/
iorw.py
559 lines (431 loc) Β· 15.7 KB
/
iorw.py
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# -*- coding: utf-8 -*-
import io
import os
import sys
import json
import yaml
import fnmatch
import nbformat
import requests
import warnings
import entrypoints
from contextlib import contextmanager
from tenacity import retry, retry_if_exception_type, stop_after_attempt, wait_exponential
from . import __version__
from .exceptions import (
PapermillException,
PapermillRateLimitException,
missing_dependency_generator,
missing_environment_variable_generator,
)
from .log import logger
from .utils import chdir
try:
from .s3 import S3
except ImportError:
S3 = missing_dependency_generator("boto3", "s3")
try:
from .adl import ADL
except ImportError:
ADL = missing_dependency_generator("azure.datalake.store", "azure")
except KeyError as exc:
if exc.args[0] == "APPDATA":
ADL = missing_environment_variable_generator("azure.datalake.store", "APPDATA")
else:
raise
try:
from .abs import AzureBlobStore
except ImportError:
AzureBlobStore = missing_dependency_generator("azure.storage.blob", "azure")
try:
from gcsfs import GCSFileSystem
except ImportError:
GCSFileSystem = missing_dependency_generator("gcsfs", "gcs")
try:
from pyarrow.fs import HadoopFileSystem, FileSelector
except ImportError:
HadoopFileSystem = missing_dependency_generator("pyarrow", "hdfs")
try:
from github import Github
except ImportError:
Github = missing_dependency_generator("pygithub", "github")
def fallback_gs_is_retriable(e):
try:
print(e.code)
return e.code is None or e.code == 429
except AttributeError:
print(e)
return False
try:
try:
# Default to gcsfs library's retry logic
from gcsfs.retry import is_retriable as gs_is_retriable
except ImportError:
from gcsfs.utils import is_retriable as gs_is_retriable
except ImportError:
gs_is_retriable = fallback_gs_is_retriable
try:
FileNotFoundError
except NameError:
FileNotFoundError = IOError
class PapermillIO(object):
'''
The holder which houses any io system registered with the system.
This object is used in a singleton manner to save and load particular
named Handler objects for reference externally.
'''
def __init__(self):
self.reset()
def read(self, path, extensions=['.ipynb', '.json']):
# Handle https://github.com/nteract/papermill/issues/317
notebook_metadata = self.get_handler(path, extensions).read(path)
if isinstance(notebook_metadata, (bytes, bytearray)):
return notebook_metadata.decode('utf-8')
return notebook_metadata
def write(self, buf, path, extensions=['.ipynb', '.json']):
return self.get_handler(path, extensions).write(buf, path)
def listdir(self, path):
return self.get_handler(path).listdir(path)
def pretty_path(self, path):
return self.get_handler(path).pretty_path(path)
def reset(self):
self._handlers = []
def register(self, scheme, handler):
# Keep these ordered as LIFO
self._handlers.insert(0, (scheme, handler))
def register_entry_points(self):
# Load handlers provided by other packages
for entrypoint in entrypoints.get_group_all("papermill.io"):
self.register(entrypoint.name, entrypoint.load())
def get_handler(self, path, extensions=None):
'''Get I/O Handler based on a notebook path
Parameters
----------
path : str or nbformat.NotebookNode or None
extensions : list of str, optional
Required file extension options for the path (if path is a string), which
will log a warning if there is no match. Defaults to None, which does not
check for any extensions
Raises
------
PapermillException: If a valid I/O handler could not be found for the input path
Returns
-------
I/O Handler
'''
if path is None:
return NoIOHandler()
if isinstance(path, nbformat.NotebookNode):
return NotebookNodeHandler()
if extensions:
if not fnmatch.fnmatch(os.path.basename(path).split('?')[0], '*.*'):
warnings.warn(
"the file is not specified with any extension : " + os.path.basename(path)
)
elif not any(
fnmatch.fnmatch(os.path.basename(path).split('?')[0], '*' + ext)
for ext in extensions
):
warnings.warn(
"The specified file ({}) does not end in one of {}".format(path, extensions)
)
local_handler = None
for scheme, handler in self._handlers:
if scheme == 'local':
local_handler = handler
if path.startswith(scheme):
return handler
if local_handler is None:
raise PapermillException(
"Could not find a registered schema handler for: {}".format(path)
)
return local_handler
class HttpHandler(object):
@classmethod
def read(cls, path):
return requests.get(path, headers={'Accept': 'application/json'}).text
@classmethod
def listdir(cls, path):
raise PapermillException('listdir is not supported by HttpHandler')
@classmethod
def write(cls, buf, path):
result = requests.put(path, json=json.loads(buf))
result.raise_for_status()
@classmethod
def pretty_path(cls, path):
return path
class LocalHandler(object):
def __init__(self):
self._cwd = None
def read(self, path):
try:
with chdir(self._cwd):
with io.open(path, 'r', encoding="utf-8") as f:
return f.read()
except IOError as e:
try:
# Check if path could be a notebook passed in as a
# string
json.loads(path)
return path
except ValueError:
# Propagate the IOError
raise e
def listdir(self, path):
with chdir(self._cwd):
return [os.path.join(path, fn) for fn in os.listdir(path)]
def write(self, buf, path):
with chdir(self._cwd):
dirname = os.path.dirname(path)
if dirname and not os.path.exists(dirname):
raise FileNotFoundError("output folder {} doesn't exist.".format(dirname))
with io.open(path, 'w', encoding="utf-8") as f:
f.write(buf)
def pretty_path(self, path):
return path
def cwd(self, new_path):
'''Sets the cwd during reads and writes'''
old_cwd = self._cwd
self._cwd = new_path
return old_cwd
class S3Handler(object):
@classmethod
def read(cls, path):
return "\n".join(S3().read(path))
@classmethod
def listdir(cls, path):
return S3().listdir(path)
@classmethod
def write(cls, buf, path):
return S3().cp_string(buf, path)
@classmethod
def pretty_path(cls, path):
return path
class ADLHandler(object):
def __init__(self):
self._client = None
def _get_client(self):
if self._client is None:
self._client = ADL()
return self._client
def read(self, path):
lines = self._get_client().read(path)
return "\n".join(lines)
def listdir(self, path):
return self._get_client().listdir(path)
def write(self, buf, path):
return self._get_client().write(buf, path)
def pretty_path(self, path):
return path
class ABSHandler(object):
def __init__(self):
self._client = None
def _get_client(self):
if self._client is None:
self._client = AzureBlobStore()
return self._client
def read(self, path):
lines = self._get_client().read(path)
return "\n".join(lines)
def listdir(self, path):
return self._get_client().listdir(path)
def write(self, buf, path):
return self._get_client().write(buf, path)
def pretty_path(self, path):
return path
class GCSHandler(object):
RATE_LIMIT_RETRIES = 3
RETRY_DELAY = 1
RETRY_MULTIPLIER = 1
RETRY_MAX_DELAY = 4
def __init__(self):
self._client = None
def _get_client(self):
if self._client is None:
self._client = GCSFileSystem()
return self._client
def read(self, path):
with self._get_client().open(path) as f:
return f.read()
def listdir(self, path):
return self._get_client().ls(path)
def write(self, buf, path):
# Wrapped so we can mock retry options during testing
@retry(
retry=retry_if_exception_type(PapermillRateLimitException),
stop=stop_after_attempt(self.RATE_LIMIT_RETRIES),
wait=wait_exponential(
multiplier=self.RETRY_MULTIPLIER, min=self.RETRY_DELAY, max=self.RETRY_MAX_DELAY
),
reraise=True,
)
def retry_write():
try:
with self._get_client().open(path, 'w') as f:
return f.write(buf)
except Exception as e:
try:
message = e.message
except AttributeError:
message = "Generic exception {} raised".format(type(e))
if gs_is_retriable(e):
raise PapermillRateLimitException(message)
# Reraise the original exception without retries
raise
return retry_write()
def pretty_path(self, path):
return path
class HDFSHandler(object):
def __init__(self):
self._client = None
def _get_client(self):
if self._client is None:
self._client = HadoopFileSystem(host="default")
return self._client
def read(self, path):
with self._get_client().open_input_stream(path) as f:
return f.read()
def listdir(self, path):
return [f.path for f in self._get_client().get_file_info(FileSelector(path))]
def write(self, buf, path):
with self._get_client().open_output_stream(path) as f:
return f.write(str.encode(buf))
def pretty_path(self, path):
return path
class GithubHandler(object):
def __init__(self):
self._client = None
def _get_client(self):
if self._client is None:
token = os.environ.get('GITHUB_ACCESS_TOKEN', None)
if token:
self._client = Github(token)
else:
self._client = Github()
return self._client
def read(self, path):
splits = path.split('/')
org_id = splits[3]
repo_id = splits[4]
ref_id = splits[6]
sub_path = '/'.join(splits[7:])
repo = self._get_client().get_repo(org_id + '/' + repo_id)
content = repo.get_contents(sub_path, ref=ref_id)
return content.decoded_content
def listdir(self, path):
raise PapermillException('listdir is not supported by GithubHandler')
def write(self, buf, path):
raise PapermillException('write is not supported by GithubHandler')
def pretty_path(self, path):
return path
class StreamHandler(object):
'''Handler for Stdin/Stdout streams'''
def read(self, path):
return sys.stdin.read()
def listdir(self, path):
raise PapermillException('listdir is not supported by Stream Handler')
def write(self, buf, path):
try:
return sys.stdout.buffer.write(buf.encode('utf-8'))
except AttributeError:
# Originally required by https://github.com/nteract/papermill/issues/420
# Support Buffer.io objects
return sys.stdout.write(buf.encode('utf-8'))
def pretty_path(self, path):
return path
class NotebookNodeHandler(object):
'''Handler for input_path of nbformat.NotebookNode object'''
def read(self, path):
return nbformat.writes(path)
def listdir(self, path):
raise PapermillException('listdir is not supported by NotebookNode Handler')
def write(self, buf, path):
raise PapermillException('write is not supported by NotebookNode Handler')
def pretty_path(self, path):
return 'NotebookNode object'
class NoIOHandler(object):
'''Handler for output_path of None - intended to not write anything'''
def read(self, path):
raise PapermillException('read is not supported by NoIOHandler')
def listdir(self, path):
raise PapermillException('listdir is not supported by NoIOHandler')
def write(self, buf, path):
return
def pretty_path(self, path):
return 'Notebook will not be saved'
# Hack to make YAML loader not auto-convert datetimes
# https://stackoverflow.com/a/52312810
class NoDatesSafeLoader(yaml.SafeLoader):
yaml_implicit_resolvers = {
k: [r for r in v if r[0] != 'tag:yaml.org,2002:timestamp']
for k, v in yaml.SafeLoader.yaml_implicit_resolvers.items()
}
# Instantiate a PapermillIO instance and register Handlers.
papermill_io = PapermillIO()
papermill_io.register("local", LocalHandler())
papermill_io.register("s3://", S3Handler)
papermill_io.register("adl://", ADLHandler())
papermill_io.register("abs://", ABSHandler())
papermill_io.register("http://", HttpHandler)
papermill_io.register("https://", HttpHandler)
papermill_io.register("gs://", GCSHandler())
papermill_io.register("hdfs://", HDFSHandler())
papermill_io.register("http://github.com/", GithubHandler())
papermill_io.register("https://github.com/", GithubHandler())
papermill_io.register("-", StreamHandler())
papermill_io.register_entry_points()
def read_yaml_file(path):
"""Reads a YAML file from the location specified at 'path'."""
return yaml.load(papermill_io.read(path, ['.json', '.yaml', '.yml']), Loader=NoDatesSafeLoader)
def write_ipynb(nb, path):
"""Saves a notebook object to the specified path.
Args:
nb_node (nbformat.NotebookNode): Notebook object to save.
notebook_path (str): Path to save the notebook object to.
"""
papermill_io.write(nbformat.writes(nb), path)
def load_notebook_node(notebook_path):
"""Returns a notebook object with papermill metadata loaded from the specified path.
Args:
notebook_path (str): Path to the notebook file.
Returns:
nbformat.NotebookNode
"""
nb = nbformat.reads(papermill_io.read(notebook_path), as_version=4)
nb_upgraded = nbformat.v4.upgrade(nb)
if nb_upgraded is not None:
nb = nb_upgraded
if not hasattr(nb.metadata, 'papermill'):
nb.metadata['papermill'] = {
'default_parameters': dict(),
'parameters': dict(),
'environment_variables': dict(),
'version': __version__,
}
for cell in nb.cells:
if not hasattr(cell.metadata, 'tags'):
cell.metadata['tags'] = [] # Create tags attr if one doesn't exist.
if not hasattr(cell.metadata, 'papermill'):
cell.metadata['papermill'] = dict()
return nb
def list_notebook_files(path):
"""Returns a list of all the notebook files in a directory."""
return [p for p in papermill_io.listdir(path) if p.endswith('.ipynb')]
def get_pretty_path(path):
return papermill_io.pretty_path(path)
@contextmanager
def local_file_io_cwd(path=None):
try:
local_handler = papermill_io.get_handler("local")
except PapermillException:
logger.warning("No local file handler detected")
else:
try:
old_cwd = local_handler.cwd(path or os.getcwd())
except AttributeError:
logger.warning("Local file handler does not support cwd assignment")
else:
try:
yield
finally:
local_handler.cwd(old_cwd)