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19
.build.yml
19
.build.yml
@ -1,19 +0,0 @@
|
||||
image: archlinux
|
||||
packages:
|
||||
- python-pipenv
|
||||
sources:
|
||||
- https://git.sr.ht/~alanorth/csv-metadata-quality
|
||||
tasks:
|
||||
- setup: |
|
||||
cd csv-metadata-quality
|
||||
pipenv install --dev
|
||||
- pytest: |
|
||||
cd csv-metadata-quality
|
||||
pipenv run pytest
|
||||
- testcli: |
|
||||
cd csv-metadata-quality
|
||||
pipenv run pip install .
|
||||
pipenv run csv-metadata-quality -i data/test.csv -o /tmp/test.csv -u --agrovoc-fields dc.subject,cg.coverage.country
|
||||
environment:
|
||||
PIPENV_NOSPIN: 'True'
|
||||
PIPENV_HIDE_EMOJIS: 'True'
|
49
.drone.yml
Normal file
49
.drone.yml
Normal file
@ -0,0 +1,49 @@
|
||||
---
|
||||
kind: pipeline
|
||||
type: docker
|
||||
name: python39
|
||||
|
||||
steps:
|
||||
- name: test
|
||||
image: python:3.9-slim
|
||||
commands:
|
||||
- id
|
||||
- python -V
|
||||
- pip install -r requirements-dev.txt
|
||||
- pytest
|
||||
- python setup.py install
|
||||
- csv-metadata-quality -i data/test.csv -o /tmp/test.csv -e -u --agrovoc-fields dc.subject,cg.coverage.country
|
||||
|
||||
---
|
||||
kind: pipeline
|
||||
type: docker
|
||||
name: python38
|
||||
|
||||
steps:
|
||||
- name: test
|
||||
image: python:3.8-slim
|
||||
commands:
|
||||
- id
|
||||
- python -V
|
||||
- pip install -r requirements-dev.txt
|
||||
- pytest
|
||||
- python setup.py install
|
||||
- csv-metadata-quality -i data/test.csv -o /tmp/test.csv -e -u --agrovoc-fields dc.subject,cg.coverage.country
|
||||
|
||||
---
|
||||
kind: pipeline
|
||||
type: docker
|
||||
name: python37
|
||||
|
||||
steps:
|
||||
- name: test
|
||||
image: python:3.7-slim
|
||||
commands:
|
||||
- id
|
||||
- python -V
|
||||
- pip install -r requirements-dev.txt
|
||||
- pytest
|
||||
- python setup.py install
|
||||
- csv-metadata-quality -i data/test.csv -o /tmp/test.csv -e -u --agrovoc-fields dc.subject,cg.coverage.country
|
||||
|
||||
# vim: ts=2 sw=2 et
|
41
.github/workflows/python-app.yml
vendored
Normal file
41
.github/workflows/python-app.yml
vendored
Normal file
@ -0,0 +1,41 @@
|
||||
# This workflow will install Python dependencies, run tests and lint with a single version of Python
|
||||
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
|
||||
|
||||
name: Build and Test
|
||||
|
||||
on:
|
||||
push:
|
||||
branches: [ master ]
|
||||
pull_request:
|
||||
branches: [ master ]
|
||||
|
||||
jobs:
|
||||
build:
|
||||
|
||||
runs-on: ubuntu-latest
|
||||
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
- name: Set up Python 3.8
|
||||
uses: actions/setup-python@v2
|
||||
with:
|
||||
python-version: 3.8
|
||||
- name: Install dependencies
|
||||
run: |
|
||||
python -m pip install --upgrade pip
|
||||
pip install flake8 pytest
|
||||
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
|
||||
if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
|
||||
- name: Lint with flake8
|
||||
run: |
|
||||
# stop the build if there are Python syntax errors or undefined names
|
||||
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
|
||||
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
|
||||
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
|
||||
- name: Test with pytest
|
||||
run: |
|
||||
pytest
|
||||
- name: Test CLI
|
||||
run: |
|
||||
python setup.py install
|
||||
csv-metadata-quality -i data/test.csv -o /tmp/test.csv -e -u --agrovoc-fields dc.subject,cg.coverage.country
|
11
.travis.yml
11
.travis.yml
@ -1,11 +0,0 @@
|
||||
dist: xenial
|
||||
language: python
|
||||
python:
|
||||
- "3.6"
|
||||
- "3.7"
|
||||
install:
|
||||
- "pip install pipenv --upgrade-strategy=only-if-needed"
|
||||
- "pipenv install --dev"
|
||||
script: pytest
|
||||
|
||||
# vim: ts=2 sw=2 et
|
69
CHANGELOG.md
69
CHANGELOG.md
@ -4,9 +4,76 @@ 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).
|
||||
|
||||
## [0.4.3] - 2021-01-26
|
||||
### Changed
|
||||
- Reformat with black
|
||||
- Requires Python 3.7+ for pandas 1.2.0
|
||||
|
||||
### Updated
|
||||
- Run `poetry update`
|
||||
- Expand check/fix for multi-value separators to include metadata with invalid
|
||||
separators at the end, for example "Kenya||Tanzania||"
|
||||
|
||||
## [0.4.2] - 2020-07-06
|
||||
### Changed
|
||||
- Add field name to the output for more fixes and checks to help identify where
|
||||
the error is
|
||||
- Minor optimizations to AGROVOC subject lookup
|
||||
- Use Poetry instead of Pipenv
|
||||
|
||||
### Updated
|
||||
- Update python dependencies to latest versions
|
||||
|
||||
## [0.4.1] - 2020-01-15
|
||||
### Changed
|
||||
- Reduce minimum Python version to 3.6 by working around the `is_normalized()`
|
||||
that only works in Python >= 3.8
|
||||
|
||||
## [0.4.0] - 2020-01-15
|
||||
### Added
|
||||
- Unicode normalization (enable with `--unsafe-fixes`, see README.md)
|
||||
|
||||
### Updated
|
||||
- Update python dependencies to latest versions, including numpy 1.18.1, pandas
|
||||
1.0.0rc0, flake8 3.7.9, pytest 5.3.2, and black 19.10b0
|
||||
- Regenerate requirements.txt and requirements-dev.txt
|
||||
|
||||
### Changed
|
||||
- Use Python 3.8.0 for pipenv
|
||||
- Use Ubuntu 18.04 "Bionic" for TravisCI builds
|
||||
- Test Python 3.8 in TravisCI builds
|
||||
|
||||
## [0.3.1] - 2019-10-01
|
||||
## Changed
|
||||
- Replace non-breaking spaces (U+00A0) with space instead of removing them
|
||||
- Harmonize language of script output when fixing various issues
|
||||
|
||||
## [0.3.0] - 2019-09-26
|
||||
### Updated
|
||||
- Update python dependencies to latest versions, including numpy 1.17.2, pandas
|
||||
0.25.1, pytest 5.1.3, and requests-cache 0.5.2
|
||||
|
||||
### Added
|
||||
- csvkit to dev requirements (csvcut etc are useful during development)
|
||||
- Experimental language validation using the Python `langid` library (enable with `-e`, see README.md)
|
||||
|
||||
### Changed
|
||||
- Re-formatted code with black and isort
|
||||
|
||||
## [0.2.2] - 2019-08-27
|
||||
### Changed
|
||||
- Output of date checks to include column names (helps debugging in case there are multiple date fields)
|
||||
|
||||
### Added
|
||||
- Ability to exclude certain fields using `--exclude-fields`
|
||||
- Fix for missing space after a comma, ie "Orth,Alan S."
|
||||
|
||||
### Improved
|
||||
- AGROVOC lookup code
|
||||
|
||||
## [0.2.1] - 2019-08-11
|
||||
### Added
|
||||
- Check for uncommon filename extensions
|
||||
- Check for uncommon filename extensions
|
||||
- Replacement of unneccessary Unicode characters like soft hyphens (U+00AD)
|
||||
|
||||
## [0.2.0] - 2019-08-09
|
||||
|
25
Pipfile
25
Pipfile
@ -1,25 +0,0 @@
|
||||
[[source]]
|
||||
name = "pypi"
|
||||
url = "https://pypi.org/simple"
|
||||
verify_ssl = true
|
||||
|
||||
[dev-packages]
|
||||
pytest = "*"
|
||||
ipython = "*"
|
||||
flake8 = "*"
|
||||
pytest-clarity = "*"
|
||||
|
||||
[packages]
|
||||
pandas = "*"
|
||||
python-stdnum = "*"
|
||||
xlrd = "*"
|
||||
requests = "*"
|
||||
requests-cache = "*"
|
||||
pycountry = "*"
|
||||
csv-metadata-quality = {editable = true,path = "."}
|
||||
|
||||
[requires]
|
||||
python_version = "3.7"
|
||||
|
||||
[pipenv]
|
||||
allow_prereleases = true
|
376
Pipfile.lock
generated
376
Pipfile.lock
generated
@ -1,376 +0,0 @@
|
||||
{
|
||||
"_meta": {
|
||||
"hash": {
|
||||
"sha256": "f8f0a9f208ec41f4d8183ecfc68356b40674b083b2f126c37468b3c9533ba5df"
|
||||
},
|
||||
"pipfile-spec": 6,
|
||||
"requires": {
|
||||
"python_version": "3.7"
|
||||
},
|
||||
"sources": [
|
||||
{
|
||||
"name": "pypi",
|
||||
"url": "https://pypi.org/simple",
|
||||
"verify_ssl": true
|
||||
}
|
||||
]
|
||||
},
|
||||
"default": {
|
||||
"certifi": {
|
||||
"hashes": [
|
||||
"sha256:046832c04d4e752f37383b628bc601a7ea7211496b4638f6514d0e5b9acc4939",
|
||||
"sha256:945e3ba63a0b9f577b1395204e13c3a231f9bc0223888be653286534e5873695"
|
||||
],
|
||||
"version": "==2019.6.16"
|
||||
},
|
||||
"chardet": {
|
||||
"hashes": [
|
||||
"sha256:84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae",
|
||||
"sha256:fc323ffcaeaed0e0a02bf4d117757b98aed530d9ed4531e3e15460124c106691"
|
||||
],
|
||||
"version": "==3.0.4"
|
||||
},
|
||||
"csv-metadata-quality": {
|
||||
"editable": true,
|
||||
"path": "."
|
||||
},
|
||||
"idna": {
|
||||
"hashes": [
|
||||
"sha256:c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407",
|
||||
"sha256:ea8b7f6188e6fa117537c3df7da9fc686d485087abf6ac197f9c46432f7e4a3c"
|
||||
],
|
||||
"version": "==2.8"
|
||||
},
|
||||
"numpy": {
|
||||
"hashes": [
|
||||
"sha256:03e311b0a4c9f5755da7d52161280c6a78406c7be5c5cc7facfbcebb641efb7e",
|
||||
"sha256:0cdd229a53d2720d21175012ab0599665f8c9588b3b8ffa6095dd7b90f0691dd",
|
||||
"sha256:312bb18e95218bedc3563f26fcc9c1c6bfaaf9d453d15942c0839acdd7e4c473",
|
||||
"sha256:464b1c48baf49e8505b1bb754c47a013d2c305c5b14269b5c85ea0625b6a988a",
|
||||
"sha256:5adfde7bd3ee4864536e230bcab1c673f866736698724d5d28c11a4d63672658",
|
||||
"sha256:7724e9e31ee72389d522b88c0d4201f24edc34277999701ccd4a5392e7d8af61",
|
||||
"sha256:8d36f7c53ae741e23f54793ffefb2912340b800476eb0a831c6eb602e204c5c4",
|
||||
"sha256:910d2272403c2ea8a52d9159827dc9f7c27fb4b263749dca884e2e4a8af3b302",
|
||||
"sha256:951fefe2fb73f84c620bec4e001e80a80ddaa1b84dce244ded7f1e0cbe0ed34a",
|
||||
"sha256:9588c6b4157f493edeb9378788dcd02cb9e6a6aeaa518b511a1c79d06cbd8094",
|
||||
"sha256:9ce8300950f2f1d29d0e49c28ebfff0d2f1e2a7444830fbb0b913c7c08f31511",
|
||||
"sha256:be39cca66cc6806652da97103605c7b65ee4442c638f04ff064a7efd9a81d50a",
|
||||
"sha256:c3ab2d835b95ccb59d11dfcd56eb0480daea57cdf95d686d22eff35584bc4554",
|
||||
"sha256:eb0fc4a492cb896346c9e2c7a22eae3e766d407df3eb20f4ce027f23f76e4c54",
|
||||
"sha256:ec0c56eae6cee6299f41e780a0280318a93db519bbb2906103c43f3e2be1206c",
|
||||
"sha256:f4e4612de60a4f1c4d06c8c2857cdcb2b8b5289189a12053f37d3f41f06c60d0"
|
||||
],
|
||||
"version": "==1.17.0"
|
||||
},
|
||||
"pandas": {
|
||||
"hashes": [
|
||||
"sha256:074a032f99bb55d178b93bd98999c971542f19317829af08c99504febd9e9b8b",
|
||||
"sha256:20f1728182b49575c2f6f681b3e2af5fac9e84abdf29488e76d569a7969b362e",
|
||||
"sha256:2745ba6e16c34d13d765c3657bb64fa20a0e2daf503e6216a36ed61770066179",
|
||||
"sha256:32c44e5b628c48ba17703f734d59f369d4cdcb4239ef26047d6c8a8bfda29a6b",
|
||||
"sha256:3b9f7dcee6744d9dcdd53bce19b91d20b4311bf904303fa00ef58e7df398e901",
|
||||
"sha256:544f2033250980fb6f069ce4a960e5f64d99b8165d01dc39afd0b244eeeef7d7",
|
||||
"sha256:58f9ef68975b9f00ba96755d5702afdf039dea9acef6a0cfd8ddcde32918a79c",
|
||||
"sha256:9023972a92073a495eba1380824b197ad1737550fe1c4ef8322e65fe58662888",
|
||||
"sha256:914341ad2d5b1ea522798efa4016430b66107d05781dbfe7cf05eba8f37df995",
|
||||
"sha256:9d151bfb0e751e2c987f931c57792871c8d7ff292bcdfcaa7233012c367940ee",
|
||||
"sha256:b932b127da810fef57d427260dde1ad54542c136c44b227a1e367551bb1a684b",
|
||||
"sha256:cfb862aa37f4dd5be0730731fdb8185ac935aba8b51bf3bd035658111c9ee1c9",
|
||||
"sha256:de7ecb4b120e98b91e8a2a21f186571266a8d1faa31d92421e979c7ca67d8e5c",
|
||||
"sha256:df7e1933a0b83920769611c5d6b9a1bf301e3fa6a544641c6678c67621fe9843"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==0.25.0"
|
||||
},
|
||||
"pycountry": {
|
||||
"hashes": [
|
||||
"sha256:68e58bfd3bedeea49ba9d4b38f2bd5e042f9753628eba9a819fb03f551d89096"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==19.7.15"
|
||||
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|
||||
"python-dateutil": {
|
||||
"hashes": [
|
||||
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|
||||
"sha256:c89805f6f4d64db21ed966fda138f8a5ed7a4fdbc1a8ee329ce1b74e3c74da9e"
|
||||
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|
||||
"version": "==2.8.0"
|
||||
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|
||||
"python-stdnum": {
|
||||
"hashes": [
|
||||
"sha256:d5f0af1bee9ddd9a20b398b46ce062dbd4d41fcc9646940f2667256a44df3854",
|
||||
"sha256:f445ec32bf5246c90389204cabba465f494545371c29a83fa2d30e6c872a6763"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==1.11"
|
||||
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|
||||
"pytz": {
|
||||
"hashes": [
|
||||
"sha256:26c0b32e437e54a18161324a2fca3c4b9846b74a8dccddd843113109e1116b32",
|
||||
"sha256:c894d57500a4cd2d5c71114aaab77dbab5eabd9022308ce5ac9bb93a60a6f0c7"
|
||||
],
|
||||
"version": "==2019.2"
|
||||
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|
||||
"requests": {
|
||||
"hashes": [
|
||||
"sha256:11e007a8a2aa0323f5a921e9e6a2d7e4e67d9877e85773fba9ba6419025cbeb4",
|
||||
"sha256:9cf5292fcd0f598c671cfc1e0d7d1a7f13bb8085e9a590f48c010551dc6c4b31"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==2.22.0"
|
||||
},
|
||||
"requests-cache": {
|
||||
"hashes": [
|
||||
"sha256:6822f788c5ee248995c4bfbd725de2002ad710182ba26a666e85b64981866060",
|
||||
"sha256:73a7211870f7d67af5fd81cad2f67cfe1cd3eb4ee6a85155e07613968cc72dfc"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==0.5.0"
|
||||
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|
||||
"six": {
|
||||
"hashes": [
|
||||
"sha256:3350809f0555b11f552448330d0b52d5f24c91a322ea4a15ef22629740f3761c",
|
||||
"sha256:d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73"
|
||||
],
|
||||
"version": "==1.12.0"
|
||||
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|
||||
"urllib3": {
|
||||
"hashes": [
|
||||
"sha256:b246607a25ac80bedac05c6f282e3cdaf3afb65420fd024ac94435cabe6e18d1",
|
||||
"sha256:dbe59173209418ae49d485b87d1681aefa36252ee85884c31346debd19463232"
|
||||
],
|
||||
"version": "==1.25.3"
|
||||
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|
||||
"xlrd": {
|
||||
"hashes": [
|
||||
"sha256:546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2",
|
||||
"sha256:e551fb498759fa3a5384a94ccd4c3c02eb7c00ea424426e212ac0c57be9dfbde"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==1.2.0"
|
||||
}
|
||||
},
|
||||
"develop": {
|
||||
"atomicwrites": {
|
||||
"hashes": [
|
||||
"sha256:03472c30eb2c5d1ba9227e4c2ca66ab8287fbfbbda3888aa93dc2e28fc6811b4",
|
||||
"sha256:75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6"
|
||||
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|
||||
"version": "==1.3.0"
|
||||
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|
||||
"attrs": {
|
||||
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|
||||
"sha256:69c0dbf2ed392de1cb5ec704444b08a5ef81680a61cb899dc08127123af36a79",
|
||||
"sha256:f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399"
|
||||
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|
||||
"version": "==19.1.0"
|
||||
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|
||||
"backcall": {
|
||||
"hashes": [
|
||||
"sha256:38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4",
|
||||
"sha256:bbbf4b1e5cd2bdb08f915895b51081c041bac22394fdfcfdfbe9f14b77c08bf2"
|
||||
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|
||||
"version": "==0.1.0"
|
||||
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|
||||
"decorator": {
|
||||
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|
||||
"sha256:86156361c50488b84a3f148056ea716ca587df2f0de1d34750d35c21312725de",
|
||||
"sha256:f069f3a01830ca754ba5258fde2278454a0b5b79e0d7f5c13b3b97e57d4acff6"
|
||||
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|
||||
"version": "==4.4.0"
|
||||
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|
||||
"entrypoints": {
|
||||
"hashes": [
|
||||
"sha256:589f874b313739ad35be6e0cd7efde2a4e9b6fea91edcc34e58ecbb8dbe56d19",
|
||||
"sha256:c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451"
|
||||
],
|
||||
"version": "==0.3"
|
||||
},
|
||||
"flake8": {
|
||||
"hashes": [
|
||||
"sha256:19241c1cbc971b9962473e4438a2ca19749a7dd002dd1a946eaba171b4114548",
|
||||
"sha256:8e9dfa3cecb2400b3738a42c54c3043e821682b9c840b0448c0503f781130696"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==3.7.8"
|
||||
},
|
||||
"importlib-metadata": {
|
||||
"hashes": [
|
||||
"sha256:23d3d873e008a513952355379d93cbcab874c58f4f034ff657c7a87422fa64e8",
|
||||
"sha256:80d2de76188eabfbfcf27e6a37342c2827801e59c4cc14b0371c56fed43820e3"
|
||||
],
|
||||
"version": "==0.19"
|
||||
},
|
||||
"ipython": {
|
||||
"hashes": [
|
||||
"sha256:1d3a1692921e932751bc1a1f7bb96dc38671eeefdc66ed33ee4cbc57e92a410e",
|
||||
"sha256:537cd0176ff6abd06ef3e23f2d0c4c2c8a4d9277b7451544c6cbf56d1c79a83d"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==7.7.0"
|
||||
},
|
||||
"ipython-genutils": {
|
||||
"hashes": [
|
||||
"sha256:72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8",
|
||||
"sha256:eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8"
|
||||
],
|
||||
"version": "==0.2.0"
|
||||
},
|
||||
"jedi": {
|
||||
"hashes": [
|
||||
"sha256:53c850f1a7d3cfcd306cc513e2450a54bdf5cacd7604b74e42dd1f0758eaaf36",
|
||||
"sha256:e07457174ef7cb2342ff94fa56484fe41cec7ef69b0059f01d3f812379cb6f7c"
|
||||
],
|
||||
"version": "==0.14.1"
|
||||
},
|
||||
"mccabe": {
|
||||
"hashes": [
|
||||
"sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42",
|
||||
"sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"
|
||||
],
|
||||
"version": "==0.6.1"
|
||||
},
|
||||
"more-itertools": {
|
||||
"hashes": [
|
||||
"sha256:409cd48d4db7052af495b09dec721011634af3753ae1ef92d2b32f73a745f832",
|
||||
"sha256:92b8c4b06dac4f0611c0729b2f2ede52b2e1bac1ab48f089c7ddc12e26bb60c4"
|
||||
],
|
||||
"version": "==7.2.0"
|
||||
},
|
||||
"packaging": {
|
||||
"hashes": [
|
||||
"sha256:a7ac867b97fdc07ee80a8058fe4435ccd274ecc3b0ed61d852d7d53055528cf9",
|
||||
"sha256:c491ca87294da7cc01902edbe30a5bc6c4c28172b5138ab4e4aa1b9d7bfaeafe"
|
||||
],
|
||||
"version": "==19.1"
|
||||
},
|
||||
"parso": {
|
||||
"hashes": [
|
||||
"sha256:63854233e1fadb5da97f2744b6b24346d2750b85965e7e399bec1620232797dc",
|
||||
"sha256:666b0ee4a7a1220f65d367617f2cd3ffddff3e205f3f16a0284df30e774c2a9c"
|
||||
],
|
||||
"version": "==0.5.1"
|
||||
},
|
||||
"pexpect": {
|
||||
"hashes": [
|
||||
"sha256:2094eefdfcf37a1fdbfb9aa090862c1a4878e5c7e0e7e7088bdb511c558e5cd1",
|
||||
"sha256:9e2c1fd0e6ee3a49b28f95d4b33bc389c89b20af6a1255906e90ff1262ce62eb"
|
||||
],
|
||||
"markers": "sys_platform != 'win32'",
|
||||
"version": "==4.7.0"
|
||||
},
|
||||
"pickleshare": {
|
||||
"hashes": [
|
||||
"sha256:87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca",
|
||||
"sha256:9649af414d74d4df115d5d718f82acb59c9d418196b7b4290ed47a12ce62df56"
|
||||
],
|
||||
"version": "==0.7.5"
|
||||
},
|
||||
"pluggy": {
|
||||
"hashes": [
|
||||
"sha256:0825a152ac059776623854c1543d65a4ad408eb3d33ee114dff91e57ec6ae6fc",
|
||||
"sha256:b9817417e95936bf75d85d3f8767f7df6cdde751fc40aed3bb3074cbcb77757c"
|
||||
],
|
||||
"version": "==0.12.0"
|
||||
},
|
||||
"prompt-toolkit": {
|
||||
"hashes": [
|
||||
"sha256:11adf3389a996a6d45cc277580d0d53e8a5afd281d0c9ec71b28e6f121463780",
|
||||
"sha256:2519ad1d8038fd5fc8e770362237ad0364d16a7650fb5724af6997ed5515e3c1",
|
||||
"sha256:977c6583ae813a37dc1c2e1b715892461fcbdaa57f6fc62f33a528c4886c8f55"
|
||||
],
|
||||
"version": "==2.0.9"
|
||||
},
|
||||
"ptyprocess": {
|
||||
"hashes": [
|
||||
"sha256:923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0",
|
||||
"sha256:d7cc528d76e76342423ca640335bd3633420dc1366f258cb31d05e865ef5ca1f"
|
||||
],
|
||||
"version": "==0.6.0"
|
||||
},
|
||||
"py": {
|
||||
"hashes": [
|
||||
"sha256:64f65755aee5b381cea27766a3a147c3f15b9b6b9ac88676de66ba2ae36793fa",
|
||||
"sha256:dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53"
|
||||
],
|
||||
"version": "==1.8.0"
|
||||
},
|
||||
"pycodestyle": {
|
||||
"hashes": [
|
||||
"sha256:95a2219d12372f05704562a14ec30bc76b05a5b297b21a5dfe3f6fac3491ae56",
|
||||
"sha256:e40a936c9a450ad81df37f549d676d127b1b66000a6c500caa2b085bc0ca976c"
|
||||
],
|
||||
"version": "==2.5.0"
|
||||
},
|
||||
"pyflakes": {
|
||||
"hashes": [
|
||||
"sha256:17dbeb2e3f4d772725c777fabc446d5634d1038f234e77343108ce445ea69ce0",
|
||||
"sha256:d976835886f8c5b31d47970ed689944a0262b5f3afa00a5a7b4dc81e5449f8a2"
|
||||
],
|
||||
"version": "==2.1.1"
|
||||
},
|
||||
"pygments": {
|
||||
"hashes": [
|
||||
"sha256:71e430bc85c88a430f000ac1d9b331d2407f681d6f6aec95e8bcfbc3df5b0127",
|
||||
"sha256:881c4c157e45f30af185c1ffe8d549d48ac9127433f2c380c24b84572ad66297"
|
||||
],
|
||||
"version": "==2.4.2"
|
||||
},
|
||||
"pyparsing": {
|
||||
"hashes": [
|
||||
"sha256:6f98a7b9397e206d78cc01df10131398f1c8b8510a2f4d97d9abd82e1aacdd80",
|
||||
"sha256:d9338df12903bbf5d65a0e4e87c2161968b10d2e489652bb47001d82a9b028b4"
|
||||
],
|
||||
"version": "==2.4.2"
|
||||
},
|
||||
"pytest": {
|
||||
"hashes": [
|
||||
"sha256:6ef6d06de77ce2961156013e9dff62f1b2688aa04d0dc244299fe7d67e09370d",
|
||||
"sha256:a736fed91c12681a7b34617c8fcefe39ea04599ca72c608751c31d89579a3f77"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==5.0.1"
|
||||
},
|
||||
"pytest-clarity": {
|
||||
"hashes": [
|
||||
"sha256:3f40d5ae7cb21cc95e622fc4f50d9466f80ae0f91460225b8c95c07afbf93e20"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==0.2.0a1"
|
||||
},
|
||||
"six": {
|
||||
"hashes": [
|
||||
"sha256:3350809f0555b11f552448330d0b52d5f24c91a322ea4a15ef22629740f3761c",
|
||||
"sha256:d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73"
|
||||
],
|
||||
"version": "==1.12.0"
|
||||
},
|
||||
"termcolor": {
|
||||
"hashes": [
|
||||
"sha256:1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b"
|
||||
],
|
||||
"version": "==1.1.0"
|
||||
},
|
||||
"traitlets": {
|
||||
"hashes": [
|
||||
"sha256:9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835",
|
||||
"sha256:c6cb5e6f57c5a9bdaa40fa71ce7b4af30298fbab9ece9815b5d995ab6217c7d9"
|
||||
],
|
||||
"version": "==4.3.2"
|
||||
},
|
||||
"wcwidth": {
|
||||
"hashes": [
|
||||
"sha256:3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e",
|
||||
"sha256:f4ebe71925af7b40a864553f761ed559b43544f8f71746c2d756c7fe788ade7c"
|
||||
],
|
||||
"version": "==0.1.7"
|
||||
},
|
||||
"zipp": {
|
||||
"hashes": [
|
||||
"sha256:4970c3758f4e89a7857a973b1e2a5d75bcdc47794442f2e2dd4fe8e0466e809a",
|
||||
"sha256:8a5712cfd3bb4248015eb3b0b3c54a5f6ee3f2425963ef2a0125b8bc40aafaec"
|
||||
],
|
||||
"version": "==0.5.2"
|
||||
}
|
||||
}
|
||||
}
|
55
README.md
55
README.md
@ -1,34 +1,36 @@
|
||||
# CSV Metadata Quality [](https://travis-ci.org/alanorth/csv-metadata-quality) [](https://builds.sr.ht/~alanorth/csv-metadata-quality?)
|
||||
A simple, but opinionated metadata quality checker and fixer designed to work with CSVs in the DSpace ecosystem. 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.
|
||||
# CSV Metadata Quality  [](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.
|
||||
|
||||
Requires Python 3.6 or greater. 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 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.
|
||||
|
||||
## Functionality
|
||||
|
||||
- Validate dates, ISSNs, ISBNs, and multi-value separators ("||")
|
||||
- Validate languages against ISO 639-2 and ISO 639-3
|
||||
- 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)
|
||||
- Fix leading, trailing, and excessive (ie, more than one) whitespace
|
||||
- Fix invalid multi-value separators (`|`) using `--unsafe-fixes`
|
||||
- Fix invalid and unnecessary multi-value separators (`|`) using `--unsafe-fixes`
|
||||
- Fix problematic newlines (line feeds) using `--unsafe-fixes`
|
||||
- Remove unnecessary Unicode like [non-breaking spaces](https://en.wikipedia.org/wiki/Non-breaking_space), [replacement characters](https://en.wikipedia.org/wiki/Specials_(Unicode_block)#Replacement_character), etc
|
||||
- Check for "suspicious" characters that indicate encoding or copy/paste issues, for example "foreˆt" should be "forêt"
|
||||
- Remove duplicate metadata values
|
||||
- Perform [Unicode normalization](https://withblue.ink/2019/03/11/why-you-need-to-normalize-unicode-strings.html) on strings using `--unsafe-fixes`
|
||||
|
||||
## Installation
|
||||
The easiest way to install CSV Metadata Quality is with [pipenv](https://github.com/pypa/pipenv):
|
||||
The easiest way to install CSV Metadata Quality is with [poetry](https://python-poetry.org):
|
||||
|
||||
```
|
||||
$ git clone https://git.sr.ht/~alanorth/csv-metadata-quality
|
||||
$ git clone https://github.com/ilri/csv-metadata-quality.git
|
||||
$ cd csv-metadata-quality
|
||||
$ pipenv install
|
||||
$ pipenv shell
|
||||
$ poetry install
|
||||
$ poetry shell
|
||||
```
|
||||
|
||||
Otherwise, if you don't have pipenv, you can use a vanilla Python virtual environment:
|
||||
Otherwise, if you don't have poetry, you can use a vanilla Python virtual environment:
|
||||
|
||||
```
|
||||
$ git clone https://git.sr.ht/~alanorth/csv-metadata-quality
|
||||
$ git clone https://github.com/ilri/csv-metadata-quality.git
|
||||
$ cd csv-metadata-quality
|
||||
$ python3 -m venv venv
|
||||
$ source venv/bin/activate
|
||||
@ -54,9 +56,19 @@ You can enable several "unsafe" fixes with the `--unsafe-fixes` option. Currentl
|
||||
### Invalid Multi-Value Separators
|
||||
This is considered "unsafe" because it is *theoretically* possible for a single `|` character to be used legitimately in a metadata value, though in my experience it is always a typo. For example, if a user mistakenly writes `Kenya|Tanzania` when attempting to indicate two countries, the result will be one metadata value with the literal text `Kenya|Tanzania`. The `--unsafe-fixes` option will correct the invalid multi-value separator so that there are two metadata values, ie `Kenya||Tanzania`.
|
||||
|
||||
This will also remove unnecessary trailing multi-value separators, for example `Kenya||Tanzania||`.
|
||||
|
||||
### Newlines
|
||||
This is considered "unsafe" because some systems give special importance to vertical space and render it properly. DSpace does not support rendering newlines in its XMLUI and has, at times, suffered from parsing errors that cause the import process to fail if an input file had newlines. The `--unsafe-fixes` option strips Unix line feeds (U+000A).
|
||||
|
||||
### Unicode Normalization
|
||||
[Unicode](https://en.wikipedia.org/wiki/Unicode) is a standard for encoding text. As the standard aims to support most of the world's languages, characters can often be represented in different ways and still be valid Unicode. This leads to interesting problems that can be confusing unless you know what's going on behind the scenes. For example, the characters `é` and `é` *look* the same, but are not — technically they refer to different code points in the Unicode standard:
|
||||
|
||||
- `é` is the Unicode code point `U+00E9`
|
||||
- `é` is the Unicode code points `U+0065` + `U+0301`
|
||||
|
||||
Read more about [Unicode normalization](https://withblue.ink/2019/03/11/why-you-need-to-normalize-unicode-strings.html).
|
||||
|
||||
## AGROVOC Validation
|
||||
You can enable validation of metadata values in certain fields against the AGROVOC REST API with the `--agrovoc-fields` option. For example, in addition to agricultural subjects, many countries and regions are also present AGROVOC. Enable this validation by specifying a comma-separated list of fields:
|
||||
|
||||
@ -69,11 +81,32 @@ Invalid AGROVOC (cg.coverage.country): KENYAA
|
||||
|
||||
*Note: Requests to the AGROVOC REST API are cached using [requests_cache](https://pypi.org/project/requests-cache/) to speed up subsequent runs with the same data and to be kind to the system's administrators.*
|
||||
|
||||
## Experimental Checks
|
||||
You can enable experimental support for validating whether the value of an item's `dc.language.iso` or `dcterms.language` field matches the actual language used in its title, abstract, and citation.
|
||||
|
||||
```
|
||||
$ csv-metadata-quality -i data/test.csv -o /tmp/test.csv -e
|
||||
...
|
||||
Possibly incorrect language es (detected en): Incorrect ISO 639-1 language
|
||||
Possibly incorrect language spa (detected eng): Incorrect ISO 639-3 language
|
||||
```
|
||||
|
||||
This currently uses the [Python langid](https://github.com/saffsd/langid.py) library. In the future I would like to move to the fastText library, but there is currently an [issue with their Python bindings](https://github.com/facebookresearch/fastText/issues/909) that makes this unfeasible.
|
||||
|
||||
## Todo
|
||||
|
||||
- Reporting / summary
|
||||
- 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!)
|
||||
|
||||
## License
|
||||
This work is licensed under the [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html).
|
||||
|
@ -1,10 +1,11 @@
|
||||
from csv_metadata_quality import app
|
||||
from sys import argv
|
||||
|
||||
from csv_metadata_quality import app
|
||||
|
||||
|
||||
def main():
|
||||
app.run(argv)
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
|
@ -1,20 +1,54 @@
|
||||
from csv_metadata_quality.version import VERSION
|
||||
import argparse
|
||||
import csv_metadata_quality.check as check
|
||||
import csv_metadata_quality.fix as fix
|
||||
import pandas as pd
|
||||
import re
|
||||
import signal
|
||||
import sys
|
||||
|
||||
import pandas as pd
|
||||
|
||||
import csv_metadata_quality.check as check
|
||||
import csv_metadata_quality.experimental as experimental
|
||||
import csv_metadata_quality.fix as fix
|
||||
from csv_metadata_quality.version import VERSION
|
||||
|
||||
|
||||
def parse_args(argv):
|
||||
parser = argparse.ArgumentParser(description='Metadata quality checker and fixer.')
|
||||
parser.add_argument('--agrovoc-fields', '-a', help='Comma-separated list of fields to validate against AGROVOC, for example: dc.subject,cg.coverage.country')
|
||||
parser.add_argument('--input-file', '-i', help='Path to input file. Can be UTF-8 CSV or Excel XLSX.', required=True, type=argparse.FileType('r', encoding='UTF-8'))
|
||||
parser.add_argument('--output-file', '-o', help='Path to output file (always CSV).', required=True, type=argparse.FileType('w', encoding='UTF-8'))
|
||||
parser.add_argument('--unsafe-fixes', '-u', help='Perform unsafe fixes.', action='store_true')
|
||||
parser.add_argument('--version', '-V', action='version', version=f'CSV Metadata Quality v{VERSION}')
|
||||
parser = argparse.ArgumentParser(description="Metadata quality checker and fixer.")
|
||||
parser.add_argument(
|
||||
"--agrovoc-fields",
|
||||
"-a",
|
||||
help="Comma-separated list of fields to validate against AGROVOC, for example: dc.subject,cg.coverage.country",
|
||||
)
|
||||
parser.add_argument(
|
||||
"--experimental-checks",
|
||||
"-e",
|
||||
help="Enable experimental checks like language detection",
|
||||
action="store_true",
|
||||
)
|
||||
parser.add_argument(
|
||||
"--input-file",
|
||||
"-i",
|
||||
help="Path to input file. Can be UTF-8 CSV or Excel XLSX.",
|
||||
required=True,
|
||||
type=argparse.FileType("r", encoding="UTF-8"),
|
||||
)
|
||||
parser.add_argument(
|
||||
"--output-file",
|
||||
"-o",
|
||||
help="Path to output file (always CSV).",
|
||||
required=True,
|
||||
type=argparse.FileType("w", encoding="UTF-8"),
|
||||
)
|
||||
parser.add_argument(
|
||||
"--unsafe-fixes", "-u", help="Perform unsafe fixes.", action="store_true"
|
||||
)
|
||||
parser.add_argument(
|
||||
"--version", "-V", action="version", version=f"CSV Metadata Quality v{VERSION}"
|
||||
)
|
||||
parser.add_argument(
|
||||
"--exclude-fields",
|
||||
"-x",
|
||||
help="Comma-separated list of fields to skip, for example: dc.contributor.author,dc.identifier.citation",
|
||||
)
|
||||
args = parser.parse_args()
|
||||
|
||||
return args
|
||||
@ -33,63 +67,106 @@ def run(argv):
|
||||
# Read all fields as strings so dates don't get converted from 1998 to 1998.0
|
||||
df = pd.read_csv(args.input_file, dtype=str)
|
||||
|
||||
for column in df.columns.values.tolist():
|
||||
for column in df.columns:
|
||||
# Check if the user requested to skip any fields
|
||||
if args.exclude_fields:
|
||||
skip = False
|
||||
# Split the list of excludes on ',' so we can test exact matches
|
||||
# rather than fuzzy matches with regexes or "if word in string"
|
||||
for exclude in args.exclude_fields.split(","):
|
||||
if column == exclude and skip is False:
|
||||
skip = True
|
||||
if skip:
|
||||
print(f"Skipping {column}")
|
||||
|
||||
continue
|
||||
|
||||
# Fix: whitespace
|
||||
df[column] = df[column].apply(fix.whitespace)
|
||||
df[column] = df[column].apply(fix.whitespace, field_name=column)
|
||||
|
||||
# Fix: newlines
|
||||
if args.unsafe_fixes:
|
||||
df[column] = df[column].apply(fix.newlines)
|
||||
|
||||
# Fix: missing space after comma. Only run on author and citation
|
||||
# fields for now, as this problem is mostly an issue in names.
|
||||
if args.unsafe_fixes:
|
||||
match = re.match(r"^.*?(author|citation).*$", column)
|
||||
if match is not None:
|
||||
df[column] = df[column].apply(fix.comma_space, field_name=column)
|
||||
|
||||
# Fix: perform Unicode normalization (NFC) to convert decomposed
|
||||
# characters into their canonical forms.
|
||||
if args.unsafe_fixes:
|
||||
df[column] = df[column].apply(fix.normalize_unicode, field_name=column)
|
||||
|
||||
# Fix: unnecessary Unicode
|
||||
df[column] = df[column].apply(fix.unnecessary_unicode)
|
||||
|
||||
# Check: invalid multi-value separator
|
||||
df[column] = df[column].apply(check.separators)
|
||||
# Check: invalid and unnecessary multi-value separators
|
||||
df[column] = df[column].apply(check.separators, field_name=column)
|
||||
|
||||
# Check: suspicious characters
|
||||
df[column] = df[column].apply(check.suspicious_characters, field_name=column)
|
||||
|
||||
# Fix: invalid multi-value separator
|
||||
# Fix: invalid and unnecessary multi-value separators
|
||||
if args.unsafe_fixes:
|
||||
df[column] = df[column].apply(fix.separators)
|
||||
df[column] = df[column].apply(fix.separators, field_name=column)
|
||||
# Run whitespace fix again after fixing invalid separators
|
||||
df[column] = df[column].apply(fix.whitespace)
|
||||
df[column] = df[column].apply(fix.whitespace, field_name=column)
|
||||
|
||||
# Fix: duplicate metadata values
|
||||
df[column] = df[column].apply(fix.duplicates)
|
||||
df[column] = df[column].apply(fix.duplicates, field_name=column)
|
||||
|
||||
# Check: invalid AGROVOC subject
|
||||
if args.agrovoc_fields:
|
||||
# Identify fields the user wants to validate against AGROVOC
|
||||
for field in args.agrovoc_fields.split(','):
|
||||
for field in args.agrovoc_fields.split(","):
|
||||
if column == field:
|
||||
df[column] = df[column].apply(check.agrovoc, field_name=column)
|
||||
|
||||
# Check: invalid language
|
||||
match = re.match(r'^.*?language.*$', column)
|
||||
match = re.match(r"^.*?language.*$", column)
|
||||
if match is not None:
|
||||
df[column] = df[column].apply(check.language)
|
||||
|
||||
# Check: invalid ISSN
|
||||
match = re.match(r'^.*?issn.*$', column)
|
||||
match = re.match(r"^.*?issn.*$", column)
|
||||
if match is not None:
|
||||
df[column] = df[column].apply(check.issn)
|
||||
|
||||
# Check: invalid ISBN
|
||||
match = re.match(r'^.*?isbn.*$', column)
|
||||
match = re.match(r"^.*?isbn.*$", column)
|
||||
if match is not None:
|
||||
df[column] = df[column].apply(check.isbn)
|
||||
|
||||
# Check: invalid date
|
||||
match = re.match(r'^.*?date.*$', column)
|
||||
match = re.match(r"^.*?date.*$", column)
|
||||
if match is not None:
|
||||
df[column] = df[column].apply(check.date)
|
||||
df[column] = df[column].apply(check.date, field_name=column)
|
||||
|
||||
# Check: filename extension
|
||||
if column == 'filename':
|
||||
if column == "filename":
|
||||
df[column] = df[column].apply(check.filename_extension)
|
||||
|
||||
##
|
||||
# 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
|
||||
# the language used in the title and abstract matches the language indi-
|
||||
# cated in the language field, for example.
|
||||
#
|
||||
# This is slower and apparently frowned upon in the Pandas community be-
|
||||
# cause it requires iterating over rows rather than using apply over a
|
||||
# column. For now it will have to do.
|
||||
##
|
||||
|
||||
if args.experimental_checks:
|
||||
# Transpose the DataFrame so we can consider each row as a column
|
||||
df_transposed = df.T
|
||||
|
||||
for column in df_transposed.columns:
|
||||
experimental.correct_language(df_transposed[column])
|
||||
|
||||
# Write
|
||||
df.to_csv(args.output_file, index=False)
|
||||
|
||||
|
@ -1,4 +1,9 @@
|
||||
from datetime import datetime, timedelta
|
||||
|
||||
import pandas as pd
|
||||
import requests
|
||||
import requests_cache
|
||||
from pycountry import languages
|
||||
|
||||
|
||||
def issn(field):
|
||||
@ -18,10 +23,10 @@ def issn(field):
|
||||
return
|
||||
|
||||
# Try to split multi-value field on "||" separator
|
||||
for value in field.split('||'):
|
||||
for value in field.split("||"):
|
||||
|
||||
if not issn.is_valid(value):
|
||||
print(f'Invalid ISSN: {value}')
|
||||
print(f"Invalid ISSN: {value}")
|
||||
|
||||
return field
|
||||
|
||||
@ -43,16 +48,20 @@ def isbn(field):
|
||||
return
|
||||
|
||||
# Try to split multi-value field on "||" separator
|
||||
for value in field.split('||'):
|
||||
for value in field.split("||"):
|
||||
|
||||
if not isbn.is_valid(value):
|
||||
print(f'Invalid ISBN: {value}')
|
||||
print(f"Invalid ISBN: {value}")
|
||||
|
||||
return field
|
||||
|
||||
|
||||
def separators(field):
|
||||
"""Check for invalid multi-value separators (ie "|" or "|||").
|
||||
def separators(field, field_name):
|
||||
"""Check for invalid and unnecessary multi-value separators, for example:
|
||||
|
||||
value|value
|
||||
value|||value
|
||||
value||value||
|
||||
|
||||
Prints the field with the invalid multi-value separator.
|
||||
"""
|
||||
@ -64,18 +73,24 @@ def separators(field):
|
||||
return
|
||||
|
||||
# Try to split multi-value field on "||" separator
|
||||
for value in field.split('||'):
|
||||
for value in field.split("||"):
|
||||
# Check if the current value is blank
|
||||
if value == "":
|
||||
print(f"Unnecessary multi-value separator ({field_name}): {field}")
|
||||
|
||||
continue
|
||||
|
||||
# After splitting, see if there are any remaining "|" characters
|
||||
match = re.findall(r'^.*?\|.*$', value)
|
||||
match = re.findall(r"^.*?\|.*$", value)
|
||||
|
||||
# Check if there was a match
|
||||
if match:
|
||||
print(f'Invalid multi-value separator: {field}')
|
||||
print(f"Invalid multi-value separator ({field_name}): {field}")
|
||||
|
||||
return field
|
||||
|
||||
|
||||
def date(field):
|
||||
def date(field, field_name):
|
||||
"""Check if a date is valid.
|
||||
|
||||
In DSpace the issue date is usually 1990, 1990-01, or 1990-01-01, but it
|
||||
@ -85,25 +100,24 @@ def date(field):
|
||||
|
||||
Prints the date if invalid.
|
||||
"""
|
||||
from datetime import datetime
|
||||
|
||||
if pd.isna(field):
|
||||
print(f'Missing date.')
|
||||
print(f"Missing date ({field_name}).")
|
||||
|
||||
return
|
||||
|
||||
# Try to split multi-value field on "||" separator
|
||||
multiple_dates = field.split('||')
|
||||
multiple_dates = field.split("||")
|
||||
|
||||
# We don't allow multi-value date fields
|
||||
if len(multiple_dates) > 1:
|
||||
print(f'Multiple dates not allowed: {field}')
|
||||
print(f"Multiple dates not allowed ({field_name}): {field}")
|
||||
|
||||
return field
|
||||
|
||||
try:
|
||||
# Check if date is valid YYYY format
|
||||
datetime.strptime(field, '%Y')
|
||||
datetime.strptime(field, "%Y")
|
||||
|
||||
return field
|
||||
except ValueError:
|
||||
@ -111,7 +125,7 @@ def date(field):
|
||||
|
||||
try:
|
||||
# Check if date is valid YYYY-MM format
|
||||
datetime.strptime(field, '%Y-%m')
|
||||
datetime.strptime(field, "%Y-%m")
|
||||
|
||||
return field
|
||||
except ValueError:
|
||||
@ -119,11 +133,11 @@ def date(field):
|
||||
|
||||
try:
|
||||
# Check if date is valid YYYY-MM-DD format
|
||||
datetime.strptime(field, '%Y-%m-%d')
|
||||
datetime.strptime(field, "%Y-%m-%d")
|
||||
|
||||
return field
|
||||
except ValueError:
|
||||
print(f'Invalid date: {field}')
|
||||
print(f"Invalid date ({field_name}): {field}")
|
||||
|
||||
return field
|
||||
|
||||
@ -140,7 +154,7 @@ def suspicious_characters(field, field_name):
|
||||
return
|
||||
|
||||
# List of suspicious characters, for example: ́ˆ~`
|
||||
suspicious_characters = ['\u00B4', '\u02C6', '\u007E', '\u0060']
|
||||
suspicious_characters = ["\u00B4", "\u02C6", "\u007E", "\u0060"]
|
||||
|
||||
for character in suspicious_characters:
|
||||
# Find the position of the suspicious character in the string
|
||||
@ -156,20 +170,20 @@ 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}'
|
||||
print(f'{suspicious_character_msg:1.80}')
|
||||
suspicious_character_msg = (
|
||||
f"Suspicious character ({field_name}): {field_subset}"
|
||||
)
|
||||
print(f"{suspicious_character_msg:1.80}")
|
||||
|
||||
return field
|
||||
|
||||
|
||||
def language(field):
|
||||
"""Check if a language is valid ISO 639-2 or ISO 639-3.
|
||||
"""Check if a language is valid ISO 639-1 (alpha 2) or ISO 639-3 (alpha 3).
|
||||
|
||||
Prints the value if it is invalid.
|
||||
"""
|
||||
|
||||
from pycountry import languages
|
||||
|
||||
# Skip fields with missing values
|
||||
if pd.isna(field):
|
||||
return
|
||||
@ -177,22 +191,22 @@ def language(field):
|
||||
# need to handle "Other" values here...
|
||||
|
||||
# Try to split multi-value field on "||" separator
|
||||
for value in field.split('||'):
|
||||
for value in field.split("||"):
|
||||
|
||||
# After splitting, check if language value is 2 or 3 characters so we
|
||||
# can check it against ISO 639-2 or ISO 639-3 accordingly.
|
||||
# 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 639-2 language: {value}')
|
||||
print(f"Invalid ISO 639-1 language: {value}")
|
||||
|
||||
pass
|
||||
elif len(value) == 3:
|
||||
if not languages.get(alpha_3=value):
|
||||
print(f'Invalid ISO 639-3 language: {value}')
|
||||
print(f"Invalid ISO 639-3 language: {value}")
|
||||
|
||||
pass
|
||||
else:
|
||||
print(f'Invalid language: {value}')
|
||||
print(f"Invalid language: {value}")
|
||||
|
||||
return field
|
||||
|
||||
@ -211,46 +225,30 @@ def agrovoc(field, field_name):
|
||||
Prints a warning if the value is invalid.
|
||||
"""
|
||||
|
||||
from datetime import timedelta
|
||||
import re
|
||||
import requests
|
||||
import requests_cache
|
||||
|
||||
# Skip fields with missing values
|
||||
if pd.isna(field):
|
||||
return
|
||||
|
||||
# enable transparent request cache with thirty days expiry
|
||||
expire_after = timedelta(days=30)
|
||||
requests_cache.install_cache("agrovoc-response-cache", expire_after=expire_after)
|
||||
|
||||
# prune old cache entries
|
||||
requests_cache.core.remove_expired_responses()
|
||||
|
||||
# Try to split multi-value field on "||" separator
|
||||
for value in field.split('||'):
|
||||
# match lines beginning with words, paying attention to subjects with
|
||||
# special characters like spaces, quotes, dashes, parentheses, etc:
|
||||
# SUBJECT
|
||||
# ANOTHER SUBJECT
|
||||
# XANTHOMONAS CAMPESTRIS PV. MANIHOTIS
|
||||
# WOMEN'S PARTICIPATION
|
||||
# COMMUNITY-BASED FOREST MANAGEMENT
|
||||
# INTERACCIÓN GENOTIPO AMBIENTE
|
||||
# COCOA (PLANT)
|
||||
pattern = re.compile(r'^[\w\-\.\'\(\)]+?[\w\s\-\.\'\(\)]+$')
|
||||
for value in field.split("||"):
|
||||
request_url = "http://agrovoc.uniroma2.it/agrovoc/rest/v1/agrovoc/search"
|
||||
request_params = {"query": value}
|
||||
|
||||
if pattern.match(value):
|
||||
request_url = f'http://agrovoc.uniroma2.it/agrovoc/rest/v1/agrovoc/search?query={value}'
|
||||
request = requests.get(request_url, params=request_params)
|
||||
|
||||
# enable transparent request cache with thirty days expiry
|
||||
expire_after = timedelta(days=30)
|
||||
requests_cache.install_cache('agrovoc-response-cache', expire_after=expire_after)
|
||||
if request.status_code == requests.codes.ok:
|
||||
data = request.json()
|
||||
|
||||
request = requests.get(request_url)
|
||||
|
||||
# prune old cache entries
|
||||
requests_cache.core.remove_expired_responses()
|
||||
|
||||
if request.status_code == requests.codes.ok:
|
||||
data = request.json()
|
||||
|
||||
# check if there are any results
|
||||
if len(data['results']) == 0:
|
||||
print(f'Invalid AGROVOC ({field_name}): {value}')
|
||||
# check if there are any results
|
||||
if len(data["results"]) == 0:
|
||||
print(f"Invalid AGROVOC ({field_name}): {value}")
|
||||
|
||||
return field
|
||||
|
||||
@ -273,10 +271,18 @@ def filename_extension(field):
|
||||
return
|
||||
|
||||
# Try to split multi-value field on "||" separator
|
||||
values = field.split('||')
|
||||
values = field.split("||")
|
||||
|
||||
# List of common filename extentions
|
||||
common_filename_extensions = ['.pdf', '.doc', '.docx', '.ppt', '.pptx', '.xls', '.xlsx']
|
||||
common_filename_extensions = [
|
||||
".pdf",
|
||||
".doc",
|
||||
".docx",
|
||||
".ppt",
|
||||
".pptx",
|
||||
".xls",
|
||||
".xlsx",
|
||||
]
|
||||
|
||||
# Iterate over all values
|
||||
for value in values:
|
||||
@ -285,7 +291,7 @@ def filename_extension(field):
|
||||
|
||||
for filename_extension in common_filename_extensions:
|
||||
# Check for extension at the end of the filename
|
||||
pattern = re.escape(filename_extension) + r'$'
|
||||
pattern = re.escape(filename_extension) + r"$"
|
||||
match = re.search(pattern, value, re.IGNORECASE)
|
||||
|
||||
if match is not None:
|
||||
@ -295,6 +301,6 @@ def filename_extension(field):
|
||||
break
|
||||
|
||||
if filename_extension_match is False:
|
||||
print(f'Filename with uncommon extension: {value}')
|
||||
print(f"Filename with uncommon extension: {value}")
|
||||
|
||||
return field
|
||||
|
95
csv_metadata_quality/experimental.py
Normal file
95
csv_metadata_quality/experimental.py
Normal file
@ -0,0 +1,95 @@
|
||||
import pandas as pd
|
||||
|
||||
|
||||
def correct_language(row):
|
||||
"""Analyze the text used in the title, abstract, and citation fields to pre-
|
||||
dict the language being used and compare it with the item's dc.language.iso
|
||||
field.
|
||||
|
||||
Function prints an error if the language field does not match the detected
|
||||
language and returns the value in the language field if it does match.
|
||||
"""
|
||||
|
||||
from pycountry import languages
|
||||
import langid
|
||||
import re
|
||||
|
||||
# Initialize some variables at global scope so that we can set them in the
|
||||
# loop scope below and still be able to access them afterwards.
|
||||
language = ""
|
||||
sample_strings = list()
|
||||
title = None
|
||||
|
||||
# Iterate over the labels of the current row's values. Before we transposed
|
||||
# the DataFrame these were the columns in the CSV, ie dc.title and dc.type.
|
||||
for label in row.axes[0]:
|
||||
# Skip fields with missing values
|
||||
if pd.isna(row[label]):
|
||||
continue
|
||||
|
||||
# Check if current row has multiple language values (separated by "||")
|
||||
match = re.match(r"^.*?language.*$", label)
|
||||
if match is not None:
|
||||
# Skip fields with multiple language values
|
||||
if "||" in row[label]:
|
||||
return
|
||||
|
||||
language = row[label]
|
||||
|
||||
# Extract title if it is present
|
||||
match = re.match(r"^.*?title.*$", label)
|
||||
if match is not None:
|
||||
title = row[label]
|
||||
# Append title to sample strings
|
||||
sample_strings.append(row[label])
|
||||
|
||||
# Extract abstract if it is present
|
||||
match = re.match(r"^.*?abstract.*$", label)
|
||||
if match is not None:
|
||||
sample_strings.append(row[label])
|
||||
|
||||
# Extract citation if it is present
|
||||
match = re.match(r"^.*?citation.*$", label)
|
||||
if match is not None:
|
||||
sample_strings.append(row[label])
|
||||
|
||||
# Make sure language is not blank and is valid ISO 639-1/639-3 before proceeding with language prediction
|
||||
if language != "":
|
||||
# Check language value like "es"
|
||||
if len(language) == 2:
|
||||
if not languages.get(alpha_2=language):
|
||||
return
|
||||
# Check language value like "spa"
|
||||
elif len(language) == 3:
|
||||
if not languages.get(alpha_3=language):
|
||||
return
|
||||
# Language value is something else like "Span", do not proceed
|
||||
else:
|
||||
return
|
||||
# Language is blank, do not proceed
|
||||
else:
|
||||
return
|
||||
|
||||
# Concatenate all sample strings into one string
|
||||
sample_text = " ".join(sample_strings)
|
||||
|
||||
# Restrict the langid detection space to reduce false positives
|
||||
langid.set_languages(
|
||||
["ar", "de", "en", "es", "fr", "hi", "it", "ja", "ko", "pt", "ru", "vi", "zh"]
|
||||
)
|
||||
langid_classification = langid.classify(sample_text)
|
||||
|
||||
# langid returns an ISO 639-1 (alpha 2) representation of the detected language, but the current item's language field might be ISO 639-3 (alpha 3) so we should use a pycountry Language object to compare both represenations and give appropriate error messages that match the format used by in the input file.
|
||||
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}"
|
||||
)
|
||||
|
||||
elif len(language) == 3 and language != detected_language.alpha_3:
|
||||
print(
|
||||
f"Possibly incorrect language {language} (detected {detected_language.alpha_3}): {title}"
|
||||
)
|
||||
|
||||
else:
|
||||
return language
|
@ -1,8 +1,12 @@
|
||||
import pandas as pd
|
||||
import re
|
||||
from unicodedata import normalize
|
||||
|
||||
import pandas as pd
|
||||
|
||||
from csv_metadata_quality.util import is_nfc
|
||||
|
||||
|
||||
def whitespace(field):
|
||||
def whitespace(field, field_name):
|
||||
"""Fix whitespace issues.
|
||||
|
||||
Return string with leading, trailing, and consecutive whitespace trimmed.
|
||||
@ -16,29 +20,36 @@ def whitespace(field):
|
||||
values = list()
|
||||
|
||||
# Try to split multi-value field on "||" separator
|
||||
for value in field.split('||'):
|
||||
for value in field.split("||"):
|
||||
# Strip leading and trailing whitespace
|
||||
value = value.strip()
|
||||
|
||||
# Replace excessive whitespace (>2) with one space
|
||||
pattern = re.compile(r'\s{2,}')
|
||||
pattern = re.compile(r"\s{2,}")
|
||||
match = re.findall(pattern, value)
|
||||
|
||||
if match:
|
||||
print(f'Excessive whitespace: {value}')
|
||||
value = re.sub(pattern, ' ', value)
|
||||
print(f"Removing excessive whitespace ({field_name}): {value}")
|
||||
value = re.sub(pattern, " ", value)
|
||||
|
||||
# Save cleaned value
|
||||
values.append(value)
|
||||
|
||||
# Create a new field consisting of all values joined with "||"
|
||||
new_field = '||'.join(values)
|
||||
new_field = "||".join(values)
|
||||
|
||||
return new_field
|
||||
|
||||
|
||||
def separators(field):
|
||||
"""Fix for invalid multi-value separators (ie "|")."""
|
||||
def separators(field, field_name):
|
||||
"""Fix for invalid and unnecessary multi-value separators, for example:
|
||||
|
||||
value|value
|
||||
value|||value
|
||||
value||value||
|
||||
|
||||
Prints the field with the invalid multi-value separator.
|
||||
"""
|
||||
|
||||
# Skip fields with missing values
|
||||
if pd.isna(field):
|
||||
@ -48,21 +59,27 @@ def separators(field):
|
||||
values = list()
|
||||
|
||||
# Try to split multi-value field on "||" separator
|
||||
for value in field.split('||'):
|
||||
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}")
|
||||
|
||||
continue
|
||||
|
||||
# After splitting, see if there are any remaining "|" characters
|
||||
pattern = re.compile(r'\|')
|
||||
pattern = re.compile(r"\|")
|
||||
match = re.findall(pattern, value)
|
||||
|
||||
if match:
|
||||
print(f'Fixing invalid multi-value separator: {value}')
|
||||
print(f"Fixing invalid multi-value separator ({field_name}): {value}")
|
||||
|
||||
value = re.sub(pattern, '||', value)
|
||||
value = re.sub(pattern, "||", value)
|
||||
|
||||
# Save cleaned value
|
||||
values.append(value)
|
||||
|
||||
# Create a new field consisting of all values joined with "||"
|
||||
new_field = '||'.join(values)
|
||||
new_field = "||".join(values)
|
||||
|
||||
return new_field
|
||||
|
||||
@ -73,10 +90,10 @@ def unnecessary_unicode(field):
|
||||
Removes unnecessary Unicode characters like:
|
||||
- Zero-width space (U+200B)
|
||||
- Replacement character (U+FFFD)
|
||||
- No-break space (U+00A0)
|
||||
|
||||
Replaces unnecessary Unicode characters like:
|
||||
- Soft hyphen (U+00AD) → hyphen
|
||||
- No-break space (U+00A0) → space
|
||||
|
||||
Return string with characters removed or replaced.
|
||||
"""
|
||||
@ -86,41 +103,41 @@ def unnecessary_unicode(field):
|
||||
return
|
||||
|
||||
# Check for zero-width space characters (U+200B)
|
||||
pattern = re.compile(r'\u200B')
|
||||
pattern = re.compile(r"\u200B")
|
||||
match = re.findall(pattern, field)
|
||||
|
||||
if match:
|
||||
print(f'Removing unnecessary Unicode (U+200B): {field}')
|
||||
field = re.sub(pattern, '', field)
|
||||
print(f"Removing unnecessary Unicode (U+200B): {field}")
|
||||
field = re.sub(pattern, "", field)
|
||||
|
||||
# Check for replacement characters (U+FFFD)
|
||||
pattern = re.compile(r'\uFFFD')
|
||||
pattern = re.compile(r"\uFFFD")
|
||||
match = re.findall(pattern, field)
|
||||
|
||||
if match:
|
||||
print(f'Removing unnecessary Unicode (U+FFFD): {field}')
|
||||
field = re.sub(pattern, '', field)
|
||||
print(f"Removing unnecessary Unicode (U+FFFD): {field}")
|
||||
field = re.sub(pattern, "", field)
|
||||
|
||||
# Check for no-break spaces (U+00A0)
|
||||
pattern = re.compile(r'\u00A0')
|
||||
pattern = re.compile(r"\u00A0")
|
||||
match = re.findall(pattern, field)
|
||||
|
||||
if match:
|
||||
print(f'Removing unnecessary Unicode (U+00A0): {field}')
|
||||
field = re.sub(pattern, '', field)
|
||||
print(f"Replacing unnecessary Unicode (U+00A0): {field}")
|
||||
field = re.sub(pattern, " ", field)
|
||||
|
||||
# Check for soft hyphens (U+00AD), sometimes preceeded with a normal hyphen
|
||||
pattern = re.compile(r'\u002D*?\u00AD')
|
||||
pattern = re.compile(r"\u002D*?\u00AD")
|
||||
match = re.findall(pattern, field)
|
||||
|
||||
if match:
|
||||
print(f'Replacing unnecessary Unicode (U+00AD): {field}')
|
||||
field = re.sub(pattern, '-', field)
|
||||
print(f"Replacing unnecessary Unicode (U+00AD): {field}")
|
||||
field = re.sub(pattern, "-", field)
|
||||
|
||||
return field
|
||||
|
||||
|
||||
def duplicates(field):
|
||||
def duplicates(field, field_name):
|
||||
"""Remove duplicate metadata values."""
|
||||
|
||||
# Skip fields with missing values
|
||||
@ -128,7 +145,7 @@ def duplicates(field):
|
||||
return
|
||||
|
||||
# Try to split multi-value field on "||" separator
|
||||
values = field.split('||')
|
||||
values = field.split("||")
|
||||
|
||||
# Initialize an empty list to hold the de-duplicated values
|
||||
new_values = list()
|
||||
@ -139,10 +156,10 @@ def duplicates(field):
|
||||
if value not in new_values:
|
||||
new_values.append(value)
|
||||
else:
|
||||
print(f'Dropping duplicate value: {value}')
|
||||
print(f"Removing duplicate value ({field_name}): {value}")
|
||||
|
||||
# Create a new field consisting of all values joined with "||"
|
||||
new_field = '||'.join(new_values)
|
||||
new_field = "||".join(new_values)
|
||||
|
||||
return new_field
|
||||
|
||||
@ -169,10 +186,55 @@ def newlines(field):
|
||||
return
|
||||
|
||||
# Check for Unix line feed (LF)
|
||||
match = re.findall(r'\n', field)
|
||||
match = re.findall(r"\n", field)
|
||||
|
||||
if match:
|
||||
print(f'Removing newline: {field}')
|
||||
field = field.replace('\n', '')
|
||||
print(f"Removing newline: {field}")
|
||||
field = field.replace("\n", "")
|
||||
|
||||
return field
|
||||
|
||||
|
||||
def comma_space(field, field_name):
|
||||
"""Fix occurrences of commas missing a trailing space, for example:
|
||||
|
||||
Orth,Alan S.
|
||||
|
||||
This is a very common mistake in author and citation fields.
|
||||
|
||||
Return string with a space added.
|
||||
"""
|
||||
|
||||
# Skip fields with missing values
|
||||
if pd.isna(field):
|
||||
return
|
||||
|
||||
# Check for comma followed by a word character
|
||||
match = re.findall(r",\w", field)
|
||||
|
||||
if match:
|
||||
print(f"Adding space after comma ({field_name}): {field}")
|
||||
field = re.sub(r",(\w)", r", \1", field)
|
||||
|
||||
return field
|
||||
|
||||
|
||||
def normalize_unicode(field, field_name):
|
||||
"""Fix occurrences of decomposed Unicode characters by normalizing them
|
||||
with NFC to their canonical forms, for example:
|
||||
|
||||
Ouédraogo, Mathieu → Ouédraogo, Mathieu
|
||||
|
||||
Return normalized string.
|
||||
"""
|
||||
|
||||
# Skip fields with missing values
|
||||
if pd.isna(field):
|
||||
return
|
||||
|
||||
# Check if the current string is using normalized Unicode (NFC)
|
||||
if not is_nfc(field):
|
||||
print(f"Normalizing Unicode ({field_name}): {field}")
|
||||
field = normalize("NFC", field)
|
||||
|
||||
return field
|
||||
|
14
csv_metadata_quality/util.py
Normal file
14
csv_metadata_quality/util.py
Normal file
@ -0,0 +1,14 @@
|
||||
def is_nfc(field):
|
||||
"""Utility function to check whether a string is using normalized Unicode.
|
||||
Python's built-in unicodedata library has the is_normalized() function, but
|
||||
it was only introduced in Python 3.8. By using a simple utility function we
|
||||
are able to run on Python >= 3.6 again.
|
||||
|
||||
See: https://docs.python.org/3/library/unicodedata.html
|
||||
|
||||
Return boolean.
|
||||
"""
|
||||
|
||||
from unicodedata import normalize
|
||||
|
||||
return field == normalize("NFC", field)
|
@ -1 +1 @@
|
||||
VERSION = '0.2.1'
|
||||
VERSION = "0.4.3"
|
||||
|
@ -1,4 +1,4 @@
|
||||
dc.contributor.author,birthdate,dc.identifier.issn,dc.identifier.isbn,dc.language.iso,dc.subject,cg.coverage.country,filename
|
||||
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,,,,,,
|
||||
@ -13,8 +13,8 @@ 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 639-2 language,2019-07-29,,,jp,,,
|
||||
Invalid ISO 639-3 language,2019-07-29,,,chi,,,
|
||||
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
|
||||
@ -23,3 +23,9 @@ 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||,,,,,
|
||||
|
|
1211
poetry.lock
generated
Normal file
1211
poetry.lock
generated
Normal file
File diff suppressed because it is too large
Load Diff
31
pyproject.toml
Normal file
31
pyproject.toml
Normal file
@ -0,0 +1,31 @@
|
||||
[tool.poetry]
|
||||
name = "csv-metadata-quality"
|
||||
version = "0.4.3"
|
||||
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.dependencies]
|
||||
python = "^3.8"
|
||||
pandas = "^1.0.4"
|
||||
python-stdnum = "^1.13"
|
||||
xlrd = "^1.2.0"
|
||||
requests = "^2.23.0"
|
||||
requests-cache = "^0.5.2"
|
||||
pycountry = "^19.8.18"
|
||||
langid = "^1.1.6"
|
||||
|
||||
[tool.poetry.dev-dependencies]
|
||||
pytest = "^6.1.1"
|
||||
ipython = { version = "^7.18.1", python = "^3.7" }
|
||||
flake8 = "^3.8.4"
|
||||
pytest-clarity = "^0.3.0-alpha.0"
|
||||
black = "20.8b1"
|
||||
isort = "^5.5.4"
|
||||
csvkit = "^1.0.5"
|
||||
|
||||
[build-system]
|
||||
requires = ["poetry>=0.12"]
|
||||
build-backend = "poetry.masonry.api"
|
@ -1,5 +1,5 @@
|
||||
[pytest]
|
||||
addopts= -rsxX -s -v --strict --capture=sys
|
||||
addopts= -rsxX -s -v --strict-markers --capture=sys
|
||||
filterwarnings =
|
||||
error::UserWarning
|
||||
ignore:.*U.* is deprecated:DeprecationWarning
|
||||
|
@ -1,32 +1,71 @@
|
||||
-i https://pypi.org/simple
|
||||
atomicwrites==1.3.0
|
||||
attrs==19.1.0
|
||||
backcall==0.1.0
|
||||
decorator==4.4.0
|
||||
entrypoints==0.3
|
||||
flake8==3.7.8
|
||||
importlib-metadata==0.19
|
||||
ipython-genutils==0.2.0
|
||||
ipython==7.7.0
|
||||
jedi==0.14.1
|
||||
agate==1.6.1
|
||||
agate-dbf==0.2.2
|
||||
agate-excel==0.2.3
|
||||
agate-sql==0.5.5
|
||||
appdirs==1.4.4
|
||||
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
|
||||
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"
|
||||
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"
|
||||
ipython-genutils==0.2.0; python_version >= "3.7" and python_version < "4.0"
|
||||
isodate==0.6.0
|
||||
isort==5.7.0
|
||||
jdcal==1.4.1
|
||||
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
|
||||
more-itertools==7.2.0
|
||||
packaging==19.1
|
||||
parso==0.5.1
|
||||
pexpect==4.7.0 ; sys_platform != 'win32'
|
||||
pickleshare==0.7.5
|
||||
pluggy==0.12.0
|
||||
prompt-toolkit==2.0.9
|
||||
ptyprocess==0.6.0
|
||||
py==1.8.0
|
||||
pycodestyle==2.5.0
|
||||
pyflakes==2.1.1
|
||||
pygments==2.4.2
|
||||
pyparsing==2.4.2
|
||||
pytest-clarity==0.2.0a1
|
||||
pytest==5.0.1
|
||||
six==1.12.0
|
||||
mypy-extensions==0.4.3
|
||||
numpy==1.19.5
|
||||
openpyxl==3.0.6
|
||||
packaging==20.8
|
||||
pandas==1.2.1
|
||||
parsedatetime==2.6
|
||||
parso==0.8.1; python_version >= "3.7" and python_version < "4.0"
|
||||
pathspec==0.8.1
|
||||
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"
|
||||
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
|
||||
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
|
||||
pytimeparse==1.1.8
|
||||
pytz==2020.5
|
||||
regex==2020.11.13
|
||||
requests==2.25.1
|
||||
requests-cache==0.5.2
|
||||
six==1.15.0
|
||||
sqlalchemy==1.3.22
|
||||
termcolor==1.1.0
|
||||
traitlets==4.3.2
|
||||
wcwidth==0.1.7
|
||||
zipp==0.5.2
|
||||
text-unidecode==1.3
|
||||
toml==0.10.2
|
||||
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
|
||||
|
@ -1,16 +1,15 @@
|
||||
-i https://pypi.org/simple
|
||||
-e .
|
||||
certifi==2019.6.16
|
||||
chardet==3.0.4
|
||||
idna==2.8
|
||||
numpy==1.17.0
|
||||
pandas==0.25.0
|
||||
pycountry==19.7.15
|
||||
python-dateutil==2.8.0
|
||||
python-stdnum==1.11
|
||||
pytz==2019.2
|
||||
requests-cache==0.5.0
|
||||
requests==2.22.0
|
||||
six==1.12.0
|
||||
urllib3==1.25.3
|
||||
certifi==2020.12.5
|
||||
chardet==4.0.0
|
||||
idna==2.10
|
||||
langid==1.1.6
|
||||
numpy==1.19.5
|
||||
pandas==1.2.1
|
||||
pycountry==19.8.18
|
||||
python-dateutil==2.8.1
|
||||
python-stdnum==1.15
|
||||
pytz==2020.5
|
||||
requests==2.25.1
|
||||
requests-cache==0.5.2
|
||||
six==1.15.0
|
||||
urllib3==1.26.2
|
||||
xlrd==1.2.0
|
||||
|
6
setup.cfg
Normal file
6
setup.cfg
Normal file
@ -0,0 +1,6 @@
|
||||
[isort]
|
||||
multi_line_output=3
|
||||
include_trailing_comma=True
|
||||
force_grid_wrap=0
|
||||
use_parentheses=True
|
||||
line_length=88
|
26
setup.py
26
setup.py
@ -4,16 +4,17 @@ with open("README.md", "r") as fh:
|
||||
long_description = fh.read()
|
||||
|
||||
install_requires = [
|
||||
'pandas',
|
||||
'python-stdnum',
|
||||
'requests',
|
||||
'requests-cache',
|
||||
'pycountry'
|
||||
"pandas",
|
||||
"python-stdnum",
|
||||
"requests",
|
||||
"requests-cache",
|
||||
"pycountry",
|
||||
"langid",
|
||||
]
|
||||
|
||||
setuptools.setup(
|
||||
name="csv-metadata-quality",
|
||||
version="0.2.1",
|
||||
version="0.4.3",
|
||||
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.",
|
||||
@ -22,17 +23,16 @@ setuptools.setup(
|
||||
long_description_content_type="text/markdown",
|
||||
url="https://github.com/alanorth/csv-metadata-quality",
|
||||
classifiers=[
|
||||
"Programming Language :: Python :: 3.6",
|
||||
"Programming Language :: Python :: 3.7",
|
||||
"Programming Language :: Python :: 3.8",
|
||||
"Programming Language :: Python :: 3.9",
|
||||
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
|
||||
"Operating System :: OS Independent",
|
||||
"Development Status :: 4 - Beta"
|
||||
"Development Status :: 4 - Beta",
|
||||
],
|
||||
packages=['csv_metadata_quality'],
|
||||
packages=["csv_metadata_quality"],
|
||||
entry_points={
|
||||
'console_scripts': [
|
||||
'csv-metadata-quality = csv_metadata_quality.__main__:main'
|
||||
]
|
||||
"console_scripts": ["csv-metadata-quality = csv_metadata_quality.__main__:main"]
|
||||
},
|
||||
install_requires=install_requires
|
||||
install_requires=install_requires,
|
||||
)
|
||||
|
@ -1,21 +1,24 @@
|
||||
import pandas as pd
|
||||
|
||||
import csv_metadata_quality.check as check
|
||||
import csv_metadata_quality.experimental as experimental
|
||||
|
||||
|
||||
def test_check_invalid_issn(capsys):
|
||||
'''Test checking invalid ISSN.'''
|
||||
"""Test checking invalid ISSN."""
|
||||
|
||||
value = '2321-2302'
|
||||
value = "2321-2302"
|
||||
|
||||
check.issn(value)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Invalid ISSN: {value}\n'
|
||||
assert captured.out == f"Invalid ISSN: {value}\n"
|
||||
|
||||
|
||||
def test_check_valid_issn():
|
||||
'''Test checking valid ISSN.'''
|
||||
"""Test checking valid ISSN."""
|
||||
|
||||
value = '0024-9319'
|
||||
value = "0024-9319"
|
||||
|
||||
result = check.issn(value)
|
||||
|
||||
@ -23,20 +26,20 @@ def test_check_valid_issn():
|
||||
|
||||
|
||||
def test_check_invalid_isbn(capsys):
|
||||
'''Test checking invalid ISBN.'''
|
||||
"""Test checking invalid ISBN."""
|
||||
|
||||
value = '99921-58-10-6'
|
||||
value = "99921-58-10-6"
|
||||
|
||||
check.isbn(value)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Invalid ISBN: {value}\n'
|
||||
assert captured.out == f"Invalid ISBN: {value}\n"
|
||||
|
||||
|
||||
def test_check_valid_isbn():
|
||||
'''Test checking valid ISBN.'''
|
||||
"""Test checking valid ISBN."""
|
||||
|
||||
value = '99921-58-10-7'
|
||||
value = "99921-58-10-7"
|
||||
|
||||
result = check.isbn(value)
|
||||
|
||||
@ -44,86 +47,113 @@ def test_check_valid_isbn():
|
||||
|
||||
|
||||
def test_check_invalid_separators(capsys):
|
||||
'''Test checking invalid multi-value separators.'''
|
||||
"""Test checking invalid multi-value separators."""
|
||||
|
||||
value = 'Alan|Orth'
|
||||
value = "Alan|Orth"
|
||||
|
||||
check.separators(value)
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
check.separators(value, field_name)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Invalid multi-value separator: {value}\n'
|
||||
assert captured.out == f"Invalid multi-value separator ({field_name}): {value}\n"
|
||||
|
||||
|
||||
def test_check_unnecessary_separators(capsys):
|
||||
"""Test checking unnecessary multi-value separators."""
|
||||
|
||||
field = "Alan||Orth||"
|
||||
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
check.separators(field, field_name)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert (
|
||||
captured.out == f"Unnecessary multi-value separator ({field_name}): {field}\n"
|
||||
)
|
||||
|
||||
|
||||
def test_check_valid_separators():
|
||||
'''Test checking valid multi-value separators.'''
|
||||
"""Test checking valid multi-value separators."""
|
||||
|
||||
value = 'Alan||Orth'
|
||||
value = "Alan||Orth"
|
||||
|
||||
result = check.separators(value)
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
result = check.separators(value, field_name)
|
||||
|
||||
assert result == value
|
||||
|
||||
|
||||
def test_check_missing_date(capsys):
|
||||
'''Test checking missing date.'''
|
||||
"""Test checking missing date."""
|
||||
|
||||
value = None
|
||||
|
||||
check.date(value)
|
||||
field_name = "dc.date.issued"
|
||||
|
||||
check.date(value, field_name)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Missing date.\n'
|
||||
assert captured.out == f"Missing date ({field_name}).\n"
|
||||
|
||||
|
||||
def test_check_multiple_dates(capsys):
|
||||
'''Test checking multiple dates.'''
|
||||
"""Test checking multiple dates."""
|
||||
|
||||
value = '1990||1991'
|
||||
value = "1990||1991"
|
||||
|
||||
check.date(value)
|
||||
field_name = "dc.date.issued"
|
||||
|
||||
check.date(value, field_name)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Multiple dates not allowed: {value}\n'
|
||||
assert captured.out == f"Multiple dates not allowed ({field_name}): {value}\n"
|
||||
|
||||
|
||||
def test_check_invalid_date(capsys):
|
||||
'''Test checking invalid ISO8601 date.'''
|
||||
"""Test checking invalid ISO8601 date."""
|
||||
|
||||
value = '1990-0'
|
||||
value = "1990-0"
|
||||
|
||||
check.date(value)
|
||||
field_name = "dc.date.issued"
|
||||
|
||||
check.date(value, field_name)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Invalid date: {value}\n'
|
||||
assert captured.out == f"Invalid date ({field_name}): {value}\n"
|
||||
|
||||
|
||||
def test_check_valid_date():
|
||||
'''Test checking valid ISO8601 date.'''
|
||||
"""Test checking valid ISO8601 date."""
|
||||
|
||||
value = '1990'
|
||||
value = "1990"
|
||||
|
||||
result = check.date(value)
|
||||
field_name = "dc.date.issued"
|
||||
|
||||
result = check.date(value, field_name)
|
||||
|
||||
assert result == value
|
||||
|
||||
|
||||
def test_check_suspicious_characters(capsys):
|
||||
'''Test checking for suspicious characters.'''
|
||||
"""Test checking for suspicious characters."""
|
||||
|
||||
value = 'foreˆt'
|
||||
value = "foreˆt"
|
||||
|
||||
field_name = 'dc.contributor.author'
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
check.suspicious_characters(value, field_name)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Suspicious character ({field_name}): ˆt\n'
|
||||
assert captured.out == f"Suspicious character ({field_name}): ˆt\n"
|
||||
|
||||
|
||||
def test_check_valid_iso639_2_language():
|
||||
'''Test valid ISO 639-2 language.'''
|
||||
def test_check_valid_iso639_1_language():
|
||||
"""Test valid ISO 639-1 (alpha 2) language."""
|
||||
|
||||
value = 'ja'
|
||||
value = "ja"
|
||||
|
||||
result = check.language(value)
|
||||
|
||||
@ -131,65 +161,65 @@ def test_check_valid_iso639_2_language():
|
||||
|
||||
|
||||
def test_check_valid_iso639_3_language():
|
||||
'''Test invalid ISO 639-3 language.'''
|
||||
"""Test valid ISO 639-3 (alpha 3) language."""
|
||||
|
||||
value = 'eng'
|
||||
value = "eng"
|
||||
|
||||
result = check.language(value)
|
||||
|
||||
assert result == value
|
||||
|
||||
|
||||
def test_check_invalid_iso639_2_language(capsys):
|
||||
'''Test invalid ISO 639-2 language.'''
|
||||
def test_check_invalid_iso639_1_language(capsys):
|
||||
"""Test invalid ISO 639-1 (alpha 2) language."""
|
||||
|
||||
value = 'jp'
|
||||
value = "jp"
|
||||
|
||||
check.language(value)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Invalid ISO 639-2 language: {value}\n'
|
||||
assert captured.out == f"Invalid ISO 639-1 language: {value}\n"
|
||||
|
||||
|
||||
def test_check_invalid_iso639_3_language(capsys):
|
||||
'''Test invalid ISO 639-3 language.'''
|
||||
"""Test invalid ISO 639-3 (alpha 3) language."""
|
||||
|
||||
value = 'chi'
|
||||
value = "chi"
|
||||
|
||||
check.language(value)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Invalid ISO 639-3 language: {value}\n'
|
||||
assert captured.out == f"Invalid ISO 639-3 language: {value}\n"
|
||||
|
||||
|
||||
def test_check_invalid_language(capsys):
|
||||
'''Test invalid language.'''
|
||||
"""Test invalid language."""
|
||||
|
||||
value = 'Span'
|
||||
value = "Span"
|
||||
|
||||
check.language(value)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Invalid language: {value}\n'
|
||||
assert captured.out == f"Invalid language: {value}\n"
|
||||
|
||||
|
||||
def test_check_invalid_agrovoc(capsys):
|
||||
'''Test invalid AGROVOC subject.'''
|
||||
"""Test invalid AGROVOC subject."""
|
||||
|
||||
value = 'FOREST'
|
||||
field_name = 'dc.subject'
|
||||
value = "FOREST"
|
||||
field_name = "dc.subject"
|
||||
|
||||
check.agrovoc(value, field_name)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Invalid AGROVOC ({field_name}): {value}\n'
|
||||
assert captured.out == f"Invalid AGROVOC ({field_name}): {value}\n"
|
||||
|
||||
|
||||
def test_check_valid_agrovoc():
|
||||
'''Test valid AGROVOC subject.'''
|
||||
"""Test valid AGROVOC subject."""
|
||||
|
||||
value = 'FORESTS'
|
||||
field_name = 'dc.subject'
|
||||
value = "FORESTS"
|
||||
field_name = "dc.subject"
|
||||
|
||||
result = check.agrovoc(value, field_name)
|
||||
|
||||
@ -197,21 +227,89 @@ def test_check_valid_agrovoc():
|
||||
|
||||
|
||||
def test_check_uncommon_filename_extension(capsys):
|
||||
'''Test uncommon filename extension.'''
|
||||
"""Test uncommon filename extension."""
|
||||
|
||||
value = 'file.pdf.lck'
|
||||
value = "file.pdf.lck"
|
||||
|
||||
check.filename_extension(value)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert captured.out == f'Filename with uncommon extension: {value}\n'
|
||||
assert captured.out == f"Filename with uncommon extension: {value}\n"
|
||||
|
||||
|
||||
def test_check_common_filename_extension():
|
||||
'''Test common filename extension.'''
|
||||
"""Test common filename extension."""
|
||||
|
||||
value = 'file.pdf'
|
||||
value = "file.pdf"
|
||||
|
||||
result = check.filename_extension(value)
|
||||
|
||||
assert result == value
|
||||
|
||||
|
||||
def test_check_incorrect_iso_639_1_language(capsys):
|
||||
"""Test incorrect ISO 639-1 language, as determined by comparing the item's language field with the actual language predicted in the item's title."""
|
||||
|
||||
title = "A randomised vaccine field trial in Kenya demonstrates protection against wildebeest-associated malignant catarrhal fever in cattle"
|
||||
language = "es"
|
||||
|
||||
# Create a dictionary to mimic Pandas series
|
||||
row = {"dc.title": title, "dc.language.iso": language}
|
||||
series = pd.Series(row)
|
||||
|
||||
experimental.correct_language(series)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert (
|
||||
captured.out
|
||||
== f"Possibly incorrect language {language} (detected en): {title}\n"
|
||||
)
|
||||
|
||||
|
||||
def test_check_incorrect_iso_639_3_language(capsys):
|
||||
"""Test incorrect ISO 639-3 language, as determined by comparing the item's language field with the actual language predicted in the item's title."""
|
||||
|
||||
title = "A randomised vaccine field trial in Kenya demonstrates protection against wildebeest-associated malignant catarrhal fever in cattle"
|
||||
language = "spa"
|
||||
|
||||
# Create a dictionary to mimic Pandas series
|
||||
row = {"dc.title": title, "dc.language.iso": language}
|
||||
series = pd.Series(row)
|
||||
|
||||
experimental.correct_language(series)
|
||||
|
||||
captured = capsys.readouterr()
|
||||
assert (
|
||||
captured.out
|
||||
== f"Possibly incorrect language {language} (detected eng): {title}\n"
|
||||
)
|
||||
|
||||
|
||||
def test_check_correct_iso_639_1_language():
|
||||
"""Test correct ISO 639-1 language, as determined by comparing the item's language field with the actual language predicted in the item's title."""
|
||||
|
||||
title = "A randomised vaccine field trial in Kenya demonstrates protection against wildebeest-associated malignant catarrhal fever in cattle"
|
||||
language = "en"
|
||||
|
||||
# Create a dictionary to mimic Pandas series
|
||||
row = {"dc.title": title, "dc.language.iso": language}
|
||||
series = pd.Series(row)
|
||||
|
||||
result = experimental.correct_language(series)
|
||||
|
||||
assert result == language
|
||||
|
||||
|
||||
def test_check_correct_iso_639_3_language():
|
||||
"""Test correct ISO 639-3 language, as determined by comparing the item's language field with the actual language predicted in the item's title."""
|
||||
|
||||
title = "A randomised vaccine field trial in Kenya demonstrates protection against wildebeest-associated malignant catarrhal fever in cattle"
|
||||
language = "eng"
|
||||
|
||||
# Create a dictionary to mimic Pandas series
|
||||
row = {"dc.title": title, "dc.language.iso": language}
|
||||
series = pd.Series(row)
|
||||
|
||||
result = experimental.correct_language(series)
|
||||
|
||||
assert result == language
|
||||
|
@ -2,57 +2,109 @@ import csv_metadata_quality.fix as fix
|
||||
|
||||
|
||||
def test_fix_leading_whitespace():
|
||||
'''Test fixing leading whitespace.'''
|
||||
"""Test fixing leading whitespace."""
|
||||
|
||||
value = ' Alan'
|
||||
value = " Alan"
|
||||
|
||||
assert fix.whitespace(value) == 'Alan'
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
assert fix.whitespace(value, field_name) == "Alan"
|
||||
|
||||
|
||||
def test_fix_trailing_whitespace():
|
||||
'''Test fixing trailing whitespace.'''
|
||||
"""Test fixing trailing whitespace."""
|
||||
|
||||
value = 'Alan '
|
||||
value = "Alan "
|
||||
|
||||
assert fix.whitespace(value) == 'Alan'
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
assert fix.whitespace(value, field_name) == "Alan"
|
||||
|
||||
|
||||
def test_fix_excessive_whitespace():
|
||||
'''Test fixing excessive whitespace.'''
|
||||
"""Test fixing excessive whitespace."""
|
||||
|
||||
value = 'Alan Orth'
|
||||
value = "Alan Orth"
|
||||
|
||||
assert fix.whitespace(value) == 'Alan Orth'
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
assert fix.whitespace(value, field_name) == "Alan Orth"
|
||||
|
||||
|
||||
def test_fix_invalid_separators():
|
||||
'''Test fixing invalid multi-value separators.'''
|
||||
"""Test fixing invalid multi-value separators."""
|
||||
|
||||
value = 'Alan|Orth'
|
||||
value = "Alan|Orth"
|
||||
|
||||
assert fix.separators(value) == 'Alan||Orth'
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
assert fix.separators(value, field_name) == "Alan||Orth"
|
||||
|
||||
|
||||
def test_fix_unnecessary_separators():
|
||||
"""Test fixing unnecessary multi-value separators."""
|
||||
|
||||
field = "Alan||Orth||"
|
||||
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
assert fix.separators(field, field_name) == "Alan||Orth"
|
||||
|
||||
|
||||
def test_fix_unnecessary_unicode():
|
||||
'''Test fixing unnecessary Unicode.'''
|
||||
"""Test fixing unnecessary Unicode."""
|
||||
|
||||
value = 'Alan Orth'
|
||||
value = "Alan Orth"
|
||||
|
||||
assert fix.unnecessary_unicode(value) == 'Alan Orth'
|
||||
assert fix.unnecessary_unicode(value) == "Alan Orth"
|
||||
|
||||
|
||||
def test_fix_duplicates():
|
||||
'''Test fixing duplicate metadata values.'''
|
||||
"""Test fixing duplicate metadata values."""
|
||||
|
||||
value = 'Kenya||Kenya'
|
||||
value = "Kenya||Kenya"
|
||||
|
||||
assert fix.duplicates(value) == 'Kenya'
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
assert fix.duplicates(value, field_name) == "Kenya"
|
||||
|
||||
|
||||
def test_fix_newlines():
|
||||
'''Test fixing newlines.'''
|
||||
"""Test fixing newlines."""
|
||||
|
||||
value = '''Ken
|
||||
ya'''
|
||||
value = """Ken
|
||||
ya"""
|
||||
|
||||
assert fix.newlines(value) == 'Kenya'
|
||||
assert fix.newlines(value) == "Kenya"
|
||||
|
||||
|
||||
def test_fix_comma_space():
|
||||
"""Test adding space after comma."""
|
||||
|
||||
value = "Orth,Alan S."
|
||||
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
assert fix.comma_space(value, field_name) == "Orth, Alan S."
|
||||
|
||||
|
||||
def test_fix_normalized_unicode():
|
||||
"""Test fixing a string that is already in its normalized (NFC) Unicode form."""
|
||||
|
||||
# string using the normalized canonical form of é
|
||||
value = "Ouédraogo, Mathieu"
|
||||
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
assert fix.normalize_unicode(value, field_name) == "Ouédraogo, Mathieu"
|
||||
|
||||
|
||||
def test_fix_decomposed_unicode():
|
||||
"""Test fixing a string that contains Unicode string."""
|
||||
|
||||
# string using the decomposed form of é
|
||||
value = "Ouédraogo, Mathieu"
|
||||
|
||||
field_name = "dc.contributor.author"
|
||||
|
||||
assert fix.normalize_unicode(value, field_name) == "Ouédraogo, Mathieu"
|
||||
|
Reference in New Issue
Block a user