treewide: make sure we use ruamel.yaml in a thread safe manner

we have multiple tests failing with the following:
```
>       self.stream.write(data)
E       ValueError: I/O operation on closed file.

../scylla/.local/lib/python3.12/site-packages/ruamel/yaml/emitter.py:1249: ValueError
```

seems like it start when we have calls from multiple thread that might be
updating the same files, or sharing the same state.

this change make sure we create `YAML` instances as needed,
so they won't be shared between threads

Ref: https://sourceforge.net/p/ruamel-yaml/tickets/367/
(cherry picked from commit 1e6e8b1)

ccmlib/cluster.py

@@ -15,8 +15,6 @@
 from ccmlib.common import logger
 from ccmlib.utils.version import parse_version
 
-yaml = YAML()
-yaml.default_flow_style = False
 
 class Cluster(object):
 
@@ -677,7 +675,7 @@ def _update_config(self, install_dir=None):
             cluster_config['sni_proxy_listen_port'] = self.sni_proxy_listen_port
 
         with open(filename, 'w') as f:
-            yaml.dump(cluster_config, f)
+            YAML().dump(cluster_config, f)
 
     def __update_pids(self, started):
         for node, p, _ in started:

ccmlib/cluster_factory.py

@@ -10,8 +10,6 @@
 from ccmlib import repository
 from ccmlib.node import Node
 
-yaml = YAML()
-yaml.default_flow_style = False
 
 class ClusterFactory():
 
@@ -20,7 +18,7 @@ def load(path, name):
         cluster_path = os.path.join(path, name)
         filename = os.path.join(cluster_path, 'cluster.conf')
         with open(filename, 'r') as f:
-            data = yaml.load(f)
+            data = YAML().load(f)
         try:
             install_dir = None
             scylla_manager_install_path = data.get('scylla_manager_install_path')

ccmlib/common.py

@@ -27,8 +27,6 @@
 from botocore import UNSIGNED
 from botocore.client import Config
 
-yaml = YAML()
-yaml.default_flow_style = False
 
 BIN_DIR = "bin"
 CASSANDRA_CONF_DIR = "conf"
@@ -817,6 +815,7 @@ def normalize_interface(itf):
 
 def parse_settings(args):
     settings = {}
+    yaml = YAML()
     for s in args:
         splitted = s.split(':', 1)
         if len(splitted) != 2:
@@ -888,7 +887,7 @@ def get_version_from_build(install_dir=None, node_path=None):
 def get_default_scylla_yaml(install_dir):
     scylla_yaml_path = Path(install_dir) / SCYLLA_CONF_DIR / SCYLLA_CONF
     with scylla_yaml_path.open() as f:
-        return yaml.load(f)
+        return YAML().load(f)
 
 def _get_scylla_version(install_dir):
     scylla_version_files = [
@@ -970,7 +969,7 @@ def is_dse_cluster(path):
             cluster_path = os.path.join(path, name)
             filename = os.path.join(cluster_path, 'cluster.conf')
             with open(filename, 'r') as f:
-                data = yaml.load(f)
+                data = YAML().load(f)
             if 'dse_dir' in data:
                 return True
     except IOError:

ccmlib/dse_node.py

@@ -14,9 +14,6 @@
 from ccmlib import common
 from ccmlib.node import Node, NodeError
 
-yaml = YAML()
-yaml.default_flow_style = False
-
 
 class DseNode(Node):
 
@@ -296,7 +293,7 @@ def import_bin_files(self):
     def __update_yaml(self):
         conf_file = os.path.join(self.get_path(), 'resources', 'dse', 'conf', 'dse.yaml')
         with open(conf_file, 'r') as f:
-            data = yaml.load(f)
+            data = YAML().load(f)
 
         data['system_key_directory'] = os.path.join(self.get_path(), 'keys')
 
@@ -313,7 +310,7 @@ def __update_yaml(self):
                 data[name] = full_options[name]
 
         with open(conf_file, 'w') as f:
-            yaml.dump(data, f)
+            YAML().dump(data, f)
 
     def _update_log4j(self):
         super(DseNode, self)._update_log4j()

ccmlib/node.py

@@ -24,8 +24,6 @@
 from ccmlib.repository import setup
 from ccmlib.utils.version import parse_version
 
-yaml = YAML()
-yaml.default_flow_style = False
 
 class Status():
     UNINITIALIZED = "UNINITIALIZED"
@@ -138,7 +136,7 @@ def load(path, name, cluster):
         node_path = os.path.join(path, name)
         filename = os.path.join(node_path, 'node.conf')
         with open(filename, 'r') as f:
-            data = yaml.load(f)
+            data = YAML().load(f)
         try:
             itf = data['interfaces']
             initial_token = None
@@ -1586,12 +1584,12 @@ def _update_config(self):
         if self.workload is not None:
             values['workload'] = self.workload
         with open(filename, 'w') as f:
-            yaml.dump(values, f)
+            YAML().dump(values, f)
 
     def __update_yaml(self):
         conf_file = os.path.join(self.get_conf_dir(), common.CASSANDRA_CONF)
         with open(conf_file, 'r') as f:
-            data = yaml.load(f)
+            data = YAML().load(f)
 
         with open(conf_file, 'r') as f:
             yaml_text = f.read()
@@ -1641,7 +1639,7 @@ def __update_yaml(self):
                     data[name] = full_options[name]
 
         with open(conf_file, 'w') as f:
-            yaml.dump(data, f)
+            YAML().dump(data, f)
 
     def _update_log4j(self):
         append_pattern = 'log4j.appender.R.File='
@@ -1963,7 +1961,7 @@ def _clean_win_jmx(self):
     def get_conf_option(self, option):
         conf_file = os.path.join(self.get_conf_dir(), common.CASSANDRA_CONF)
         with open(conf_file, 'r') as f:
-            data = yaml.load(f)
+            data = YAML().load(f)
 
         if option in data:
             return data[option]

ccmlib/scylla_cluster.py

@@ -19,8 +19,6 @@
 
 SNITCH = 'org.apache.cassandra.locator.GossipingPropertyFileSnitch'
 
-yaml = YAML()
-yaml.default_flow_style = False
 
 class ScyllaCluster(Cluster):
 
@@ -246,7 +244,7 @@ def _update_config(self, install_dir=None):
         filename = os.path.join(self.get_path(), 'cluster.conf')
 
         with open(filename, 'r') as f:
-            data = yaml.load(f)
+            data = YAML().load(f)
 
         if self.is_scylla_reloc():
             data['scylla_version'] = self.scylla_version
@@ -255,7 +253,7 @@ def _update_config(self, install_dir=None):
             data['scylla_manager_install_path'] = self._scylla_manager.install_dir
 
         with open(filename, 'w') as f:
-            yaml.dump(data, f)
+            YAML().dump(data, f)
 
     def sctool(self, cmd):
         if self._scylla_manager == None:
@@ -315,7 +313,7 @@ def _get_api_address(self):
     def _update_config(self, install_dir=None):
         conf_file = os.path.join(self._get_path(), common.SCYLLAMANAGER_CONF)
         with open(conf_file, 'r') as f:
-            data = yaml.load(f)
+            data = YAML().load(f)
         data['http'] = self._get_api_address()
         if not 'database' in data:
             data['database'] = {}
@@ -351,7 +349,7 @@ def _update_config(self, install_dir=None):
         for key in keys_to_delete:
             del data[key]
         with open(conf_file, 'w') as f:
-            yaml.dump(data, f)
+            YAML().dump(data, f)
 
     def _copy_config_files(self, install_dir):
         conf_dir = os.path.join(install_dir, 'etc')

ccmlib/scylla_docker_cluster.py

@@ -12,8 +12,6 @@
 
 LOGGER = logging.getLogger("ccm")
 
-yaml = YAML()
-yaml.default_flow_style = False
 
 class ScyllaDockerCluster(ScyllaCluster):
     def __init__(self, *args, **kwargs):
@@ -139,7 +137,7 @@ def update_yaml(self):
                     copyfile(src=file_path, dst=os.path.join(keys_dir_path, file_name))
                     server_encryption_options[key] = os.path.join(self.base_data_path, "keys", file_name)
         with open(conf_file, 'w') as f:
-            yaml.safe_dump(data, f, default_flow_style=False)
+            YAML().dump(data, f)
 
     def create_docker(self, args):
         # TODO: handle smp correctly via the correct param/api (or only via commandline params)

ccmlib/scylla_node.py

@@ -19,10 +19,10 @@
 import logging
 
 import psutil
-from ruamel.yaml import YAML
 import glob
 import re
 import requests
+from ruamel.yaml import YAML
 
 from ccmlib.common import CASSANDRA_SH, BIN_DIR, wait_for, copy_directory, print_if_standalone
 
@@ -35,9 +35,6 @@
 from ccmlib.utils.version import parse_version
 
 
-yaml = YAML(typ='safe')
-yaml.default_flow_style = False
-
 class ScyllaNode(Node):
 
     """
@@ -117,7 +114,7 @@ def has_jmx(self):
 
     @property
     def scylla_yaml(self) -> Dict[str, Any]:
-        return yaml.load(Path(self.get_conf_dir()) / common.SCYLLA_CONF)
+        return YAML().load(Path(self.get_conf_dir()) / common.SCYLLA_CONF)
 
     @property
     def api_port(self) -> int:
@@ -383,18 +380,18 @@ def _create_agent_config(self):
         data['s3'] = {"endpoint": os.getenv("AWS_S3_ENDPOINT"), "provider": "Minio"}
 
         with open(conf_file, 'w') as f:
-            yaml.dump(data, f)
+            YAML().dump(data, f)
         return conf_file
 
     def update_agent_config(self, new_settings, restart_agent_after_change=True):
         conf_file = os.path.join(self.get_conf_dir(), 'scylla-manager-agent.yaml')
         with open(conf_file, 'r') as f:
-            current_config = yaml.load(f)
+            current_config = YAML().load(f)
 
         current_config.update(new_settings)
 
         with open(conf_file, 'w') as f:
-            yaml.dump(current_config, f)
+            YAML().dump(current_config, f)
 
         if restart_agent_after_change:
             self.restart_scylla_manager_agent(gently=True, recreate_config=False)
@@ -427,7 +424,7 @@ def start_scylla_manager_agent(self, create_config=True):
             pid_file.write(str(self._process_agent.pid))
 
         with open(config_file, 'r') as f:
-            current_config = yaml.load(f)
+            current_config = YAML().load(f)
             # Extracting currently configured port
             current_listening_port = int(current_config['https'].split(":")[1])
 
@@ -580,7 +577,7 @@ def start(self, join_ring=True, no_wait=False, verbose=False,
         # from config file scylla#59
         conf_file = os.path.join(self.get_conf_dir(), common.SCYLLA_CONF)
         with open(conf_file, 'r') as f:
-            data = yaml.load(f)
+            data = YAML().load(f)
         jvm_args = jvm_args + ['--api-address', data['api_address']]
 
         args = [launch_bin, '--options-file', options_file, '--log-to-stdout', '1']
@@ -1155,7 +1152,7 @@ def update_yaml(self):
         # TODO: copied from node.py
         conf_file = os.path.join(self.get_conf_dir(), common.SCYLLA_CONF)
         with open(conf_file, 'r') as f:
-            data = yaml.load(f)
+            data = YAML().load(f)
 
         data['cluster_name'] = self.cluster.name
         data['auto_bootstrap'] = self.auto_bootstrap
@@ -1216,7 +1213,7 @@ def update_yaml(self):
         if 'alternator_port' in data or 'alternator_https_port' in data:
             data['alternator_address'] = data['listen_address']
         with open(conf_file, 'w') as f:
-            yaml.dump(data, f)
+            YAML().dump(data, f)
 
         # TODO: - for now create a cassandra conf file leaving only
         # cassandra config items - this should be removed once tools are
@@ -1326,7 +1323,7 @@ def update_yaml(self):
                 cassandra_data[key] = data[key]
 
         with open(cassandra_conf_file, 'w') as f:
-            yaml.dump(cassandra_data, f)
+            YAML().dump(cassandra_data, f)
 
     def __update_yaml_dse(self):
         raise NotImplementedError('ScyllaNode.__update_yaml_dse')

ccmlib/scylla_repository.py

@@ -14,18 +14,15 @@
 from typing import NamedTuple, Literal
 
 import requests
-from ruamel.yaml import YAML
 import packaging.version
+from ruamel.yaml import YAML
 
 from ccmlib.common import (
     ArgumentError, CCMError, get_default_path, rmdirs, validate_install_dir, get_scylla_version, aws_bucket_ls,
     DOWNLOAD_IN_PROGRESS_FILE, print_if_standalone, LockFile, get_installed_scylla_package_hash)
 from ccmlib.utils.download import download_file, download_version_from_s3, get_url_hash, save_source_file
 from ccmlib.utils.version import parse_version
 
-yaml = YAML()
-yaml.default_flow_style = False
-
 
 GIT_REPO = "http://github.com/scylladb/scylla.git"
 
@@ -189,7 +186,7 @@ def read_build_manifest(url):
     #
     #    url-id: 2022-08-29T08:05:34Z
     #    docker-image-name: scylla-nightly:5.2.0-dev-0.20220829.67c91e8bcd61
-    return yaml.load(res.content)
+    return YAML().load(res.content)
 
 
 def normalize_scylla_version(version):

ccmlib/utils/sni_proxy.py

@@ -18,8 +18,6 @@
 
 logger = logging.getLogger(__name__)
 
-yaml = YAML()
-yaml.default_flow_style = False
 
 @contextmanager
 def file_or_memory(path=None, data=None):
@@ -67,7 +65,7 @@ def encode_base64(filename):
                   currentContext='default')
 
     with open(os.path.join(ssl_dir, 'config_data.yaml'), 'w') as config_file:
-        yaml.dump(config, config_file)
+        YAML().dump(config, config_file)
 
     datacenters = {}
 
@@ -86,7 +84,7 @@ def encode_base64(filename):
                   currentContext='default')
 
     with open(os.path.join(ssl_dir, 'config_path.yaml'), 'w') as config_file:
-        yaml.dump(config, config_file)
+        YAML().dump(config, config_file)
 
     return os.path.join(ssl_dir, 'config_data.yaml'), os.path.join(ssl_dir, 'config_path.yaml')