[plugins,distros] Resolve code alerts for file not always closed

Fix a number of outstanding "File is not always closed" errors highlighted by
GitHub's code scanning.

This involves (almost exclusively) changing such as:

   for line in open('/some/file', 'r').read().splitlines():

To using a context manager to ensure the file is always closed:

   with open('/some/file', 'r') as sfile:
       for line in sfile.read().splitlines():

...or something similar. Overall the logic of what a specific block of code was
doing (mostly in plugins) is not changed however.

Signed-off-by: Jake Hunsaker <jacob.r.hunsaker@gmail.com>

14 files changed, 122 insertions, 110 deletions

diff --git a/sos/archive.py b/sos/archive.py
index d76b7aa0..2a9706a2 100644
--- a/sos/archive.py
+++ b/sos/archive.py
@@ -390,14 +390,14 @@ class FileCacheArchive(Archive):
             # on file content.
             dest = self.check_path(dest, P_FILE, force=True)
 
-            f = codecs.open(dest, mode, encoding='utf-8')
-            if isinstance(content, bytes):
-                content = content.decode('utf8', 'ignore')
-            f.write(content)
-            if os.path.exists(src):
-                self._copy_attributes(src, dest)
-            self.log_debug("added string at '%s' to FileCacheArchive '%s'"
-                           % (src, self._archive_root))
+            with codecs.open(dest, mode, encoding='utf-8') as f:
+                if isinstance(content, bytes):
+                    content = content.decode('utf8', 'ignore')
+                f.write(content)
+                if os.path.exists(src):
+                    self._copy_attributes(src, dest)
+                self.log_debug("added string at '%s' to FileCacheArchive '%s'"
+                               % (src, self._archive_root))
 
     def add_binary(self, content, dest):
         with self._path_lock:
@@ -405,8 +405,8 @@ class FileCacheArchive(Archive):
             if not dest:
                 return
 
-            f = codecs.open(dest, 'wb', encoding=None)
-            f.write(content)
+            with codecs.open(dest, 'wb', encoding=None) as f:
+                f.write(content)
             self.log_debug("added binary content at '%s' to archive '%s'"
                            % (dest, self._archive_root))
 
diff --git a/sos/cleaner/__init__.py b/sos/cleaner/__init__.py
index fbcaa9c3..9aabd9c4 100644
--- a/sos/cleaner/__init__.py
+++ b/sos/cleaner/__init__.py
@@ -525,15 +525,14 @@ third party.
         """
         try:
             hash_size = 1024**2  # Hash 1MiB of content at a time.
-            archive_fp = open(archive_path, 'rb')
-            digest = hashlib.new(self.hash_name)
-            while True:
-                hashdata = archive_fp.read(hash_size)
-                if not hashdata:
-                    break
-                digest.update(hashdata)
-            archive_fp.close()
-            return digest.hexdigest() + '\n'
+            with open(archive_path, 'rb') as archive_fp:
+                digest = hashlib.new(self.hash_name)
+                while True:
+                    hashdata = archive_fp.read(hash_size)
+                    if not hashdata:
+                        break
+                    digest.update(hashdata)
+                return digest.hexdigest() + '\n'
         except Exception as err:
             self.log_debug("Could not generate new checksum: %s" % err)
         return None
diff --git a/sos/policies/distros/redhat.py b/sos/policies/distros/redhat.py
index 8085aae8..15241e27 100644
--- a/sos/policies/distros/redhat.py
+++ b/sos/policies/distros/redhat.py
@@ -466,8 +466,9 @@ support representative.
         if not os.path.exists(host_release):
             return False
         try:
-            for line in open(host_release, "r").read().splitlines():
-                atomic |= ATOMIC_RELEASE_STR in line
+            with open(host_release, 'r') as afile:
+                for line in afile.read().splitlines():
+                    atomic |= ATOMIC_RELEASE_STR in line
         except IOError:
             pass
         return atomic
@@ -551,8 +552,9 @@ support representative.
             return coreos
         host_release = os.environ[ENV_HOST_SYSROOT] + OS_RELEASE
         try:
-            for line in open(host_release, 'r').read().splitlines():
-                coreos |= 'Red Hat Enterprise Linux CoreOS' in line
+            with open(host_release, 'r') as hfile:
+                for line in hfile.read().splitlines():
+                    coreos |= 'Red Hat Enterprise Linux CoreOS' in line
         except IOError:
             pass
         return coreos
diff --git a/sos/report/plugins/__init__.py b/sos/report/plugins/__init__.py
index 60910c39..b43bc4ea 100644
--- a/sos/report/plugins/__init__.py
+++ b/sos/report/plugins/__init__.py
@@ -3175,10 +3175,9 @@ class Plugin():
             _pfname = self._make_command_filename(fname, subdir=subdir)
             self.archive.check_path(_pfname, P_FILE)
             _name = self.archive.dest_path(_pfname)
-            _file = open(_name, 'w')
-            self._log_debug(f"manual collection file opened: {_name}")
-            yield _file
-            _file.close()
+            with open(_name, 'w') as _file:
+                self._log_debug(f"manual collection file opened: {_name}")
+                yield _file
             end = time()
             run = end - start
             self._log_info(f"manual collection '{fname}' finished in {run}")
@@ -3447,10 +3446,10 @@ class Plugin():
         try:
             cmd_line_paths = glob.glob(cmd_line_glob)
             for path in cmd_line_paths:
-                f = open(self.path_join(path), 'r')
-                cmd_line = f.read().strip()
-                if process in cmd_line:
-                    status = True
+                with open(self.path_join(path), 'r') as pfile:
+                    cmd_line = pfile.read().strip()
+                    if process in cmd_line:
+                        status = True
         except IOError:
             return False
         return status
diff --git a/sos/report/plugins/candlepin.py b/sos/report/plugins/candlepin.py
index 67dc8d2e..9c14ea2d 100644
--- a/sos/report/plugins/candlepin.py
+++ b/sos/report/plugins/candlepin.py
@@ -30,7 +30,9 @@ class Candlepin(Plugin, RedHatPlugin):
         self.dbpasswd = ""
         cfg_file = "/etc/candlepin/candlepin.conf"
         try:
-            for line in open(cfg_file).read().splitlines():
+            with open(cfg_file, 'r') as cfile:
+                candle_lines = cfile.read().splitlines()
+            for line in candle_lines:
                 # skip empty lines and lines with comments
                 if not line or line[0] == '#':
                     continue
diff --git a/sos/report/plugins/firewall_tables.py b/sos/report/plugins/firewall_tables.py
index 590e9849..372e6e47 100644
--- a/sos/report/plugins/firewall_tables.py
+++ b/sos/report/plugins/firewall_tables.py
@@ -77,7 +77,8 @@ class firewall_tables(Plugin, IndependentPlugin):
         # do collect them only when relevant nft list ruleset exists
         default_ip_tables = "mangle\nfilter\nnat\n"
         try:
-            ip_tables_names = open("/proc/net/ip_tables_names").read()
+            with open('/proc/net/ip_tables_names', 'r') as ifile:
+                ip_tables_names = ifile.read()
         except IOError:
             ip_tables_names = default_ip_tables
         for table in ip_tables_names.splitlines():
@@ -85,7 +86,8 @@ class firewall_tables(Plugin, IndependentPlugin):
                 self.collect_iptable(table)
         # collect the same for ip6tables
         try:
-            ip_tables_names = open("/proc/net/ip6_tables_names").read()
+            with open('/proc/net/ip6_tables_names', 'r') as ipfile:
+                ip_tables_names = ipfile.read()
         except IOError:
             ip_tables_names = default_ip_tables
         for table in ip_tables_names.splitlines():
diff --git a/sos/report/plugins/foreman.py b/sos/report/plugins/foreman.py
index cea68ae2..a3ee81b7 100644
--- a/sos/report/plugins/foreman.py
+++ b/sos/report/plugins/foreman.py
@@ -43,7 +43,9 @@ class Foreman(Plugin):
         self.dbhost = "localhost"
         self.dbpasswd = ""
         try:
-            for line in open("/etc/foreman/database.yml").read().splitlines():
+            with open('/etc/foreman/database.yml', 'r') as dfile:
+                foreman_lines = dfile.read().splitlines()
+            for line in foreman_lines:
                 # skip empty lines and lines with comments
                 if not line or line[0] == '#':
                     continue
diff --git a/sos/report/plugins/haproxy.py b/sos/report/plugins/haproxy.py
index 1b3a26d2..5d71e223 100644
--- a/sos/report/plugins/haproxy.py
+++ b/sos/report/plugins/haproxy.py
@@ -48,11 +48,12 @@ class HAProxy(Plugin, RedHatPlugin, DebianPlugin):
         matched = None
         provision_ip = None
         try:
-            for line in open("/etc/haproxy/haproxy.cfg").read().splitlines():
-                if matched:
-                    provision_ip = line.split()[1]
-                    break
-                matched = match(r".*haproxy\.stats.*", line)
+            with open("/etc/haproxy/haproxy.cfg", 'r') as hfile:
+                for line in hfile.read().splitlines():
+                    if matched:
+                        provision_ip = line.split()[1]
+                        break
+                    matched = match(r".*haproxy\.stats.*", line)
         except IOError:
             # fallback when the cfg file is not accessible
             pass
diff --git a/sos/report/plugins/libvirt.py b/sos/report/plugins/libvirt.py
index c36bd022..60c439ef 100644
--- a/sos/report/plugins/libvirt.py
+++ b/sos/report/plugins/libvirt.py
@@ -69,9 +69,10 @@ class Libvirt(Plugin, IndependentPlugin):
 
         # get details of processes of KVM hosts
         for pidfile in glob.glob("/run/libvirt/*/*.pid"):
-            pid = open(pidfile).read().splitlines()[0]
-            for pf in ["environ", "cgroup", "maps", "numa_maps", "limits"]:
-                self.add_copy_spec("/proc/%s/%s" % (pid, pf))
+            with open(pidfile, 'r') as pfile:
+                pid = pfile.read().splitlines()[0]
+                for pf in ["environ", "cgroup", "maps", "numa_maps", "limits"]:
+                    self.add_copy_spec("/proc/%s/%s" % (pid, pf))
 
         self.add_file_tags({
             "/run/libvirt/qemu/*.xml": "var_qemu_xml",
diff --git a/sos/report/plugins/mssql.py b/sos/report/plugins/mssql.py
index d9dce0f9..9a4d643c 100644
--- a/sos/report/plugins/mssql.py
+++ b/sos/report/plugins/mssql.py
@@ -43,19 +43,20 @@ class MsSQL(Plugin, RedHatPlugin):
         sqlagent_errorlogfile = '/var/opt/mssql/log/sqlagentstartup.log'
         kerberoskeytabfile = None
         try:
-            for line in open(mssql_conf).read().splitlines():
-                if line.startswith('['):
-                    section = line
-                    continue
-                words = line.split('=')
-                if words[0].strip() == 'errorlogfile':
-                    if section == '[filelocation]':
-                        errorlogfile = words[1].strip()
-                    elif section == '[sqlagent]':
-                        sqlagent_errorlogfile = words[1].strip()
-                elif words[0].strip() == 'kerberoskeytabfile':
-                    if section == '[network]':
-                        kerberoskeytabfile = words[1].strip()
+            with open(mssql_conf, 'r') as mfile:
+                for line in mfile.read().splitlines():
+                    if line.startswith('['):
+                        section = line
+                        continue
+                    words = line.split('=')
+                    if words[0].strip() == 'errorlogfile':
+                        if section == '[filelocation]':
+                            errorlogfile = words[1].strip()
+                        elif section == '[sqlagent]':
+                            sqlagent_errorlogfile = words[1].strip()
+                    elif words[0].strip() == 'kerberoskeytabfile':
+                        if section == '[network]':
+                            kerberoskeytabfile = words[1].strip()
         except IOError as ex:
             self._log_error('Could not open conf file %s: %s' %
                             (mssql_conf, ex))
diff --git a/sos/report/plugins/pcp.py b/sos/report/plugins/pcp.py
index a979deab..2c6772e2 100644
--- a/sos/report/plugins/pcp.py
+++ b/sos/report/plugins/pcp.py
@@ -47,9 +47,8 @@ class Pcp(Plugin, RedHatPlugin, DebianPlugin):
 
     def pcp_parse_conffile(self):
         try:
-            pcpconf = open(self.pcp_conffile, "r")
-            lines = pcpconf.readlines()
-            pcpconf.close()
+            with open(self.pcp_conffile, "r") as pcpconf:
+                lines = pcpconf.readlines()
         except IOError:
             return False
         env_vars = {}
diff --git a/sos/report/plugins/pulp.py b/sos/report/plugins/pulp.py
index 19484b07..df007168 100644
--- a/sos/report/plugins/pulp.py
+++ b/sos/report/plugins/pulp.py
@@ -45,7 +45,9 @@ class Pulp(Plugin, RedHatPlugin):
         self.messaging_cert_file = ""
         in_messaging_section = False
         try:
-            for line in open("/etc/pulp/server.conf").read().splitlines():
+            with open("/etc/pulp/server.conf", 'r') as pfile:
+                pulp_lines = pfile.read().splitlines()
+            for line in pulp_lines:
                 if match(r"^\s*seeds:\s+\S+:\S+", line):
                     uri = line.split()[1].split(',')[0].split(':')
                     self.dbhost = uri[0]
diff --git a/sos/report/plugins/pulpcore.py b/sos/report/plugins/pulpcore.py
index ad459111..04efae9f 100644
--- a/sos/report/plugins/pulpcore.py
+++ b/sos/report/plugins/pulpcore.py
@@ -45,34 +45,35 @@ class PulpCore(Plugin, IndependentPlugin):
             return val
 
         try:
-            # split the lines to "one option per line" format
-            for line in open("/etc/pulp/settings.py").read() \
-                    .replace(',', ',\n').replace('{', '{\n') \
-                    .replace('}', '\n}').splitlines():
-                # skip empty lines and lines with comments
-                if not line or line[0] == '#':
-                    continue
-                if line.startswith("DATABASES"):
-                    databases_scope = True
-                    continue
-                # example HOST line to parse:
-                #         'HOST': 'localhost',
-                pattern = r"\s*['|\"]%s['|\"]\s*:\s*\S+"
-                if databases_scope and match(pattern % 'HOST', line):
-                    self.dbhost = separate_value(line)
-                if databases_scope and match(pattern % 'PORT', line):
-                    self.dbport = separate_value(line)
-                if databases_scope and match(pattern % 'NAME', line):
-                    self.dbname = separate_value(line)
-                if databases_scope and match(pattern % 'PASSWORD', line):
-                    self.dbpasswd = separate_value(line)
-                # if line contains closing '}' database_scope end
-                if databases_scope and '}' in line:
-                    databases_scope = False
-                if line.startswith("STATIC_ROOT = "):
-                    self.staticroot = separate_value(line, sep='=')
-                if line.startswith("CHUNKED_UPLOAD_DIR = "):
-                    self.uploaddir = separate_value(line, sep='=')
+            with open("/etc/pulp/settings.py", 'r') as pfile:
+                # split the lines to "one option per line" format
+                for line in pfile.read() \
+                        .replace(',', ',\n').replace('{', '{\n') \
+                        .replace('}', '\n}').splitlines():
+                    # skip empty lines and lines with comments
+                    if not line or line[0] == '#':
+                        continue
+                    if line.startswith("DATABASES"):
+                        databases_scope = True
+                        continue
+                    # example HOST line to parse:
+                    #         'HOST': 'localhost',
+                    pattern = r"\s*['|\"]%s['|\"]\s*:\s*\S+"
+                    if databases_scope and match(pattern % 'HOST', line):
+                        self.dbhost = separate_value(line)
+                    if databases_scope and match(pattern % 'PORT', line):
+                        self.dbport = separate_value(line)
+                    if databases_scope and match(pattern % 'NAME', line):
+                        self.dbname = separate_value(line)
+                    if databases_scope and match(pattern % 'PASSWORD', line):
+                        self.dbpasswd = separate_value(line)
+                    # if line contains closing '}' database_scope end
+                    if databases_scope and '}' in line:
+                        databases_scope = False
+                    if line.startswith("STATIC_ROOT = "):
+                        self.staticroot = separate_value(line, sep='=')
+                    if line.startswith("CHUNKED_UPLOAD_DIR = "):
+                        self.uploaddir = separate_value(line, sep='=')
         except IOError:
             # fallback when the cfg file is not accessible
             pass
diff --git a/sos/report/plugins/sos_extras.py b/sos/report/plugins/sos_extras.py
index 55bc4dc0..71cc8787 100644
--- a/sos/report/plugins/sos_extras.py
+++ b/sos/report/plugins/sos_extras.py
@@ -61,28 +61,29 @@ class SosExtras(Plugin, IndependentPlugin):
                 _file = self.path_join(path, f)
                 self._log_warn("Collecting data from extras file %s" % _file)
                 try:
-                    for line in open(_file).read().splitlines():
-                        # ignore empty lines or comments
-                        if len(line.split()) == 0 or line.startswith('#'):
-                            continue
-                        # lines starting by ':' specify file pattern to collect
-                        # optionally followed by sizelimit
-                        if line.startswith(':'):
-                            words = line.split()
-                            limit = None
-                            if len(words) > 1:
-                                try:
-                                    limit = int(words[1])
-                                except ValueError:
-                                    self._log_warn("Can't decode integer"
-                                                   " sizelimit on line '%s'"
-                                                   " in file %s, using"
-                                                   " default."
-                                                   % (line, _file))
-                            self.add_copy_spec(words[0][1:], sizelimit=limit)
-                        else:
-                            # command to execute
-                            self.add_cmd_output(line, subdir=f)
+                    with open(_file, 'r') as sfile:
+                        for line in sfile.read().splitlines():
+                            # ignore empty lines or comments
+                            if len(line.split()) == 0 or line.startswith('#'):
+                                continue
+                            # lines starting by ':' specify file pattern to
+                            # collect optionally followed by sizelimit
+                            if line.startswith(':'):
+                                words = line.split()
+                                limit = None
+                                if len(words) > 1:
+                                    try:
+                                        limit = int(words[1])
+                                    except ValueError:
+                                        self._log_warn(
+                                            f"Can't decode size limit on line"
+                                            f"{line} in {_file}, using default"
+                                        )
+                                self.add_copy_spec(words[0][1:],
+                                                   sizelimit=limit)
+                            else:
+                                # command to execute
+                                self.add_cmd_output(line, subdir=f)
 
                 except IOError:
                     self._log_warn("unable to read extras file %s" % _file)