"""Find files on the local filesystem."""
from __future__ import annotations
import itertools
import logging
import os
import re
from dataclasses import dataclass
from glob import glob
from pathlib import Path
from typing import TYPE_CHECKING, Any
import isodate
from cf_units import Unit
from netCDF4 import Dataset, Variable
from .config import CFG
from .config._config import get_project_config
from .exceptions import RecipeError
if TYPE_CHECKING:
from collections.abc import Iterable
from .esgf import ESGFFile
from .typing import Facets, FacetValue
logger = logging.getLogger(__name__)
def _get_from_pattern(
pattern: str,
date_range_pattern: str,
stem: str,
group: str,
) -> tuple[str | None, str | None]:
"""Get time, date or datetime from date range patterns in file names."""
# Next string allows to test that there is an allowed delimiter (or
# string start or end) close to date range (or to single date)
start_point: str | None = None
end_point: str | None = None
context = r"(?:^|[-_]|$)"
# First check for a block of two potential dates
date_range_pattern_with_context = context + date_range_pattern + context
daterange = re.search(date_range_pattern_with_context, stem)
if not daterange:
# Retry with extended context for CMIP3
context = r"(?:^|[-_.]|$)"
date_range_pattern_with_context = (
context + date_range_pattern + context
)
daterange = re.search(date_range_pattern_with_context, stem)
if daterange:
start_point = daterange.group(group)
end_group = f"{group}_end"
end_point = daterange.group(end_group)
else:
# Check for single dates in the filename
single_date_pattern = context + pattern + context
dates = re.findall(single_date_pattern, stem)
if len(dates) == 1:
start_point = end_point = dates[0][0]
elif len(dates) > 1:
# Check for dates at start or (exclusive or) end of filename
start = re.search(r"^" + pattern, stem)
end = re.search(pattern + r"$", stem)
if start and not end:
start_point = end_point = start.group(group)
elif end:
start_point = end_point = end.group(group)
return start_point, end_point
def _get_var_name(variable: Variable) -> str:
"""Get variable name (following Iris' Cube.name())."""
for attr in ("standard_name", "long_name"):
if attr in variable.ncattrs():
return str(variable.getncattr(attr))
return str(variable.name)
def _get_start_end_date(
file: str | Path | LocalFile | ESGFFile,
) -> tuple[str, str]:
"""Get the start and end dates as a string from a file name.
Examples of allowed dates: 1980, 198001, 1980-01, 19801231, 1980-12-31,
1980123123, 19801231T23, 19801231T2359, 19801231T235959, 19801231T235959Z
(ISO 8601).
Dates must be surrounded by '-', '_' or '.' (the latter is used by CMIP3
data), or string start or string end (after removing filename suffix).
Look first for two dates separated by '-', '_' or '_cat_' (the latter is
used by CMIP3 data), then for one single date, and if there are multiple,
for one date at start or end.
Parameters
----------
file:
The file to read the start and end data from.
Returns
-------
tuple[str, str]
The start and end date.
Raises
------
ValueError
Start or end date cannot be determined.
"""
if hasattr(file, "name"): # noqa: SIM108
# Path, LocalFile, ESGFFile
stem = Path(file.name).stem
else:
# str
stem = Path(file).stem
start_date = end_date = None
# Build regex
time_pattern = (
r"(?P<hour>[0-2][0-9]"
r"(?P<minute>[0-5][0-9]"
r"(?P<second>[0-5][0-9])?)?Z?)"
)
date_pattern = (
r"(?P<year>[0-9]{4})"
r"(?P<month>-?[01][0-9]"
r"(?P<day>-?[0-3][0-9]"
rf"(T?{time_pattern})?)?)?"
)
datetime_pattern = rf"(?P<datetime>{date_pattern})"
end_datetime_pattern = datetime_pattern.replace(">", "_end>")
# Dates can either be delimited by '-', '_', or '_cat_' (the latter for
# CMIP3)
date_range_pattern = (
datetime_pattern + r"[-_](?:cat_)?" + end_datetime_pattern
)
# Find dates using the regex
start_date, end_date = _get_from_pattern(
datetime_pattern,
date_range_pattern,
stem,
"datetime",
)
# As final resort, try to get the dates from the file contents
if (
(start_date is None or end_date is None)
and isinstance(file, (str, Path))
and Path(file).exists()
):
logger.debug("Must load file %s for daterange ", file)
with Dataset(file) as dataset:
for variable in dataset.variables.values():
var_name = _get_var_name(variable)
if var_name == "time" and "units" in variable.ncattrs():
time_units = Unit(variable.getncattr("units"))
start_date = isodate.date_isoformat(
time_units.num2date(variable[0]),
format=isodate.isostrf.DATE_BAS_COMPLETE,
)
end_date = isodate.date_isoformat(
time_units.num2date(variable[-1]),
format=isodate.isostrf.DATE_BAS_COMPLETE,
)
break
if start_date is None or end_date is None:
msg = (
f"File {file} datetimes do not match a recognized pattern and "
f"time coordinate can not be read from the file"
)
raise ValueError(msg)
# Remove potential '-' characters from datetimes
start_date = start_date.replace("-", "")
end_date = end_date.replace("-", "")
return start_date, end_date
def _get_start_end_year(
file: str | Path | LocalFile | ESGFFile,
) -> tuple[int, int]:
"""Get the start and end year as int from a file name.
See :func:`_get_start_end_date`.
"""
(start_date, end_date) = _get_start_end_date(file)
return (int(start_date[:4]), int(end_date[:4]))
def _dates_to_timerange(start_date: int | str, end_date: int | str) -> str:
"""Convert ``start_date`` and ``end_date`` to ``timerange``.
Note
----
This function ensures that dates in years format follow the pattern YYYY
(i.e., that they have at least 4 digits). Other formats, such as wildcards
(``'*'``) and relative time ranges (e.g., ``'P6Y'``) are used unchanged.
Parameters
----------
start_date:
Start date.
end_date:
End date.
Returns
-------
str
``timerange`` in the form ``'start_date/end_date'``.
"""
start_date = str(start_date)
end_date = str(end_date)
# Pad years with 0s if not wildcard or relative time range
if start_date != "*" and not start_date.startswith("P"):
start_date = start_date.zfill(4)
if end_date != "*" and not end_date.startswith("P"):
end_date = end_date.zfill(4)
return f"{start_date}/{end_date}"
def _replace_years_with_timerange(variable: dict[str, Any]) -> None:
"""Set `timerange` tag from tags `start_year` and `end_year`."""
start_year = variable.get("start_year")
end_year = variable.get("end_year")
if start_year and end_year:
variable["timerange"] = _dates_to_timerange(start_year, end_year)
elif start_year:
variable["timerange"] = _dates_to_timerange(start_year, start_year)
elif end_year:
variable["timerange"] = _dates_to_timerange(end_year, end_year)
variable.pop("start_year", None)
variable.pop("end_year", None)
def _parse_period(timerange: FacetValue) -> tuple[str, str]:
"""Parse `timerange` values given as duration periods.
Sum the duration periods to the `timerange` value given as a
reference point in order to compute the start and end dates needed
for file selection.
"""
if not isinstance(timerange, str):
msg = f"`timerange` should be a `str`, got {type(timerange)}"
raise TypeError(msg)
start_date: str | None = None
end_date: str | None = None
time_format = None
datetime_format = (
isodate.DATE_BAS_COMPLETE + "T" + isodate.TIME_BAS_COMPLETE
)
if timerange.split("/")[0].startswith("P"):
try:
end_date = isodate.parse_datetime(timerange.split("/")[1])
time_format = datetime_format
except isodate.ISO8601Error:
end_date = isodate.parse_date(timerange.split("/")[1])
time_format = isodate.DATE_BAS_COMPLETE
delta = isodate.parse_duration(timerange.split("/")[0])
start_date = end_date - delta
elif timerange.split("/")[1].startswith("P"):
try:
start_date = isodate.parse_datetime(timerange.split("/")[0])
time_format = datetime_format
except isodate.ISO8601Error:
start_date = isodate.parse_date(timerange.split("/")[0])
time_format = isodate.DATE_BAS_COMPLETE
delta = isodate.parse_duration(timerange.split("/")[1])
end_date = start_date + delta
if time_format == datetime_format:
start_date = str(
isodate.datetime_isoformat(start_date, format=datetime_format),
)
end_date = str(
isodate.datetime_isoformat(end_date, format=datetime_format),
)
elif time_format == isodate.DATE_BAS_COMPLETE:
start_date = str(
isodate.date_isoformat(start_date, format=time_format),
)
end_date = str(isodate.date_isoformat(end_date, format=time_format))
if start_date is None:
start_date = timerange.split("/")[0]
if end_date is None:
end_date = timerange.split("/")[1]
return start_date, end_date
def _truncate_dates(date: str, file_date: str) -> tuple[int, int]:
"""Truncate dates of different lengths and convert to integers.
This allows to compare the dates chronologically. For example, this allows
comparisons between the formats 'YYYY' and 'YYYYMM', and 'YYYYMM' and
'YYYYMMDD'.
Warning
-------
This function assumes that the years in ``date`` and ``file_date`` have the
same number of digits. If this is not the case, pad the dates with leading
zeros (e.g., use ``date='0100'`` and ``file_date='199901'`` for a correct
comparison).
"""
date = re.sub("[^0-9]", "", date)
file_date = re.sub("[^0-9]", "", file_date)
if len(date) < len(file_date):
file_date = file_date[0 : len(date)]
elif len(date) > len(file_date):
date = date[0 : len(file_date)]
return int(date), int(file_date)
def _select_files(
filenames: Iterable[LocalFile],
timerange: FacetValue,
) -> list[LocalFile]:
"""Select files containing data between a given timerange.
If the timerange is given as a period, the file selection occurs
taking only the years into account.
Otherwise, the file selection occurs taking into account the time
resolution of the file.
"""
if not isinstance(timerange, str):
msg = f"`timerange` should be a `str`, got {type(timerange)}"
raise TypeError(msg)
if "*" in timerange:
# TODO: support * combined with a period
return list(filenames)
selection: list[LocalFile] = []
for filename in filenames:
start_date, end_date = _parse_period(timerange)
start, end = _get_start_end_date(filename)
start_date_int, end_int = _truncate_dates(start_date, end)
end_date_int, start_int = _truncate_dates(end_date, start)
if start_int <= end_date_int and end_int >= start_date_int:
selection.append(filename)
return selection
def _replace_tags(
paths: str | list[str],
variable: Facets,
) -> list[Path]:
"""Replace tags in the config-developer's file with actual values."""
pathset: Iterable[str]
if isinstance(paths, str):
pathset = {paths.strip("/")}
else:
pathset = {path.strip("/") for path in paths}
tlist: set[str] = set()
for path in pathset:
tlist = tlist.union(re.findall(r"{([^}]*)}", path))
if "sub_experiment" in variable:
new_paths: set[str] = set()
for path in pathset:
new_paths.update(
(
re.sub(r"(\b{ensemble}\b)", r"{sub_experiment}-\1", path),
re.sub(r"({ensemble})", r"{sub_experiment}-\1", path),
),
)
tlist.add("sub_experiment")
pathset = new_paths
for tag in tlist:
original_tag = tag
tag, _, _ = _get_caps_options(tag)
if tag in variable:
replacewith = variable[tag]
elif tag == "version":
replacewith = "*"
else:
msg = (
f"Dataset key '{tag}' must be specified for {variable}, check "
f"your recipe entry and/or extra facet file(s)"
)
raise RecipeError(msg)
pathset = _replace_tag(pathset, original_tag, replacewith)
return [Path(p) for p in pathset]
def _replace_tag(
paths: Iterable[str],
tag: str,
replacewith: FacetValue,
) -> list[str]:
"""Replace tag by replacewith in paths."""
_, lower, upper = _get_caps_options(tag)
result: list[str] = []
if isinstance(replacewith, (list, tuple)):
for item in replacewith:
result.extend(_replace_tag(paths, tag, item))
else:
text = _apply_caps(str(replacewith), lower, upper)
result.extend(p.replace("{" + tag + "}", text) for p in paths)
return list(set(result))
def _get_caps_options(tag: str) -> tuple[str, bool, bool]:
lower = False
upper = False
if tag.endswith(".lower"):
lower = True
tag = tag[0:-6]
elif tag.endswith(".upper"):
upper = True
tag = tag[0:-6]
return tag, lower, upper
def _apply_caps(original: str, lower: bool, upper: bool) -> str:
if lower:
return original.lower()
if upper:
return original.upper()
return original
def _select_drs(input_type: str, project: str, structure: str) -> list[str]:
"""Select the directory structure of input path."""
cfg = get_project_config(project)
input_path_patterns = cfg[input_type]
if isinstance(input_path_patterns, str):
return [input_path_patterns]
if structure in input_path_patterns:
value = input_path_patterns[structure]
if isinstance(value, str):
value = [value]
return value
msg = f"drs {structure} for {project} project not specified in config-developer file"
raise KeyError(msg)
[docs]
@dataclass(order=True)
class DataSource:
"""Class for storing a data source and finding the associated files."""
rootpath: Path
dirname_template: str
filename_template: str
def __post_init__(self) -> None:
"""Set further attributes."""
self._regex_pattern = self._templates_to_regex()
@property
def regex_pattern(self) -> str:
"""Get regex pattern that can be used to extract facets from paths."""
return self._regex_pattern
[docs]
def get_glob_patterns(self, **facets) -> list[Path]:
"""Compose the globs that will be used to look for files."""
dirname_globs = _replace_tags(self.dirname_template, facets)
filename_globs = _replace_tags(self.filename_template, facets)
return sorted(
self.rootpath / d / f
for d in dirname_globs
for f in filename_globs
)
[docs]
def find_files(self, **facets) -> list[LocalFile]:
"""Find files."""
globs = self.get_glob_patterns(**facets)
logger.debug("Looking for files matching %s", globs)
files: list[LocalFile] = []
for glob_ in globs:
for filename in glob(str(glob_)):
file = LocalFile(filename)
file.facets.update(self.path2facets(file))
files.append(file)
files.sort() # sorting makes it easier to see what was found
if "timerange" in facets:
files = _select_files(files, facets["timerange"])
return files
[docs]
def path2facets(self, path: Path) -> dict[str, str]:
"""Extract facets from path."""
facets: dict[str, str] = {}
match = re.search(self.regex_pattern, str(path))
if match is None:
return facets
for facet, value in match.groupdict().items():
if value:
facets[facet] = value
return facets
def _templates_to_regex(self) -> str:
r"""Convert template strings to regex pattern.
The resulting regex pattern can be used to extract facets from paths
using :func:`re.search`.
Note
----
Facets must not contain "/" or "_".
Examples
--------
- rootpath: "/root"
dirname_template: "{f2.upper}"
filename_template: "{f3}[._]{f4}*"
--> regex_pattern:
"/root/(?P<f2>[^_/]*?)/(?P<f3>[^_/]*?)[\._](?P<f4>[^_/]*?).*?"
- rootpath: "/root"
dirname_template: "{f1}/{f1}-{f2}"
filename_template: "*.nc"
--> regex_pattern:
"/root/(?P<f1>[^_/]*?)/(?P=f1)\-(?P<f2>[^_/]*?)/.*?\.nc"
- rootpath: "/root"
dirname_template: "{f1}/{f2}{f3}"
filename_template: "*.nc"
--> regex_pattern:
"/root/(?P<f1>[^_/]*?)/(?:[^_/]*?)/.*?\.nc"
"""
dirname_template = self.dirname_template
filename_template = self.filename_template
# Templates must not be absolute paths (i.e., start with /), otherwise
# the roopath is ignored (see
# https://docs.python.org/3/library/pathlib.html#operators)
if self.dirname_template.startswith(os.sep):
dirname_template = dirname_template[1:]
if self.filename_template.startswith(os.sep):
filename_template = filename_template[1:]
pattern = re.escape(
str(self.rootpath / dirname_template / filename_template),
)
# Remove all tags that are in between other tags, e.g.,
# {tag1}{tag2}{tag3} -> {tag1}{tag2} (there is no way to reliably
# extract facets from those)
pattern = re.sub(r"(?<=\})\\\{[^\}]+?\\\}(?=\\(?=\{))", "", pattern)
# Replace consecutive tags, e.g. {tag1}{tag2} with non-capturing groups
# (?:[^_/]*?) (there is no way to reliably extract facets from those)
# Note: This assumes that facets do NOT contain / or _
pattern = re.sub(
r"\\\{[^\{]+?\}\\\{[^\}]+?\\\}",
rf"(?:[^_{os.sep}]*?)",
pattern,
)
# Convert tags {tag} to named capture groups (?P<tag>[^_/]*?); for
# duplicates use named backreferences (?P=tag)
# Note: This assumes that facets do NOT contain / or _
already_used_tags: set[str] = set()
for full_tag in re.findall(r"\\\{(.+?)\\\}", pattern):
# Ignore .upper and .lower (full_tag: {tag.lower}, tag: {tag})
if full_tag.endswith((r"\.upper", r"\.lower")):
tag = full_tag[:-7]
else:
tag = full_tag
old_str = rf"\{{{full_tag}\}}"
if tag in already_used_tags:
new_str = rf"(?P={tag})"
else:
new_str = rf"(?P<{tag}>[^_{os.sep}]*?)"
already_used_tags.add(tag)
pattern = pattern.replace(old_str, new_str, 1)
# Convert fnmatch wildcards * and [] to regex wildcards
pattern = pattern.replace(r"\*", ".*?")
for chars in re.findall(r"\\\[(.*?)\\\]", pattern):
pattern = pattern.replace(rf"\[{chars}\]", f"[{chars}]")
return pattern
_ROOTPATH_WARNED: set[tuple[str, tuple[str]]] = set()
def _get_data_sources(project: str) -> list[DataSource]:
"""Get a list of data sources."""
rootpaths = CFG["rootpath"]
for key in (project, "default"):
if key in rootpaths:
paths = rootpaths[key]
nonexistent = tuple(p for p in paths if not os.path.exists(p))
if nonexistent and (key, nonexistent) not in _ROOTPATH_WARNED:
logger.warning(
"Configured '%s' rootpaths '%s' do not exist",
key,
", ".join(str(p) for p in nonexistent),
)
_ROOTPATH_WARNED.add((key, nonexistent))
if isinstance(paths, list):
structure = CFG["drs"].get(project, "default")
paths = dict.fromkeys(paths, structure)
sources: list[DataSource] = []
for path, structure in paths.items():
path = Path(path)
dir_templates = _select_drs("input_dir", project, structure)
file_templates = _select_drs("input_file", project, structure)
sources.extend(
DataSource(path, d, f)
for d in dir_templates
for f in file_templates
)
return sources
msg = (
f"No '{project}' or 'default' path specified under 'rootpath' in "
"the configuration."
)
raise KeyError(msg)
def _get_output_file(variable: dict[str, Any], preproc_dir: Path) -> Path:
"""Return the full path to the output (preprocessed) file."""
cfg = get_project_config(variable["project"])
# Join different experiment names
if isinstance(variable.get("exp"), (list, tuple)):
variable = dict(variable)
variable["exp"] = "-".join(variable["exp"])
outfile = _replace_tags(cfg["output_file"], variable)[0]
if "timerange" in variable:
timerange = variable["timerange"].replace("/", "-")
outfile = Path(f"{outfile}_{timerange}")
outfile = Path(f"{outfile}.nc")
return Path(
preproc_dir,
variable.get("diagnostic", ""),
variable.get("variable_group", ""),
outfile,
)
def _get_multiproduct_filename(attributes: dict, preproc_dir: Path) -> Path:
"""Get ensemble/multi-model filename depending on settings."""
relevant_keys = [
"project",
"dataset",
"exp",
"ensemble_statistics",
"multi_model_statistics",
"mip",
"short_name",
]
filename_segments = []
for key in relevant_keys:
if key in attributes:
attribute = attributes[key]
if isinstance(attribute, (list, tuple)):
attribute = "-".join(attribute)
filename_segments.extend(attribute.split("_"))
# Remove duplicate segments:
filename_segments = list(dict.fromkeys(filename_segments))
# Add time period if possible
if "timerange" in attributes:
filename_segments.append(
f"{attributes['timerange'].replace('/', '-')}",
)
filename = f"{'_'.join(filename_segments)}.nc"
return Path(
preproc_dir,
attributes["diagnostic"],
attributes["variable_group"],
filename,
)
def _filter_versions_called_latest(
files: list[LocalFile],
) -> list[LocalFile]:
"""Filter out versions called 'latest' if they are duplicates.
On compute clusters it is usual to have a symbolic link to the
latest version called 'latest'. Those need to be skipped in order to
find valid version names and avoid duplicate results.
"""
resolved_valid_versions = {
f.resolve(strict=False)
for f in files
if f.facets.get("version") != "latest"
}
return [
f
for f in files
if f.facets.get("version") != "latest"
or f.resolve(strict=False) not in resolved_valid_versions
]
def _select_latest_version(files: list[LocalFile]) -> list[LocalFile]:
"""Select only the latest version of files."""
def filename(file):
return file.name
def version(file):
return file.facets.get("version", "")
result = []
for _, group in itertools.groupby(
sorted(files, key=filename),
key=filename,
):
duplicates = sorted(group, key=version)
latest = duplicates[-1]
result.append(latest)
return result
[docs]
def find_files(
*,
debug: bool = False,
**facets: FacetValue,
) -> list[LocalFile] | tuple[list[LocalFile], list[Path]]:
"""Find files on the local filesystem.
The directories that are searched for files are defined in
:data:`esmvalcore.config.CFG` under the ``'rootpath'`` key using the
directory structure defined under the ``'drs'`` key.
If ``esmvalcore.config.CFG['rootpath']`` contains a key that matches the
value of the ``project`` facet, those paths will be used. If there is no
project specific key, the directories in
``esmvalcore.config.CFG['rootpath']['default']`` will be searched.
See :ref:`findingdata` for extensive instructions on configuring ESMValCore
so it can find files locally.
Parameters
----------
debug
When debug is set to :obj:`True`, the function will return a tuple
with the first element containing the files that were found
and the second element containing the :func:`glob.glob` patterns that
were used to search for files.
**facets
Facets used to search for files. An ``'*'`` can be used to match
any value. By default, only the latest version of a file will
be returned. To select all versions use ``version='*'``. It is also
possible to specify multiple values for a facet, e.g.
``exp=['historical', 'ssp585']`` will match any file that belongs
to either the historical or ssp585 experiment.
The ``timerange`` facet can be specified in `ISO 8601 format
<https://en.wikipedia.org/wiki/ISO_8601>`__.
Note
----
A value of ``timerange='*'`` is supported, but combining a ``'*'`` with
a time or period :ref:`as supported in the recipe <datasets>` is currently
not supported and will return all found files.
Examples
--------
Search for files containing surface air temperature from any CMIP6 model
for the historical experiment:
>>> esmvalcore.local.find_files(
... project='CMIP6',
... activity='CMIP',
... mip='Amon',
... short_name='tas',
... exp='historical',
... dataset='*',
... ensemble='*',
... grid='*',
... institute='*',
... ) # doctest: +SKIP
[LocalFile('/home/bandela/climate_data/CMIP6/CMIP/BCC/BCC-ESM1/historical/r1i1p1f1/Amon/tas/gn/v20181214/tas_Amon_BCC-ESM1_historical_r1i1p1f1_gn_185001-201412.nc')]
Returns
-------
list[LocalFile]
The files that were found.
"""
facets = dict(facets)
if "original_short_name" in facets:
facets["short_name"] = facets["original_short_name"]
files = []
filter_latest = False
data_sources = _get_data_sources(facets["project"]) # type: ignore
for data_source in data_sources:
for file in data_source.find_files(**facets):
if file.facets.get("version") == "latest":
filter_latest = True
files.append(file)
if filter_latest:
files = _filter_versions_called_latest(files)
if "version" not in facets:
files = _select_latest_version(files)
files.sort() # sorting makes it easier to see what was found
if debug:
globs = []
for data_source in data_sources:
globs.extend(data_source.get_glob_patterns(**facets))
return files, sorted(globs)
return files
[docs]
class LocalFile(type(Path())): # type: ignore
"""File on the local filesystem."""
@property
def facets(self) -> Facets:
"""Facets describing the file.
Note
----
When using :func:`find_files`, facets are read from the directory
structure. Facets stored in filenames are not yet supported.
"""
if not hasattr(self, "_facets"):
self._facets: Facets = {}
return self._facets
@facets.setter
def facets(self, value: Facets) -> None:
self._facets = value
