Source code for yt.sample_data.api

"""
This is a collection of helper functions to yt.load_sample
"""
import json
import re
from functools import lru_cache
from itertools import chain
from pathlib import Path
from typing import Optional, Union
from warnings import warn

from yt.config import ytcfg
from yt.funcs import mylog
from yt.utilities.on_demand_imports import (
    _pandas as pd,
    _pooch as pooch,
    _requests as requests,
)

num_exp = re.compile(r"\d*(\.\d*)?")
byte_unit_exp = re.compile(r"[KMGT]?B")


def _parse_byte_size(s: str):
    """
    Convert a string size specification to integer byte size.

    This function should be insensitive to case and whitespace.

    It doesn't always return an int, as a temporary measure to deal with missing
    or corrupted data in the registry. This should be fixed in the future.

    Examples
    --------
    # most of the following examples are adapted from
    # https://stackoverflow.com/a/31631711/5489622
    >>> _parse_byte_size(None)
    <NA>
    >>> from numpy import nan
    >>> _parse_byte_size(nan)
    <NA>
    >>> _parse_byte_size("1B")
    1
    >>> _parse_byte_size("1.00 KB")
    1024
    >>> _parse_byte_size("488.28 KB")
    500000
    >>> _parse_byte_size("1.00 MB")
    1049000
    >>> _parse_byte_size("47.68 MB")
    50000000
    >>> _parse_byte_size("1.00 GB")
    1074000000
    >>> _parse_byte_size("4.66 GB")
    5004000000
    >>> _parse_byte_size("1.00 TB")
    1100000000000
    >>> _parse_byte_size("4.55 TB")
    5003000000000
    """
    try:
        s = s.upper()
    except AttributeError:
        # input is not a string (likely a np.nan)
        return pd.NA

    match = re.search(num_exp, s)
    if match is None:
        raise ValueError
    val = float(match.group())

    match = re.search(byte_unit_exp, s)
    if match is None:
        raise ValueError
    unit = match.group()
    prefixes = ["B", "K", "M", "G", "T"]
    raw_res = val * 1024 ** prefixes.index(unit[0])
    return int(float(f"{raw_res:.3e}"))


[docs]@lru_cache(maxsize=128) def get_data_registry_table(): """ Load the sample data registry as a pandas.Dataframe instance. This function is considered experimental and is exposed for exploratory purposed. The output format is subject to change. The output of this function is cached so it will only generate one request per session. """ import pkg_resources # it would be nicer to have an actual api on the yt website server, # but this will do for now api_url = "https://raw.githubusercontent.com/yt-project/website/master/data/datafiles.json" response = requests.get(api_url) if not response.ok: raise RuntimeError( "Could not retrieve registry data. Please check your network setup." ) website_json = response.json() # this dict follows this schema: {frontend_name: {flat dataframe-like}} columns = ["code", "filename", "size", "url", "description"] website_table = pd.concat(pd.DataFrame(d) for d in website_json.values())[columns] # add a int-type byte size column # note that we cast to pandas specific type "Int64" because we expect missing values # see https://pandas.pydata.org/pandas-docs/stable/user_guide/missing_data.html#integer-dtypes-and-missing-data website_table["byte_size"] = ( website_table["size"].apply(_parse_byte_size).astype("Int64") ) # normalize urls to match the local json website_table["url"] = website_table["url"].apply( lambda u: u.replace("http:", "https:") ) # load local data with pkg_resources.resource_stream("yt", "sample_data_registry.json") as fh: pooch_json = json.load(fh) pooch_table = pd.DataFrame(pooch_json.values()) # merge tables unified_table = website_table.merge(pooch_table, on="url", how="outer") # PR 3089 # ideally we should be able to do this, but it's not possible # at the time of writing because fhe "filename" is incomplete # see the companion comment in load_sample # unified_table.set_index("filename", inplace=True) # unified_table.index.rename("id", inplace=True) return unified_table
def _get_test_data_dir_path(): p = Path(ytcfg.get("yt", "test_data_dir")) if p.is_dir(): return p warn( "Storage directory from yt config doesn't exist " f"(currently set to '{p}'). " "Current working directory will be used instead." ) return Path.cwd()
[docs]def lookup_on_disk_data(fn) -> Path: """ Look for data file/dir on disk. Returns ------- pathlib.Path to a file/dir matching fn if any Raises ------ FileNotFoundError """ path = Path(fn).expanduser() if path.exists(): return path err_msg = f"No such file or directory: '{fn}'." test_data_dir = _get_test_data_dir_path() if not test_data_dir.is_dir(): raise FileNotFoundError(err_msg) alt_path = _get_test_data_dir_path() / fn if alt_path != path: if alt_path.exists(): return alt_path err_msg += f"\n(Also tried '{alt_path}')." raise FileNotFoundError(err_msg)
@lru_cache(maxsize=128) def _get_pooch_instance(): import pkg_resources data_registry = get_data_registry_table() cache_storage = _get_test_data_dir_path() / "yt_download_cache" with pkg_resources.resource_stream("yt", "sample_data_registry.json") as fh: sample_data_registry = json.load(fh) registry = {k: v["hash"] for k, v in sample_data_registry.items()} return pooch.create( path=cache_storage, base_url="https://yt-project.org/data/", registry=registry ) def _download_sample_data_file( filename, progressbar=True, timeout: Optional[int] = None ): """ Download a file by url. Returns ------- storage_filename : location of the downloaded file """ downloader = pooch.HTTPDownloader(progressbar=progressbar, timeout=timeout) poochie = _get_pooch_instance() poochie.fetch(filename, downloader=downloader) return Path.joinpath(poochie.path, filename)