def _load_gigantum_data(self) -> None:
"""Method to load the labbook YAML file to a dictionary
Returns:
None
"""
if not self.root_dir:
raise GigantumException("No root directory assigned to lab book. "
"Failed to get root directory.")
schema_path = os.path.join(self.root_dir, '.gigantum', 'project.yaml')
old_schema_path = os.path.join(self.root_dir, ".gigantum", "labbook.yaml")
if os.path.exists(schema_path):
with open(schema_path, 'rt') as lbfile:
d = yaml.safe_load(lbfile)
self._data = d
elif os.path.exists(old_schema_path):
# For backward compatibility
with open(old_schema_path, 'rt') as lbfile:
d = yaml.safe_load(lbfile)
# "Virtualize" old schemas into new schemas to support back-compatability
self._data = translate_schema(d, self.root_dir)
else:
if 'gm.workspace' in self.get_branches()['local']:
logger.warning("Master branch empty, attempting to load gm.workspace")
self.checkout_branch('gm.workspace')
self._load_gigantum_data()
else:
raise GigantumException('Cannot find configuration yaml file')
if self.schema == 2:
# Make sure untracked directory exists (it and its contents are ignored)
os.makedirs(os.path.join(self.root_dir, 'output', 'untracked'), exist_ok=True)
def checkout_branch(self, branch_name: str, new: bool = False) -> None:
"""
Checkout a Git branch. Create a new branch locally.
Args:
branch_name(str): Name of branch to checkout or create
new(bool): Indicates this branch should be created.
Return:
None
"""
if not self.is_repo_clean:
raise GigantumException(f"Cannot checkout {branch_name}: Untracked and/or uncommitted changes")
try:
if new:
logger.info(f"Creating a new branch {branch_name}...")
self.git.create_branch(branch_name)
logger.info(f"Checking out branch {branch_name}...")
self.git.checkout(branch_name=branch_name)
# Clear out checkout context
if self._root_dir and os.path.exists(os.path.join(self._root_dir, ".gigantum", ".checkout")):
os.remove(os.path.join(self._root_dir, ".gigantum", ".checkout"))
self._checkout_id = None
except ValueError as e:
logger.error(f"Cannot checkout branch {branch_name}: {e}")
raise GigantumException(e)
def _clone(remote_url: str, working_dir: str) -> str:
clone_tokens = f"git clone {remote_url}".split()
call_subprocess(clone_tokens, cwd=working_dir)
# Affirm there is only one directory created
dirs = os.listdir(working_dir)
if len(dirs) != 1:
raise GigantumException('Git clone produced extra directories')
p = os.path.join(working_dir, dirs[0])
if not os.path.exists(p):
raise GigantumException(
'Could not find expected path of repo after clone')
try:
# This is for backward compatibility -- old projects will clone to
# branch "gm.workspace" by default -- even if it has already been migrated.
# This will therefore set the user to the proper branch if the project has been
# migrated, and will have no affect if it hasn't
r = call_subprocess("git checkout master".split(), cwd=p)
except Exception as e:
logger.error(e)
return p
def _start_dev_tool(cls, labbook: LabBook, username: str, dev_tool: str, container_override_id: str = None):
router = ProxyRouter.get_proxy(labbook.client_config.config['proxy'])
bam = BundledAppManager(labbook)
bundled_apps = bam.get_bundled_apps()
bundled_app_names = [x for x in bundled_apps]
if dev_tool == "rstudio":
suffix = cls._start_rstudio(labbook, router, username)
elif dev_tool in ["jupyterlab", "notebook"]:
# Note that starting the dev tool is identical whether we're targeting jupyterlab or notebook
suffix = cls._start_jupyter_tool(labbook, router, username, container_override_id)
elif dev_tool in bundled_app_names:
app_data = bundled_apps[dev_tool]
app_data['name'] = dev_tool
suffix = cls._start_bundled_app(labbook, router, username, app_data, container_override_id)
else:
raise GigantumException(f"'{dev_tool}' not currently supported as a Dev Tool")
# Don't include the port in the path if running on 80
apparent_proxy_port = labbook.client_config.config['proxy']["apparent_proxy_port"]
if apparent_proxy_port == 80:
path = suffix
else:
path = f':{apparent_proxy_port}{suffix}'
return path
def start_rserver(labbook: LabBook,
username: str,
tag: Optional[str] = None,
check_reachable: bool = True) -> None:
""" Main entrypoint to launch rstudio-server. Note, the caller must
determine for themselves the host and port.
Raises an exception if there's a problem.
Returns:
Path to rstudio-server
"""
owner = InventoryManager().query_owner(labbook)
lb_key = tag or infer_docker_image_name(
labbook_name=labbook.name, owner=owner, username=username)
docker_client = get_docker_client()
lb_container = docker_client.containers.get(lb_key)
if lb_container.status != 'running':
raise GigantumException(f"{str(labbook)} container is not running")
rserver_ps = ps_search(lb_container, 'rserver')
if len(rserver_ps) == 1:
# we have an existing rstudio-server instance
return
elif len(rserver_ps) == 0:
_start_rserver_process(lb_container)
else:
# If "ps aux" for rserver returns multiple hits - this should never happen.
for n, l in enumerate(rserver_ps):
logger.error(
f'Multiple RStudio-Server instances - ({n+1} of {len(rserver_ps)}) - {l}'
)
raise ValueError(
f'Multiple ({len(rserver_ps)}) RStudio Server instances detected')
def _start_dev_tool(cls,
lb: LabBook,
username: str,
dev_tool: str,
container_override_id: str = None):
pr = ProxyRouter.get_proxy(lb.client_config.config['proxy'])
if dev_tool == "rstudio":
suffix = cls._start_rstudio(lb, pr, username)
elif dev_tool in ["jupyterlab", "notebook"]:
# Note that starting the dev tool is identical whether we're targeting jupyterlab or notebook
suffix = cls._start_jupyter_tool(lb, pr, username,
container_override_id)
else:
raise GigantumException(
f"'{dev_tool}' not currently supported as a Dev Tool")
# Don't include the port in the path if running on 80
apparent_proxy_port = lb.client_config.config['proxy'][
"apparent_proxy_port"]
if apparent_proxy_port == 80:
path = suffix
else:
path = f':{apparent_proxy_port}{suffix}'
return path
def start_bundled_app(labbook: LabBook, username: str, command: str, tag: Optional[str] = None) -> None:
""" Method to start a bundled app by running the user specified command inside the running Project container
Args:
labbook: labbook instance
username: current logged in user
command: user specified command to run
tag: optional tag for the container override id
Returns:
"""
if len(command) == 0:
return
owner = InventoryManager().query_owner(labbook)
lb_key = tag or infer_docker_image_name(labbook_name=labbook.name,
owner=owner,
username=username)
docker_client = get_docker_client()
lb_container = docker_client.containers.get(lb_key)
if lb_container.status != 'running':
raise GigantumException(f"{str(labbook)} container is not running. Start it before starting a bundled app.")
lb_container.exec_run(f'sh -c "{command}"', detach=True, user='******')
def start_mitm_proxy(cls, lb_endpoint: str, key: str) -> str:
"""Launch a proxy cointainer between client and labbook.
Args:
lb_endpoint: the specific target running a dev tool
key: a unique key for this instance (related to the monitored Project container - e.g., RStudio)
Returns:
str that contains the proxy endpoint as http://{ip}:{port}
"""
# setup the environment - note that UID is obtained inside the container based on labmanager_share_vol
# (mounted at /mnt/share)
env_var = [f"LBENDPOINT={lb_endpoint}", f"PROXYID={key}"]
nametag = f"gmitmproxy.{key}"
volumes_dict = {
'labmanager_share_vol': {'bind': '/mnt/share', 'mode': 'rw'}
}
docker_client = get_docker_client()
container = docker_client.containers.run("gigantum/mitmproxy_proxy:" + CURRENT_MITMPROXY_TAG, detach=True,
init=True, name=nametag, volumes=volumes_dict,
environment=env_var)
# For now, we hammer repeatedly for 5 seconds
# Plan for a better solution is mentioned in #434
for _ in range(50):
time.sleep(.1)
# Hope that our container is actually up and reload
container.reload()
container_ip = container.attrs['NetworkSettings']['Networks']['bridge']['IPAddress']
if container_ip:
break
if not container_ip:
raise GigantumException("Unable to get mitmproxy_proxy IP address.")
mitm_endpoint = f'http://{container_ip}:8079'
# register the proxy in KV store
redis_conn = redis.Redis(db=1)
redis_conn.set(f"{lb_endpoint}-mitm-endpoint", mitm_endpoint)
redis_conn.set(f"{lb_endpoint}-mitm-container_id", container.id)
redis_conn.set(f"{lb_endpoint}-mitm-key", key)
# make sure proxy is up.
for timeout in range(10):
time.sleep(1)
ec, new_ps_list = container.exec_run(
f'sh -c "ps aux | grep nginx | grep -v \' grep \'"')
new_ps_list = new_ps_list.decode().split('\n')
if any('nginx' in l for l in new_ps_list):
logger.info(f"Proxy to rserver started within {timeout + 1} seconds")
break
else:
raise ValueError('mitmproxy failed to start after 10 seconds')
return mitm_endpoint
def modify_tag_visibility(self, tag: str, show: str):
"""Modify all detail objecvts with matching tag to have visibility specified in show"""
if not self._in_modify:
raise GigantumException(
"Attempt to use ActivityRecord.modify_tag_visibility() outside of "
"ActivityRecord.inspect_detail_objects()")
# We'll actually do the modifications in one pass when we exit the with-context
self._tags_to_update[tag] = show
def remote(self) -> Optional[str]:
try:
r = self.git.list_remotes()
if r:
return r[0]['url']
else:
return None
except Exception as e:
logger.exception(e)
raise GigantumException(e)
def remove_remote(self, remote_name: Optional[str] = "origin") -> None:
"""Remove a remove from the git config
Args:
remote_name: Optional name of remote (default "origin")
"""
try:
logger.info(f"Removing remote {remote_name} from {str(self)}")
self.git.remove_remote(remote_name)
except Exception as e:
raise GigantumException(e)
def has_remote(self):
"""Return True if the Repository has a remote that it can push/pull to/from
Returns:
bool indicating whether a remote is set.
"""
try:
return len(self.git.list_remotes()) > 0
except Exception as e:
logger.exception(e)
raise GigantumException(e)
def add_remote(self, remote_name: str, url: str) -> None:
"""Add a new git remote
Args:
remote_name: Name of remote, e.g., "origin"
url: Path to remote Git repository.
"""
try:
logger.info(f"Adding new remote {remote_name} at {url}")
self.git.add_remote(remote_name, url)
self.git.fetch(remote=remote_name)
except Exception as e:
raise GigantumException(e)
def get_storage_backend(storage_type: str) -> Union[ManagedStorageBackend, UnmanagedStorageBackend]:
"""
Args:
storage_type(str): Identifier to load class
Returns:
gtmcore.dataset.storage.backend.StorageBackend
"""
if storage_type in SUPPORTED_STORAGE_BACKENDS.keys():
module, package = SUPPORTED_STORAGE_BACKENDS.get(storage_type) # type: ignore
imported = importlib.import_module(module, package)
class_instance = getattr(imported, package)
return class_instance()
else:
raise GigantumException(f"Unsupported Dataset Storage Type: {storage_type}")
def get_branches(self) -> Dict[str, List[str]]:
"""Return all branches a Dict of Lists. Dict contains two keys "local" and "remote".
Args:
None
Returns:
Dictionary of lists for "remote" and "local" branches.
"""
try:
# Note - do NOT fetch here - fetch should be done before this is called.
return self.git.list_branches()
except Exception as e:
# Unsure what specific exception add_remote creates, so make a catchall.
logger.exception(e)
raise GigantumException(e)
def update_detail_object(self, obj: ActivityDetailRecord,
index: int) -> None:
"""Method to update a detail object in place
Can only be used while in the context of self.inspect_detail_objects
Args:
obj: detail record to add
index: index to update
"""
if not self._in_modify:
raise GigantumException(
"Attempt to use ActivityRecord.update_detail_object() outside of "
"ActivityRecord.inspect_detail_objects()")
if index < 0 or index >= len(self._detail_objects):
raise ValueError("Index out of range when updating detail object")
self._detail_objects[index] = (obj.show, obj.type.value,
obj.importance, obj)
def check_jupyter_reachable(ip_address: str, port: int, prefix: str):
for n in range(20):
test_url = f'http://{ip_address}:{port}{prefix}/api'
logger.debug(
f"Attempt {n + 1}: Testing if JupyerLab is up at {test_url}...")
try:
r = requests.get(test_url, timeout=0.5)
if r.status_code != 200:
time.sleep(0.5)
else:
if "version" in r.json():
logger.info(
f'Found JupyterLab up at {test_url} after {n/2.0} seconds'
)
break
else:
time.sleep(0.5)
except requests.exceptions.ConnectionError:
# Assume API isn't up at all yet, so no connection can be made
time.sleep(0.5)
else:
raise GigantumException(
f'Could not reach JupyterLab at {test_url} after timeout')
def get_cache_manager_class(config: Configuration) -> Callable:
"""
Args:
config(Configuration): Configuration for the client
Returns:
gtmcore.dataset.cache.CacheManager
"""
dataset_config = config.config.get('datasets')
if not dataset_config:
# Fallback to default host manager
manager_str = 'host'
else:
manager_str = dataset_config.get('cache_manager')
if manager_str in SUPPORTED_CACHE_MANAGERS.keys():
module, package = SUPPORTED_CACHE_MANAGERS.get(manager_str) # type: ignore
imported = importlib.import_module(module, package)
class_instance = getattr(imported, package)
return class_instance
else:
raise GigantumException(f"Unsupported Dataset File Cache Manager: {manager_str}")
def start_mitm_proxy(cls, devtool_endpoint: str, target_key: str) -> str:
"""Launch a proxy cointainer between client and labbook.
Args:
devtool_endpoint: the specific target running a dev tool
target_key: a unique key for this instance (related to the monitored Project container - e.g., RStudio)
Returns:
str that contains the proxy endpoint as http://{ip}:{port}
"""
hkey = cls.get_mitm_redis_key(target_key)
# setup the environment - note that UID is obtained inside the container based on labmanager_share_vol
# (mounted at /mnt/share)
logfile_path = f'/mnt/share/{cls.logfile_dir}/{target_key}.rserver.dump'
env_var = [
f"LBENDPOINT={devtool_endpoint}", f"LOGFILE_NAME={logfile_path}"
]
nametag = f"gmitmproxy.{target_key}"
volumes_dict = {
'labmanager_share_vol': {
'bind': '/mnt/share',
'mode': 'rw'
}
}
docker_client = get_docker_client()
container = docker_client.containers.run("gigantum/mitmproxy_proxy:" +
CURRENT_MITMPROXY_TAG,
detach=True,
init=True,
name=nametag,
volumes=volumes_dict,
environment=env_var)
# We hammer repeatedly for 5 seconds (this should be very fast since it's a small, simple container)
for _ in range(10):
time.sleep(.5)
# Hope that our container is actually up and reload
container.reload()
mitm_ip = container.attrs['NetworkSettings']['Networks']['bridge'][
'IPAddress']
if mitm_ip:
break
if not mitm_ip:
raise GigantumException(
"Unable to get mitmproxy_proxy IP address.")
# This is the port for NGINX
mitm_endpoint = f'http://{mitm_ip}:8079'
# register the proxy in KV store
redis_conn = redis.Redis(db=1)
redis_conn.hset(hkey, "endpoint", mitm_endpoint)
redis_conn.hset(hkey, "container_id", container.id)
redis_conn.hset(hkey, "logfile_path", logfile_path)
redis_conn.hset(hkey, "devtool_endpoint", devtool_endpoint)
# make sure proxy is up.
for timeout in range(10):
time.sleep(1)
if ps_search(container, 'nginx'):
logger.info(
f"Proxy to rserver started within {timeout + 1} seconds")
break
else:
raise ValueError('mitmproxy failed to start after 10 seconds')
return mitm_endpoint
def start_jupyter(labbook: LabBook,
username: str,
tag: Optional[str] = None,
check_reachable: bool = True,
proxy_prefix: Optional[str] = None) -> str:
""" Main entrypoint to launching Jupyter. Note, the caller must
determine for themselves the host and port.
Returns:
Path to jupyter (e.g., "/lab?token=xyz")
"""
owner = InventoryManager().query_owner(labbook)
lb_key = tag or infer_docker_image_name(
labbook_name=labbook.name, owner=owner, username=username)
docker_client = get_docker_client()
lb_container = docker_client.containers.get(lb_key)
if lb_container.status != 'running':
raise GigantumException(
f"{str(labbook)} container is not running. Start it before launch a dev tool."
)
jupyter_ps = ps_search(lb_container, 'jupyter lab')
# Get IP of container on Docker Bridge Network
lb_ip_addr = get_container_ip(lb_key)
if len(jupyter_ps) == 1:
logger.info(f'Found existing Jupyter instance for {str(labbook)}.')
# Get token from PS in container
t = re.search("token='?([a-zA-Z\d-]+)'?", jupyter_ps[0])
if not t:
raise GigantumException('Cannot detect Jupyter Lab token')
token = t.groups()[0]
suffix = f'{proxy_prefix or ""}/lab/tree/code?token={token}'
if check_reachable:
check_jupyter_reachable(lb_ip_addr, DEFAULT_JUPYTER_PORT,
f'{proxy_prefix or ""}')
return suffix
elif len(jupyter_ps) == 0:
token = str(uuid.uuid4()).replace('-', '')
if proxy_prefix and proxy_prefix[0] != '/':
proxy_prefix = f'/{proxy_prefix}'
_start_jupyter_process(labbook, lb_container, username, lb_key, token,
proxy_prefix)
suffix = f'{proxy_prefix or ""}/lab/tree/code?token={token}'
if check_reachable:
check_jupyter_reachable(lb_ip_addr, DEFAULT_JUPYTER_PORT,
f'{proxy_prefix or ""}')
return suffix
else:
# If "ps aux" for jupyterlab returns multiple hits - this should never happen.
for n, l in enumerate(jupyter_ps):
logger.error(
f'Multiple JupyerLab instances - ({n+1} of {len(jupyter_ps)}) - {l}'
)
raise ValueError(
f'Multiple Jupyter Lab instances detected in project env. You should restart the container.'
)