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"^3.8" click = ">=8.1.6" -curies = ">=0.6.4" +curies = ">=0.7.2" linkml-runtime = ">=1.5.5" importlib-metadata = ">=6.8.0" pandas = ">1.0.3" diff --git a/src/sssom/io.py b/src/sssom/io.py index 648e131c..28f9eaf8 100644 --- a/src/sssom/io.py +++ b/src/sssom/io.py @@ -4,8 +4,9 @@ import os import re from collections import ChainMap +from itertools import chain from pathlib import Path -from typing import List, Optional, TextIO, Tuple, Union +from typing import Iterable, List, Optional, TextIO, Tuple, Union import curies import pandas as pd @@ -26,14 +27,7 @@ ) from .context import get_converter from .parsers import get_parsing_function, parse_sssom_table, split_dataframe -from .util import ( - MappingSetDataFrame, - are_params_slots, - augment_metadata, - is_curie, - is_iri, - raise_for_bad_path, -) +from .util import MappingSetDataFrame, are_params_slots, augment_metadata, raise_for_bad_path from .writers import get_writer_function, write_table, write_tables @@ -167,20 +161,14 @@ def _merge_converter(converter: Converter, prefix_map_mode: str = None) -> Conve raise ValueError(f"Invalid prefix map mode: {prefix_map_mode}") -def get_list_of_predicate_iri(predicate_filter: tuple, converter: Converter) -> list: +def get_list_of_predicate_iri(predicate_filter: Iterable[str], converter: Converter) -> list: """Return a list of IRIs for predicate CURIEs passed. :param predicate_filter: CURIE OR list of CURIEs OR file path containing the same. :param converter: Prefix map of mapping set (possibly) containing custom prefix:IRI combination. :return: A list of IRIs. """ - pred_filter_list = list(predicate_filter) - iri_list = [] - for p in pred_filter_list: - p_iri = extract_iri(p, converter) - if p_iri: - iri_list.extend(p_iri) - return list(set(iri_list)) + return sorted(set(chain.from_iterable(extract_iri(p, converter) for p in predicate_filter))) def extract_iri(input: str, converter: Converter) -> List[str]: @@ -192,25 +180,18 @@ def extract_iri(input: str, converter: Converter) -> List[str]: :return: A list of IRIs. :rtype: list """ - if is_iri(input): - return [input] - elif is_curie(input): - p_iri = converter.expand(input) - if p_iri: - return [p_iri] + if converter.is_uri(input): + return [converter.standardize_uri(input, strict=True)] + elif converter.is_curie(input): + return [converter.expand(input, strict=True)] elif os.path.isfile(input): pred_list = Path(input).read_text().splitlines() - iri_list: List[str] = [] - for p in pred_list: - p_iri = extract_iri(p, converter) - if p_iri: - iri_list.extend(p_iri) - return iri_list + return sorted(set(chain.from_iterable(extract_iri(p, converter) for p in pred_list))) else: logging.warning( - f"{input} is neither a valid curie, nor an IRI, nor a local file path, " + f"{input} is neither a local file path nor a valid CURIE or URI w.r.t. the given converter. " f"skipped from processing." ) return [] diff --git a/src/sssom/util.py b/src/sssom/util.py index ce72f628..1f094906 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -18,6 +18,7 @@ import validators import yaml from curies import Converter +from deprecation import deprecated from jsonschema import ValidationError from linkml_runtime.linkml_model.types import Uriorcurie from sssom_schema import Mapping as SSSOM_Mapping @@ -294,10 +295,12 @@ def _standardize_curie_or_iri(curie_or_iri: str, *, converter: Converter) -> str - If the string represents a CURIE, tries to standardize it. If not possible, returns the original value - Otherwise, return the original value """ - if is_iri(curie_or_iri): - return converter.standardize_uri(curie_or_iri) or curie_or_iri - if is_curie(curie_or_iri): - return converter.standardize_curie(curie_or_iri) or curie_or_iri + if converter.is_uri(curie_or_iri): + # TODO switch to compress, or fully replace _standardize_curie_or_iri with + # https://curies.readthedocs.io/en/latest/tutorial.html#extended-expansion-and-compression + return converter.standardize_uri(curie_or_iri, strict=True) + if converter.is_curie(curie_or_iri): + return converter.standardize_curie(curie_or_iri, strict=True) return curie_or_iri @@ -1091,22 +1094,47 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> return map_dict -CURIE_RE = re.compile(r"[A-Za-z0-9_.]+[:][A-Za-z0-9_]") +CURIE_PATTERN = r"[A-Za-z0-9_.]+[:][A-Za-z0-9_]" +CURIE_RE = re.compile(CURIE_PATTERN) +@deprecated( + deprecated_in="0.4.0", + details="sssom.util.is_curie is deprecated. This functionality was not supposed to be exposed from " + "the public interface from SSSOM-py. Instead, we suggest instantiating a curies.Converter based on " + "your context's prefix map and using curies.Converter.is_curie(). If you're looking for global syntax " + f"checking for CURIEs, try matching against {CURIE_PATTERN}", +) def is_curie(string: str) -> bool: + """Check if the string is a CURIE.""" + return _is_curie(string) + + +def _is_curie(string: str) -> bool: """Check if the string is a CURIE.""" return bool(CURIE_RE.match(string)) +@deprecated( + deprecated_in="0.4.0", + details="sssom.util.is_iri is deprecated. This functionality was not supposed to be exposed from " + "the public interface from SSSOM-py. Instead, we suggest instantiating a curies.Converter based on " + "your context's prefix map and using curies.Converter.is_uri(). If you're looking for a globally valid " + "URI checker, use validators.url()", +) def is_iri(string: str) -> bool: + """Check if the string is an IRI.""" + return _is_iri(string) + + +def _is_iri(string: str) -> bool: """Check if the string is an IRI.""" return validators.url(string) def get_prefix_from_curie(curie: str) -> str: """Get the prefix from a CURIE.""" - if is_curie(curie): + if _is_curie(curie): return curie.split(":")[0] else: return "" @@ -1123,7 +1151,10 @@ def get_prefixes_used_in_table(df: pd.DataFrame, converter: Converter) -> Set[st prefixes.update( converter.parse_curie(row).prefix for row in df[col] - if not is_iri(row) and is_curie(row) + # we don't use the converter here since get_prefixes_used_in_table + # is often used to identify prefixes that are not properly registered + # in the converter + if not _is_iri(row) and _is_curie(row) ) return set(prefixes) @@ -1461,7 +1492,9 @@ def safe_compress(uri: str, converter: Converter) -> str: :param converter: Converter used for compression :return: A CURIE """ - if not is_curie(uri): + # TODO replace with https://curies.readthedocs.io/en/latest/tutorial.html#extended-expansion-and-compression + # when it's available + if not converter.is_curie(uri): return converter.compress_strict(uri) rv = converter.standardize_curie(uri) if rv is None: diff --git a/tests/test_utils.py b/tests/test_utils.py index 0b9a2a27..86b3b39c 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -8,7 +8,7 @@ from sssom.constants import OBJECT_ID, SUBJECT_ID from sssom.context import SSSOM_BUILT_IN_PREFIXES, ensure_converter -from sssom.io import extract_iri +from sssom.io import get_list_of_predicate_iri from sssom.parsers import parse_sssom_table from sssom.util import ( MappingSetDataFrame, @@ -33,15 +33,17 @@ def setUp(self) -> None: def test_broken_predicate_list(self): """Test merging of multiple msdfs.""" - pred_filter_list = ["skos:relatedMatch", f"{data_dir}/predicate_list3.txt"] + predicate_filter = ["skos:relatedMatch", f"{data_dir}/predicate_list3.txt"] prefix_map = {"skos": "http://www.w3.org/2004/02/skos/core#"} converter = Converter.from_prefix_map(prefix_map) - iri_list = [] - for p in pred_filter_list: - p_iri = extract_iri(p, converter) - if p_iri: - iri_list.extend(p_iri) - self.assertEqual(3, len(iri_list)) + iri_list = get_list_of_predicate_iri(converter=converter, predicate_filter=predicate_filter) + self.assertEqual( + [ + "http://www.w3.org/2004/02/skos/core#narrowMatch", + "http://www.w3.org/2004/02/skos/core#relatedMatch", + ], + iri_list, + ) def test_filter_prefixes_any(self): """Test filtering MSDF.df by prefixes provided."""