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

Issue:
--register-unsafely-without-email prints message even with --quiet
## My operating system is (include version):

Ubuntu 16.04

## I installed Certbot with (certbot-auto, OS package manager, pip, etc):

`sudo pip install certbot`

## I ran this command and it produced this output:

```
$ certbot register --non-interactive --quiet --agree-tos --register-unsafely-without-email
Registering without email!
```

## Certbot's behavior differed from what I expected because:

From `certbot --help all`:

```
  -q, --quiet           Silence all output except errors. Useful for
                        automation via cron. Implies --non-interactive.
                        (default: False)
```

## Here is a Certbot log showing the issue (if available):
###### Logs are stored in `/var/log/letsencrypt` by default. Feel free to redact domains, e-mail and IP addresses as you see fit.



Discussion:
ooh - seems like a bug in --quiet, pinging @ohemorange, do you think this is an easy fix?
Yup, this is a bug, and should definitely be an easy fix.

Resolving patch:
diff --git a/certbot/client.py b/certbot/client.py
--- a/certbot/client.py
+++ b/certbot/client.py
@@ -118,7 +118,7 @@ def register(config, account_storage, tos_cb=None):
             logger.warning(msg)
             raise errors.Error(msg)
         if not config.dry_run:
-            logger.warning("Registering without email!")
+            logger.info("Registering without email!")
 
     # Each new registration shall use a fresh new key
     key = jose.JWKRSA(key=jose.ComparableRSAKey(


Test patch:
diff --git a/certbot/tests/client_test.py b/certbot/tests/client_test.py
--- a/certbot/tests/client_test.py
+++ b/certbot/tests/client_test.py
@@ -102,7 +102,7 @@ def test_without_email(self, mock_logger):
                     self.config.register_unsafely_without_email = True
                     self.config.dry_run = False
                     self._call()
-                    mock_logger.warning.assert_called_once_with(mock.ANY)
+                    mock_logger.info.assert_called_once_with(mock.ANY)
                     self.assertTrue(mock_handle.called)
 
     def test_unsupported_error(self):
Repository: certbot/certbot

Issue:
Preserve permissions on renewal conf files during renewal
Ensure that permissions are preserved when renewal data is written to conf files. This allows users to limit access to the file, if they wish.

See #4430.


Discussion:

Resolving patch:
diff --git a/certbot/storage.py b/certbot/storage.py
--- a/certbot/storage.py
+++ b/certbot/storage.py
@@ -4,6 +4,7 @@
 import logging
 import os
 import re
+import stat
 
 import configobj
 import parsedatetime
@@ -117,10 +118,20 @@ def write_renewal_config(o_filename, n_filename, archive_dir, target, relevant_d
     # TODO: add human-readable comments explaining other available
     #       parameters
     logger.debug("Writing new config %s.", n_filename)
+
+    # Ensure that the file exists
+    open(n_filename, 'a').close()
+
+    # Copy permissions from the old version of the file, if it exists.
+    if os.path.exists(o_filename):
+        current_permissions = stat.S_IMODE(os.lstat(o_filename).st_mode)
+        os.chmod(n_filename, current_permissions)
+
     with open(n_filename, "wb") as f:
         config.write(outfile=f)
     return config
 
+
 def rename_renewal_config(prev_name, new_name, cli_config):
     """Renames cli_config.certname's config to cli_config.new_certname.
 


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
@@ -3,6 +3,7 @@
 import datetime
 import os
 import shutil
+import stat
 import unittest
 
 import configobj
@@ -758,13 +759,16 @@ def test_write_renewal_config(self):
         with open(temp, "w") as f:
             f.write("[renewalparams]\nuseful = value # A useful value\n"
                     "useless = value # Not needed\n")
+        os.chmod(temp, 0o640)
         target = {}
         for x in ALL_FOUR:
             target[x] = "somewhere"
         archive_dir = "the_archive"
         relevant_data = {"useful": "new_value"}
+
         from certbot import storage
         storage.write_renewal_config(temp, temp2, archive_dir, target, relevant_data)
+
         with open(temp2, "r") as f:
             content = f.read()
         # useful value was updated
@@ -775,6 +779,9 @@ def test_write_renewal_config(self):
         self.assertTrue("useless" not in content)
         # check version was stored
         self.assertTrue("version = {0}".format(certbot.__version__) in content)
+        # ensure permissions are copied
+        self.assertEqual(stat.S_IMODE(os.lstat(temp).st_mode),
+                         stat.S_IMODE(os.lstat(temp2).st_mode))
 
     def test_update_symlinks(self):
         from certbot import storage
Repository: certbot/certbot

Issue:
/etc/nginx.conf should probably be /etc/nginx/nginx.conf
https://github.com/certbot/certbot/blob/master/certbot-nginx/certbot_nginx/configurator.py#L821


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
@@ -820,7 +820,7 @@ def cleanup(self, achalls):
             self.restart()
 
 
-def nginx_restart(nginx_ctl, nginx_conf="/etc/nginx.conf"):
+def nginx_restart(nginx_ctl, nginx_conf):
     """Restarts the Nginx Server.
 
     .. todo:: Nginx restart is fatal if the configuration references


Test patch:
Repository: certbot/certbot

Issue:
Cannot find Apache control command apache2ctl on Arch Linux
I have this problem when using certbot for apache following this guide http://letsencrypt.readthedocs.io/en/latest/using.html#apache

```
$ sudo certbot --apache
Saving debug log to /var/log/letsencrypt/letsencrypt.log
Failed to find apache2ctl in expanded PATH: /usr/local/sbin:/usr/local/bin:/usr/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/usr/sbin
The apache plugin is not working; there may be problems with your existing configuration.
The error was: NoInstallationError('Cannot find Apache control command apache2ctl',)
```
I am on Arch Linux, and it seems that there is no apache2ctl for Arch but certbot requires it?

I tried to installed it but no luck:

```
$ sudo pacman -S apache2
error: target not found: apache2
```

My Apache's version:

```
$ httpd -v
Server version: Apache/2.4.25 (Unix)
Server built:   Dec 20 2016 13:02:2
```



Discussion:

Resolving patch:
diff --git a/certbot-apache/certbot_apache/constants.py b/certbot-apache/certbot_apache/constants.py
--- a/certbot-apache/certbot_apache/constants.py
+++ b/certbot-apache/certbot_apache/constants.py
@@ -110,6 +110,24 @@
     MOD_SSL_CONF_SRC=pkg_resources.resource_filename(
         "certbot_apache", "options-ssl-apache.conf")
 )
+CLI_DEFAULTS_ARCH = dict(
+    server_root="/etc/httpd",
+    vhost_root="/etc/httpd/conf",
+    vhost_files="*.conf",
+    logs_root="/var/log/httpd",
+    version_cmd=['apachectl', '-v'],
+    define_cmd=['apachectl', '-t', '-D', 'DUMP_RUN_CFG'],
+    restart_cmd=['apachectl', 'graceful'],
+    conftest_cmd=['apachectl', 'configtest'],
+    enmod=None,
+    dismod=None,
+    le_vhost_ext="-le-ssl.conf",
+    handle_mods=False,
+    handle_sites=False,
+    challenge_location="/etc/httpd/conf",
+    MOD_SSL_CONF_SRC=pkg_resources.resource_filename(
+        "certbot_apache", "options-ssl-apache.conf")
+)
 CLI_DEFAULTS = {
     "default": CLI_DEFAULTS_DEFAULT,
     "debian": CLI_DEFAULTS_DEBIAN,
@@ -125,6 +143,7 @@
     "darwin": CLI_DEFAULTS_DARWIN,
     "opensuse": CLI_DEFAULTS_SUSE,
     "suse": CLI_DEFAULTS_SUSE,
+    "arch": CLI_DEFAULTS_ARCH,
 }
 """CLI defaults."""
 


Test patch:
Repository: certbot/certbot

Issue:
Don't mention locations of CSR and privkey
It seems like users are getting confused at least sometimes by Certbot's mention of how it's created a private key and CSR (*not* in the `live` directory!)

https://community.letsencrypt.org/t/trouble-renewing-with-secondary-domains/32806

I would suggest that we change these messages so they at least don't print a full file path, since almost nobody will manage to use these files productively. I think the particular trouble is

https://github.com/certbot/certbot/blob/master/certbot/crypto_util.py#L63

and

https://github.com/certbot/certbot/blob/master/certbot/crypto_util.py#L98


Discussion:

Resolving patch:
diff --git a/certbot/crypto_util.py b/certbot/crypto_util.py
--- a/certbot/crypto_util.py
+++ b/certbot/crypto_util.py
@@ -54,13 +54,13 @@ def init_save_key(key_size, key_dir, keyname="key-certbot.pem"):
                             config.strict_permissions)
     if config.dry_run:
         key_path = None
-        logger.info("Generating key (%d bits), not saving to file", key_size)
+        logger.debug("Generating key (%d bits), not saving to file", key_size)
     else:
         key_f, key_path = util.unique_file(
             os.path.join(key_dir, keyname), 0o600, "wb")
         with key_f:
             key_f.write(key_pem)
-        logger.info("Generating key (%d bits): %s", key_size, key_path)
+        logger.debug("Generating key (%d bits): %s", key_size, key_path)
 
     return util.Key(key_path, key_pem)
 
@@ -89,13 +89,13 @@ def init_save_csr(privkey, names, path):
                                config.strict_permissions)
     if config.dry_run:
         csr_filename = None
-        logger.info("Creating CSR: not saving to file")
+        logger.debug("Creating CSR: not saving to file")
     else:
         csr_f, csr_filename = util.unique_file(
             os.path.join(path, "csr-certbot.pem"), 0o644, "wb")
         with csr_f:
             csr_f.write(csr_pem)
-        logger.info("Creating CSR: %s", csr_filename)
+        logger.debug("Creating CSR: %s", csr_filename)
 
     return util.CSR(csr_filename, csr_pem, "pem")
 


Test patch:
Repository: certbot/certbot

Issue:
Simplify http instructions in manual plugin
Right now when you run the manual plugin for an HTTP challenge, you get the following message:

```
Make sure your web server displays the following content at
http://4544ad.com/.well-known/acme-challenge/UlK01OTOxzjsZO74kSzj53goMdIaJKlf6xEVoAlImBE before continuing:

UlK01OTOxzjsZO74kSzj53goMdIaJKlf6xEVoAlImBE.W1iiTykicy7OqjL-Fu3XxEut3RTonSfTtbV6mRA2u4g

If you don't have HTTP server configured, you can run the following
command on the target server (as root):

mkdir -p /tmp/certbot/public_html/.well-known/acme-challenge
cd /tmp/certbot/public_html
printf "%s" UlK01OTOxzjsZO74kSzj53goMdIaJKlf6xEVoAlImBE.W1iiTykicy7OqjL-Fu3XxEut3RTonSfTtbV6mRA2u4g > .well-known/acme-challenge/UlK01OTOxzjsZO74kSzj53goMdIaJKlf6xEVoAlImBE
# run only once per server:
$(command -v python2 || command -v python2.7 || command -v python2.6) -c \
"import BaseHTTPServer, SimpleHTTPServer; \
s = BaseHTTPServer.HTTPServer(('', 5002), SimpleHTTPServer.SimpleHTTPRequestHandler); \
s.serve_forever()" 
```

I would argue that the code at the bottom is visual noise and distracts from the more important information up top. I also think that most people using the manual plugin with the HTTP challenge don't want these instructions to set up a Python server, because they are probably planning to push the challenge file to an already-running web server of some sort.

I think we should rip out everything below "If you don't have...". Note that the integration tests, last I checked, expect to parse out this message and run it, so that integration test will need to be updated.


Discussion:
Also, "Make sure your web server displays the following content at" is ambiguous. Should I expect that my web server already displays that content, and I'm just double-checking? We should update this message to say something like "put a file containing this data on your web server at this url."

Resolving patch:
diff --git a/certbot/plugins/manual.py b/certbot/plugins/manual.py
--- a/certbot/plugins/manual.py
+++ b/certbot/plugins/manual.py
@@ -44,22 +44,14 @@ class Authenticator(common.Plugin):
 
 Before continuing, verify the record is deployed."""
     _HTTP_INSTRUCTIONS = """\
-Make sure your web server displays the following content at
-{uri} before continuing:
+Create a file containing just this data:
 
 {validation}
 
-If you don't have HTTP server configured, you can run the following
-command on the target server (as root):
-
-mkdir -p /tmp/certbot/public_html/{achall.URI_ROOT_PATH}
-cd /tmp/certbot/public_html
-printf "%s" {validation} > {achall.URI_ROOT_PATH}/{encoded_token}
-# run only once per server:
-$(command -v python2 || command -v python2.7 || command -v python2.6) -c \\
-"import BaseHTTPServer, SimpleHTTPServer; \\
-s = BaseHTTPServer.HTTPServer(('', {port}), SimpleHTTPServer.SimpleHTTPRequestHandler); \\
-s.serve_forever()" """
+And make it available on your web server at this URL:
+
+{uri}
+"""
 
     def __init__(self, *args, **kwargs):
         super(Authenticator, self).__init__(*args, **kwargs)


Test patch:
Repository: certbot/certbot

Issue:
bad text formatting in manual domain prompt
There are two problems going on with the manual prompts. One is that there are two spaces between the prompt determined by ops.py and the prompt from utils.py this is likely because it joins them at some point with a space. Additionally the space at the end (after the colon) is stripped. 
Below is an example of the text as just given to me on my server:

Please enter in your domain name(s) (comma and/or space separated)  (Enter 'c'
to cancel):x.example.com



Discussion:

Resolving patch:
diff --git a/certbot/display/util.py b/certbot/display/util.py
--- a/certbot/display/util.py
+++ b/certbot/display/util.py
@@ -176,12 +176,9 @@ def input(self, message, default=None,
         if self._return_default(message, default, cli_flag, force_interactive):
             return OK, default
 
-        ans = input_with_timeout(
-            textwrap.fill(
-                "%s (Enter 'c' to cancel): " % message,
-                80,
-                break_long_words=False,
-                break_on_hyphens=False))
+        # Trailing space must be added outside of _wrap_lines to be preserved
+        message = _wrap_lines("%s (Enter 'c' to cancel):" % message) + " "
+        ans = input_with_timeout(message)
 
         if ans == "c" or ans == "C":
             return CANCEL, "-1"
@@ -392,12 +389,8 @@ def _print_menu(self, message, choices):
 
         # Write out the menu choices
         for i, desc in enumerate(choices, 1):
-            self.outfile.write(
-                textwrap.fill(
-                    "{num}: {desc}".format(num=i, desc=desc),
-                    80,
-                    break_long_words=False,
-                    break_on_hyphens=False))
+            msg = "{num}: {desc}".format(num=i, desc=desc)
+            self.outfile.write(_wrap_lines(msg))
 
             # Keep this outside of the textwrap
             self.outfile.write(os.linesep)


Test patch:
Repository: certbot/certbot

Issue:
Nginx should give a prompt when it can't find a server_name
When the nginx plugin can't find a server name it doesn't give you any
advice on what to do. It should tell you to add a server_name directive
to your nginx config and hint at where that might be.


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
@@ -236,7 +236,11 @@ def choose_vhost(self, target_name):
         if not vhost:
             # No matches. Raise a misconfiguration error.
             raise errors.MisconfigurationError(
-                        "Cannot find a VirtualHost matching domain %s." % (target_name))
+                        ("Cannot find a VirtualHost matching domain %s. "
+                         "In order for Certbot to correctly perform the challenge "
+                         "please add a corresponding server_name directive to your "
+                         "nginx configuration: "
+                         "https://nginx.org/en/docs/http/server_names.html") % (target_name))
         else:
             # Note: if we are enhancing with ocsp, vhost should already be ssl.
             if not vhost.ssl:


Test patch:
Repository: certbot/certbot

Issue:
add the word `instead` to renew error
I tried to renew a certificate:

```sh
# ~/certbot-auto -d server.example.com renew
Saving debug log to /var/log/letsencrypt/letsencrypt.log
Currently, the renew verb is capable of either renewing all installed certificates that are due to be renewed or renewing a single certificate specified by its name. If you would like to renew specific certificates by their domains, use the certonly command. The renew verb may provide other options for selecting certificates to renew in the future.
```

I'm not sure why my original command was rejected, I only specified one domain.
So, I naively tried to fix my command:
```sh
# ~/certbot-auto certonly -d server.example.com renew
usage:
  certbot-auto [SUBCOMMAND] [options] [-d DOMAIN] [-d DOMAIN] ...

Certbot can obtain and install HTTPS/TLS/SSL certificates.  By default,
it will attempt to use a webserver both for obtaining and installing the


cert.


certbot: error: unrecognized arguments: certonly
```

Suggestions:
1. Accept the input I provided (my guess is that the order `-d foo renew` confused renew and had I used `renew -d foo` it would have been ok)
1. Change `the certonly command` to `the certonly command instead`. I'm not really sure why I think the word "instead" would have queued my brain to drop the word renew from the command, but I think it would have.


Discussion:
Actually you (currently) can't use `-d/--domains` with `renew` (see #4096), but we can certainly add "instead" to the error message.

Resolving patch:
diff --git a/certbot/renewal.py b/certbot/renewal.py
--- a/certbot/renewal.py
+++ b/certbot/renewal.py
@@ -372,8 +372,8 @@ def handle_renewal_request(config):
                            "renewing all installed certificates that are due "
                            "to be renewed or renewing a single certificate specified "
                            "by its name. If you would like to renew specific "
-                           "certificates by their domains, use the certonly "
-                           "command. The renew verb may provide other options "
+                           "certificates by their domains, use the certonly command "
+                           "instead. The renew verb may provide other options "
                            "for selecting certificates to renew in the future.")
 
     if config.certname:


Test patch:
Repository: certbot/certbot

Issue:
the help message should be more explicit about the effect of the -d option
#### Hypothetical language

A suggestion, possibly mostly correct:

If the -d option is mentioned more than once on the command line, a _single_ certificate will be created to cover all the domains that were mentioned.  In particular:
- The first-mentioned domain will be the Subject CN of the certificate.
- All the domains (including the first) will be version-3 Subject Alternative Names on the certificate.
- The certificate will be stored with a filename derived from the first-mentioned domain.
#### Question

Suppose there are multiple inequivalent certificates having the same first domain but different additional domains.  There is the potential for conflict with the filename.  How is this conflict resolved?
#### Suggestion

The stated goal is to make the process easy.  To this end, it would be helpful for somebody who understands the process to document it in the help message.



Discussion:
I agree this could be more clear.

To answer your question, if there is a conflict with filenames, a number is appended to the name of the directory. For example, if you have `example.com`, the next directory will be called `example.com-0001`, followed by `example.com-0002`, etc.

This should still be mentioned in the documentation

Resolving patch:
diff --git a/certbot/cli.py b/certbot/cli.py
--- a/certbot/cli.py
+++ b/certbot/cli.py
@@ -891,11 +891,15 @@ def prepare_and_parse_args(plugins, args, detect_defaults=False):  # pylint: dis
         metavar="DOMAIN", action=_DomainsAction, default=[],
         help="Domain names to apply. For multiple domains you can use "
              "multiple -d flags or enter a comma separated list of domains "
-             "as a parameter. The first provided domain will be used in "
-             "some software user interfaces and file paths for the "
+             "as a parameter. The first domain provided will be the "
+             "subject CN of the certificate, and all domains will be "
+             "Subject Alternative Names on the certificate. "
+             "The first domain will also be used in "
+             "some software user interfaces and as the file paths for the "
              "certificate and related material unless otherwise "
-             "specified or you already have a certificate for the same "
-             "domains. (default: Ask)")
+             "specified or you already have a certificate with the same "
+             "name. In the case of a name collision it will append a number "
+             "like 0001 to the file path name. (default: Ask)")
     helpful.add(
         [None, "run", "certonly", "manage", "delete", "certificates"],
         "--cert-name", dest="certname",


Test patch:
Repository: certbot/certbot

Issue:
--deploy-hook value on command line not being used during renewal
## I ran this command and it produced this output:
```
$ certbot certonly -d example.org --standalone --deploy-hook "touch foo"
...
$ certbot renew --force-renewal --deploy-hook "touch bar"
...
$ grep bar /etc/letsencrypt/renewal/example.org.conf || echo "Why wasn't my deploy hook set?"
Why wasn't my deploy hook set?
$
```

## Certbot's behavior differed from what I expected because:
The deploy hook value should be set. I think this is due to renew hook to deploy hook rename and default detection. I think `certbot.cli.VAR_MODIFIERS` needs to be changed for this interaction to be handled proerply.


Discussion:

Resolving patch:
diff --git a/certbot/cli.py b/certbot/cli.py
--- a/certbot/cli.py
+++ b/certbot/cli.py
@@ -129,6 +129,7 @@
 # This dictionary is used recursively, so if A modifies B and B modifies C,
 # it is determined that C was modified by the user if A was modified.
 VAR_MODIFIERS = {"account": set(("server",)),
+                 "renew_hook": set(("deploy_hook",)),
                  "server": set(("dry_run", "staging",)),
                  "webroot_map": set(("webroot_path",))}
 


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
@@ -438,6 +438,10 @@ class SetByCliTest(unittest.TestCase):
     def setUp(self):
         reload_module(cli)
 
+    def test_deploy_hook(self):
+        self.assertTrue(_call_set_by_cli(
+            'renew_hook', '--deploy-hook foo'.split(), 'renew'))
+
     def test_webroot_map(self):
         args = '-w /var/www/html -d example.com'.split()
         verb = 'renew'