        """
-
     def save(title=None, temporary=False):
         """Saves all changes to the configuration files.
 
diff --git a/certbot/plugins/null.py b/certbot/plugins/null.py
--- a/certbot/plugins/null.py
+++ b/certbot/plugins/null.py
@@ -40,9 +40,6 @@ def enhance(self, domain, enhancement, options=None):
     def supported_enhancements(self):
         return []
 
-    def get_all_certs_keys(self):
-        return []
-
     def save(self, title=None, temporary=False):
         pass  # pragma: no cover
 


Test patch:
diff --git a/certbot/plugins/null_test.py b/certbot/plugins/null_test.py
--- a/certbot/plugins/null_test.py
+++ b/certbot/plugins/null_test.py
@@ -15,7 +15,6 @@ def test_it(self):
         self.assertTrue(isinstance(self.installer.more_info(), str))
         self.assertEqual([], self.installer.get_all_names())
         self.assertEqual([], self.installer.supported_enhancements())
-        self.assertEqual([], self.installer.get_all_certs_keys())
 
 
 if __name__ == "__main__":
Repository: certbot/certbot

Issue:
`certbot-auto --version` still says `letsencrypt 0.9.3` (should say `certbot 0.9.3`?)
Given the systematic renaming of this client from `letsencrypt` to `certbot` some while ago, I was surprised to receive this output:

```
$ certbot-auto --version
letsencrypt 0.9.3
```

I.e. the software still refers to itself as `letsencrypt` instead of `certbot`.

In case it is not desired (which I think so), I am letting you know.



Discussion:
I was also surprised by this output reading the issue, however, I've repoed the problem and know the cause. If you're curious, `certbot-auto` still installs the shim package `letsencrypt` for backwards compatibility. It also uses the command `letsencrypt` to call into Certbot for no other reason than we saw no reason to change it. Turns out that `argv[0]` is used to print the version string, so when calling into Certbot through the `letsencrypt` shim, you see `letsencrypt` rather than `certbot`.

This is a one line fix and will be changed in our next release. Thanks for reporting the problem.

@bmw I have submitted a pull request to resolve this issue. I have solved it by setting `argparse`'s `prog` attribute to "certbot". This was a one line change, so it seemed to be what you referred to. The other way that occurred to me was to modify `letsencrypt-auto-source.template` to call the `certbot` script instead of `letsencrypt`. However, that seemed a bit more difficult and I probably don't understand the `letsencrypt-auto-source` script well enough to do that at this point.


Resolving patch:
diff --git a/certbot/cli.py b/certbot/cli.py
--- a/certbot/cli.py
+++ b/certbot/cli.py
@@ -335,6 +335,7 @@ def __init__(self, args, plugins, detect_defaults=False):
         self.help_topics = HELP_TOPICS + plugin_names + [None]
         usage, short_usage = usage_strings(plugins)
         self.parser = configargparse.ArgParser(
+            prog="certbot",
             usage=short_usage,
             formatter_class=argparse.ArgumentDefaultsHelpFormatter,
             args_for_setting_config_path=["-c", "--config"],


Test patch:
diff --git a/certbot/tests/cli_test.py b/certbot/tests/cli_test.py
--- a/certbot/tests/cli_test.py
+++ b/certbot/tests/cli_test.py
@@ -143,6 +143,21 @@ def test_help(self):
         out = self._help_output(['-h'])
         self.assertTrue(cli.usage_strings(plugins)[0] in out)
 
+    def test_version_string_program_name(self):
+        toy_out = six.StringIO()
+        toy_err = six.StringIO()
+        with mock.patch('certbot.main.sys.stdout', new=toy_out):
+            with mock.patch('certbot.main.sys.stderr', new=toy_err):
+                try:
+                    main.main(["--version"])
+                except SystemExit:
+                    pass
+                finally:
+                    output = toy_out.getvalue() or toy_err.getvalue()
+                    self.assertTrue("certbot" in output, "Output is {0}".format(output))
+        toy_out.close()
+        toy_err.close()
+
     def _cli_missing_flag(self, args, message):
         "Ensure that a particular error raises a missing cli flag error containing message"
         exc = None
Repository: certbot/certbot

Issue:
Git master certbot is making executable renewal conf files?
I recently added an additional cert on my test system, and then noticed that the renewal conf file was executable!

```
ubuntu@isnot:/etc/letsencrypt/renewal$ ls -lF
total 20
-rw-r--r-- 1 root root  431 Oct  4 22:30 demo.reworld.org.conf
-rw-r--r-- 1 root root 1566 Dec  2  2015 goxogle.com.conf
-rw-r--r-- 1 root root  423 Oct  4 22:30 isnot.org-0001.conf
-rw-r--r-- 1 root root  453 Oct 27 23:14 isnot.org.conf
-rwxr-xr-x 1 root root  533 Dec  1 00:50 www.isnot.org.conf*
```


Discussion:

Resolving patch:
diff --git a/certbot/util.py b/certbot/util.py
--- a/certbot/util.py
+++ b/certbot/util.py
@@ -181,7 +181,7 @@ def unique_file(path, chmod=0o777, mode="w"):
         count=0, chmod=chmod, mode=mode)
 
 
-def unique_lineage_name(path, filename, chmod=0o777, mode="w"):
+def unique_lineage_name(path, filename, chmod=0o644, mode="w"):
     """Safely finds a unique file using lineage convention.
 
     :param str path: directory path


Test patch:
Repository: certbot/certbot

Issue:
Mention line in (Apache) conf file in case of Augeas parse/syntax error
See also the community thread [Certbot renew fails on current fedora 24 w/ apache](https://community.letsencrypt.org/t/certbot-renew-fails-on-current-fedora-24-w-apache/25046).

In summary:

When a syntax/parse error occurs when Augeas tries to parse Apache configuration files, `certbot` raises an error and mentions the file in question and the Augeaus error message.

Unfortunately, the *message* itself doesn't contain a line number, so the user has to spit through all the lines, perhaps not even knowing why Augeas complains in the first place. It would be very helpful if the error message also would contain a line number.

On [some blog post](https://stomp.colorado.edu/blog/blog/2011/01/07/on-finding-and-fixing-augeas-parse-errors/) I found Augeas does provide a line number, but this is separate from the message. And `certbot` [only fetches the message, not the line number](https://github.com/certbot/certbot/blob/master/certbot-apache/certbot_apache/augeas_configurator.py#L73).

Could we, for example, change the code to something like:

                msg = (
                    "There has been an error in parsing the file %s on line %s: %s",
                    # Strip off /augeas/files and /error
                    path[13:len(path) - 6], self.aug.get(path + "/line"), self.aug.get(path + "/message"))

If deemed helpful, would it need a check if there's a line number present in the Augeas error? Or does it always come with a line number? (I'm not familiar with Augeas...)

(Untested code by the way :stuck_out_tongue:)


Discussion:
@osirisinferi test it and send us a PR!

Resolving patch:
diff --git a/certbot-apache/certbot_apache/augeas_configurator.py b/certbot-apache/certbot_apache/augeas_configurator.py
--- a/certbot-apache/certbot_apache/augeas_configurator.py
+++ b/certbot-apache/certbot_apache/augeas_configurator.py
@@ -68,9 +68,12 @@ def check_parsing_errors(self, lens):
             # As aug.get may return null
             if lens_path and lens in lens_path:
                 msg = (
-                    "There has been an error in parsing the file (%s): %s",
+                    "There has been an error in parsing the file {0} on line {1}: "
+                    "{2}".format(
                     # Strip off /augeas/files and /error
-                    path[13:len(path) - 6], self.aug.get(path + "/message"))
+                    path[13:len(path) - 6],
+                    self.aug.get(path + "/line"),
+                    self.aug.get(path + "/message")))
                 raise errors.PluginError(msg)
 
     # TODO: Cleanup this function


Test patch:
Repository: certbot/certbot

Issue:
Incorrect success condition in nginx
`Cannot find a cert or key directive in /etc/nginx/sites-enabled/site.conf for set(['sitecom']). VirtualHost was not modified.`

After getting this message, we still ask about Easy or Secure, and then print a success message. That is incorrect.



Discussion:
```
server {
  listen 443 ssl;
  server_name site.com;
}
```

Resolving patch:
diff --git a/certbot-nginx/certbot_nginx/configurator.py b/certbot-nginx/certbot_nginx/configurator.py
--- a/certbot-nginx/certbot_nginx/configurator.py
+++ b/certbot-nginx/certbot_nginx/configurator.py
@@ -191,11 +191,9 @@ def deploy_cert(self, domain, cert_path, key_path,
                         vhost.filep, vhost.names)
         except errors.MisconfigurationError as error:
             logger.debug(error)
-            logger.warning(
-                "Cannot find a cert or key directive in %s for %s. "
-                "VirtualHost was not modified.", vhost.filep, vhost.names)
             # Presumably break here so that the virtualhost is not modified
-            return False
+            raise errors.PluginError("Cannot find a cert or key directive in {0} for {1}. "
+                "VirtualHost was not modified.".format(vhost.filep, vhost.names))
 
         self.save_notes += ("Changed vhost at %s with addresses of %s\n" %
                             (vhost.filep,
diff --git a/certbot/client.py b/certbot/client.py
--- a/certbot/client.py
+++ b/certbot/client.py
@@ -376,7 +376,8 @@ def deploy_certificate(self, domains, privkey_path,
 
         chain_path = None if chain_path is None else os.path.abspath(chain_path)
 
-        with error_handler.ErrorHandler(self.installer.recovery_routine):
+        msg = ("Unable to install the certificate")
+        with error_handler.ErrorHandler(self._recovery_routine_with_msg, msg):
             for dom in domains:
                 self.installer.deploy_cert(
                     domain=dom, cert_path=os.path.abspath(cert_path),


Test patch:
diff --git a/certbot-nginx/certbot_nginx/tests/configurator_test.py b/certbot-nginx/certbot_nginx/tests/configurator_test.py
--- a/certbot-nginx/certbot_nginx/tests/configurator_test.py
+++ b/certbot-nginx/certbot_nginx/tests/configurator_test.py
@@ -158,6 +158,18 @@ def test_deploy_cert_requires_fullchain_path(self):
             "example/chain.pem",
             None)
 
+    @mock.patch('certbot_nginx.parser.NginxParser.add_server_directives')
+    def test_deploy_cert_raise_on_add_error(self, mock_add_server_directives):
+        mock_add_server_directives.side_effect = errors.MisconfigurationError()
+        self.assertRaises(
+            errors.PluginError,
+            self.config.deploy_cert,
+            "migration.com",
+            "example/cert.pem",
+            "example/key.pem",
+            "example/chain.pem",
+            "example/fullchain.pem")
+
     def test_deploy_cert(self):
         server_conf = self.config.parser.abs_path('server.conf')
         nginx_conf = self.config.parser.abs_path('nginx.conf')
Repository: certbot/certbot

Issue:
Put update_symlinks in certbot --help manage



Discussion:

Resolving patch:
diff --git a/certbot/cli.py b/certbot/cli.py
--- a/certbot/cli.py
+++ b/certbot/cli.py
@@ -383,7 +383,7 @@ def _get_help_string(self, action):
         "opts": 'Options for for the "plugins" subcommand'
     }),
     ("update_symlinks", {
-        "short": "Recreate symlinks in your /live/ directory",
+        "short": "Recreate symlinks in your /etc/letsencrypt/live/ directory",
         "opts": ("Recreates cert and key symlinks in {0}, if you changed them by hand "
                  "or edited a renewal configuration file".format(
                   os.path.join(flag_default("config_dir"), "live")))
@@ -780,7 +780,7 @@ def _add_all_groups(helpful):
     helpful.add_group("paths", description="Arguments changing execution paths & servers")
     helpful.add_group("manage",
         description="Various subcommands and flags are available for managing your certificates:",
-        verbs=["certificates", "delete", "renew", "revoke"])
+        verbs=["certificates", "delete", "renew", "revoke", "update_symlinks"])
 
     # VERBS
     for verb, docs in VERB_HELP:


Test patch:
Repository: certbot/certbot

Issue:
Remove extra space introduced by #3994
An extra space was introduced in the error message in #3994.  It should be removed.  
Remove extra space introduced by #3994
An extra space was introduced in the error message in #3994.  It should be removed.  
Error message for empty domain name is incorrect
In a recent commit that [Fix FQDN checks](https://github.com/certbot/certbot/commit/6156b452bcf7c924f12c334e7094ff5a9049ee37),
 the error message fails to address the case where domain name is an empty string. See below.

`--domain` is a CSV string, but the 2nd DNS name is parsed to be an empty string, which caused 
and error message `Requested domain  is not a FQDN because label  is too long.`. 

It would have been more logically to say `Requested domain "" is not a FQDN because label  is either empty or too long.`

The check it failed is here: https://github.com/certbot/certbot/blob/6156b452bcf7c924f12c334e7094ff5a9049ee37/certbot/util.py#L432

``` bash
$ docker run --rm -it --entrypoint bash quay.io/letsencrypt/letsencrypt:latest
root@4b80271cdd6c:/opt/certbot# certbot certonly \
>     --webroot \
>     --non-interactive \
>     --agree-tos \
>     --email test@test.com \
>     --webroot-path /var/lib/letsencrypt \
>     --domain www.example.com,,test1.example.com \
>     --no-verify-ssl \
>     --debug \
>    --test-cert
Requested domain  is not a FQDN because label  is too long.
```



Discussion:


@pde I suppose I could help to fix this - any pointers for the contributing guidelines? Much appreciated!

Taken.

@jpluimers Good news. But by whom? Shouldn't this be mentioned so that an association can be established?

I've taken it (;

#3445 still needs a bit of work. Just commenting here to keep the issue up to date in case anyone else would like to take this issue.


Resolving patch:
diff --git a/certbot/util.py b/certbot/util.py
--- a/certbot/util.py
+++ b/certbot/util.py
@@ -478,9 +478,9 @@ def enforce_domain_sanity(domain):
     # FQDN checks according to RFC 2181: domain name should be less than 255
     # octets (inclusive). And each label is 1 - 63 octets (inclusive).
     # https://tools.ietf.org/html/rfc2181#section-11
-    msg = "Requested domain {0} is not a FQDN because ".format(domain)
+    msg = "Requested domain {0} is not a FQDN because".format(domain)
     if len(domain) > 255:
-        raise errors.ConfigurationError(msg + "it is too long.")
+        raise errors.ConfigurationError("{0} it is too long.".format(msg))
     labels = domain.split('.')
     for l in labels:
         if not l:


Test patch:
Repository: certbot/certbot

Issue:
IndexError: list index out of range
I got an error when running ./certbot-auto for letsencrypt: 

> IndexError: list index out of range

certbot.log showed:

> Traceback (most recent call last):
>   File "/root/.local/share/letsencrypt/bin/letsencrypt", line 11, in <module>
>     sys.exit(main())
>   File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot/main.py", line 861, in main
>     args = cli.prepare_and_parse_args(plugins, cli_args)
>   File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot/cli.py", line 814, in prepare_and_parse_args
>     helpful = HelpfulArgumentParser(args, plugins, detect_defaults)
>   File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot/cli.py", line 442, in __init__
>     if self.args[0] == 'help':
> IndexError: list index out of range


Discussion:
Thanks for reporting this. I've repoed the problem and I'll be releasing 0.11.1 shortly.

Resolving patch:
diff --git a/certbot/cli.py b/certbot/cli.py
--- a/certbot/cli.py
+++ b/certbot/cli.py
@@ -439,7 +439,7 @@ def __init__(self, args, plugins, detect_defaults=False):
         self.detect_defaults = detect_defaults
         self.args = args
 
-        if self.args[0] == 'help':
+        if self.args and self.args[0] == 'help':
             self.args[0] = '--help'
 
         self.determine_verb()


Test patch:
diff --git a/certbot/tests/cli_test.py b/certbot/tests/cli_test.py
--- a/certbot/tests/cli_test.py
+++ b/certbot/tests/cli_test.py
@@ -60,6 +60,11 @@ def _help_output(self, args):
                 self.assertRaises(SystemExit, self.parse, args, output)
         return output.getvalue()
 
+    def test_no_args(self):
+        namespace = self.parse([])
+        for d in ('config_dir', 'logs_dir', 'work_dir'):
+            self.assertEqual(getattr(namespace, d), cli.flag_default(d))
+
     def test_install_abspath(self):
         cert = 'cert'
         key = 'key'
Repository: certbot/certbot

Issue:
Plugin renewalparams not saved in renewal config files
I'm using the s3front plugin and I set various args via the commandline (e.g. --certbot-s3front:auth-s3-bucket). However, these args are not saved in the renewal config file. So when certbot detects the cert needs renewing it fails as no args for the plugin were given.

Any ideas why this is?

(using 0.11.1)


Discussion:
Example of args saved in a renewal file:

```
[renewalparams]
installer = certbot-s3front:installer
config_dir = ...
authenticator = certbot-s3front:auth
account = ...
logs_dir = ...
```
But no `certbot-s3front:auth-s3-bucket` even though it was used in creating the cert.
@bmw any idea how we should be handling this?
We should be saving these values not dropping them.

Thanks for reporting the bug @code-tree. I've reproduced it and am working on a fix now.

Resolving patch:
diff --git a/certbot/storage.py b/certbot/storage.py
--- a/certbot/storage.py
+++ b/certbot/storage.py
@@ -19,6 +19,9 @@
 from certbot import error_handler
 from certbot import util
 
+from certbot.plugins import common as plugins_common
+from certbot.plugins import disco as plugins_disco
+
 logger = logging.getLogger(__name__)
 
 ALL_FOUR = ("cert", "privkey", "chain", "fullchain")
@@ -179,13 +182,12 @@ def _relevant(option):
 
     :rtype: bool
     """
-    # The list() here produces a list of the plugin names as strings.
     from certbot import renewal
-    from certbot.plugins import disco as plugins_disco
-    plugins = list(plugins_disco.PluginsRegistry.find_all())
+    plugins = plugins_disco.PluginsRegistry.find_all()
+    namespaces = [plugins_common.dest_namespace(plugin) for plugin in plugins]
 
     return (option in renewal.CONFIG_ITEMS or
-            any(option.startswith(x + "_") for x in plugins))
+            any(option.startswith(namespace) for namespace in namespaces))
 
 
 def relevant_values(all_values):


Test patch:
diff --git a/certbot/tests/storage_test.py b/certbot/tests/storage_test.py
--- a/certbot/tests/storage_test.py
+++ b/certbot/tests/storage_test.py
@@ -581,6 +581,15 @@ def test_relevant_values_str(self):
         self.assertEqual(
             self._test_relevant_values_common(values), values)
 
+    @mock.patch("certbot.cli.set_by_cli")
+    @mock.patch("certbot.plugins.disco.PluginsRegistry.find_all")
+    def test_relevant_values_namespace(self, mock_find_all, mock_set_by_cli):
+        mock_set_by_cli.return_value = True
+        mock_find_all.return_value = ["certbot-foo:bar"]
+        values = {"certbot_foo:bar_baz": 42}
+        self.assertEqual(
+            self._test_relevant_values_common(values), values)
+
     @mock.patch("certbot.storage.relevant_values")
     def test_new_lineage(self, mock_rv):
         """Test for new_lineage() class method."""