"""
Argo specific layer on top of fsspec
This allows for file/memory/http/ftp stores with Argo dedicated methods
fs = filestore()
fs = memorystore()
fs = httpstore()
fs = ftpstore()
fs = httpstore_erddap_auth(payload = {"user": None, "password": None})
fs.open_dataset
fs.open_json
fs.open_mfdataset
fs.open_mfjson
fs.read_csv
"""
import os
import types
import xarray as xr
import pandas as pd
import fsspec
import aiohttp
import shutil
import pickle # nosec B403 only used with internal files/assets
import json
import time
import tempfile
import logging
from packaging import version
from typing import Union
from urllib.parse import urlparse, parse_qs
from functools import lru_cache
from abc import ABC, abstractmethod
import concurrent.futures
import multiprocessing
from ..options import OPTIONS
from ..errors import (
FileSystemHasNoCache,
CacheFileNotFound,
DataNotFound,
InvalidMethod,
ErddapHTTPUnauthorized,
ErddapHTTPNotFound,
)
from ..utils.transform import (
drop_variables_not_in_all_datasets,
fill_variables_not_in_all_datasets,
)
from ..utils.monitored_threadpool import MyThreadPoolExecutor as MyExecutor
from ..utils.accessories import Registry
from ..utils.format import UriCName
log = logging.getLogger("argopy.stores")
try:
from tqdm import tqdm
except ModuleNotFoundError:
log.debug("argopy needs tqdm installed to display progress bars")
def tqdm(fct, **kw):
return fct
try:
import distributed
has_distributed = True
except ModuleNotFoundError:
log.debug("argopy needs distributed to use Dask cluster/client")
has_distributed = False
def new_fs(
protocol: str = "",
cache: bool = False,
cachedir: str = OPTIONS["cachedir"],
cache_expiration: int = OPTIONS["cache_expiration"],
**kwargs,
):
"""Create a new fsspec file system
Parameters
----------
protocol: str (optional)
cache: bool (optional)
Use a filecache system on top of the protocol. Default: False
cachedir: str
Define path to cache directory.
**kwargs: (optional)
Other arguments passed to :class:`fsspec.filesystem`
"""
# Load default FSSPEC kwargs:
default_fsspec_kwargs = {"simple_links": True, "block_size": 0}
if protocol == "http":
default_fsspec_kwargs = {
**default_fsspec_kwargs,
**{"client_kwargs": {"trust_env": OPTIONS["trust_env"]}},
}
elif protocol == "ftp":
default_fsspec_kwargs = {
**default_fsspec_kwargs,
**{"block_size": 1000 * (2**20)},
}
# Merge default with user arguments:
fsspec_kwargs = {**default_fsspec_kwargs, **kwargs}
# Create filesystem:
if not cache:
fs = fsspec.filesystem(protocol, **fsspec_kwargs)
cache_registry = None
log_msg = (
"Opening a fsspec [file] system for '%s' protocol with options: %s"
% (protocol, str(fsspec_kwargs))
)
else:
# https://filesystem-spec.readthedocs.io/en/latest/_modules/fsspec/implementations/cached.html#WholeFileCacheFileSystem
fs = fsspec.filesystem(
"filecache",
target_protocol=protocol,
target_options={**fsspec_kwargs},
cache_storage=cachedir,
expiry_time=cache_expiration,
cache_check=10,
)
# We use a refresh rate for cache of 1 day,
# since this is the update frequency of the Ifremer erddap
cache_registry = Registry(
name="Cache"
) # Will hold uri cached by this store instance
log_msg = (
"Opening a fsspec [filecache, storage='%s'] system for '%s' protocol with options: %s"
% (cachedir, protocol, str(fsspec_kwargs))
)
if protocol == "file" and os.path.sep != fs.sep:
# For some reasons (see https://github.com/fsspec/filesystem_spec/issues/937), the property fs.sep is
# not '\' under Windows. So, using this dirty fix to overwrite it:
fs.sep = os.path.sep
# fsspec folks recommend to use posix internally. But I don't see how to handle this. So keeping this fix
# because it solves issues with failing tests under Windows. Enough at this time.
# todo: Revisit this choice in a while
# log_msg = "%s\n[sys sep=%s] vs [fs sep=%s]" % (log_msg, os.path.sep, fs.sep)
# log.warning(log_msg)
log.debug(log_msg)
# log_argopy_callerstack()
return fs, cache_registry
[docs]class argo_store_proto(ABC):
"""Argo Abstract File System
Provide a prototype for Argo file systems
Should this class inherits from fsspec.spec.AbstractFileSystem ?
"""
protocol = ""
"""str: File system name, one in fsspec.registry.known_implementations"""
[docs] def __init__(self, cache: bool = False, cachedir: str = "", **kwargs):
"""Create a file storage system for Argo data
Parameters
----------
cache: bool (False)
cachedir: str (from OPTIONS)
**kwargs: (optional)
Other arguments passed to :class:`fsspec.filesystem`
"""
self.cache = cache
self.cachedir = OPTIONS["cachedir"] if cachedir == "" else cachedir
self._fsspec_kwargs = {**kwargs}
self.fs, self.cache_registry = new_fs(
self.protocol, self.cache, self.cachedir, **self._fsspec_kwargs
)
def open(self, path, *args, **kwargs):
self.register(path)
# log.debug("Opening path: %s" % path)
return self.fs.open(path, *args, **kwargs)
def glob(self, path, **kwargs):
return self.fs.glob(path, **kwargs)
def exists(self, path, *args):
return self.fs.exists(path, *args)
def expand_path(self, path):
if self.protocol != "http" and self.protocol != "https":
return self.fs.expand_path(path)
else:
return [path]
def store_path(self, uri):
path = uri
path = self.expand_path(path)[0]
if not path.startswith(self.fs.target_protocol) and version.parse(
fsspec.__version__
) <= version.parse("0.8.3"):
path = self.fs.target_protocol + "://" + path
return path
def register(self, uri):
"""Keep track of files open with this instance"""
if self.cache:
path = self.store_path(uri)
if path not in self.cache_registry:
self.cache_registry.commit(path)
@property
def cached_files(self):
if version.parse(fsspec.__version__) <= version.parse("2023.6.0"):
return self.fs.cached_files
else:
# See https://github.com/euroargodev/argopy/issues/294
return self.fs._metadata.cached_files
def cachepath(self, uri: str, errors: str = "raise"):
"""Return path to cached file for a given URI"""
if not self.cache:
if errors == "raise":
raise FileSystemHasNoCache("%s has no cache system" % type(self.fs))
elif uri is not None:
store_path = self.store_path(uri)
self.fs.load_cache() # Read set of stored blocks from file and populate self.cached_files
if store_path in self.cached_files[-1]:
return os.path.sep.join(
[self.cachedir, self.cached_files[-1][store_path]["fn"]]
)
elif errors == "raise":
raise CacheFileNotFound(
"No cached file found in %s for: \n%s" % (self.fs.storage[-1], uri)
)
else:
raise CacheFileNotFound(
"No cached file found in %s for: \n%s" % (self.fs.storage[-1], uri)
)
def _clear_cache_item(self, uri):
"""Remove medadata and file for fsspec cache uri"""
fn = os.path.join(self.fs.storage[-1], "cache")
self.fs.load_cache() # Read set of stored blocks from file and populate self.cached_files
cache = self.cached_files[-1]
# Read cache metadata:
if os.path.exists(fn):
if version.parse(fsspec.__version__) <= version.parse("2023.6.0"):
with open(fn, "rb") as f:
cached_files = pickle.load(f) # nosec B301 because files controlled internally
else:
with open(fn, "r") as f:
cached_files = json.load(f)
else:
cached_files = cache
# Build new metadata without uri to delete, and delete corresponding cached file:
cache = {}
for k, v in cached_files.items():
if k != uri:
cache[k] = v.copy()
else:
# Delete file:
os.remove(os.path.join(self.fs.storage[-1], v["fn"]))
# log.debug("Removed %s -> %s" % (uri, v['fn']))
# Update cache metadata file:
if version.parse(fsspec.__version__) <= version.parse("2023.6.0"):
with tempfile.NamedTemporaryFile(mode="wb", delete=False) as f:
pickle.dump(cache, f)
shutil.move(f.name, fn)
else:
with fsspec.utils.atomic_write(fn, mode="w") as f:
json.dump(cache, f)
def clear_cache(self):
"""Remove cache files and entry from uri open with this store instance"""
if self.cache:
for uri in self.cache_registry:
# log.debug("Removing from cache %s" % uri)
self._clear_cache_item(uri)
self.cache_registry.clear() # Reset registry
@abstractmethod
def open_dataset(self, *args, **kwargs):
raise NotImplementedError("Not implemented")
@abstractmethod
def read_csv(self):
raise NotImplementedError("Not implemented")
[docs]class filestore(argo_store_proto):
"""Argo local file system
Relies on :class:`fsspec.implementations.local.LocalFileSystem`
"""
protocol = "file"
def open_json(self, url, **kwargs):
"""Return a json from a path, or verbose errors
Parameters
----------
path: str
Path to resources passed to :func:`json.loads`
*args, **kwargs:
Other arguments passed to :func:`json.loads`
Returns
-------
json
"""
with self.open(url) as of:
js = json.load(of, **kwargs)
if len(js) == 0:
js = None
return js
[docs] def open_dataset(self, path, *args, **kwargs):
"""Return a xarray.dataset from a path.
Parameters
----------
path: str
Path to resources passed to xarray.open_dataset
*args, **kwargs:
Other arguments are passed to :func:`xarray.open_dataset`
Returns
-------
:class:`xarray.DataSet`
"""
xr_opts = {}
if "xr_opts" in kwargs:
xr_opts.update(kwargs["xr_opts"])
with self.open(path) as of:
# log.debug("Opening dataset: '%s'" % path) # Redundant with fsspec logger
ds = xr.open_dataset(of, *args, **xr_opts)
ds.load()
if "source" not in ds.encoding:
if isinstance(path, str):
ds.encoding["source"] = path
return ds.copy()
def _mfprocessor(
self,
url,
preprocess=None,
preprocess_opts={},
open_dataset_opts={},
*args,
**kwargs,
):
# Load data
ds = self.open_dataset(url, **open_dataset_opts)
# Pre-process
if isinstance(preprocess, types.FunctionType) or isinstance(
preprocess, types.MethodType
):
ds = preprocess(ds, **preprocess_opts)
return ds
[docs] def open_mfdataset(
self, # noqa: C901
urls,
concat_dim="row",
max_workers: int = 6,
method: str = "thread",
progress: bool = False,
concat: bool = True,
preprocess=None,
preprocess_opts={},
open_dataset_opts={},
errors: str = "ignore",
*args,
**kwargs,
):
"""Open multiple urls as a single xarray dataset.
This is a version of the ``open_dataset`` method that is able to handle a list of urls/paths
sequentially or in parallel.
Use a Threads Pool by default for parallelization.
Parameters
----------
urls: list(str)
List of url/path to open
concat_dim: str
Name of the dimension to use to concatenate all datasets (passed to :class:`xarray.concat`)
max_workers: int
Maximum number of threads or processes
method: str
The parallelization method to execute calls asynchronously:
- ``thread`` (Default): use a pool of at most ``max_workers`` threads
- ``process``: use a pool of at most ``max_workers`` processes
- (XFAIL) a :class:`distributed.client.Client` object (:class:`distributed.client.Client`)
Use 'seq' to simply open data sequentially
progress: bool
Display a progress bar (True by default)
preprocess: callable (optional)
If provided, call this function on each dataset prior to concatenation
errors: str
Should it 'raise' or 'ignore' errors. Default: 'ignore'
Returns
-------
:class:`xarray.Dataset`
"""
if not isinstance(urls, list):
urls = [urls]
results = []
if method in ["thread", "process"]:
if method == "thread":
ConcurrentExecutor = concurrent.futures.ThreadPoolExecutor(
max_workers=max_workers
)
else:
if max_workers == 6:
max_workers = multiprocessing.cpu_count()
ConcurrentExecutor = concurrent.futures.ProcessPoolExecutor(
max_workers=max_workers
)
with ConcurrentExecutor as executor:
future_to_url = {
executor.submit(
self._mfprocessor,
url,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
): url
for url in urls
}
futures = concurrent.futures.as_completed(future_to_url)
if progress:
futures = tqdm(
futures, total=len(urls), disable="disable" in [progress]
)
for future in futures:
data = None
# url = future_to_url[future]
try:
data = future.result()
except Exception as e:
if errors == "ignore":
log.debug(
"Ignored error with this file: %s\nException raised: %s"
% (future_to_url[future], str(e.args))
)
pass
else:
raise
finally:
results.append(data)
elif has_distributed and isinstance(method, distributed.client.Client):
# Use a dask client:
if progress:
from dask.diagnostics import ProgressBar
with ProgressBar():
futures = method.map(
self._mfprocessor,
urls,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
)
results = method.gather(futures)
else:
futures = method.map(
self._mfprocessor,
urls,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
)
results = method.gather(futures)
elif method in ["seq", "sequential"]:
if progress:
urls = tqdm(urls, total=len(urls), disable="disable" in [progress])
for url in urls:
data = None
try:
data = self._mfprocessor(
url,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
)
except Exception as e:
if errors == "ignore":
log.debug(
"Ignored error with this url: %s\nException raised: %s"
% (url, str(e.args))
)
pass
else:
raise
finally:
results.append(data)
else:
raise InvalidMethod(method)
# Post-process results
results = [r for r in results if r is not None] # Only keep non-empty results
if len(results) > 0:
if concat:
# ds = xr.concat(results, dim=concat_dim, data_vars='all', coords='all', compat='override')
ds = xr.concat(
results,
dim=concat_dim,
data_vars="minimal",
coords="minimal",
compat="override",
)
return ds
else:
return results
else:
raise DataNotFound(urls)
[docs] def read_csv(self, path, **kwargs):
"""Return a pandas.dataframe from a path that is a csv resource
Parameters
----------
Path: str
Path to csv resources passed to :func:`pandas.read_csv`
Returns
-------
:class:`pandas.DataFrame`
"""
log.debug("Reading csv: %s" % path)
with self.open(path) as of:
df = pd.read_csv(of, **kwargs)
return df
[docs]class memorystore(filestore):
"""Argo in-memory file system (global)
Note that this inherits from :class:`argopy.stores.filestore`, not the:class:`argopy.stores.argo_store_proto`.
Relies on :class:`fsspec.implementations.memory.MemoryFileSystem`
"""
protocol = "memory"
[docs] def exists(self, path, *args):
"""Check if path can be open or not
Special handling for memory store
The fsspec.exists() will return False even if the path is in cache.
Here we bypass this in order to return True if the path is in cache.
This assumes that the goal of fs.exists is to determine if we can load the path or not.
If the path is in cache, it can be loaded.
"""
guess = self.fs.exists(path, *args)
if not guess:
try:
self.cachepath(path)
return True
except CacheFileNotFound:
pass
except FileSystemHasNoCache:
pass
return guess
[docs]class httpstore(argo_store_proto):
"""Argo http file system
Relies on :class:`fsspec.implementations.http.HTTPFileSystem`
This store intends to make argopy: safer to failures from http requests and to provide higher levels methods to
work with our datasets
This store is primarily used by the Erddap/Argovis data/index fetchers
"""
protocol = "http"
def curateurl(self, url):
"""Possibly replace server of a given url by a local argopy option value
This is intended to be used by tests and dev
"""
return url
# if OPTIONS["server"] is not None:
# # log.debug("Replaced '%s' with '%s'" % (urlparse(url).netloc, OPTIONS["netloc"]))
#
# if urlparse(url).scheme == "":
# patternA = "//%s" % (urlparse(url).netloc)
# else:
# patternA = "%s://%s" % (urlparse(url).scheme, urlparse(url).netloc)
#
# patternB = "%s://%s" % (urlparse(OPTIONS["server"]).scheme, urlparse(OPTIONS["server"]).netloc)
# log.debug(patternA)
# log.debug(patternB)
#
# new_url = url.replace(patternA, patternB)
# # log.debug(url)
# # log.debug(new_url)
# return new_url
# else:
# # log.debug("'%s' left unchanged" % urlparse(url).netloc)
# log.debug(url)
# return url
def download_url(
self,
url,
n_attempt: int = 1,
max_attempt: int = 5,
cat_opts: dict = {},
*args,
**kwargs,
):
"""URL data downloader
This is basically a fsspec.cat_file that is able tho handle a 429 "Too many requests" error from a server, by
waiting and sending requests several time.
"""
def make_request(
ffs, url, n_attempt: int = 1, max_attempt: int = 5, cat_opts: dict = {}
):
data = None
if n_attempt <= max_attempt:
try:
data = ffs.cat_file(url, **cat_opts)
except aiohttp.ClientResponseError as e:
if e.status == 413:
log.debug(
"Error %i (Payload Too Large) raised with %s"
% (e.status, url)
)
raise
elif e.status == 429:
retry_after = int(e.headers.get("Retry-After", 5))
log.debug(
f"Error {e.status} (Too many requests). Retry after {retry_after} seconds. Tentative {n_attempt}/{max_attempt}"
)
time.sleep(retry_after)
n_attempt += 1
make_request(ffs, url, n_attempt=n_attempt, cat_opts=cat_opts)
else:
# Handle other client response errors
print(f"Error: {e}")
except aiohttp.ClientError:
# Handle other request exceptions
# print(f"Error: {e}")
raise
else:
raise ValueError(
f"Error: All attempts failed to download this url: {url}"
)
return data, n_attempt
url = self.curateurl(url)
data, n = make_request(
self.fs,
url,
n_attempt=n_attempt,
max_attempt=max_attempt,
cat_opts=cat_opts,
)
if data is None:
raise FileNotFoundError(url)
return data
[docs] def open_dataset(self, url, **kwargs):
"""Open and decode a xarray dataset from an url
Parameters
----------
url: str
kwargs: dict
The 'dwn_opts' key is passed to self.download_url
The 'xr_opts' key is passed to xr.open_dataset
Returns
-------
:class:`xarray.Dataset`
"""
dwn_opts = {}
if "download_url_opts" in kwargs:
dwn_opts.update(kwargs["download_url_opts"])
data = self.download_url(url, **dwn_opts)
if data[0:3] != b"CDF":
raise TypeError(
"We didn't get a CDF binary data as expected ! We get: %s" % data
)
xr_opts = {}
if "xr_opts" in kwargs:
xr_opts.update(kwargs["xr_opts"])
ds = xr.open_dataset(data, **xr_opts)
if "source" not in ds.encoding:
if isinstance(url, str):
ds.encoding["source"] = url
self.register(url)
return ds
def _mfprocessor_dataset(
self,
url,
preprocess=None,
preprocess_opts={},
open_dataset_opts={},
*args,
**kwargs,
):
"""Used by httpstore.open_mfdataset"""
# Load data
ds = self.open_dataset(url, **open_dataset_opts)
# Pre-process
if isinstance(preprocess, types.FunctionType) or isinstance(
preprocess, types.MethodType
):
ds = preprocess(ds, **preprocess_opts)
return ds
def _open_mfdataset_from_erddap(
self,
urls: list,
concat_dim="rows",
max_workers: int = 6,
preprocess=None,
preprocess_opts: {} = None,
concat: bool = True,
progress: bool = True,
compute_details: bool = False,
*args,
**kwargs,
):
"""
Method used by httpstore.open_mfdataset dedicated to handle the case where we need to create a dataset from
multiples erddap urls download/preprocessing and need a visual feedback of the procedure up to the final merge.
- httpstore.open_dataset is distributed is handle by a pool of threads
"""
strUrl = lambda x: x.replace("https://", "").replace( # noqa: E731
"http://", ""
)
@lru_cache
def task_fct(url):
try:
ds = self.open_dataset(url)
ds.attrs['Fetched_url'] = url
ds.attrs['Fetched_constraints'] = UriCName(url).cname
return ds, True
except FileNotFoundError:
log.debug("task_fct: This url returned no data: %s" % strUrl(url))
return DataNotFound(url), True
except Exception as e:
log.debug("task_fct: Unexpected error when opening a remote dataset: '%s'" % str(e))
return None, False
def postprocessing_fct(obj, **kwargs):
if isinstance(obj, xr.Dataset):
try:
ds = preprocess(obj, **kwargs)
return ds, True
except Exception as e:
log.debug("postprocessing_fct: Unexpected error when post-processing dataset: '%s'" % str(e))
return None, False
elif isinstance(obj, DataNotFound):
return obj, True
elif obj is None:
# This is because some un-expected Exception was raised in task_fct(url)
return None, False
else:
log.debug("postprocessing_fct: Unexpected object: '%s'" % type(obj))
return None, False
def finalize(obj_list, **kwargs):
try:
# Read list of datasets from the list of objects:
ds_list = [v for v in dict(sorted(obj_list.items())).values()]
# Only keep non-empty results:
ds_list = [r for r in ds_list if (r is not None and not isinstance(r, DataNotFound))]
# log.debug(ds_list)
if len(ds_list) > 0:
if "data_vars" in kwargs and kwargs["data_vars"] == "all":
# log.info('fill_variables_not_in_all_datasets')
ds_list = fill_variables_not_in_all_datasets(
ds_list, concat_dim=concat_dim
)
else:
# log.info('drop_variables_not_in_all_datasets')
ds_list = drop_variables_not_in_all_datasets(ds_list)
log.info("Nb of dataset to concat: %i" % len(ds_list))
# log.debug(concat_dim)
# for ds in ds_list:
# log.debug(ds[concat_dim])
log.info(
"Dataset sizes before concat: %s"
% [len(ds[concat_dim]) for ds in ds_list]
)
ds = xr.concat(
ds_list,
dim=concat_dim,
data_vars="minimal",
coords="minimal",
compat="override",
)
log.info("Dataset size after concat: %i" % len(ds[concat_dim]))
return ds, True
else:
ds_list = [v for v in dict(sorted(obj_list.items())).values()]
# Is the ds_list full of None or DataNotFound ?
if len([r for r in ds_list if (r is None)]) == len(ds_list):
log.debug("finalize: An error occurred with all URLs !")
return ValueError("An un-expected error occurred with all URLs, check log file for more "
"information"), True
elif len([r for r in ds_list if isinstance(r, DataNotFound)]) == len(ds_list):
log.debug("finalize: All URLs returned DataNotFound !")
return DataNotFound("All URLs returned DataNotFound !"), True
except Exception as e:
log.debug("finalize: Unexpected error when finalize request: '%s'" % str(e))
return None, False
if ".nc" in urls[0]:
task_legend = {
"w": "Downloading netcdf from the erddap",
"p": "Formatting xarray dataset",
"c": "Callback",
"f": "Failed or No Data",
}
else:
task_legend = {"w": "Working", "p": "Post-processing", "c": "Callback"}
if concat:
finalize_fct = finalize
else:
finalize_fct = None
run = MyExecutor(
max_workers=max_workers,
task_fct=task_fct,
postprocessing_fct=postprocessing_fct,
postprocessing_fct_kwargs=preprocess_opts,
finalize_fct=finalize_fct,
finalize_fct_kwargs=kwargs["final_opts"] if "final_opts" in kwargs else {},
task_legend=task_legend,
final_legend={
"task": "Processing data chunks",
"final": "Merging chunks of xarray dataset",
},
show=progress,
)
results, failed = run.execute(urls, list_failed=True)
if concat:
# results = Union[xr.DataSet, DataNotFound, None]
if isinstance(results, xr.Dataset):
if not compute_details:
return results
else:
return results, failed, len(results)
elif results is None:
raise DataNotFound("An error occurred while finalizing the dataset")
else:
raise results
elif len(failed) == len(urls):
raise ValueError(
"Errors happened with all URLs, this could be due to an internal impossibility to read returned content"
)
else:
if len([r for r in results if r == DataNotFound]) == len(urls):
raise DataNotFound("All URLs returned DataNotFound !")
else:
if not compute_details:
return results
else:
return results, failed, len(results)
[docs] def open_mfdataset(
self, # noqa: C901
urls,
max_workers: int = 6,
method: str = "thread",
progress: Union[bool, str] = False,
concat: bool = True,
concat_dim="row",
preprocess=None,
preprocess_opts={},
open_dataset_opts={},
errors: str = "ignore",
compute_details: bool = False,
*args,
**kwargs,
):
"""Open multiple urls as a single xarray dataset.
This is a version of the :class:`argopy.stores.httpstore.open_dataset` method that is able to
handle a list of urls/paths sequentially or in parallel.
Use a Threads Pool by default for parallelization.
Parameters
----------
urls: list(str)
List of url/path to open
max_workers: int, default: 6
Maximum number of threads or processes
method: str, default: ``thread``
The parallelization method to execute calls asynchronously:
- ``thread`` (default): use a pool of at most ``max_workers`` threads
- ``process``: use a pool of at most ``max_workers`` processes
- :class:`distributed.client.Client`: Experimental, expect this method to fail !
- ``seq``: open data sequentially, no parallelization applied
- ``erddap``: use a pool of at most ``max_workers`` threads, comes with a nice dashboard dedicated
to erddap server requests.
progress: bool, default: False
Display a progress bar
concat: bool, default: True
Concatenate results in a single :class:`xarray.Dataset` or not (in this case, function will return a
list of :class:`xarray.Dataset`)
concat_dim: str, default: ``row``
Name of the dimension to use to concatenate all datasets (passed to :class:`xarray.concat`)
preprocess: callable (optional)
If provided, call this function on each dataset prior to concatenation
preprocess_opts: dict (optional)
If ``preprocess`` is provided, pass this as options
errors: str, default: ``ignore``
Define how to handle errors raised during data URIs fetching:
- ``raise``: Raise any error encountered
- ``ignore`` (default): Do not stop processing, simply issue a debug message in logging console
- ``silent``: Do not stop processing and do not issue log message
Other args and kwargs: other options passed to :class:`argopy.stores.httpstore.open_dataset`.
Returns
-------
output: :class:`xarray.Dataset` or list of :class:`xarray.Dataset`
"""
strUrl = lambda x: x.replace("https://", "").replace( # noqa: E731
"http://", ""
)
if not isinstance(urls, list):
urls = [urls]
urls = [self.curateurl(url) for url in urls]
results = []
failed = []
################################
if method == "erddap":
return self._open_mfdataset_from_erddap(
urls=urls,
concat_dim=concat_dim,
max_workers=max_workers,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
concat=concat,
progress=progress,
compute_details=compute_details,
*args,
**kwargs,
)
################################
if method == "thread":
ConcurrentExecutor = concurrent.futures.ThreadPoolExecutor(
max_workers=max_workers
)
with ConcurrentExecutor as executor:
future_to_url = {
executor.submit(
self._mfprocessor_dataset,
url,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
): url
for url in urls
}
futures = concurrent.futures.as_completed(future_to_url)
if progress:
futures = tqdm(
futures, total=len(urls), disable="disable" in [progress]
)
for future in futures:
data = None
try:
data = future.result()
except Exception:
failed.append(future_to_url[future])
if errors == "ignore":
log.debug(
"Ignored error with this url: %s"
% strUrl(future_to_url[future])
)
# See fsspec.http logger for more
pass
elif errors == "silent":
pass
else:
raise
finally:
results.append(data)
################################
elif method == "process":
if max_workers == 6:
max_workers = multiprocessing.cpu_count()
ConcurrentExecutor = concurrent.futures.ProcessPoolExecutor(
max_workers=max_workers
)
with ConcurrentExecutor as executor:
future_to_url = {
executor.submit(
self._mfprocessor_dataset,
url,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
): url
for url in urls
}
futures = concurrent.futures.as_completed(future_to_url)
if progress:
futures = tqdm(
futures, total=len(urls), disable="disable" in [progress]
)
for future in futures:
data = None
try:
data = future.result()
except Exception:
failed.append(future_to_url[future])
if errors == "ignore":
log.debug(
"Ignored error with this url: %s"
% strUrl(future_to_url[future])
)
# See fsspec.http logger for more
pass
elif errors == "silent":
pass
else:
raise
finally:
results.append(data)
################################
elif has_distributed and isinstance(method, distributed.client.Client):
# Use a dask client:
if progress:
from dask.diagnostics import ProgressBar
with ProgressBar():
futures = method.map(
self._mfprocessor_dataset,
urls,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
)
results = method.gather(futures)
else:
futures = method.map(
self._mfprocessor_dataset,
urls,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
)
results = method.gather(futures)
################################
elif method in ["seq", "sequential"]:
if progress:
urls = tqdm(urls, total=len(urls), disable="disable" in [progress])
for url in urls:
data = None
try:
data = self._mfprocessor_dataset(
url,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
)
except Exception:
failed.append(url)
if errors == "ignore":
log.debug(
"Ignored error with this url: %s" % strUrl(url)
) # See fsspec.http logger for more
pass
elif errors == "silent":
pass
else:
raise
finally:
results.append(data)
################################
else:
raise InvalidMethod(method)
################################
# Post-process results
results = [r for r in results if r is not None] # Only keep non-empty results
if len(results) > 0:
if concat:
# ds = xr.concat(results, dim=concat_dim, data_vars='all', coords='all', compat='override')
results = drop_variables_not_in_all_datasets(results)
ds = xr.concat(
results,
dim=concat_dim,
data_vars="minimal",
coords="minimal",
compat="override",
)
if not compute_details:
return ds
else:
return ds, failed, len(results)
else:
return results
elif len(failed) == len(urls):
raise ValueError(
"Errors happened with all URLs, this could be due to an internal impossibility to read returned content."
)
else:
raise DataNotFound(urls)
[docs] def read_csv(self, url, **kwargs):
"""Read a comma-separated values (csv) url into Pandas DataFrame.
Parameters
----------
url: str
**kwargs: Arguments passed to :class:`pandas.read_csv`
Returns
-------
:class:`pandas.DataFrame`
"""
url = self.curateurl(url)
# log.debug("Opening/reading csv from: %s" % url)
with self.open(url) as of:
df = pd.read_csv(of, **kwargs)
return df
[docs] def open_json(self, url, **kwargs):
"""Return a json from an url, or verbose errors
Parameters
----------
url: str
Returns
-------
json
"""
data = self.download_url(url)
js = json.loads(data, **kwargs)
if len(js) == 0:
js = None
self.register(url)
return js
def _mfprocessor_json(
self, url, preprocess=None, url_follow=False, *args, **kwargs
):
# Load data
data = self.open_json(url, **kwargs)
# Pre-process
if data is None:
raise DataNotFound(url)
elif isinstance(preprocess, types.FunctionType) or isinstance(
preprocess, types.MethodType
):
if url_follow:
data = preprocess(data, url=url, **kwargs)
else:
data = preprocess(data)
return data
[docs] def open_mfjson(
self, # noqa: C901
urls,
max_workers: int = 6,
method: str = "thread",
progress: Union[bool, str] = False,
preprocess=None,
url_follow=False,
errors: str = "ignore",
*args,
**kwargs,
):
"""Open multiple json urls
This is a parallelized version of ``open_json``.
Use a Threads Pool by default for parallelization.
Parameters
----------
urls: list(str)
max_workers: int
Maximum number of threads or processes.
method:
The parallelization method to execute calls asynchronously:
- 'thread' (Default): use a pool of at most ``max_workers`` threads
- 'process': use a pool of at most ``max_workers`` processes
- (XFAIL) Dask client object: use a Dask distributed client object
Use 'seq' to simply open data sequentially
progress: bool
Display a progress bar (True by default, not for dask client method)
preprocess: (callable, optional)
If provided, call this function on each json set
url_follow: bool, False
Follow the URL to the preprocess method as ``url`` argument.
Returns
-------
list()
"""
strUrl = lambda x: x.replace("https://", "").replace( # noqa: E731
"http://", ""
)
if not isinstance(urls, list):
urls = [urls]
urls = [self.curateurl(url) for url in urls]
results = []
failed = []
if method in ["thread", "process"]:
if method == "thread":
ConcurrentExecutor = concurrent.futures.ThreadPoolExecutor(
max_workers=max_workers
)
else:
if max_workers == 6:
max_workers = multiprocessing.cpu_count()
ConcurrentExecutor = concurrent.futures.ProcessPoolExecutor(
max_workers=max_workers
)
with ConcurrentExecutor as executor:
future_to_url = {
executor.submit(
self._mfprocessor_json,
url,
preprocess=preprocess,
url_follow=url_follow,
*args,
**kwargs,
): url
for url in urls
}
futures = concurrent.futures.as_completed(future_to_url)
if progress:
futures = tqdm(
futures, total=len(urls), disable="disable" in [progress]
)
for future in futures:
data = None
try:
data = future.result()
except Exception:
failed.append(future_to_url[future])
if errors == "ignore":
log.debug(
"Ignored error with this url: %s"
% strUrl(future_to_url[future])
)
# See fsspec.http logger for more
pass
elif errors == "silent":
pass
else:
raise
finally:
results.append(data)
# elif type(method) == distributed.client.Client:
# # Use a dask client:
# futures = method.map(self._mfprocessor_json, urls, preprocess=preprocess, *args, **kwargs)
# results = method.gather(futures)
elif method in ["seq", "sequential"]:
if progress:
# log.debug("We asked for a progress bar !")
urls = tqdm(urls, total=len(urls), disable="disable" in [progress])
for url in urls:
data = None
try:
data = self._mfprocessor_json(
url,
preprocess=preprocess,
url_follow=url_follow,
*args,
**kwargs,
)
except Exception:
failed.append(url)
if errors == "ignore":
log.debug("Ignored error with this url: %s" % strUrl(url))
# See fsspec.http logger for more
pass
elif errors == "silent":
pass
else:
raise
finally:
results.append(data)
else:
raise InvalidMethod(method)
# Post-process results
results = [r for r in results if r is not None] # Only keep non-empty results
if len(results) > 0:
return results
else:
raise DataNotFound(urls)
[docs]class ftpstore(httpstore):
"""Argo ftp file system
Relies on :class:`fsspec.implementations.ftp.FTPFileSystem`
"""
protocol = "ftp"
[docs] def open_dataset(self, url, *args, **kwargs):
"""Open and decode a xarray dataset from an ftp url
Parameters
----------
url: str
Returns
-------
:class:`xarray.Dataset`
"""
try:
this_url = self.fs._strip_protocol(url)
data = self.fs.cat_file(this_url)
except Exception:
log.debug("Error with: %s" % url)
# except aiohttp.ClientResponseError as e:
raise
xr_opts = {}
if "xr_opts" in kwargs:
xr_opts.update(kwargs["xr_opts"])
ds = xr.open_dataset(data, *args, **xr_opts)
if "source" not in ds.encoding:
if isinstance(url, str):
ds.encoding["source"] = url
self.register(this_url)
self.register(url)
return ds
def _mfprocessor_dataset(
self,
url,
preprocess=None,
preprocess_opts={},
open_dataset_opts={},
*args,
**kwargs,
):
# Load data
ds = self.open_dataset(url, **open_dataset_opts)
# Pre-process
if isinstance(preprocess, types.FunctionType) or isinstance(
preprocess, types.MethodType
):
ds = preprocess(ds, **preprocess_opts)
return ds
[docs] def open_mfdataset(
self, # noqa: C901
urls,
max_workers: int = 6,
method: str = "seq",
progress: bool = False,
concat: bool = True,
concat_dim="row",
preprocess=None,
preprocess_opts={},
open_dataset_opts={},
errors: str = "ignore",
*args,
**kwargs,
):
"""Open multiple ftp urls as a single xarray dataset.
This is a version of the :class:`argopy.stores.ftpstore.open_dataset` method that is able
to handle a list of urls/paths sequentially or in parallel.
Use a Threads Pool by default for parallelization.
Parameters
----------
urls: list(str)
List of url/path to open
max_workers: int, default: 6
Maximum number of threads or processes
method: str, default: ``thread``
The parallelization method to execute calls asynchronously:
- ``seq`` (default): open data sequentially, no parallelization applied
- ``process``: use a pool of at most ``max_workers`` processes
- :class:`distributed.client.Client`: Experimental, expect this method to fail !
progress: bool, default: False
Display a progress bar
concat: bool, default: True
Concatenate results in a single :class:`xarray.Dataset` or not (in this case, function will return a
list of :class:`xarray.Dataset`)
concat_dim: str, default: ``row``
Name of the dimension to use to concatenate all datasets (passed to :class:`xarray.concat`)
preprocess: callable (optional)
If provided, call this function on each dataset prior to concatenation
preprocess_opts: dict (optional)
If ``preprocess`` is provided, pass this as options
errors: str, default: ``ignore``
Define how to handle errors raised during data URIs fetching:
- ``raise``: Raise any error encountered
- ``ignore`` (default): Do not stop processing, simply issue a debug message in logging console
- ``silent``: Do not stop processing and do not issue log message
Other args and kwargs: other options passed to :class:`argopy.stores.httpstore.open_dataset`.
Returns
-------
output: :class:`xarray.Dataset` or list of :class:`xarray.Dataset`
"""
strUrl = lambda x: x.replace("ftps://", "").replace("ftp://", "") # noqa: E731
if not isinstance(urls, list):
urls = [urls]
results = []
failed = []
if method in ["process"]:
if max_workers == 6:
max_workers = multiprocessing.cpu_count()
ConcurrentExecutor = concurrent.futures.ProcessPoolExecutor(
max_workers=max_workers
)
with ConcurrentExecutor as executor:
future_to_url = {
executor.submit(
self._mfprocessor_dataset,
url,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
): url
for url in urls
}
futures = concurrent.futures.as_completed(future_to_url)
if progress:
futures = tqdm(
futures, total=len(urls), disable="disable" in [progress]
)
for future in futures:
data = None
try:
data = future.result()
except Exception:
failed.append(future_to_url[future])
if errors == "ignore":
log.debug(
"Ignored error with this url: %s"
% strUrl(future_to_url[future])
)
# See fsspec.http logger for more
pass
elif errors == "silent":
pass
else:
raise
finally:
results.append(data)
elif has_distributed and isinstance(method, distributed.client.Client):
# Use a dask client:
if progress:
from dask.diagnostics import ProgressBar
with ProgressBar():
futures = method.map(
self._mfprocessor_dataset,
urls,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
)
results = method.gather(futures)
else:
futures = method.map(
self._mfprocessor_dataset,
urls,
preprocess=preprocess,
*args,
**kwargs,
)
results = method.gather(futures)
elif method in ["seq", "sequential"]:
if progress:
urls = tqdm(urls, total=len(urls), disable="disable" in [progress])
for url in urls:
data = None
try:
data = self._mfprocessor_dataset(
url,
preprocess=preprocess,
preprocess_opts=preprocess_opts,
open_dataset_opts=open_dataset_opts,
*args,
**kwargs,
)
except Exception:
failed.append(url)
if errors == "ignore":
log.debug(
"Ignored error with this url: %s" % strUrl(url)
) # See fsspec.http logger for more
pass
elif errors == "silent":
pass
else:
raise
finally:
results.append(data)
else:
raise InvalidMethod(method)
# Post-process results
results = [r for r in results if r is not None] # Only keep non-empty results
if len(results) > 0:
if concat:
# ds = xr.concat(results, dim=concat_dim, data_vars='all', coords='all', compat='override')
results = drop_variables_not_in_all_datasets(results)
ds = xr.concat(
results,
dim=concat_dim,
data_vars="minimal",
coords="minimal",
compat="override",
)
return ds
else:
return results
else:
raise DataNotFound(urls)
class httpstore_erddap_auth(httpstore):
async def get_auth_client(self, **kwargs):
session = aiohttp.ClientSession(**kwargs)
async with session.post(self._login_page, data=self._login_payload) as resp:
resp_query = dict(parse_qs(urlparse(str(resp.url)).query))
if resp.status == 404:
raise ErddapHTTPNotFound(
"Error %s: %s. This erddap server does not support log-in"
% (resp.status, resp.reason)
)
elif resp.status == 200:
has_expected = (
"message" in resp_query
) # only available when there is a form page response
if has_expected:
message = resp_query["message"][0]
if "failed" in message:
raise ErddapHTTPUnauthorized(
"Error %i: %s (%s)" % (401, message, self._login_payload)
)
else:
raise ErddapHTTPUnauthorized(
"This erddap server does not support log-in with a user/password"
)
else:
log.debug("resp.status", resp.status)
log.debug("resp.reason", resp.reason)
log.debug("resp.headers", resp.headers)
log.debug("resp.url", urlparse(str(resp.url)))
log.debug("resp.url.query", resp_query)
data = await resp.read()
log.debug("data", data)
return session
def __init__(
self,
cache: bool = False,
cachedir: str = "",
login: str = None,
payload: dict = {"user": None, "password": None},
auto: bool = True,
**kwargs,
):
if login is None:
raise ValueError("Invalid login url")
else:
self._login_page = login
self._login_auto = (
auto # Should we try to log-in automatically at instantiation ?
)
self._login_payload = payload.copy()
if "user" in self._login_payload and self._login_payload["user"] is None:
self._login_payload["user"] = OPTIONS["user"]
if (
"password" in self._login_payload
and self._login_payload["password"] is None
):
self._login_payload["password"] = OPTIONS["password"]
fsspec_kwargs = {**kwargs, **{"get_client": self.get_auth_client}}
super().__init__(cache=cache, cachedir=cachedir, **fsspec_kwargs)
if auto:
assert isinstance(self.connect(), bool)
# def __repr__(self):
# # summary = ["<httpstore_erddap_auth.%i>" % id(self)]
# summary = ["<httpstore_erddap_auth>"]
# summary.append("login page: %s" % self._login_page)
# summary.append("login data: %s" % (self._login_payload))
# if hasattr(self, '_connected'):
# summary.append("connected: %s" % (self._connected))
# else:
# summary.append("connected: ?")
# return "\n".join(summary)
def _repr_html_(self):
td_title = (
lambda title: '<td colspan="2"><div style="vertical-align: middle;text-align:left"><strong>%s</strong></div></td>'
% title
) # noqa: E731
tr_title = lambda title: "<thead><tr>%s</tr></thead>" % td_title( # noqa: E731
title
)
a_link = lambda url, txt: '<a href="%s">%s</a>' % (url, txt) # noqa: E731
td_key = ( # noqa: E731
lambda prop: '<td style="border-width:0px;padding-left:10px;text-align:left">%s</td>'
% str(prop)
)
td_val = (
lambda label: '<td style="border-width:0px;padding-left:10px;text-align:left">%s</td>'
% str(label)
) # noqa: E731
tr_tick = lambda key, value: "<tr>%s%s</tr>" % ( # noqa: E731
td_key(key),
td_val(value),
)
td_vallink = (
lambda url, label: '<td style="border-width:0px;padding-left:10px;text-align:left">%s</td>'
% a_link(url, label)
)
tr_ticklink = lambda key, url, value: "<tr>%s%s</tr>" % ( # noqa: E731
td_key(key),
td_vallink(url, value),
)
html = []
html.append("<table style='border-collapse:collapse;border-spacing:0'>")
html.append("<thead>")
html.append(tr_title("httpstore_erddap_auth"))
html.append("</thead>")
html.append("<tbody>")
html.append(tr_ticklink("login page", self._login_page, self._login_page))
html.append(tr_tick("login data", self._login_payload))
if hasattr(self, "_connected"):
html.append(tr_tick("connected", "✅" if self._connected else "⛔"))
else:
html.append(tr_tick("connected", "?"))
html.append("</tbody>")
html.append("</table>")
html = "\n".join(html)
return html
def connect(self):
try:
log.info(
"Try to log-in to '%s' page with %s data ..."
% (self._login_page, self._login_payload)
)
self.fs.info(self._login_page)
self._connected = True
except ErddapHTTPUnauthorized:
self._connected = False
except: # noqa: E722
raise
return self._connected
@property
def connected(self):
if not hasattr(self, "_connected"):
self.connect()
return self._connected
def httpstore_erddap(url: str = "", cache: bool = False, cachedir: str = "", **kwargs):
login_page = "%s/login.html" % url.rstrip("/")
login_store = httpstore_erddap_auth(
cache=cache, cachedir=cachedir, login=login_page, auto=False, **kwargs
)
try:
login_store.connect()
keep = True
except ErddapHTTPNotFound:
keep = False
pass
if keep:
return login_store
else:
return httpstore(cache=cache, cachedir=cachedir, **kwargs)
