1
0
mirror of https://github.com/ilri/csv-metadata-quality.git synced 2025-05-09 14:46:00 +02:00

15 Commits

Author SHA1 Message Date
d76e72532a Move unreleased changes to v0.4.4
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2021-02-21 13:25:22 +02:00
13980d2dde CHANGELOG.md: Add note about colored output 2021-02-21 13:12:26 +02:00
9aaaa62461 Update requirements
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Generated with poetry export:

    $ poetry export --without-hashes -f requirements.txt > requirements.txt
    $ poetry export --without-hashes --dev -f requirements.txt > requirements-dev.txt

I am trying `--without-hashes` to work around an error on pip install
when running in CI:

    ERROR: In --require-hashes mode, all requirements must have their versions pinned with ==.
2021-02-21 13:10:52 +02:00
a7fc5a246c Colorize output
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Messages will be colorized:

- Red for errors
- Yellow for warnings or information
- Green for fixes
2021-02-21 13:01:25 +02:00
7fb8acb866 Add colorama for colored output
Red for errors, yellow for warnings or information, and green for
fixes.
2021-02-21 13:00:31 +02:00
9f5d2c2c4f poetry.lock: Run poetry update
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2021-02-15 15:13:12 +02:00
202abf140c CHANGELOG.md: Add note about poetry
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2021-02-04 21:48:12 +02:00
0cd6d3dfe6 Update requirements
Generated with poetry export:

    $ poetry export --without-hashes -f requirements.txt > requirements.txt
    $ poetry export --without-hashes --dev -f requirements.txt > requirements-dev.txt

I am trying `--without-hashes` to work around an error on pip install
when running in CI:

    ERROR: In --require-hashes mode, all requirements must have their versions pinned with ==.
2021-02-04 21:46:49 +02:00
a458beac55 poetry.lock: Run poetry update 2021-02-04 21:45:30 +02:00
e62ecb0a8f CHANGELOG.md: Add note about new date format 2021-02-04 21:43:44 +02:00
de92f32ab6 csv_metadata_quality/check.py: More date formats
We should also allow ISO 8601 extended in combined date and time
format. DSpace does not have a problem with dates in this format
and I have found some metadata that uses this date format.

For example: 2020-08-31T11:04:56Z

See: https://en.wikipedia.org/wiki/ISO_8601
2021-02-04 21:39:14 +02:00
dbbbc0944a README.md: Add handle to citation
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2021-01-27 10:33:37 +02:00
d17bf3033c README.md: Add citation 2021-01-27 10:32:26 +02:00
2ec52f1b73 README.md: Update description
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2021-01-26 15:43:41 +02:00
aa1abf15a7 README.md: Adjust title 2021-01-26 15:35:21 +02:00
12 changed files with 335 additions and 291 deletions

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@ -4,6 +4,16 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [0.4.4] - 2021-02-21
### Added
- Accept dates formatted in ISO 8601 extended with combined date and time, for
example: 2020-08-31T11:04:56Z
- Colorized output: red for errors, yellow for warnings and information, green
for changes
### Updated
- Run `poetry update` to update project dependencies
## [0.4.3] - 2021-01-26
### Changed
- Reformat with black

View File

@ -1,8 +1,12 @@
# CSV Metadata Quality ![GitHub Actions](https://github.com/ilri/csv-metadata-quality/workflows/Build%20and%20Test/badge.svg) [![Build Status](https://ci.mjanja.ch/api/badges/alanorth/csv-metadata-quality/status.svg)](https://ci.mjanja.ch/alanorth/csv-metadata-quality)
A simple, but opinionated metadata quality checker and fixer designed to work with CSVs in the DSpace ecosystem (though it could theoretically work on any CSV that uses Dublin Core fields as columns). The implementation is essentially a pipeline of checks and fixes that begins with splitting multi-value fields on the standard DSpace "||" separator, trimming leading/trailing whitespace, and then proceeding to more specialized cases like ISSNs, ISBNs, languages, etc.
# DSpace CSV Metadata Quality Checker ![GitHub Actions](https://github.com/ilri/csv-metadata-quality/workflows/Build%20and%20Test/badge.svg) [![Build Status](https://ci.mjanja.ch/api/badges/alanorth/csv-metadata-quality/status.svg)](https://ci.mjanja.ch/alanorth/csv-metadata-quality)
A simple, but opinionated metadata quality checker and fixer designed to work with CSVs in the DSpace ecosystem (though it could theoretically work on any CSV that uses Dublin Core fields as columns). The implementation is essentially a pipeline of checks and fixes that begins with splitting multi-value fields on the standard DSpace "||" separator, trimming leading/trailing whitespace, and then proceeding to more specialized cases like ISSNs, ISBNs, languages, unnecessary Unicode, AGROVOC terms, etc.
Requires Python 3.7 or greater (3.8 recommended). CSV and Excel support comes from the [Pandas](https://pandas.pydata.org/) library, though your mileage may vary with Excel because this is much less tested.
If you use the DSpace CSV metadata quality checker please cite:
*Orth, A. 2019. DSpace CSV metadata quality checker. Nairobi, Kenya: ILRI. https://hdl.handle.net/10568/110997.*
## Functionality
- Validate dates, ISSNs, ISBNs, and multi-value separators ("||")

View File

@ -4,6 +4,7 @@ import signal
import sys
import pandas as pd
from colorama import Fore
import csv_metadata_quality.check as check
import csv_metadata_quality.experimental as experimental
@ -77,7 +78,7 @@ def run(argv):
if column == exclude and skip is False:
skip = True
if skip:
print(f"Skipping {column}")
print(f"{Fore.YELLOW}Skipping {Fore.RESET}{column}")
continue

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@ -3,6 +3,7 @@ from datetime import datetime, timedelta
import pandas as pd
import requests
import requests_cache
from colorama import Fore
from pycountry import languages
@ -26,7 +27,7 @@ def issn(field):
for value in field.split("||"):
if not issn.is_valid(value):
print(f"Invalid ISSN: {value}")
print(f"{Fore.RED}Invalid ISSN: {Fore.RESET}{value}")
return field
@ -51,7 +52,7 @@ def isbn(field):
for value in field.split("||"):
if not isbn.is_valid(value):
print(f"Invalid ISBN: {value}")
print(f"{Fore.RED}Invalid ISBN: {Fore.RESET}{value}")
return field
@ -76,7 +77,9 @@ def separators(field, field_name):
for value in field.split("||"):
# Check if the current value is blank
if value == "":
print(f"Unnecessary multi-value separator ({field_name}): {field}")
print(
f"{Fore.RED}Unnecessary multi-value separator ({field_name}): {Fore.RESET}{field}"
)
continue
@ -85,7 +88,9 @@ def separators(field, field_name):
# Check if there was a match
if match:
print(f"Invalid multi-value separator ({field_name}): {field}")
print(
f"{Fore.RED}Invalid multi-value separator ({field_name}): {Fore.RESET}{field}"
)
return field
@ -102,7 +107,7 @@ def date(field, field_name):
"""
if pd.isna(field):
print(f"Missing date ({field_name}).")
print(f"{Fore.RED}Missing date ({field_name}).{Fore.RESET}")
return
@ -111,7 +116,9 @@ def date(field, field_name):
# We don't allow multi-value date fields
if len(multiple_dates) > 1:
print(f"Multiple dates not allowed ({field_name}): {field}")
print(
f"{Fore.RED}Multiple dates not allowed ({field_name}): {Fore.RESET}{field}"
)
return field
@ -137,7 +144,15 @@ def date(field, field_name):
return field
except ValueError:
print(f"Invalid date ({field_name}): {field}")
pass
try:
# Check if date is valid YYYY-MM-DDTHH:MM:SSZ format
datetime.strptime(field, "%Y-%m-%dT%H:%M:%SZ")
return field
except ValueError:
print(f"{Fore.RED}Invalid date ({field_name}): {Fore.RESET}{field}")
return field
@ -170,9 +185,7 @@ def suspicious_characters(field, field_name):
# character and spanning enough of the rest to give a preview,
# but not too much to cause the line to break in terminals with
# a default of 80 characters width.
suspicious_character_msg = (
f"Suspicious character ({field_name}): {field_subset}"
)
suspicious_character_msg = f"{Fore.YELLOW}Suspicious character ({field_name}): {Fore.RESET}{field_subset}"
print(f"{suspicious_character_msg:1.80}")
return field
@ -197,16 +210,16 @@ def language(field):
# can check it against ISO 639-1 or ISO 639-3 accordingly.
if len(value) == 2:
if not languages.get(alpha_2=value):
print(f"Invalid ISO 639-1 language: {value}")
print(f"{Fore.RED}Invalid ISO 639-1 language: {Fore.RESET}{value}")
pass
elif len(value) == 3:
if not languages.get(alpha_3=value):
print(f"Invalid ISO 639-3 language: {value}")
print(f"{Fore.RED}Invalid ISO 639-3 language: {Fore.RESET}{value}")
pass
else:
print(f"Invalid language: {value}")
print(f"{Fore.RED}Invalid language: {Fore.RESET}{value}")
return field
@ -248,7 +261,7 @@ def agrovoc(field, field_name):
# check if there are any results
if len(data["results"]) == 0:
print(f"Invalid AGROVOC ({field_name}): {value}")
print(f"{Fore.RED}Invalid AGROVOC ({field_name}): {Fore.RESET}{value}")
return field
@ -301,6 +314,6 @@ def filename_extension(field):
break
if filename_extension_match is False:
print(f"Filename with uncommon extension: {value}")
print(f"{Fore.YELLOW}Filename with uncommon extension: {Fore.RESET}{value}")
return field

View File

@ -1,4 +1,5 @@
import pandas as pd
from colorama import Fore
def correct_language(row):
@ -10,10 +11,11 @@ def correct_language(row):
language and returns the value in the language field if it does match.
"""
from pycountry import languages
import langid
import re
import langid
from pycountry import languages
# Initialize some variables at global scope so that we can set them in the
# loop scope below and still be able to access them afterwards.
language = ""
@ -83,12 +85,12 @@ def correct_language(row):
detected_language = languages.get(alpha_2=langid_classification[0])
if len(language) == 2 and language != detected_language.alpha_2:
print(
f"Possibly incorrect language {language} (detected {detected_language.alpha_2}): {title}"
f"{Fore.YELLOW}Possibly incorrect language {language} (detected {detected_language.alpha_2}): {Fore.RESET}{title}"
)
elif len(language) == 3 and language != detected_language.alpha_3:
print(
f"Possibly incorrect language {language} (detected {detected_language.alpha_3}): {title}"
f"{Fore.YELLOW}Possibly incorrect language {language} (detected {detected_language.alpha_3}): {Fore.RESET}{title}"
)
else:

View File

@ -2,6 +2,7 @@ import re
from unicodedata import normalize
import pandas as pd
from colorama import Fore
from csv_metadata_quality.util import is_nfc
@ -29,7 +30,9 @@ def whitespace(field, field_name):
match = re.findall(pattern, value)
if match:
print(f"Removing excessive whitespace ({field_name}): {value}")
print(
f"{Fore.GREEN}Removing excessive whitespace ({field_name}): {Fore.RESET}{value}"
)
value = re.sub(pattern, " ", value)
# Save cleaned value
@ -62,7 +65,9 @@ def separators(field, field_name):
for value in field.split("||"):
# Check if the value is blank and skip it
if value == "":
print(f"Fixing unnecessary multi-value separator ({field_name}): {field}")
print(
f"{Fore.GREEN}Fixing unnecessary multi-value separator ({field_name}): {Fore.RESET}{field}"
)
continue
@ -71,7 +76,9 @@ def separators(field, field_name):
match = re.findall(pattern, value)
if match:
print(f"Fixing invalid multi-value separator ({field_name}): {value}")
print(
f"{Fore.RED}Fixing invalid multi-value separator ({field_name}): {Fore.RESET}{value}"
)
value = re.sub(pattern, "||", value)
@ -107,7 +114,7 @@ def unnecessary_unicode(field):
match = re.findall(pattern, field)
if match:
print(f"Removing unnecessary Unicode (U+200B): {field}")
print(f"{Fore.GREEN}Removing unnecessary Unicode (U+200B): {Fore.RESET}{field}")
field = re.sub(pattern, "", field)
# Check for replacement characters (U+FFFD)
@ -115,7 +122,7 @@ def unnecessary_unicode(field):
match = re.findall(pattern, field)
if match:
print(f"Removing unnecessary Unicode (U+FFFD): {field}")
print(f"{Fore.GREEN}Removing unnecessary Unicode (U+FFFD): {Fore.RESET}{field}")
field = re.sub(pattern, "", field)
# Check for no-break spaces (U+00A0)
@ -123,7 +130,9 @@ def unnecessary_unicode(field):
match = re.findall(pattern, field)
if match:
print(f"Replacing unnecessary Unicode (U+00A0): {field}")
print(
f"{Fore.GREEN}Replacing unnecessary Unicode (U+00A0): {Fore.RESET}{field}"
)
field = re.sub(pattern, " ", field)
# Check for soft hyphens (U+00AD), sometimes preceeded with a normal hyphen
@ -131,7 +140,9 @@ def unnecessary_unicode(field):
match = re.findall(pattern, field)
if match:
print(f"Replacing unnecessary Unicode (U+00AD): {field}")
print(
f"{Fore.GREEN}Replacing unnecessary Unicode (U+00AD): {Fore.RESET}{field}"
)
field = re.sub(pattern, "-", field)
return field
@ -156,7 +167,9 @@ def duplicates(field, field_name):
if value not in new_values:
new_values.append(value)
else:
print(f"Removing duplicate value ({field_name}): {value}")
print(
f"{Fore.GREEN}Removing duplicate value ({field_name}): {Fore.RESET}{value}"
)
# Create a new field consisting of all values joined with "||"
new_field = "||".join(new_values)
@ -189,7 +202,7 @@ def newlines(field):
match = re.findall(r"\n", field)
if match:
print(f"Removing newline: {field}")
print(f"{Fore.GREEN}Removing newline: {Fore.RESET}{field}")
field = field.replace("\n", "")
return field
@ -213,7 +226,9 @@ def comma_space(field, field_name):
match = re.findall(r",\w", field)
if match:
print(f"Adding space after comma ({field_name}): {field}")
print(
f"{Fore.GREEN}Adding space after comma ({field_name}): {Fore.RESET}{field}"
)
field = re.sub(r",(\w)", r", \1", field)
return field
@ -234,7 +249,7 @@ def normalize_unicode(field, field_name):
# Check if the current string is using normalized Unicode (NFC)
if not is_nfc(field):
print(f"Normalizing Unicode ({field_name}): {field}")
print(f"{Fore.GREEN}Normalizing Unicode ({field_name}): {Fore.RESET}{field}")
field = normalize("NFC", field)
return field

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@ -1 +1 @@
VERSION = "0.4.3"
VERSION = "0.4.4"

332
poetry.lock generated
View File

@ -67,7 +67,6 @@ description = "Disable App Nap on macOS >= 10.9"
category = "dev"
optional = false
python-versions = "*"
marker = "python_version >= \"3.7\" and python_version < \"4.0\" and sys_platform == \"darwin\""
[[package]]
name = "atomicwrites"
@ -76,7 +75,6 @@ description = "Atomic file writes."
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
marker = "sys_platform == \"win32\""
[[package]]
name = "attrs"
@ -87,10 +85,10 @@ optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[package.extras]
dev = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"]
dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"]
docs = ["furo", "sphinx", "zope.interface"]
tests = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
tests_no_zope = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
[[package]]
name = "babel"
@ -110,7 +108,6 @@ description = "Specifications for callback functions passed in to an API"
category = "dev"
optional = false
python-versions = "*"
marker = "python_version >= \"3.7\" and python_version < \"4.0\""
[[package]]
name = "black"
@ -120,10 +117,6 @@ category = "dev"
optional = false
python-versions = ">=3.6"
[package.extras]
colorama = ["colorama (>=0.4.3)"]
d = ["aiohttp (>=3.3.2)", "aiohttp-cors"]
[package.dependencies]
appdirs = "*"
click = ">=7.1.2"
@ -134,6 +127,10 @@ toml = ">=0.10.1"
typed-ast = ">=1.4.0"
typing-extensions = ">=3.7.4"
[package.extras]
colorama = ["colorama (>=0.4.3)"]
d = ["aiohttp (>=3.3.2)", "aiohttp-cors"]
[[package]]
name = "certifi"
version = "2020.12.5"
@ -162,10 +159,9 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
name = "colorama"
version = "0.4.4"
description = "Cross-platform colored terminal text."
category = "dev"
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
marker = "python_version >= \"3.7\" and python_version < \"4.0\" and sys_platform == \"win32\" or sys_platform == \"win32\""
[[package]]
name = "csvkit"
@ -197,7 +193,6 @@ description = "Decorators for Humans"
category = "dev"
optional = false
python-versions = ">=2.6, !=3.0.*, !=3.1.*"
marker = "python_version >= \"3.7\" and python_version < \"4.0\""
[[package]]
name = "et-xmlfile"
@ -238,12 +233,23 @@ python-versions = "*"
[[package]]
name = "ipython"
version = "7.19.0"
version = "7.20.0"
description = "IPython: Productive Interactive Computing"
category = "dev"
optional = false
python-versions = ">=3.7"
marker = "python_version >= \"3.7\" and python_version < \"4.0\""
[package.dependencies]
appnope = {version = "*", markers = "sys_platform == \"darwin\""}
backcall = "*"
colorama = {version = "*", markers = "sys_platform == \"win32\""}
decorator = "*"
jedi = ">=0.16"
pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
pickleshare = "*"
prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
pygments = "*"
traitlets = ">=4.2"
[package.extras]
all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.14)", "pygments", "qtconsole", "requests", "testpath"]
@ -256,19 +262,6 @@ parallel = ["ipyparallel"]
qtconsole = ["qtconsole"]
test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.14)"]
[package.dependencies]
appnope = "*"
backcall = "*"
colorama = "*"
decorator = "*"
jedi = ">=0.10"
pexpect = ">4.3"
pickleshare = "*"
prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
pygments = "*"
setuptools = ">=18.5"
traitlets = ">=4.2"
[[package]]
name = "ipython-genutils"
version = "0.2.0"
@ -276,7 +269,6 @@ description = "Vestigial utilities from IPython"
category = "dev"
optional = false
python-versions = "*"
marker = "python_version >= \"3.7\" and python_version < \"4.0\""
[[package]]
name = "isodate"
@ -317,15 +309,14 @@ description = "An autocompletion tool for Python that can be used for text edito
category = "dev"
optional = false
python-versions = ">=3.6"
marker = "python_version >= \"3.7\" and python_version < \"4.0\""
[package.extras]
qa = ["flake8 (3.8.3)", "mypy (0.782)"]
testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<6.0.0)"]
[package.dependencies]
parso = ">=0.8.0,<0.9.0"
[package.extras]
qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<6.0.0)"]
[[package]]
name = "langid"
version = "1.1.6"
@ -366,11 +357,11 @@ python-versions = "*"
[[package]]
name = "numpy"
version = "1.19.5"
version = "1.20.1"
description = "NumPy is the fundamental package for array computing with Python."
category = "main"
optional = false
python-versions = ">=3.6"
python-versions = ">=3.7"
[[package]]
name = "openpyxl"
@ -386,7 +377,7 @@ jdcal = "*"
[[package]]
name = "packaging"
version = "20.8"
version = "20.9"
description = "Core utilities for Python packages"
category = "dev"
optional = false
@ -397,20 +388,20 @@ pyparsing = ">=2.0.2"
[[package]]
name = "pandas"
version = "1.2.1"
version = "1.2.2"
description = "Powerful data structures for data analysis, time series, and statistics"
category = "main"
optional = false
python-versions = ">=3.7.1"
[package.extras]
test = ["pytest (>=5.0.1)", "pytest-xdist", "hypothesis (>=3.58)"]
[package.dependencies]
numpy = ">=1.16.5"
python-dateutil = ">=2.7.3"
pytz = ">=2017.3"
[package.extras]
test = ["pytest (>=5.0.1)", "pytest-xdist", "hypothesis (>=3.58)"]
[[package]]
name = "parsedatetime"
version = "2.6"
@ -426,10 +417,9 @@ description = "A Python Parser"
category = "dev"
optional = false
python-versions = ">=3.6"
marker = "python_version >= \"3.7\" and python_version < \"4.0\""
[package.extras]
qa = ["flake8 (3.8.3)", "mypy (0.782)"]
qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
testing = ["docopt", "pytest (<6.0.0)"]
[[package]]
@ -447,7 +437,6 @@ description = "Pexpect allows easy control of interactive console applications."
category = "dev"
optional = false
python-versions = "*"
marker = "python_version >= \"3.7\" and python_version < \"4.0\" and sys_platform != \"win32\""
[package.dependencies]
ptyprocess = ">=0.5"
@ -459,7 +448,6 @@ description = "Tiny 'shelve'-like database with concurrency support"
category = "dev"
optional = false
python-versions = "*"
marker = "python_version >= \"3.7\" and python_version < \"4.0\""
[[package]]
name = "pluggy"
@ -474,12 +462,11 @@ dev = ["pre-commit", "tox"]
[[package]]
name = "prompt-toolkit"
version = "3.0.14"
version = "3.0.16"
description = "Library for building powerful interactive command lines in Python"
category = "dev"
optional = false
python-versions = ">=3.6.1"
marker = "python_version >= \"3.7\" and python_version < \"4.0\""
[package.dependencies]
wcwidth = "*"
@ -491,7 +478,6 @@ description = "Run a subprocess in a pseudo terminal"
category = "dev"
optional = false
python-versions = "*"
marker = "python_version >= \"3.7\" and python_version < \"4.0\" and sys_platform != \"win32\""
[[package]]
name = "py"
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{file = "SQLAlchemy-1.3.23-cp36-cp36m-macosx_10_14_x86_64.whl", hash = "sha256:d1a85dfc5dee741bf49cb9b6b6b8d2725a268e4992507cf151cba26b17d97c37"},
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{file = "SQLAlchemy-1.3.23-cp36-cp36m-manylinux2010_x86_64.whl", hash = "sha256:e8a1750b44ad6422ace82bf3466638f1aa0862dbb9689690d5f2f48cce3476c8"},
{file = "SQLAlchemy-1.3.23-cp36-cp36m-manylinux2014_aarch64.whl", hash = "sha256:e5bb3463df697279e5459a7316ad5a60b04b0107f9392e88674d0ece70e9cf70"},
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{file = "SQLAlchemy-1.3.23-cp37-cp37m-macosx_10_14_x86_64.whl", hash = "sha256:23927c3981d1ec6b4ea71eb99d28424b874d9c696a21e5fbd9fa322718be3708"},
{file = "SQLAlchemy-1.3.23-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:d90010304abb4102123d10cbad2cdf2c25a9f2e66a50974199b24b468509bad5"},
{file = "SQLAlchemy-1.3.23-cp37-cp37m-manylinux2010_x86_64.whl", hash = "sha256:a8bfc1e1afe523e94974132d7230b82ca7fa2511aedde1f537ec54db0399541a"},
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{file = "SQLAlchemy-1.3.23-cp38-cp38-macosx_10_14_x86_64.whl", hash = "sha256:24f9569e82a009a09ce2d263559acb3466eba2617203170e4a0af91e75b4f075"},
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{file = "SQLAlchemy-1.3.23-cp39-cp39-macosx_10_14_x86_64.whl", hash = "sha256:8be835aac18ec85351385e17b8665bd4d63083a7160a017bef3d640e8e65cadb"},
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{file = "SQLAlchemy-1.3.23-cp39-cp39-manylinux2014_aarch64.whl", hash = "sha256:baeb451ee23e264de3f577fee5283c73d9bbaa8cb921d0305c0bbf700094b65b"},
{file = "SQLAlchemy-1.3.23-cp39-cp39-win32.whl", hash = "sha256:94208867f34e60f54a33a37f1c117251be91a47e3bfdb9ab8a7847f20886ad06"},
{file = "SQLAlchemy-1.3.23-cp39-cp39-win_amd64.whl", hash = "sha256:f4d972139d5000105fcda9539a76452039434013570d6059993120dc2a65e447"},
{file = "SQLAlchemy-1.3.23.tar.gz", hash = "sha256:6fca33672578666f657c131552c4ef8979c1606e494f78cd5199742dfb26918b"},
]
termcolor = [
{file = "termcolor-1.1.0.tar.gz", hash = "sha256:1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b"},
@ -1198,8 +1172,8 @@ typing-extensions = [
{file = "typing_extensions-3.7.4.3.tar.gz", hash = "sha256:99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c"},
]
urllib3 = [
{file = "urllib3-1.26.2-py2.py3-none-any.whl", hash = "sha256:d8ff90d979214d7b4f8ce956e80f4028fc6860e4431f731ea4a8c08f23f99473"},
{file = "urllib3-1.26.2.tar.gz", hash = "sha256:19188f96923873c92ccb987120ec4acaa12f0461fa9ce5d3d0772bc965a39e08"},
{file = "urllib3-1.26.3-py2.py3-none-any.whl", hash = "sha256:1b465e494e3e0d8939b50680403e3aedaa2bc434b7d5af64dfd3c958d7f5ae80"},
{file = "urllib3-1.26.3.tar.gz", hash = "sha256:de3eedaad74a2683334e282005cd8d7f22f4d55fa690a2a1020a416cb0a47e73"},
]
wcwidth = [
{file = "wcwidth-0.2.5-py2.py3-none-any.whl", hash = "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784"},

View File

@ -1,6 +1,6 @@
[tool.poetry]
name = "csv-metadata-quality"
version = "0.4.3"
version = "0.4.4"
description="A simple, but opinionated CSV quality checking and fixing pipeline for CSVs in the DSpace ecosystem."
authors = ["Alan Orth <alan.orth@gmail.com>"]
license="GPL-3.0-only"
@ -16,6 +16,7 @@ requests = "^2.23.0"
requests-cache = "^0.5.2"
pycountry = "^19.8.18"
langid = "^1.1.6"
colorama = "^0.4.4"
[tool.poetry.dev-dependencies]
pytest = "^6.1.1"

View File

@ -1,71 +1,71 @@
agate==1.6.1
agate-dbf==0.2.2
agate-excel==0.2.3
agate-sql==0.5.5
appdirs==1.4.4
agate==1.6.1
appdirs==1.4.4; python_version >= "3.6"
appnope==0.1.2; python_version >= "3.7" and python_version < "4.0" and sys_platform == "darwin"
atomicwrites==1.4.0; sys_platform == "win32"
attrs==20.3.0
babel==2.9.0
atomicwrites==1.4.0; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6")
attrs==20.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
babel==2.9.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
backcall==0.2.0; python_version >= "3.7" and python_version < "4.0"
black==20.8b1
certifi==2020.12.5
chardet==4.0.0
click==7.1.2
colorama==0.4.4; python_version >= "3.7" and python_version < "4.0" and sys_platform == "win32" or sys_platform == "win32"
black==20.8b1; python_version >= "3.6"
certifi==2020.12.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
chardet==4.0.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
click==7.1.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
colorama==0.4.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
csvkit==1.0.5
dbfread==2.0.7
decorator==4.4.2; python_version >= "3.7" and python_version < "4.0"
et-xmlfile==1.0.1
flake8==3.8.4
idna==2.10
iniconfig==1.1.1
ipython==7.19.0; python_version >= "3.7" and python_version < "4.0"
decorator==4.4.2; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4.0" or python_version >= "3.7" and python_version < "4.0" and python_full_version >= "3.2.0"
et-xmlfile==1.0.1; python_version >= "3.6"
flake8==3.8.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
idna==2.10; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
iniconfig==1.1.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
ipython-genutils==0.2.0; python_version >= "3.7" and python_version < "4.0"
ipython==7.20.0; python_version >= "3.7" and python_version < "4.0"
isodate==0.6.0
isort==5.7.0
jdcal==1.4.1
isort==5.7.0; python_version >= "3.6" and python_version < "4.0"
jdcal==1.4.1; python_version >= "3.6"
jedi==0.18.0; python_version >= "3.7" and python_version < "4.0"
langid==1.1.6
leather==0.3.3
mccabe==0.6.1
mypy-extensions==0.4.3
numpy==1.19.5
openpyxl==3.0.6
packaging==20.8
pandas==1.2.1
mccabe==0.6.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
mypy-extensions==0.4.3; python_version >= "3.6"
numpy==1.20.1; python_version >= "3.7" and python_full_version >= "3.7.1"
openpyxl==3.0.6; python_version >= "3.6"
packaging==20.9; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
pandas==1.2.2; python_full_version >= "3.7.1"
parsedatetime==2.6
parso==0.8.1; python_version >= "3.7" and python_version < "4.0"
pathspec==0.8.1
pathspec==0.8.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
pexpect==4.8.0; python_version >= "3.7" and python_version < "4.0" and sys_platform != "win32"
pickleshare==0.7.5; python_version >= "3.7" and python_version < "4.0"
pluggy==0.13.1
prompt-toolkit==3.0.14; python_version >= "3.7" and python_version < "4.0"
pluggy==0.13.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
prompt-toolkit==3.0.16; python_version >= "3.7" and python_version < "4.0" and python_full_version >= "3.6.1"
ptyprocess==0.7.0; python_version >= "3.7" and python_version < "4.0" and sys_platform != "win32"
py==1.10.0
pycodestyle==2.6.0
py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
pycodestyle==2.6.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
pycountry==19.8.18
pyflakes==2.2.0
pygments==2.7.4; python_version >= "3.7" and python_version < "4.0"
pyparsing==2.4.7
pytest==6.2.2
pytest-clarity==0.3.0a0
python-dateutil==2.8.1
python-slugify==4.0.1
python-stdnum==1.15
pyflakes==2.2.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
pygments==2.8.0; python_version >= "3.7" and python_version < "4.0"
pyparsing==2.4.7; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
pytest-clarity==0.3.0a0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
pytest==6.2.2; python_version >= "3.6"
python-dateutil==2.8.1; python_full_version >= "3.7.1"
python-slugify==4.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
python-stdnum==1.16
pytimeparse==1.1.8
pytz==2020.5
regex==2020.11.13
requests==2.25.1
pytz==2021.1; python_full_version >= "3.7.1"
regex==2020.11.13; python_version >= "3.6"
requests-cache==0.5.2
six==1.15.0
sqlalchemy==1.3.22
termcolor==1.1.0
text-unidecode==1.3
toml==0.10.2
requests==2.25.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
six==1.15.0; python_full_version >= "3.7.1"
sqlalchemy==1.3.23; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
termcolor==1.1.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
text-unidecode==1.3; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
toml==0.10.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
traitlets==5.0.5; python_version >= "3.7" and python_version < "4.0"
typed-ast==1.4.2
typing-extensions==3.7.4.3
urllib3==1.26.2
wcwidth==0.2.5; python_version >= "3.7" and python_version < "4.0"
xlrd==1.2.0
typed-ast==1.4.2; python_version >= "3.6"
typing-extensions==3.7.4.3; python_version >= "3.6"
urllib3==1.26.3; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
wcwidth==0.2.5; python_version >= "3.7" and python_version < "4.0" and python_full_version >= "3.6.1"
xlrd==1.2.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")

View File

@ -1,15 +1,16 @@
certifi==2020.12.5
chardet==4.0.0
idna==2.10
certifi==2020.12.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
chardet==4.0.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
colorama==0.4.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
idna==2.10; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
langid==1.1.6
numpy==1.19.5
pandas==1.2.1
numpy==1.20.1; python_version >= "3.7" and python_full_version >= "3.7.1"
pandas==1.2.2; python_full_version >= "3.7.1"
pycountry==19.8.18
python-dateutil==2.8.1
python-stdnum==1.15
pytz==2020.5
requests==2.25.1
python-dateutil==2.8.1; python_full_version >= "3.7.1"
python-stdnum==1.16
pytz==2021.1; python_full_version >= "3.7.1"
requests-cache==0.5.2
six==1.15.0
urllib3==1.26.2
xlrd==1.2.0
requests==2.25.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
six==1.15.0; python_full_version >= "3.7.1"
urllib3==1.26.3; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
xlrd==1.2.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")

View File

@ -1,4 +1,5 @@
import pandas as pd
from colorama import Fore
import csv_metadata_quality.check as check
import csv_metadata_quality.experimental as experimental
@ -12,7 +13,7 @@ def test_check_invalid_issn(capsys):
check.issn(value)
captured = capsys.readouterr()
assert captured.out == f"Invalid ISSN: {value}\n"
assert captured.out == f"{Fore.RED}Invalid ISSN: {Fore.RESET}{value}\n"
def test_check_valid_issn():
@ -33,7 +34,7 @@ def test_check_invalid_isbn(capsys):
check.isbn(value)
captured = capsys.readouterr()
assert captured.out == f"Invalid ISBN: {value}\n"
assert captured.out == f"{Fore.RED}Invalid ISBN: {Fore.RESET}{value}\n"
def test_check_valid_isbn():
@ -56,7 +57,10 @@ def test_check_invalid_separators(capsys):
check.separators(value, field_name)
captured = capsys.readouterr()
assert captured.out == f"Invalid multi-value separator ({field_name}): {value}\n"
assert (
captured.out
== f"{Fore.RED}Invalid multi-value separator ({field_name}): {Fore.RESET}{value}\n"
)
def test_check_unnecessary_separators(capsys):
@ -70,7 +74,8 @@ def test_check_unnecessary_separators(capsys):
captured = capsys.readouterr()
assert (
captured.out == f"Unnecessary multi-value separator ({field_name}): {field}\n"
captured.out
== f"{Fore.RED}Unnecessary multi-value separator ({field_name}): {Fore.RESET}{field}\n"
)
@ -96,7 +101,7 @@ def test_check_missing_date(capsys):
check.date(value, field_name)
captured = capsys.readouterr()
assert captured.out == f"Missing date ({field_name}).\n"
assert captured.out == f"{Fore.RED}Missing date ({field_name}).{Fore.RESET}\n"
def test_check_multiple_dates(capsys):
@ -109,7 +114,10 @@ def test_check_multiple_dates(capsys):
check.date(value, field_name)
captured = capsys.readouterr()
assert captured.out == f"Multiple dates not allowed ({field_name}): {value}\n"
assert (
captured.out
== f"{Fore.RED}Multiple dates not allowed ({field_name}): {Fore.RESET}{value}\n"
)
def test_check_invalid_date(capsys):
@ -122,7 +130,9 @@ def test_check_invalid_date(capsys):
check.date(value, field_name)
captured = capsys.readouterr()
assert captured.out == f"Invalid date ({field_name}): {value}\n"
assert (
captured.out == f"{Fore.RED}Invalid date ({field_name}): {Fore.RESET}{value}\n"
)
def test_check_valid_date():
@ -147,7 +157,10 @@ def test_check_suspicious_characters(capsys):
check.suspicious_characters(value, field_name)
captured = capsys.readouterr()
assert captured.out == f"Suspicious character ({field_name}): ˆt\n"
assert (
captured.out
== f"{Fore.YELLOW}Suspicious character ({field_name}): {Fore.RESET}ˆt\n"
)
def test_check_valid_iso639_1_language():
@ -178,7 +191,9 @@ def test_check_invalid_iso639_1_language(capsys):
check.language(value)
captured = capsys.readouterr()
assert captured.out == f"Invalid ISO 639-1 language: {value}\n"
assert (
captured.out == f"{Fore.RED}Invalid ISO 639-1 language: {Fore.RESET}{value}\n"
)
def test_check_invalid_iso639_3_language(capsys):
@ -189,7 +204,9 @@ def test_check_invalid_iso639_3_language(capsys):
check.language(value)
captured = capsys.readouterr()
assert captured.out == f"Invalid ISO 639-3 language: {value}\n"
assert (
captured.out == f"{Fore.RED}Invalid ISO 639-3 language: {Fore.RESET}{value}\n"
)
def test_check_invalid_language(capsys):
@ -200,7 +217,7 @@ def test_check_invalid_language(capsys):
check.language(value)
captured = capsys.readouterr()
assert captured.out == f"Invalid language: {value}\n"
assert captured.out == f"{Fore.RED}Invalid language: {Fore.RESET}{value}\n"
def test_check_invalid_agrovoc(capsys):
@ -212,7 +229,10 @@ def test_check_invalid_agrovoc(capsys):
check.agrovoc(value, field_name)
captured = capsys.readouterr()
assert captured.out == f"Invalid AGROVOC ({field_name}): {value}\n"
assert (
captured.out
== f"{Fore.RED}Invalid AGROVOC ({field_name}): {Fore.RESET}{value}\n"
)
def test_check_valid_agrovoc():
@ -234,7 +254,10 @@ def test_check_uncommon_filename_extension(capsys):
check.filename_extension(value)
captured = capsys.readouterr()
assert captured.out == f"Filename with uncommon extension: {value}\n"
assert (
captured.out
== f"{Fore.YELLOW}Filename with uncommon extension: {Fore.RESET}{value}\n"
)
def test_check_common_filename_extension():
@ -262,7 +285,7 @@ def test_check_incorrect_iso_639_1_language(capsys):
captured = capsys.readouterr()
assert (
captured.out
== f"Possibly incorrect language {language} (detected en): {title}\n"
== f"{Fore.YELLOW}Possibly incorrect language {language} (detected en): {Fore.RESET}{title}\n"
)
@ -281,7 +304,7 @@ def test_check_incorrect_iso_639_3_language(capsys):
captured = capsys.readouterr()
assert (
captured.out
== f"Possibly incorrect language {language} (detected eng): {title}\n"
== f"{Fore.YELLOW}Possibly incorrect language {language} (detected eng): {Fore.RESET}{title}\n"
)