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

144 Commits

Author SHA1 Message Date
cbf94490f2 Version 0.4.3 2021-01-26 15:22:40 +02:00
f3d0d5ef07 setup.py: Remove Python 3.6
I actually removed Python 3.6 support a few weeks ago after updating
to Pandas 1.2.0, but forgot to update this.
2021-01-26 15:22:08 +02:00
4b7b99c94c CHANGELOG.md: Add note about multi-value separators 2021-01-26 15:20:22 +02:00
df670e81b9 README.md: Use badge from my Drone CI
All checks were successful
continuous-integration/drone/push Build is passing
I'm not using SourceHut anymore.
2021-01-26 14:38:50 +02:00
ae357d8c6c Revert "Update requirements"
This reverts commit ca80340f7a717a9c8cd1780ba12e5bd366c9900d.

Nope, we still need the --without-hashes because this still fails
on Python 3.7, but not 3.8 or 3.9. From looking around it seems
that nobody can agree whether poetry should handle this, pip should
handle it, or upstream projects should pin their dependencies.
2021-01-26 14:15:31 +02:00
ca80340f7a Update requirements
Some checks failed
continuous-integration/drone/push Build is failing
Generated with poetry export:

    $ poetry export -f requirements.txt > requirements.txt
    $ poetry export --dev -f requirements.txt > requirements-dev.txt

Trying to see if we no longer need --without-hashes since we don't
support Python 3.6 anymore.
2021-01-26 11:46:05 +02:00
cc1743b86d Remove .build.yml
I will just use GitHub Actions and Drone.
2021-01-26 11:41:30 +02:00
bcb9885c6b 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 on Python 3.6 in Travis:

    ERROR: In --require-hashes mode, all requirements must have their versions pinned with ==.
2021-01-26 10:36:48 +02:00
b484b75178 poetry.lock: Run poetry update 2021-01-26 10:36:04 +02:00
d3880a9dfa Remove Python 3.6 support
All checks were successful
continuous-integration/drone/push Build is passing
Pandas 1.2.0 apparently requires Python 3.7.1+.
2021-01-03 15:51:53 +02:00
7edb8b19d7 tests/test_check.py: Reformat with black 2021-01-03 15:50:21 +02:00
a6709c7f82 Update requirements
Some checks failed
continuous-integration/drone/push Build is failing
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 on Python 3.6 in Travis:

    ERROR: In --require-hashes mode, all requirements must have their versions pinned with ==.
2021-01-03 15:42:00 +02:00
d489ea4609 poetry.lock: Run poetry update 2021-01-03 15:41:08 +02:00
96634cbb67 pytest.ini: Change --strict to --strict-markers
This is deprecated since pytest 6.2.0.

See: https://docs.pytest.org/en/stable/deprecations.html#the-strict-command-line-option
2021-01-03 15:40:14 +02:00
29e67a0887 Add tests for unnecessary multi-value separators 2021-01-03 15:37:18 +02:00
32cea2055f data/test.csv: Add unnecessary multi-value separator 2021-01-03 15:33:04 +02:00
0dc66c5c4e Expand check/fix for multi-value separators
I just came across some metadata that had unnecessary multi-value
separators at the end of a field, causing a blank value to be used.

For example: "Kenya||Tanzania||"
2021-01-03 15:30:03 +02:00
c26ad83534 .github: Test CLI invocation 2020-12-14 23:47:09 +02:00
72ca9d99bf setup.py: Add Python 3.9
[SKIP CI]
2020-12-14 23:44:35 +02:00
ae33a9b793 Add .drone.yml 2020-12-14 23:42:23 +02:00
fc0367bfc8 README.md: Update note about Python version 2020-12-08 10:52:24 +02:00
e33b285034 README.md: Add GitHub Actions badge 2020-12-08 10:48:31 +02:00
349fca03b8 .github/workflows/python-app.yml: Rename
This name is displayed in the badge so it should be something more
relevant.
2020-12-08 10:46:39 +02:00
52d8904870 Remove .travis.yml
They changed their free tier and I might as well use GitHub Actions
for ILRI stuff anyways.
2020-12-08 10:41:36 +02:00
971c69e535 Create python-app.yml
Try GitHub Actions for Python 3.8 using GitHub's Python example.
2020-12-08 10:38:52 +02:00
f8cc233e25 .travis.yml: Use Amazon Graviton2 ARM environment
These are the new hotness and should have faster build times.

See: https://blog.travis-ci.com/2020-09-11-arm-on-aws
2020-12-06 10:49:03 +02:00
aa7b7a9592 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 on Python 3.6 in Travis:

    ERROR: In --require-hashes mode, all requirements must have their versions pinned with ==.
2020-11-03 07:42:45 +02:00
57b455bde7 poetry.lock: Run poetry update 2020-11-03 07:40:56 +02:00
23b95fa368 .travis.yml: Use Ubuntu 20.04 "Focal" environment 2020-10-29 00:14:54 +03:00
6985f76aa3 .travis.yml: Bump Python versions
Test Python 3.9 now that it was released, and allow tests to fail
on nightly builds.
2020-10-29 00:14:36 +03:00
98a6a19e12 Update requirements-dev.txt
Generated with poetry export:

    $ poetry export --dev -f requirements.txt > requirements-dev.txt
2020-10-06 17:48:46 +03:00
f4914c414f Only install ipython on Python 3.7+ 2020-10-06 17:48:16 +03:00
d352fe8017 Update requirements
Generated with poetry export:

    $ poetry export -f requirements.txt > requirements.txt
    $ poetry export --dev -f requirements.txt > requirements-dev.txt
2020-10-06 17:21:33 +03:00
f13c360084 Update poetry package dependencies 2020-10-06 17:20:16 +03:00
7cfd4c0b59 csv_metadata_quality: Move scoped imports to global
According to PEP8 we should avoid scoped imports unless you have a
good reason. Here there are two cases where we do (issn and isbn),
but I will move the others to the global scope.
2020-10-06 17:11:39 +03:00
826509ddcf poetry.lock: Run poetry update
List of updated modules:

  - Updating numpy (1.19.1 -> 1.19.2)
  - Updating pygments (2.6.1 -> 2.7.1)
  - Updating pandas (1.1.1 -> 1.1.2)

All tests still pass according to pytest.
2020-09-26 12:18:23 +03:00
22b5c0f7a1 CHANGELOG.md: Add note about dependencies update 2020-09-08 15:04:40 +03:00
774e274b32 poetry.lock: Run poetry update
Update dependencies to latest version:

  - Updating attrs (19.3.0 -> 20.2.0)
  - Updating more-itertools (8.4.0 -> 8.5.0)
  - Updating openpyxl (3.0.4 -> 3.0.5)
  - Updating parso (0.7.0 -> 0.7.1)
  - Updating sqlalchemy (1.3.18 -> 1.3.19)
  - Updating urllib3 (1.25.9 -> 1.25.10)
  - Updating agate-dbf (0.2.1 -> 0.2.2)
  - Updating agate-sql (0.5.4 -> 0.5.5)
  - Updating jedi (0.17.1 -> 0.17.2)
  - Updating numpy (1.19.0 -> 1.19.1)
  - Updating prompt-toolkit (3.0.5 -> 3.0.7)
  - Updating regex (2020.6.8 -> 2020.7.14)
  - Updating traitlets (4.3.3 -> 5.0.4)
  - Updating ipython (7.16.1 -> 7.18.1)
  - Updating pandas (1.0.5 -> 1.1.1)
  - Updating python-stdnum (1.13 -> 1.14)

All tests still pass according to pytest.
2020-09-08 15:04:00 +03:00
db474a802f README.md: Use badge from travis-ci.com 2020-08-04 11:12:28 +03:00
e241f8461b CHANGELOG.md: Add notes 2020-07-06 14:10:46 +03:00
431e6331c8 csv_metadata_quality/check.py: Format with black 2020-07-06 14:10:19 +03:00
cb07d357d4 Version 0.4.2 2020-07-06 14:04:34 +03:00
65cd48a26f CHANGELOG.md: Update changes 2020-07-06 14:00:21 +03:00
0f883f640c Remove pipenv 2020-07-06 13:59:49 +03:00
f4c5c5781e README.md: Switch to poetry 2020-07-06 13:59:11 +03:00
6aa784ad8c Update requirements
Generated with poetry export:

    $ poetry export -f requirements.txt > requirements.txt
    $ poetry export --dev -f requirements.txt > requirements-dev.txt
2020-07-06 13:57:07 +03:00
7b8da94f41 poetry.lock: Update Python dependencies 2020-07-06 13:56:31 +03:00
2a1566af62 csv_metadata_quality/check.py: Parameterize AGROVOC request 2020-07-06 13:44:46 +03:00
5fcaa63bd5 csv_metadata_quality/check.py: Prune requests cache once
We only need to prune the requests cache once before using it, not
for every value we check.
2020-07-06 13:42:19 +03:00
aa9e23b46c pyproject.toml: Update license specifier
We need to use valid SPDX license identifiers.
2020-06-09 14:22:53 +03:00
73acb1661f Update requirements
Generated with poetry export:

    $ poetry export -f requirements.txt > requirements.txt
    $ poetry export --dev -f requirements.txt > requirements-dev.txt
2020-05-31 17:51:16 +03:00
2a068fddc4 .build.yml: Fix test 2020-05-31 17:44:37 +03:00
c6c2f13e88 .build.yml: Fix poetry install invocation
Poetry apparently installs dev dependencies by default.
2020-05-31 17:37:09 +03:00
56f16e37ed .build.yml: Use poetry in SourceHut CI 2020-05-31 17:35:04 +03:00
0c44b967b6 Add poetry project file and lock
I want to try to use poetry instead of pipenv because pipenv takes
forever to do dependency resolution sometimes. Also, I have had a
few issues with Python modules like black that don't have releases
other than pre-releases, and even including the project itself in
the dependencies (pip install -e . ...?). My initial experience is
that poetry handles this better.
2020-05-31 17:33:40 +03:00
8a267bb40b .travis.yml: Try to build with Python 3.8-dev
But allow failures.
2020-03-29 16:40:11 +03:00
8fda8f1ef1 Pipfile.lock: Run pipenv update
All tests still passing.
2020-03-20 16:22:04 +02:00
5e471813e8 CHANGELOG.md: Add note about python dependencies 2020-01-29 12:41:43 +02:00
79244b9ac3 Pipfile.lock: Run pipenv update 2020-01-29 12:39:12 +02:00
5e81a33482 CHANGELOG.md: Add note about field names 2020-01-16 12:37:11 +02:00
28b5996aa6 Output field name for more fixes and checks
This helps identify which field has the error.
2020-01-16 12:35:11 +02:00
40ba9bae6c README.md: Adjust heading size 2020-01-15 12:26:11 +02:00
0b2d211455 Version 0.4.1 2020-01-15 12:19:42 +02:00
7f1df0b47c Support Python 3.6 and 3.7 again 2020-01-15 12:19:17 +02:00
365ecda324 Add utility function to check normalization
Python's built-in unicodedata library includes the is_normalized()
function starting with Python 3.8. This utility function allows us
to do the same thing with earlier Python versions.

See: https://docs.python.org/3/library/unicodedata.html
2020-01-15 12:17:52 +02:00
550ce7fb7e .travis.yml: Only test Python 3.8
The Unicode normalization feature requires Python 3.8 because the
unicodedata.is_normalized() function only appears there. If I find
another way to check if a string is normalized without normalizing
it first I will drop the requirements back down to Python 3.6.

See: https://docs.python.org/3/library/unicodedata.html
2020-01-15 11:57:21 +02:00
705127fd28 Version 0.4.0 2020-01-15 11:44:56 +02:00
894e0a196d setup.py: Change Python requirements
The `unicodedata.is_normalized()` function requires Python 3.8.

See: https://docs.python.org/3/library/unicodedata.html
2020-01-15 11:43:25 +02:00
87181bc7b8 Run black, isort, and flake8. 2020-01-15 11:41:31 +02:00
8de5d862b6 CHANGELOG.md: Add note about Unicode normalization 2020-01-15 11:40:40 +02:00
49e3543878 Add Unicode normalization
This will check all strings for un-normalized Unicode characters.
Normalization is done using NFC. This includes tests and updated
sample data (data/test.csv).

See: https://withblue.ink/2019/03/11/why-you-need-to-normalize-unicode-strings.html
2020-01-15 11:37:54 +02:00
403b253762 CHANGELOG.md: Update python library versions 2020-01-15 10:58:44 +02:00
c5fbaf407a Update python requirements
Generated using pipenv:

  $ pipenv lock -r > requirements.txt
  $ pipenv lock -r -d > requirements-dev.txt
2020-01-15 10:51:58 +02:00
4f81f6c83c Pipfile.lock: Run pipenv update 2020-01-15 10:51:19 +02:00
4b9d1e060f setup.py: Add Python 3.8 classifier 2019-12-14 12:56:11 +02:00
c8a71e3143 Pipfile.lock: Run pipenv update 2019-12-14 12:53:39 +02:00
7964d98ca5 Pipfile: Specify exact version of black
Black only releases pre-release versions, which causes issues with
pipenv. Instead of always running pipenv with "--pre" and potenti-
ally letting in some other pre-release versions for other depende-
ncies, I would rather specify the latest black version explicitly.

See: https://github.com/psf/black/issues/517
See: https://github.com/microsoft/vscode-python/issues/5171
2019-12-14 12:41:28 +02:00
64ffc2f1da .travis.yml: Install packages from requirements.txt too 2019-11-14 23:42:28 +02:00
7b1bc29a92 .travis.yml: Try using pip instead of pipenv
The Pipfile knows it was created with Python 3.8, yet we're running
with multiple Python versions on Travis. I'm curious if would work
better to use pip to install dependencies instead of pipenv in this
case.
2019-11-14 23:37:25 +02:00
f0110d8e74 CHANGELOG.md: Add note about requirements 2019-11-14 23:30:26 +02:00
86498deee8 Update python requirements
Generated using pipenv:

  $ pipenv lock -r > requirements.txt
  $ pipenv lock -r -d > requirements-dev.txt
2019-11-14 23:28:42 +02:00
251647a15f CHANGELOG.md: Add TravisCI changes 2019-11-14 23:24:08 +02:00
0bd28e22ec .travis.yml: Test Python 3.8 2019-11-14 23:22:37 +02:00
63fdce7d13 .travis.yml: Use Ubuntu 18.04 "Bionic" 2019-11-14 23:22:19 +02:00
f068c0e16a CHANGELOG.md: Use Python 3.8.0 for pipenv 2019-11-14 23:11:43 +02:00
79b8f62a85 Use Python 3.8 for pipenv
Python 3.8.0 entered Arch Linux core repositories now and all tests
pass with Python 3.8.0 so it's time...
2019-11-14 23:10:20 +02:00
6c1e132531 CHANGELOG.md: Add unreleased changes 2019-11-14 09:19:19 +02:00
c0f3c866bd Pipfile.lock: Run pipenv update
Updates the following dependencies:

- numpy 1.17.2→1.17.4
- pandas 0.25.1→0.25.3
- flake8 3.7.8→3.7.9
- pytest 5.1.3→5.2.2
- black 19.3b0→19.10b0
2019-11-14 09:17:31 +02:00
36d0474b95 CHANGELOG.md: Move unreleased changes to v0.3.1 2019-10-01 17:11:52 +03:00
efdc3a841a Version 0.3.1 2019-10-01 17:11:13 +03:00
fd2ba6845d CHANGELOG.md: Update unreleased notes 2019-10-01 17:10:23 +03:00
e55380b4d5 csv_metadata_quality/fix.py: Harmonize language in fix output
We should always say if we're removing or replacing something.
2019-10-01 17:09:49 +03:00
85ae16d9b7 CHANGELOG.md: Add note about non-breaking spaces 2019-10-01 16:56:37 +03:00
c42f8b4812 csv_metadata_quality/fix.py: Replace non-breaking spaces
We should be replacing non-breaking spaces (U+00A0) with normal sp-
aces instead of removing them.
2019-10-01 16:55:04 +03:00
1c75608d54 README.md: Update introduction text
We should mention that this is not DSpace specific. Rather, it is
much more realistically Dublin Core specific.
2019-09-26 14:19:13 +03:00
0b15a8ed3b README.md: Remove TODO about lack of space after comma
This was added as an automatic global fix a few weeks ago.
2019-09-26 14:16:33 +03:00
9ca266f5f0 data/test.csv: Change birthdate column to dc.date.issued
More accurately reflects actual data we will be validating.
2019-09-26 14:15:48 +03:00
0d3f948708 CHANGELOG.md: Update comment about language validation 2019-09-26 14:14:57 +03:00
c04207fcfc CHANGELOG.md: Fix header formatting 2019-09-26 14:13:50 +03:00
9d4eceddc7 .build.yml: Enable experimental CLI checks on SourceHut 2019-09-26 14:11:35 +03:00
e15c98cccb Move unreleased changes to v0.3.0 2019-09-26 14:06:31 +03:00
93c4e1a993 Update python requirements
Generated using pipenv:

  $ pipenv lock -r > requirements.txt
  $ pipenv lock -r -d > requirements-dev.txt
2019-09-26 14:05:37 +03:00
9963b2bb64 Pipfile.lock: Run pipenv update 2019-09-26 14:04:50 +03:00
76291c1876 CHANGELOG.md: Add note about language validation 2019-09-26 14:03:18 +03:00
604bd5bda6 Reformat tests with black 2019-09-26 14:02:51 +03:00
e7c220039b README.md: Add note about experimental language validation 2019-09-26 13:59:50 +03:00
d7b5e378bc setup.py: Add langid 2019-09-26 13:49:32 +03:00
8435ee242d Experimental language detection using langid
Works decenty well assuming the title, abstract, and citation fields
are an accurate representation of the language as identified by the
language field. Handles ISO 639-1 (alpha 2) and ISO 639-3 (alpha 3)
values seamlessly.

This includes updated pipenv environment, test data, pytest tests
for both correct and incorrect ISO 639-1 and ISO 639-3 languages,
and a new command line option "-e".
2019-09-26 13:46:32 +03:00
7ac1c6f554 README.md: Update comment about ISO 639-3
The pycountry library is actually using ISO 639-3 apparently.

See: https://pypi.org/project/pycountry/
2019-09-26 07:51:41 +03:00
86d4623fd3 More ISO 639-1 and ISO 639-3 fixes
ISO 639-1 uses two-letter codes and ISO 639-3 uses three-letter codes.
Technically there ISO 639-2/T and ISO 639-2/B, which also uses three
letter codes, but those are not supported by the pycountry library
so I won't even worry about them.

See: https://en.wikipedia.org/wiki/List_of_ISO_639-1_codes
2019-09-26 07:44:39 +03:00
ddbe970342 data/test.csv: Update titles of language tests
ISO 639-1 is alpha 2 and ISO 639-3 is alpha 3.

See: https://en.wikipedia.org/wiki/List_of_ISO_639-1_codes
2019-09-26 07:40:27 +03:00
31c78ca6f3 data/test.csv: Rename contributor column to title
This makes more sense as a description of each test and the titles
are obviously not authors.
2019-09-26 05:50:40 +03:00
154d05b5e2 CHANGELOG.md: Update notes 2019-09-24 18:55:05 +03:00
186f146edb Pipfile.lock: Run pipenv update
Synchronizes state with the Pipfile and brings some new deps.
2019-09-24 18:54:49 +03:00
a4cb301943 CHANGELOG.md: Add note about csvkit 2019-09-24 18:49:20 +03:00
219e37526d Pipfile: Add csvkit to dev requirements
Used to inspect CSV files during testing and development.
2019-09-24 18:48:01 +03:00
f304ca6a33 csv_metadata_quality/app.py: Use simpler column iteration
I don't know where I got the other one...
2019-09-21 17:19:39 +03:00
3d5c8bdf5d CHANGELOG.md: Add notes about updated python packages 2019-09-11 16:45:39 +03:00
480956d54d Pipfile.lock: Run pipenv update 2019-09-11 16:45:16 +03:00
d9fc09f121 Fix references to ISO 639
It turns out that ISO 639-1 is the two-letter codes, and ISO 639-2
is the three-letter codes, aka alpha2 and alpha3.

See: https://en.wikipedia.org/wiki/List_of_ISO_639-1_codes
2019-09-11 16:36:53 +03:00
b5899001b7 CHANGELOG.md: Add note about black and isort 2019-08-29 01:26:11 +03:00
c92977d1ca Update requirements-dev.txt
Generated with:

  $ pipenv lock -r -d > requirements-dev.txt
2019-08-29 01:25:14 +03:00
280a99c8a8 Sort imports with isort
See: https://sourcery.ai/blog/python-best-practices/
2019-08-29 01:15:04 +03:00
0388145b81 Add configuration for isort
See: https://sourcery.ai/blog/python-best-practices/
2019-08-29 01:14:31 +03:00
d97dcd19db Format with black 2019-08-29 01:10:39 +03:00
b375f0e895 Add black and isort to pipenv dev dependencies
These do a very opinionated automatic formatting and validation of
code.

See: https://sourcery.ai/blog/python-best-practices/
2019-08-29 01:08:38 +03:00
865c61d316 Add note about updated python dependencies 2019-08-28 21:02:21 +03:00
3b2ba57b75 Update python requirements
Generated using pipenv:

  $ pipenv lock -r > requirements.txt
  $ pipenv lock -r -d > requirements-dev.txt
2019-08-28 21:01:48 +03:00
2805c556a9 Pipfile.lock: Run pipenv update
Brings numpy 1.17.1, pandas 0.25.1, requests-cache 0.5.2, and pandas
0.25.1.
2019-08-28 20:58:35 +03:00
c354a3687c Release version 0.2.2 2019-08-28 00:10:17 +03:00
07f80cb37f tests/test_fix.py: Add test for missing space after comma 2019-08-28 00:08:56 +03:00
89d72540f1 data/test.csv: Add sample for missing space after comma 2019-08-28 00:08:26 +03:00
81190d56bb Add fix for missing space after commas
This happens in names very often, for example in the contributor
and citation fields. I will limit this to those fields for now and
hide this fix behind the "unsafe fixes" option until I test it more.
2019-08-28 00:05:52 +03:00
2af714fb05 README.md: Add a handful of TODOs 2019-08-27 00:12:41 +03:00
cc863a6bdd CHANGELOG.md: Add note about excluding fields 2019-08-27 00:11:22 +03:00
113e7cd8b6 csv_metadata_quality/app.py: Add ability to skip fields
The user may want to skip the checking and fixing of certain fields
in the input file.
2019-08-27 00:10:07 +03:00
bd984f3db5 README.md: Update TravisCI badge 2019-08-22 15:07:03 +03:00
3f4e84a638 README.md: Use ILRI GitHub remote 2019-08-22 14:54:12 +03:00
c52b3ed131 CHANGELOG.md: Add note about AGROVOC 2019-08-21 16:37:49 +03:00
884e8f970d csv_metadata_quality/check.py: Simplify AGROVOC check
I recycled this code from a separate agrovoc-lookup.py script that
checks lines in a text file to see if they are valid AGROVOC terms
or not. There I was concerned about skipping comments or something
I think, but we don't need to check that here. We simply check the
term that is in the field and inform the user if it's valid or not.
2019-08-21 16:35:29 +03:00
6d02f5026a CHANGELOG.md: Add note about date checks 2019-08-21 15:35:46 +03:00
e7cb8920db tests/test_check.py: Update date tests 2019-08-21 15:34:52 +03:00
ed5612fbcf Add column name to output in date checks
This makes it easier to understand where the error is in case a CSV
has multiple date fields, for example:

    Missing date (dc.date.issued).
    Missing date (dc.date.issued[]).

If you have 126 items and you get 126 "Missing date" messages then
it's likely that 100 of the items have dates in one field, and the
others have dates in other field.
2019-08-21 15:31:12 +03:00
3247495cee CHANGELOG.md: Remove extra space 2019-08-11 10:43:27 +03:00
25 changed files with 2172 additions and 716 deletions

View File

@ -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
View 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
View 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

View File

@ -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

View File

@ -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
View File

@ -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
View File

@ -1,376 +0,0 @@
{
"_meta": {
"hash": {
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},
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"requires": {
"python_version": "3.7"
},
"sources": [
{
"name": "pypi",
"url": "https://pypi.org/simple",
"verify_ssl": true
}
]
},
"default": {
"certifi": {
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"version": "==2019.6.16"
},
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"version": "==3.0.4"
},
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"path": "."
},
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"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"
}
}
}

View File

@ -1,34 +1,36 @@
# CSV Metadata Quality [![Build Status](https://travis-ci.org/alanorth/csv-metadata-quality.svg?branch=master)](https://travis-ci.org/alanorth/csv-metadata-quality) [![builds.sr.ht status](https://builds.sr.ht/~alanorth/csv-metadata-quality.svg)](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 ![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.
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 nottechnically 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).

View File

@ -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()

View File

@ -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)

View File

@ -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

View 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

View File

@ -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

View 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)

View File

@ -1 +1 @@
VERSION = '0.2.1'
VERSION = "0.4.3"

View File

@ -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||,,,,,

1 dc.contributor.author dc.title birthdate dc.date.issued dc.identifier.issn dc.identifier.isbn dc.language.iso dc.subject cg.coverage.country filename
2 Leading space 2019-07-29
3 Trailing space 2019-07-29
4 Excessive space 2019-07-29
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 639-2 language Invalid ISO 639-1 (alpha 2) language 2019-07-29 jp
17 Invalid ISO 639-3 language 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
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

1211
poetry.lock generated Normal file

File diff suppressed because it is too large Load Diff

31
pyproject.toml Normal file
View 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"

View File

@ -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

View File

@ -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

View File

@ -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
View File

@ -0,0 +1,6 @@
[isort]
multi_line_output=3
include_trailing_comma=True
force_grid_wrap=0
use_parentheses=True
line_length=88

View File

@ -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,
)

View File

@ -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

View File

@ -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"