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mirror of https://github.com/ilri/csv-metadata-quality.git synced 2025-05-10 15:16:01 +02:00

46 Commits

Author SHA1 Message Date
46098861ed poetry.lock: Run poetry update
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2021-03-11 22:45:32 +02:00
fa84cfa440 Bump version to 0.4.6-dev 2021-03-11 22:44:36 +02:00
6cc1401f88 pyproject.toml: Minimum Python is technically 3.7.1
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See: https://pandas.pydata.org/pandas-docs/stable/whatsnew/v1.2.0.html
2021-03-11 13:41:58 +02:00
ad2cda8a41 README.md: Add note about SPDX license identifiers
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2021-03-11 12:21:34 +02:00
dc6920802e .github/workflows/python-app.yml: Use Python 3.9
I now use this version in my development environment. Eventually I
should add a matrix of versions to use, but I don't know the GitHub
Actions syntax well enough yet.
2021-03-11 12:17:57 +02:00
6ca449d8ed README.md: Update note about Python 3.8 to 3.8+
Currently the lower bound on Python version support is 3.7 because
of Pandas 1.2.0 requiring it, but I use 3.9 on my development box.
2021-03-11 12:16:07 +02:00
1554cfd5c9 Version 0.4.6 2021-03-11 12:14:54 +02:00
00b8faad6d CHANGELOG.md: Fix headers 2021-03-11 12:13:22 +02:00
b19d81abdd .drone.yml: We need some stuff to build pyicu now
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2021-03-11 12:07:28 +02:00
a0ea829f5c csv_metadata_quality/fix.py: Fixes should be green 2021-03-11 11:47:24 +02:00
0089efa914 tests/test_check.py: Use dcterms.subject instead of dc.subject
Trying to move some old DC fields to DCTERMS.
2021-03-11 11:45:25 +02:00
3dbe656f9f 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 ==.
2021-03-11 11:11:19 +02:00
7ad821dcad CHANGELOG.md: Add note about poetry dependencies 2021-03-11 11:10:27 +02:00
cd876c4fb3 poetry.lock: Run poetry update 2021-03-11 11:10:02 +02:00
d88ea56488 csv_metadata_quality/check.py: Move all imports to top of file
PEP8 recommends keeping imports at the top of the file. Also, I had
to re-work the issn/isbn so they didn't conflict with the functions
in check.py (flake8 warned about them being redefined).

Imports sorted with isort.

See: https://www.python.org/dev/peps/pep-0008/#imports
2021-03-11 10:52:20 +02:00
e0e3ca6c58 CHANGELOG.md: Add notes about DCTERMS in data/test.csv 2021-03-11 10:50:52 +02:00
abae8ca4fb data/test.csv: Move some DC fields to DCTERMS
The original Dublin Core elements set was superceded by DCTERMS in
2008 and we have started using them in our DSpace repository so I
think it's good to update them in our test data. Old DC fields are
still checked and fixed in this tool, though.

It's worth nothing that currently supported DSpace versions (4, 5,
and 6) all have hard-coded a few fields like dc.title internally so
we can't migrate those to their DCTERMS counterparts just yet.
2021-03-11 10:49:05 +02:00
d7d4d4efca CHANGELOG.md: Add note about SPDX license identifiers 2021-03-11 10:37:27 +02:00
5318953150 tests/test_check.py: Add tests for licenses 2021-03-11 10:36:26 +02:00
3b17914002 data/test.csv: Add invalid SPDX license
Now we are checking dcterms.license against the list of SPDX license
identifiers using https://pypi.org/project/spdx-license-list/.
2021-03-11 10:34:58 +02:00
6e4b0e5c1b Add validation of SPDX license identifiers
Currently this only checks the dcterms.license field and the result
will only be a warning.
2021-03-11 10:33:16 +02:00
b16fa9121f pyproject.toml: Add csv-metadata-quality as a script
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For some reason I stopped having csv-metadata-quality available in
my poetry environment after install. It seems I need to add it as a
poetry tool script? I had already done this in setup.py years ago,
which works for regular python setup.py installs, but hadn't needed
to do it in poetry for a year or more that I've been using it, until
now.
2021-03-08 09:50:05 +02:00
202bda862a Bump version to 0.4.5
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2021-03-04 21:38:10 +02:00
7479310ac0 setup.py: Bump version to 0.4.4
I missed to increase this when I actually released version 0.4.4 so
I will do it in a separate commit now before I bump the version to
0.4.5.
2021-03-04 21:35:08 +02:00
98a91bc9c2 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 ==.
2021-03-04 21:33:33 +02:00
fc5bedcc5c CHANGELOG.md: Add poetry update 2021-03-04 21:32:46 +02:00
44d12d771a poetry.lock: Run poetry update 2021-03-04 21:32:21 +02:00
4a7000e975 README.md: Add more ideas to do 2021-03-04 21:26:53 +02:00
27b2d81ca8 CHANGELOG.md: Add note about dcterms.issued
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2021-02-28 15:14:39 +02:00
91ebd0f606 README.md: Update TODOs
A few of these date things have been addressed.
2021-02-28 15:13:36 +02:00
dd2cfae047 csv_metadata_quality/app.py: Match dcterms.issued for dates
We used to only check fields that had "date" in their name because
we were using DSpace's default dc.date.* fields. Now we are using
dcterms.issued so I will add that one as well.
2021-02-28 15:11:06 +02:00
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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continuous-integration/drone/push Build is passing
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
16 changed files with 536 additions and 362 deletions

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@ -9,6 +9,7 @@ steps:
commands:
- id
- python -V
- apt update && apt install -y gcc g++ libicu-dev pkg-config
- pip install -r requirements-dev.txt
- pytest
- python setup.py install
@ -25,6 +26,7 @@ steps:
commands:
- id
- python -V
- apt update && apt install -y gcc g++ libicu-dev pkg-config
- pip install -r requirements-dev.txt
- pytest
- python setup.py install
@ -41,6 +43,7 @@ steps:
commands:
- id
- python -V
- apt update && apt install -y gcc g++ libicu-dev pkg-config
- pip install -r requirements-dev.txt
- pytest
- python setup.py install

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@ -16,10 +16,10 @@ jobs:
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: 3.8
python-version: 3.9
- name: Install dependencies
run: |
python -m pip install --upgrade pip

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@ -4,6 +4,37 @@ 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).
## [0.4.6] - 2021-03-11
### Added
- Validation of dcterms.license field against SPDX license identifiers
### Changed
- Use DCTERMS fields where possible in `data/test.csv`
### Updated
- Run `poetry update` to update project dependencies
### Fixed
- Output for all fixes should be green, because it is good
## [0.4.5] - 2021-03-04
### Added
- Check dates in dcterms.issued field as well, not just fields that have the
word "date" in them
### Updated
- Run `poetry update` to update project dependencies
## [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

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@ -1,7 +1,11 @@
# 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.
Requires Python 3.7.1 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
@ -9,6 +13,7 @@ Requires Python 3.7 or greater (3.8 recommended). CSV and Excel support comes fr
- Validate languages against ISO 639-1 (alpha2) and ISO 639-3 (alpha3)
- Experimental validation of titles and abstracts against item's Dublin Core language field
- Validate subjects against the AGROVOC REST API (see the `--agrovoc-fields` option)
- Validation of licenses against the list of [SPDX license identifiers](https://spdx.org/licenses)
- Fix leading, trailing, and excessive (ie, more than one) whitespace
- Fix invalid and unnecessary multi-value separators (`|`) using `--unsafe-fixes`
- Fix problematic newlines (line feeds) using `--unsafe-fixes`
@ -99,14 +104,18 @@ This currently uses the [Python langid](https://github.com/saffsd/langid.py) lib
- Better logging, for example with INFO, WARN, and ERR levels
- Verbose, debug, or quiet options
- Warn if an author is shorter than 3 characters?
- Validate dc.rights field against SPDX? Perhaps with an option like `-m spdx` to enable the spdx module?
- Validate DOIs? Normalize to https://doi.org format? Or use just the DOI part: 10.1016/j.worlddev.2010.06.006
- Warn if two items use the same file in `filename` column
- Add an option to drop invalid AGROVOC subjects?
- Add tests for application invocation, ie `tests/test_app.py`?
- Validate ISSNs or journal titles against CrossRef API?
- Better ISO 8601 date parsing (currently only supports simple dates, perhaps we need to use dateutil.parser.parseiso())
- Fix lazy date check (assumes field name has "date" but could be dcterms.issued etc!)
- Add configurable field validation, like specify a field name and a validation file?
- Perhaps like --validate=field.name,filename
- Add some row-based item sanity checks and fixes:
- Warn if item is Open Access, but missing a filename or URL
- Warn if item is Open Access, but missing a license
- Warn if item has an ISSN but no journal title
- Update journal titles from ISSN
## License
This work is licensed under the [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html).

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@ -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
@ -141,7 +142,7 @@ def run(argv):
df[column] = df[column].apply(check.isbn)
# Check: invalid date
match = re.match(r"^.*?date.*$", column)
match = re.match(r"^.*?(date|dcterms\.issued).*$", column)
if match is not None:
df[column] = df[column].apply(check.date, field_name=column)
@ -149,6 +150,11 @@ def run(argv):
if column == "filename":
df[column] = df[column].apply(check.filename_extension)
# Check: SPDX license identifier
match = re.match(r"dcterms\.license.*$", column)
if match is not None:
df[column] = df[column].apply(check.spdx_license_identifier)
##
# Perform some checks on rows so we can consider items as a whole rather
# than simple on a field-by-field basis. This allows us to check whether

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@ -1,9 +1,14 @@
import re
from datetime import datetime, timedelta
import pandas as pd
import requests
import requests_cache
import spdx_license_list
from colorama import Fore
from pycountry import languages
from stdnum import isbn as stdnum_isbn
from stdnum import issn as stdnum_issn
def issn(field):
@ -16,8 +21,6 @@ def issn(field):
See: https://arthurdejong.org/python-stdnum/doc/1.11/index.html#stdnum.module.is_valid
"""
from stdnum import issn
# Skip fields with missing values
if pd.isna(field):
return
@ -25,8 +28,8 @@ def issn(field):
# Try to split multi-value field on "||" separator
for value in field.split("||"):
if not issn.is_valid(value):
print(f"Invalid ISSN: {value}")
if not stdnum_issn.is_valid(value):
print(f"{Fore.RED}Invalid ISSN: {Fore.RESET}{value}")
return field
@ -41,8 +44,6 @@ def isbn(field):
See: https://arthurdejong.org/python-stdnum/doc/1.11/index.html#stdnum.module.is_valid
"""
from stdnum import isbn
# Skip fields with missing values
if pd.isna(field):
return
@ -50,8 +51,8 @@ def isbn(field):
# Try to split multi-value field on "||" separator
for value in field.split("||"):
if not isbn.is_valid(value):
print(f"Invalid ISBN: {value}")
if not stdnum_isbn.is_valid(value):
print(f"{Fore.RED}Invalid ISBN: {Fore.RESET}{value}")
return field
@ -66,8 +67,6 @@ def separators(field, field_name):
Prints the field with the invalid multi-value separator.
"""
import re
# Skip fields with missing values
if pd.isna(field):
return
@ -76,7 +75,9 @@ 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 +86,9 @@ 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 +105,7 @@ 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 +114,9 @@ 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 +142,15 @@ 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 +183,7 @@ 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 +208,16 @@ 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 +259,7 @@ 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
@ -264,8 +275,6 @@ def filename_extension(field):
than .pdf, .xls(x), .doc(x), ppt(x), case insensitive).
"""
import re
# Skip fields with missing values
if pd.isna(field):
return
@ -301,6 +310,26 @@ 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
def spdx_license_identifier(field):
"""Check if a license is a valid SPDX identifier.
Prints the value if it is invalid.
"""
# Skip fields with missing values
if pd.isna(field):
return
# Try to split multi-value field on "||" separator
for value in field.split("||"):
if value not in spdx_license_list.LICENSES:
print(f"{Fore.YELLOW}Non-SPDX license identifier: {Fore.RESET}{value}")
pass
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:

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@ -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.GREEN}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

View File

@ -1 +1 @@
VERSION = "0.4.3"
VERSION = "0.4.6-dev"

View File

@ -1,31 +1,32 @@
dc.title,dc.date.issued,dc.identifier.issn,dc.identifier.isbn,dc.language.iso,dc.subject,cg.coverage.country,filename
Leading space,2019-07-29,,,,,,
Trailing space ,2019-07-29,,,,,,
Excessive space,2019-07-29,,,,,,
Miscellaenous ||whitespace | issues ,2019-07-29,,,,,,
Duplicate||Duplicate,2019-07-29,,,,,,
Invalid ISSN,2019-07-29,2321-2302,,,,,
Invalid ISBN,2019-07-29,,978-0-306-40615-6,,,,
Multiple valid ISSNs,2019-07-29,0378-5955||0024-9319,,,,,
Multiple valid ISBNs,2019-07-29,,99921-58-10-7||978-0-306-40615-7,,,,
Invalid date,2019-07-260,,,,,,
Multiple dates,2019-07-26||2019-01-10,,,,,,
Invalid multi-value separator,2019-07-29,0378-5955|0024-9319,,,,,
Unnecessary Unicode,2019-07-29,,,,,,
Suspicious character||foreˆt,2019-07-29,,,,,,
Invalid ISO 639-1 (alpha 2) language,2019-07-29,,,jp,,,
Invalid ISO 639-3 (alpha 3) language,2019-07-29,,,chi,,,
Invalid language,2019-07-29,,,Span,,,
Invalid AGROVOC subject,2019-07-29,,,,FOREST,,
dc.title,dcterms.issued,dc.identifier.issn,dc.identifier.isbn,dcterms.language,dcterms.subject,cg.coverage.country,filename,dcterms.license
Leading space,2019-07-29,,,,,,,
Trailing space ,2019-07-29,,,,,,,
Excessive space,2019-07-29,,,,,,,
Miscellaenous ||whitespace | issues ,2019-07-29,,,,,,,
Duplicate||Duplicate,2019-07-29,,,,,,,
Invalid ISSN,2019-07-29,2321-2302,,,,,,
Invalid ISBN,2019-07-29,,978-0-306-40615-6,,,,,
Multiple valid ISSNs,2019-07-29,0378-5955||0024-9319,,,,,,
Multiple valid ISBNs,2019-07-29,,99921-58-10-7||978-0-306-40615-7,,,,,
Invalid date,2019-07-260,,,,,,,
Multiple dates,2019-07-26||2019-01-10,,,,,,,
Invalid multi-value separator,2019-07-29,0378-5955|0024-9319,,,,,,
Unnecessary Unicode,2019-07-29,,,,,,,
Suspicious character||foreˆt,2019-07-29,,,,,,,
Invalid ISO 639-1 (alpha 2) language,2019-07-29,,,jp,,,,
Invalid ISO 639-3 (alpha 3) language,2019-07-29,,,chi,,,,
Invalid language,2019-07-29,,,Span,,,,
Invalid AGROVOC subject,2019-07-29,,,,FOREST,,,
Newline (LF),2019-07-30,,,,"TANZA
NIA",,
Missing date,,,,,,,
Invalid country,2019-08-01,,,,,KENYAA,
Uncommon filename extension,2019-08-10,,,,,,file.pdf.lck
Unneccesary unicode (U+002D + U+00AD),2019-08-10,,978-­92-­9043-­823-­6,,,,
"Missing space,after comma",2019-08-27,,,,,,
Incorrect ISO 639-1 language,2019-09-26,,,es,,,
Incorrect ISO 639-3 language,2019-09-26,,,spa,,,
Composéd Unicode,2020-01-14,,,,,,
Decomposéd Unicode,2020-01-14,,,,,,
Unnecessary multi-value separator,2021-01-03,0378-5955||,,,,,
NIA",,,
Missing date,,,,,,,,
Invalid country,2019-08-01,,,,,KENYAA,,
Uncommon filename extension,2019-08-10,,,,,,file.pdf.lck,
Unneccesary unicode (U+002D + U+00AD),2019-08-10,,978-­92-­9043-­823-­6,,,,,
"Missing space,after comma",2019-08-27,,,,,,,
Incorrect ISO 639-1 language,2019-09-26,,,es,,,,
Incorrect ISO 639-3 language,2019-09-26,,,spa,,,,
Composéd Unicode,2020-01-14,,,,,,,
Decomposéd Unicode,2020-01-14,,,,,,,
Unnecessary multi-value separator,2021-01-03,0378-5955||,,,,,,
Invalid SPDX license identifier,2021-03-11,,,,,,,CC-BY

1 dc.title dc.date.issued dcterms.issued dc.identifier.issn dc.identifier.isbn dc.language.iso dcterms.language dc.subject dcterms.subject cg.coverage.country filename dcterms.license
2 Leading space 2019-07-29
3 Trailing space 2019-07-29
4 Excessive space 2019-07-29
5 Miscellaenous ||whitespace | issues 2019-07-29
6 Duplicate||Duplicate 2019-07-29
7 Invalid ISSN 2019-07-29 2321-2302
8 Invalid ISBN 2019-07-29 978-0-306-40615-6
9 Multiple valid ISSNs 2019-07-29 0378-5955||0024-9319
10 Multiple valid ISBNs 2019-07-29 99921-58-10-7||978-0-306-40615-7
11 Invalid date 2019-07-260
12 Multiple dates 2019-07-26||2019-01-10
13 Invalid multi-value separator 2019-07-29 0378-5955|0024-9319
14 Unnecessary Unicode​ 2019-07-29
15 Suspicious character||foreˆt 2019-07-29
16 Invalid ISO 639-1 (alpha 2) language 2019-07-29 jp
17 Invalid ISO 639-3 (alpha 3) language 2019-07-29 chi
18 Invalid language 2019-07-29 Span
19 Invalid AGROVOC subject 2019-07-29 FOREST
20 Newline (LF) 2019-07-30 TANZA NIA
21 Missing date
22 Invalid country 2019-08-01 KENYAA
23 Uncommon filename extension 2019-08-10 file.pdf.lck
24 Unneccesary unicode (U+002D + U+00AD) 2019-08-10 978-­92-­9043-­823-­6
25 Missing space,after comma 2019-08-27
26 Incorrect ISO 639-1 language 2019-09-26 es
27 Incorrect ISO 639-3 language 2019-09-26 spa
28 Composéd Unicode 2020-01-14
29 Decomposéd Unicode 2020-01-14
30 Unnecessary multi-value separator 2021-01-03 0378-5955||
31 Invalid SPDX license identifier 2021-03-11 CC-BY
32

421
poetry.lock generated
View File

@ -1,6 +1,6 @@
[[package]]
name = "agate"
version = "1.6.1"
version = "1.6.2"
description = "A data analysis library that is optimized for humans instead of machines."
category = "dev"
optional = false
@ -11,6 +11,7 @@ Babel = ">=2.0"
isodate = ">=0.5.4"
leather = ">=0.3.2"
parsedatetime = ">=2.1"
PyICU = ">=2.4.2"
python-slugify = ">=1.2.1"
pytimeparse = ">=1.1.5"
six = ">=1.9.0"
@ -67,7 +68,6 @@ 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 +76,6 @@ 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 +86,10 @@ 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 +109,6 @@ 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 +118,6 @@ 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 +128,10 @@ 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 +160,9 @@ 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 +194,6 @@ 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"
@ -216,6 +212,7 @@ optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
[package.dependencies]
importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
mccabe = ">=0.6.0,<0.7.0"
pycodestyle = ">=2.6.0a1,<2.7.0"
pyflakes = ">=2.2.0,<2.3.0"
@ -228,6 +225,22 @@ category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "importlib-metadata"
version = "3.7.2"
description = "Read metadata from Python packages"
category = "dev"
optional = false
python-versions = ">=3.6"
[package.dependencies]
typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
zipp = ">=0.5"
[package.extras]
docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
[[package]]
name = "iniconfig"
version = "1.1.1"
@ -238,12 +251,23 @@ python-versions = "*"
[[package]]
name = "ipython"
version = "7.19.0"
version = "7.21.0"
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 +280,6 @@ 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 +287,6 @@ description = "Vestigial utilities from IPython"
category = "dev"
optional = false
python-versions = "*"
marker = "python_version >= \"3.7\" and python_version < \"4.0\""
[[package]]
name = "isodate"
@ -302,14 +312,6 @@ pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
requirements_deprecated_finder = ["pipreqs", "pip-api"]
colors = ["colorama (>=0.4.3,<0.5.0)"]
[[package]]
name = "jdcal"
version = "1.4.1"
description = "Julian dates from proleptic Gregorian and Julian calendars."
category = "dev"
optional = false
python-versions = "*"
[[package]]
name = "jedi"
version = "0.18.0"
@ -317,15 +319,14 @@ 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"
@ -366,15 +367,15 @@ 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"
version = "3.0.6"
version = "3.0.7"
description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
category = "dev"
optional = false
@ -382,11 +383,10 @@ python-versions = ">=3.6,"
[package.dependencies]
et-xmlfile = "*"
jdcal = "*"
[[package]]
name = "packaging"
version = "20.8"
version = "20.9"
description = "Core utilities for Python packages"
category = "dev"
optional = false
@ -397,20 +397,20 @@ pyparsing = ">=2.0.2"
[[package]]
name = "pandas"
version = "1.2.1"
version = "1.2.3"
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 +426,9 @@ 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 +446,6 @@ 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 +457,6 @@ 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"
@ -469,17 +466,19 @@ category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[package.dependencies]
importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
[package.extras]
dev = ["pre-commit", "tox"]
[[package]]
name = "prompt-toolkit"
version = "3.0.14"
version = "3.0.17"
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 +490,6 @@ 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"
@ -527,12 +525,19 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "pygments"
version = "2.7.4"
version = "2.8.1"
description = "Pygments is a syntax highlighting package written in Python."
category = "dev"
optional = false
python-versions = ">=3.5"
marker = "python_version >= \"3.7\" and python_version < \"4.0\""
[[package]]
name = "pyicu"
version = "2.6"
description = "Python extension wrapping the ICU C++ API"
category = "dev"
optional = false
python-versions = "*"
[[package]]
name = "pyparsing"
@ -550,19 +555,20 @@ category = "dev"
optional = false
python-versions = ">=3.6"
[package.extras]
testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
[package.dependencies]
atomicwrites = ">=1.0"
atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
attrs = ">=19.2.0"
colorama = "*"
colorama = {version = "*", markers = "sys_platform == \"win32\""}
importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
iniconfig = "*"
packaging = "*"
pluggy = ">=0.12,<1.0.0a1"
py = ">=1.8.2"
toml = "*"
[package.extras]
testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
[[package]]
name = "pytest-clarity"
version = "0.3.0a0"
@ -594,15 +600,15 @@ category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[package.extras]
unidecode = ["Unidecode (>=1.1.1)"]
[package.dependencies]
text-unidecode = ">=1.3"
[package.extras]
unidecode = ["Unidecode (>=1.1.1)"]
[[package]]
name = "python-stdnum"
version = "1.15"
version = "1.16"
description = "Python module to handle standardized numbers and codes"
category = "main"
optional = false
@ -623,7 +629,7 @@ python-versions = "*"
[[package]]
name = "pytz"
version = "2020.5"
version = "2021.1"
description = "World timezone definitions, modern and historical"
category = "main"
optional = false
@ -645,16 +651,16 @@ category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[package.extras]
security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"]
socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7)", "win-inet-pton"]
[package.dependencies]
certifi = ">=2017.4.17"
chardet = ">=3.0.2,<5"
idna = ">=2.5,<3"
urllib3 = ">=1.21.1,<1.27"
[package.extras]
security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"]
socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"]
[[package]]
name = "requests-cache"
version = "0.5.2"
@ -674,9 +680,17 @@ category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
[[package]]
name = "spdx-license-list"
version = "0.5.2"
description = "A simple tool/library for working with SPDX license definitions."
category = "main"
optional = false
python-versions = "*"
[[package]]
name = "sqlalchemy"
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@ -689,10 +703,10 @@ mssql_pyodbc = ["pyodbc"]
mysql = ["mysqlclient"]
oracle = ["cx-oracle"]
postgresql = ["psycopg2"]
postgresql_pg8000 = ["pg8000"]
postgresql_pg8000 = ["pg8000 (<1.16.6)"]
postgresql_psycopg2binary = ["psycopg2-binary"]
postgresql_psycopg2cffi = ["psycopg2cffi"]
pymysql = ["pymysql"]
pymysql = ["pymysql (<1)", "pymysql"]
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@ -725,14 +739,13 @@ description = "Traitlets Python configuration system"
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optional = false
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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-manylinux2010_x86_64.whl", hash = "sha256:eab063a70cca4a587c28824e18be41d8ecc4457f8f15b2933584c6c6cccd30f0"},
{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 +1217,8 @@ 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"},
@ -1209,3 +1228,7 @@ xlrd = [
{file = "xlrd-1.2.0-py2.py3-none-any.whl", hash = "sha256:e551fb498759fa3a5384a94ccd4c3c02eb7c00ea424426e212ac0c57be9dfbde"},
{file = "xlrd-1.2.0.tar.gz", hash = "sha256:546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2"},
]
zipp = [
{file = "zipp-3.4.1-py3-none-any.whl", hash = "sha256:51cb66cc54621609dd593d1787f286ee42a5c0adbb4b29abea5a63edc3e03098"},
{file = "zipp-3.4.1.tar.gz", hash = "sha256:3607921face881ba3e026887d8150cca609d517579abe052ac81fc5aeffdbd76"},
]

View File

@ -1,14 +1,17 @@
[tool.poetry]
name = "csv-metadata-quality"
version = "0.4.3"
version = "0.4.6-dev"
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"
repository = "https://github.com/ilri/csv-metadata-quality"
homepage = "https://github.com/ilri/csv-metadata-quality"
[tool.poetry.scripts]
csv-metadata-quality = 'csv_metadata_quality.__main__:main'
[tool.poetry.dependencies]
python = "^3.8"
python = "^3.7.1"
pandas = "^1.0.4"
python-stdnum = "^1.13"
xlrd = "^1.2.0"
@ -16,6 +19,8 @@ requests = "^2.23.0"
requests-cache = "^0.5.2"
pycountry = "^19.8.18"
langid = "^1.1.6"
colorama = "^0.4.4"
spdx-license-list = "^0.5.2"
[tool.poetry.dev-dependencies]
pytest = "^6.1.1"

View File

@ -1,71 +1,72 @@
agate==1.6.1
agate-dbf==0.2.2
agate-excel==0.2.3
agate-sql==0.5.5
appdirs==1.4.4
agate==1.6.2
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==7.21.0; 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"
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==3.0.7; 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==1.2.3; 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==2.8.1; python_version >= "3.7" and python_version < "4.0"
pyicu==2.6
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"
spdx-license-list==0.5.2
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 +1,17 @@
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==1.2.3; 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"
spdx-license-list==0.5.2
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

@ -14,7 +14,7 @@ install_requires = [
setuptools.setup(
name="csv-metadata-quality",
version="0.4.3",
version="0.4.6-dev",
author="Alan Orth",
author_email="aorth@mjanja.ch",
description="A simple, but opinionated CSV quality checking and fixing pipeline for CSVs in the DSpace ecosystem.",

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):
@ -200,26 +217,29 @@ 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):
"""Test invalid AGROVOC subject."""
value = "FOREST"
field_name = "dc.subject"
field_name = "dcterms.subject"
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():
"""Test valid AGROVOC subject."""
value = "FORESTS"
field_name = "dc.subject"
field_name = "dcterms.subject"
result = check.agrovoc(value, field_name)
@ -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"
)
@ -313,3 +336,27 @@ def test_check_correct_iso_639_3_language():
result = experimental.correct_language(series)
assert result == language
def test_check_valid_spdx_license_identifier():
"""Test valid SPDX license identifier."""
license = "CC-BY-SA-4.0"
result = check.spdx_license_identifier(license)
assert result == license
def test_check_invalid_spdx_license_identifier(capsys):
"""Test invalid SPDX license identifier."""
license = "CC-BY-SA"
result = check.spdx_license_identifier(license)
captured = capsys.readouterr()
assert (
captured.out
== f"{Fore.YELLOW}Non-SPDX license identifier: {Fore.RESET}{license}\n"
)