mirror of
https://github.com/ilri/csv-metadata-quality.git
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Alan Orth
2cc2dbe952
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RewriteToLiteral: It's slower to call list() than using the empty literal
515 lines
13 KiB
Python
515 lines
13 KiB
Python
# SPDX-License-Identifier: GPL-3.0-only
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import pandas as pd
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from colorama import Fore
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import csv_metadata_quality.check as check
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import csv_metadata_quality.experimental as experimental
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def test_check_invalid_issn(capsys):
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"""Test checking invalid ISSN."""
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value = "2321-2302"
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check.issn(value)
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captured = capsys.readouterr()
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assert captured.out == f"{Fore.RED}Invalid ISSN: {Fore.RESET}{value}\n"
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def test_check_valid_issn():
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"""Test checking valid ISSN."""
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value = "0024-9319"
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result = check.issn(value)
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assert result is None
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def test_check_invalid_isbn(capsys):
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"""Test checking invalid ISBN."""
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value = "99921-58-10-6"
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check.isbn(value)
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captured = capsys.readouterr()
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assert captured.out == f"{Fore.RED}Invalid ISBN: {Fore.RESET}{value}\n"
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def test_check_valid_isbn():
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"""Test checking valid ISBN."""
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value = "99921-58-10-7"
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result = check.isbn(value)
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assert result is None
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def test_check_missing_date(capsys):
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"""Test checking missing date."""
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value = None
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field_name = "dc.date.issued"
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check.date(value, field_name)
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captured = capsys.readouterr()
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assert captured.out == f"{Fore.RED}Missing date ({field_name}).{Fore.RESET}\n"
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def test_check_multiple_dates(capsys):
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"""Test checking multiple dates."""
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value = "1990||1991"
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field_name = "dc.date.issued"
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check.date(value, field_name)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.RED}Multiple dates not allowed ({field_name}): {Fore.RESET}{value}\n"
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)
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def test_check_invalid_date(capsys):
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"""Test checking invalid ISO8601 date."""
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value = "1990-0"
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field_name = "dc.date.issued"
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check.date(value, field_name)
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captured = capsys.readouterr()
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assert (
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captured.out == f"{Fore.RED}Invalid date ({field_name}): {Fore.RESET}{value}\n"
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)
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def test_check_valid_date():
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"""Test checking valid ISO8601 date."""
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value = "1990"
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field_name = "dc.date.issued"
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result = check.date(value, field_name)
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assert result is None
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def test_check_suspicious_characters(capsys):
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"""Test checking for suspicious characters."""
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value = "foreˆt"
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field_name = "dc.contributor.author"
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check.suspicious_characters(value, field_name)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.YELLOW}Suspicious character ({field_name}): {Fore.RESET}ˆt\n"
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)
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def test_check_valid_iso639_1_language():
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"""Test valid ISO 639-1 (alpha 2) language."""
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value = "ja"
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result = check.language(value)
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assert result is None
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def test_check_valid_iso639_3_language():
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"""Test valid ISO 639-3 (alpha 3) language."""
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value = "eng"
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result = check.language(value)
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assert result is None
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def test_check_invalid_iso639_1_language(capsys):
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"""Test invalid ISO 639-1 (alpha 2) language."""
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value = "jp"
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check.language(value)
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captured = capsys.readouterr()
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assert (
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captured.out == f"{Fore.RED}Invalid ISO 639-1 language: {Fore.RESET}{value}\n"
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)
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def test_check_invalid_iso639_3_language(capsys):
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"""Test invalid ISO 639-3 (alpha 3) language."""
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value = "chi"
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check.language(value)
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captured = capsys.readouterr()
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assert (
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captured.out == f"{Fore.RED}Invalid ISO 639-3 language: {Fore.RESET}{value}\n"
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)
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def test_check_invalid_language(capsys):
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"""Test invalid language."""
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value = "Span"
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check.language(value)
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captured = capsys.readouterr()
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assert captured.out == f"{Fore.RED}Invalid language: {Fore.RESET}{value}\n"
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def test_check_invalid_agrovoc(capsys):
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"""Test invalid AGROVOC subject. Invalid values *will not* be dropped."""
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valid_agrovoc = "LIVESTOCK"
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invalid_agrovoc = "FOREST"
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value = f"{valid_agrovoc}||{invalid_agrovoc}"
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field_name = "dcterms.subject"
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drop = False
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new_value = check.agrovoc(value, field_name, drop)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.RED}Invalid AGROVOC ({field_name}): {Fore.RESET}{invalid_agrovoc}\n"
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)
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assert new_value == value
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def test_check_invalid_agrovoc_dropped(capsys):
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"""Test invalid AGROVOC subjects. Invalid values *will* be dropped."""
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valid_agrovoc = "LIVESTOCK"
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invalid_agrovoc = "FOREST"
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value = f"{valid_agrovoc}||{invalid_agrovoc}"
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field_name = "dcterms.subject"
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drop = True
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new_value = check.agrovoc(value, field_name, drop)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.GREEN}Dropping invalid AGROVOC ({field_name}): {Fore.RESET}{invalid_agrovoc}\n"
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)
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assert new_value == valid_agrovoc
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def test_check_valid_agrovoc():
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"""Test valid AGROVOC subject."""
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value = "FORESTS"
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field_name = "dcterms.subject"
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drop = False
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result = check.agrovoc(value, field_name, drop)
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assert result == "FORESTS"
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def test_check_uncommon_filename_extension(capsys):
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"""Test uncommon filename extension."""
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value = "file.pdf.lck"
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check.filename_extension(value)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.YELLOW}Filename with uncommon extension: {Fore.RESET}{value}\n"
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)
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def test_check_common_filename_extension():
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"""Test common filename extension."""
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value = "file.pdf"
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result = check.filename_extension(value)
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assert result is None
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def test_check_incorrect_iso_639_1_language(capsys):
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"""Test incorrect ISO 639-1 language, as determined by comparing the item's language field with the actual language predicted in the item's title."""
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title = "A randomised vaccine field trial in Kenya demonstrates protection against wildebeest-associated malignant catarrhal fever in cattle"
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language = "es"
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exclude = []
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# Create a dictionary to mimic Pandas series
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row = {"dc.title": title, "dc.language.iso": language}
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series = pd.Series(row)
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experimental.correct_language(series, exclude)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.YELLOW}Possibly incorrect language {language} (detected en): {Fore.RESET}{title}\n"
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)
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def test_check_incorrect_iso_639_3_language(capsys):
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"""Test incorrect ISO 639-3 language, as determined by comparing the item's language field with the actual language predicted in the item's title."""
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title = "A randomised vaccine field trial in Kenya demonstrates protection against wildebeest-associated malignant catarrhal fever in cattle"
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language = "spa"
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exclude = []
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# Create a dictionary to mimic Pandas series
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row = {"dc.title": title, "dc.language.iso": language}
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series = pd.Series(row)
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experimental.correct_language(series, exclude)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.YELLOW}Possibly incorrect language {language} (detected eng): {Fore.RESET}{title}\n"
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)
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def test_check_correct_iso_639_1_language():
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"""Test correct ISO 639-1 language, as determined by comparing the item's language field with the actual language predicted in the item's title."""
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title = "A randomised vaccine field trial in Kenya demonstrates protection against wildebeest-associated malignant catarrhal fever in cattle"
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language = "en"
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exclude = []
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# Create a dictionary to mimic Pandas series
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row = {"dc.title": title, "dc.language.iso": language}
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series = pd.Series(row)
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result = experimental.correct_language(series, exclude)
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assert result is None
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def test_check_correct_iso_639_3_language():
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"""Test correct ISO 639-3 language, as determined by comparing the item's language field with the actual language predicted in the item's title."""
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title = "A randomised vaccine field trial in Kenya demonstrates protection against wildebeest-associated malignant catarrhal fever in cattle"
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language = "eng"
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exclude = []
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# Create a dictionary to mimic Pandas series
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row = {"dc.title": title, "dc.language.iso": language}
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series = pd.Series(row)
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result = experimental.correct_language(series, exclude)
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assert result is None
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def test_check_valid_spdx_license_identifier():
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"""Test valid SPDX license identifier."""
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license = "CC-BY-SA-4.0"
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result = check.spdx_license_identifier(license)
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assert result is None
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def test_check_invalid_spdx_license_identifier(capsys):
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"""Test invalid SPDX license identifier."""
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license = "CC-BY-SA"
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check.spdx_license_identifier(license)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.YELLOW}Non-SPDX license identifier: {Fore.RESET}{license}\n"
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)
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def test_check_duplicate_item(capsys):
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"""Test item with duplicate title, type, and date."""
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item_title = "Title"
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item_type = "Report"
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item_date = "2021-03-17"
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d = {
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"dc.title": [item_title, item_title],
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"dcterms.type": [item_type, item_type],
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"dcterms.issued": [item_date, item_date],
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}
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df = pd.DataFrame(data=d)
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check.duplicate_items(df)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.YELLOW}Possible duplicate (dc.title): {Fore.RESET}{item_title}\n"
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)
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def test_check_no_mojibake():
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"""Test string with no mojibake."""
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field = "CIAT Publicaçao"
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field_name = "dcterms.isPartOf"
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result = check.mojibake(field, field_name)
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assert result is None
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def test_check_mojibake(capsys):
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"""Test string with mojibake."""
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field = "CIAT Publicaçao"
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field_name = "dcterms.isPartOf"
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check.mojibake(field, field_name)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.YELLOW}Possible encoding issue ({field_name}): {Fore.RESET}{field}\n"
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)
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def test_check_doi_field():
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"""Test an item with a DOI field."""
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doi = "https://doi.org/10.1186/1743-422X-9-218"
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citation = "Orth, A. 2021. Testing all the things. doi: 10.1186/1743-422X-9-218"
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# Emulate a column in a transposed dataframe (which is just a series), with
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# the citation and a DOI field.
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d = {"cg.identifier.doi": doi, "dcterms.bibliographicCitation": citation}
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series = pd.Series(data=d)
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exclude = []
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result = check.citation_doi(series, exclude)
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assert result is None
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def test_check_doi_only_in_citation(capsys):
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"""Test an item with a DOI in its citation, but no DOI field."""
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citation = "Orth, A. 2021. Testing all the things. doi: 10.1186/1743-422X-9-218"
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exclude = []
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# Emulate a column in a transposed dataframe (which is just a series), with
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# an empty DOI field and a citation containing a DOI.
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d = {"cg.identifier.doi": None, "dcterms.bibliographicCitation": citation}
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series = pd.Series(data=d)
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check.citation_doi(series, exclude)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.YELLOW}DOI in citation, but missing a DOI field: {Fore.RESET}{citation}\n"
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)
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def test_title_in_citation():
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"""Test an item with its title in the citation."""
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title = "Testing all the things"
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citation = "Orth, A. 2021. Testing all the things."
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exclude = []
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# Emulate a column in a transposed dataframe (which is just a series), with
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# the title and citation.
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d = {"dc.title": title, "dcterms.bibliographicCitation": citation}
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series = pd.Series(data=d)
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result = check.title_in_citation(series, exclude)
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assert result is None
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def test_title_not_in_citation(capsys):
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"""Test an item with its title missing from the citation."""
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title = "Testing all the things"
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citation = "Orth, A. 2021. Testing all teh things."
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exclude = []
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# Emulate a column in a transposed dataframe (which is just a series), with
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# the title and citation.
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d = {"dc.title": title, "dcterms.bibliographicCitation": citation}
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series = pd.Series(data=d)
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check.title_in_citation(series, exclude)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.YELLOW}Title is not present in citation: {Fore.RESET}{title}\n"
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)
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def test_country_matches_region():
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"""Test an item with regions matching its country list."""
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country = "Kenya"
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region = "Eastern Africa"
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exclude = []
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# Emulate a column in a transposed dataframe (which is just a series)
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d = {"cg.coverage.country": country, "cg.coverage.region": region}
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series = pd.Series(data=d)
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result = check.countries_match_regions(series, exclude)
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assert result is None
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def test_country_not_matching_region(capsys):
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"""Test an item with regions not matching its country list."""
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title = "Testing an item with no matching region."
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country = "Kenya"
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region = ""
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missing_region = "Eastern Africa"
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exclude = []
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# Emulate a column in a transposed dataframe (which is just a series)
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d = {
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"dc.title": title,
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"cg.coverage.country": country,
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"cg.coverage.region": region,
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}
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series = pd.Series(data=d)
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check.countries_match_regions(series, exclude)
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captured = capsys.readouterr()
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assert (
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captured.out
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== f"{Fore.YELLOW}Missing region ({country} → {missing_region}): {Fore.RESET}{title}\n"
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)
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