1
0
mirror of https://github.com/ilri/csv-metadata-quality.git synced 2025-05-09 22:56:01 +02:00

41 Commits

Author SHA1 Message Date
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
18 changed files with 744 additions and 266 deletions

View File

@ -13,7 +13,7 @@ tasks:
- 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
pipenv run csv-metadata-quality -i data/test.csv -o /tmp/test.csv -e -u --agrovoc-fields dc.subject,cg.coverage.country
environment:
PIPENV_NOSPIN: 'True'
PIPENV_HIDE_EMOJIS: 'True'

View File

@ -4,6 +4,23 @@ 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).
## [0.3.1] - 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)

View File

@ -8,6 +8,9 @@ pytest = "*"
ipython = "*"
flake8 = "*"
pytest-clarity = "*"
black = "*"
isort = "*"
csvkit = "*"
[packages]
pandas = "*"
@ -17,6 +20,7 @@ requests = "*"
requests-cache = "*"
pycountry = "*"
csv-metadata-quality = {editable = true,path = "."}
langid = "*"
[requires]
python_version = "3.7"

315
Pipfile.lock generated
View File

@ -1,7 +1,7 @@
{
"_meta": {
"hash": {
"sha256": "f8f0a9f208ec41f4d8183ecfc68356b40674b083b2f126c37468b3c9533ba5df"
"sha256": "59562d8c59eb09e23b49475d6901687edbf605f5b84e283e90cc8e2de518641f"
},
"pipfile-spec": 6,
"requires": {
@ -18,10 +18,10 @@
"default": {
"certifi": {
"hashes": [
"sha256:046832c04d4e752f37383b628bc601a7ea7211496b4638f6514d0e5b9acc4939",
"sha256:945e3ba63a0b9f577b1395204e13c3a231f9bc0223888be653286534e5873695"
"sha256:e4f3620cfea4f83eedc95b24abd9cd56f3c4b146dd0177e83a21b4eb49e21e50",
"sha256:fd7c7c74727ddcf00e9acd26bba8da604ffec95bf1c2144e67aff7a8b50e6cef"
],
"version": "==2019.6.16"
"version": "==2019.9.11"
},
"chardet": {
"hashes": [
@ -41,53 +41,61 @@
],
"version": "==2.8"
},
"langid": {
"hashes": [
"sha256:044bcae1912dab85c33d8e98f2811b8f4ff1213e5e9a9e9510137b84da2cb293"
],
"index": "pypi",
"version": "==1.1.6"
},
"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"
"sha256:05dbfe72684cc14b92568de1bc1f41e5f62b00f714afc9adee42f6311738091f",
"sha256:0d82cb7271a577529d07bbb05cb58675f2deb09772175fab96dc8de025d8ac05",
"sha256:10132aa1fef99adc85a905d82e8497a580f83739837d7cbd234649f2e9b9dc58",
"sha256:12322df2e21f033a60c80319c25011194cd2a21294cc66fee0908aeae2c27832",
"sha256:16f19b3aa775dddc9814e02a46b8e6ae6a54ed8cf143962b4e53f0471dbd7b16",
"sha256:3d0b0989dd2d066db006158de7220802899a1e5c8cf622abe2d0bd158fd01c2c",
"sha256:438a3f0e7b681642898fd7993d38e2bf140a2d1eafaf3e89bb626db7f50db355",
"sha256:5fd214f482ab53f2cea57414c5fb3e58895b17df6e6f5bca5be6a0bb6aea23bb",
"sha256:73615d3edc84dd7c4aeb212fa3748fb83217e00d201875a47327f55363cef2df",
"sha256:7bd355ad7496f4ce1d235e9814ec81ee3d28308d591c067ce92e49f745ba2c2f",
"sha256:7d077f2976b8f3de08a0dcf5d72083f4af5411e8fddacd662aae27baa2601196",
"sha256:a4092682778dc48093e8bda8d26ee8360153e2047826f95a3f5eae09f0ae3abf",
"sha256:b458de8624c9f6034af492372eb2fee41a8e605f03f4732f43fc099e227858b2",
"sha256:e70fc8ff03a961f13363c2c95ef8285e0cf6a720f8271836f852cc0fa64e97c8",
"sha256:ee8e9d7cad5fe6dde50ede0d2e978d81eafeaa6233fb0b8719f60214cf226578",
"sha256:f4a4f6aba148858a5a5d546a99280f71f5ee6ec8182a7d195af1a914195b21a2"
],
"version": "==1.17.0"
"version": "==1.17.2"
},
"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"
"sha256:18d91a9199d1dfaa01ad645f7540370ba630bdcef09daaf9edf45b4b1bca0232",
"sha256:3f26e5da310a0c0b83ea50da1fd397de2640b02b424aa69be7e0784228f656c9",
"sha256:4182e32f4456d2c64619e97c58571fa5ca0993d1e8c2d9ca44916185e1726e15",
"sha256:426e590e2eb0e60f765271d668a30cf38b582eaae5ec9b31229c8c3c10c5bc21",
"sha256:5eb934a8f0dc358f0e0cdf314072286bbac74e4c124b64371395e94644d5d919",
"sha256:717928808043d3ea55b9bcde636d4a52d2236c246f6df464163a66ff59980ad8",
"sha256:8145f97c5ed71827a6ec98ceaef35afed1377e2d19c4078f324d209ff253ecb5",
"sha256:8744c84c914dcc59cbbb2943b32b7664df1039d99e834e1034a3372acb89ea4d",
"sha256:c1ac1d9590d0c9314ebf01591bd40d4c03d710bfc84a3889e5263c97d7891dee",
"sha256:cb2e197b7b0687becb026b84d3c242482f20cbb29a9981e43604eb67576da9f6",
"sha256:d4001b71ad2c9b84ff18b182cea22b7b6cbf624216da3ea06fb7af28d1f93165",
"sha256:d8930772adccb2882989ab1493fa74bd87d47c8ac7417f5dd3dd834ba8c24dc9",
"sha256:dfbb0173ee2399bc4ed3caf2d236e5c0092f948aafd0a15fbe4a0e77ee61a958",
"sha256:eebfbba048f4fa8ac711b22c78516e16ff8117d05a580e7eeef6b0c2be554c18",
"sha256:f1b21bc5cf3dbea53d33615d1ead892dfdae9d7052fa8898083bec88be20dcd2"
],
"index": "pypi",
"version": "==0.25.0"
"version": "==0.25.1"
},
"pycountry": {
"hashes": [
"sha256:68e58bfd3bedeea49ba9d4b38f2bd5e042f9753628eba9a819fb03f551d89096"
"sha256:3c57aa40adcf293d59bebaffbe60d8c39976fba78d846a018dc0c2ec9c6cb3cb"
],
"index": "pypi",
"version": "==19.7.15"
"version": "==19.8.18"
},
"python-dateutil": {
"hashes": [
@ -121,11 +129,11 @@
},
"requests-cache": {
"hashes": [
"sha256:6822f788c5ee248995c4bfbd725de2002ad710182ba26a666e85b64981866060",
"sha256:73a7211870f7d67af5fd81cad2f67cfe1cd3eb4ee6a85155e07613968cc72dfc"
"sha256:813023269686045f8e01e2289cc1e7e9ae5ab22ddd1e2849a9093ab3ab7270eb",
"sha256:81e13559baee64677a7d73b85498a5a8f0639e204517b5d05ff378e44a57831a"
],
"index": "pypi",
"version": "==0.5.0"
"version": "==0.5.2"
},
"six": {
"hashes": [
@ -136,10 +144,10 @@
},
"urllib3": {
"hashes": [
"sha256:b246607a25ac80bedac05c6f282e3cdaf3afb65420fd024ac94435cabe6e18d1",
"sha256:dbe59173209418ae49d485b87d1681aefa36252ee85884c31346debd19463232"
"sha256:3de946ffbed6e6746608990594d08faac602528ac7015ac28d33cee6a45b7398",
"sha256:9a107b99a5393caf59c7aa3c1249c16e6879447533d0887f4336dde834c7be86"
],
"version": "==1.25.3"
"version": "==1.25.6"
},
"xlrd": {
"hashes": [
@ -151,6 +159,38 @@
}
},
"develop": {
"agate": {
"hashes": [
"sha256:48d6f80b35611c1ba25a642cbc5b90fcbdeeb2a54711c4a8d062ee2809334d1c",
"sha256:c93aaa500b439d71e4a5cf088d0006d2ce2c76f1950960c8843114e5f361dfd3"
],
"version": "==1.6.1"
},
"agate-dbf": {
"hashes": [
"sha256:00c93c498ec9a04cc587bf63dd7340e67e2541f0df4c9a7259d7cb3dd4ce372f"
],
"version": "==0.2.1"
},
"agate-excel": {
"hashes": [
"sha256:8f255ef2c87c436b7132049e1dd86c8e08bf82d8c773aea86f3069b461a17d52"
],
"version": "==0.2.3"
},
"agate-sql": {
"hashes": [
"sha256:9277490ba8b8e7c747a9ae3671f52fe486784b48d4a14e78ca197fb0e36f281b"
],
"version": "==0.5.4"
},
"appdirs": {
"hashes": [
"sha256:9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92",
"sha256:d8b24664561d0d34ddfaec54636d502d7cea6e29c3eaf68f3df6180863e2166e"
],
"version": "==1.4.3"
},
"atomicwrites": {
"hashes": [
"sha256:03472c30eb2c5d1ba9227e4c2ca66ab8287fbfbbda3888aa93dc2e28fc6811b4",
@ -165,6 +205,13 @@
],
"version": "==19.1.0"
},
"babel": {
"hashes": [
"sha256:af92e6106cb7c55286b25b38ad7695f8b4efb36a90ba483d7f7a6628c46158ab",
"sha256:e86135ae101e31e2c8ec20a4e0c5220f4eed12487d5cf3f78be7e98d3a57fc28"
],
"version": "==2.7.0"
},
"backcall": {
"hashes": [
"sha256:38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4",
@ -172,6 +219,35 @@
],
"version": "==0.1.0"
},
"black": {
"hashes": [
"sha256:09a9dcb7c46ed496a9850b76e4e825d6049ecd38b611f1224857a79bd985a8cf",
"sha256:68950ffd4d9169716bcb8719a56c07a2f4485354fec061cdd5910aa07369731c"
],
"index": "pypi",
"version": "==19.3b0"
},
"click": {
"hashes": [
"sha256:2335065e6395b9e67ca716de5f7526736bfa6ceead690adf616d925bdc622b13",
"sha256:5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7"
],
"version": "==7.0"
},
"csvkit": {
"hashes": [
"sha256:1353a383531bee191820edfb88418c13dfe1cdfa9dd3dc46f431c05cd2a260a0"
],
"index": "pypi",
"version": "==1.0.4"
},
"dbfread": {
"hashes": [
"sha256:07c8a9af06ffad3f6f03e8fe91ad7d2733e31a26d2b72c4dd4cfbae07ee3b73d",
"sha256:f604def58c59694fa0160d7be5d0b8d594467278d2bb6a47d46daf7162c84cec"
],
"version": "==2.0.7"
},
"decorator": {
"hashes": [
"sha256:86156361c50488b84a3f148056ea716ca587df2f0de1d34750d35c21312725de",
@ -186,6 +262,12 @@
],
"version": "==0.3"
},
"et-xmlfile": {
"hashes": [
"sha256:614d9722d572f6246302c4491846d2c393c199cfa4edc9af593437691683335b"
],
"version": "==1.0.1"
},
"flake8": {
"hashes": [
"sha256:19241c1cbc971b9962473e4438a2ca19749a7dd002dd1a946eaba171b4114548",
@ -194,20 +276,27 @@
"index": "pypi",
"version": "==3.7.8"
},
"future": {
"hashes": [
"sha256:67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8"
],
"version": "==0.17.1"
},
"importlib-metadata": {
"hashes": [
"sha256:23d3d873e008a513952355379d93cbcab874c58f4f034ff657c7a87422fa64e8",
"sha256:80d2de76188eabfbfcf27e6a37342c2827801e59c4cc14b0371c56fed43820e3"
"sha256:aa18d7378b00b40847790e7c27e11673d7fed219354109d0e7b9e5b25dc3ad26",
"sha256:d5f18a79777f3aa179c145737780282e27b508fc8fd688cb17c7a813e8bd39af"
],
"version": "==0.19"
"markers": "python_version < '3.8'",
"version": "==0.23"
},
"ipython": {
"hashes": [
"sha256:1d3a1692921e932751bc1a1f7bb96dc38671eeefdc66ed33ee4cbc57e92a410e",
"sha256:537cd0176ff6abd06ef3e23f2d0c4c2c8a4d9277b7451544c6cbf56d1c79a83d"
"sha256:c4ab005921641e40a68e405e286e7a1fcc464497e14d81b6914b4fd95e5dee9b",
"sha256:dd76831f065f17bddd7eaa5c781f5ea32de5ef217592cf019e34043b56895aa1"
],
"index": "pypi",
"version": "==7.7.0"
"version": "==7.8.0"
},
"ipython-genutils": {
"hashes": [
@ -216,12 +305,41 @@
],
"version": "==0.2.0"
},
"isodate": {
"hashes": [
"sha256:2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8",
"sha256:aa4d33c06640f5352aca96e4b81afd8ab3b47337cc12089822d6f322ac772c81"
],
"version": "==0.6.0"
},
"isort": {
"hashes": [
"sha256:54da7e92468955c4fceacd0c86bd0ec997b0e1ee80d97f67c35a78b719dccab1",
"sha256:6e811fcb295968434526407adb8796944f1988c5b65e8139058f2014cbe100fd"
],
"index": "pypi",
"version": "==4.3.21"
},
"jdcal": {
"hashes": [
"sha256:1abf1305fce18b4e8aa248cf8fe0c56ce2032392bc64bbd61b5dff2a19ec8bba",
"sha256:472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8"
],
"version": "==1.4.1"
},
"jedi": {
"hashes": [
"sha256:53c850f1a7d3cfcd306cc513e2450a54bdf5cacd7604b74e42dd1f0758eaaf36",
"sha256:e07457174ef7cb2342ff94fa56484fe41cec7ef69b0059f01d3f812379cb6f7c"
"sha256:786b6c3d80e2f06fd77162a07fed81b8baa22dde5d62896a790a331d6ac21a27",
"sha256:ba859c74fa3c966a22f2aeebe1b74ee27e2a462f56d3f5f7ca4a59af61bfe42e"
],
"version": "==0.14.1"
"version": "==0.15.1"
},
"leather": {
"hashes": [
"sha256:076d1603b5281488285718ce1a5ce78cf1027fe1e76adf9c548caf83c519b988",
"sha256:e0bb36a6d5f59fbf3c1a6e75e7c8bee29e67f06f5b48c0134407dde612eba5e2"
],
"version": "==0.3.3"
},
"mccabe": {
"hashes": [
@ -237,12 +355,25 @@
],
"version": "==7.2.0"
},
"openpyxl": {
"hashes": [
"sha256:340a1ab2069764559b9d58027a43a24db18db0e25deb80f81ecb8ca7ee5253db"
],
"version": "==3.0.0"
},
"packaging": {
"hashes": [
"sha256:a7ac867b97fdc07ee80a8058fe4435ccd274ecc3b0ed61d852d7d53055528cf9",
"sha256:c491ca87294da7cc01902edbe30a5bc6c4c28172b5138ab4e4aa1b9d7bfaeafe"
"sha256:28b924174df7a2fa32c1953825ff29c61e2f5e082343165438812f00d3a7fc47",
"sha256:d9551545c6d761f3def1677baf08ab2a3ca17c56879e70fecba2fc4dde4ed108"
],
"version": "==19.1"
"version": "==19.2"
},
"parsedatetime": {
"hashes": [
"sha256:3d817c58fb9570d1eec1dd46fa9448cd644eeed4fb612684b02dfda3a79cb84b",
"sha256:9ee3529454bf35c40a77115f5a596771e59e1aee8c53306f346c461b8e913094"
],
"version": "==2.4"
},
"parso": {
"hashes": [
@ -268,10 +399,10 @@
},
"pluggy": {
"hashes": [
"sha256:0825a152ac059776623854c1543d65a4ad408eb3d33ee114dff91e57ec6ae6fc",
"sha256:b9817417e95936bf75d85d3f8767f7df6cdde751fc40aed3bb3074cbcb77757c"
"sha256:0db4b7601aae1d35b4a033282da476845aa19185c1e6964b25cf324b5e4ec3e6",
"sha256:fa5fa1622fa6dd5c030e9cad086fa19ef6a0cf6d7a2d12318e10cb49d6d68f34"
],
"version": "==0.12.0"
"version": "==0.13.0"
},
"prompt-toolkit": {
"hashes": [
@ -325,11 +456,11 @@
},
"pytest": {
"hashes": [
"sha256:6ef6d06de77ce2961156013e9dff62f1b2688aa04d0dc244299fe7d67e09370d",
"sha256:a736fed91c12681a7b34617c8fcefe39ea04599ca72c608751c31d89579a3f77"
"sha256:813b99704b22c7d377bbd756ebe56c35252bb710937b46f207100e843440b3c2",
"sha256:cc6620b96bc667a0c8d4fa592a8c9c94178a1bd6cc799dbb057dfd9286d31a31"
],
"index": "pypi",
"version": "==5.0.1"
"version": "==5.1.3"
},
"pytest-clarity": {
"hashes": [
@ -338,6 +469,26 @@
"index": "pypi",
"version": "==0.2.0a1"
},
"python-slugify": {
"hashes": [
"sha256:575d03256a132fc1efb4c52966c6eb11c57a13b071618f0b26076057a23f6937"
],
"version": "==3.0.4"
},
"pytimeparse": {
"hashes": [
"sha256:04b7be6cc8bd9f5647a6325444926c3ac34ee6bc7e69da4367ba282f076036bd",
"sha256:e86136477be924d7e670646a98561957e8ca7308d44841e21f5ddea757556a0a"
],
"version": "==1.1.8"
},
"pytz": {
"hashes": [
"sha256:26c0b32e437e54a18161324a2fca3c4b9846b74a8dccddd843113109e1116b32",
"sha256:c894d57500a4cd2d5c71114aaab77dbab5eabd9022308ce5ac9bb93a60a6f0c7"
],
"version": "==2019.2"
},
"six": {
"hashes": [
"sha256:3350809f0555b11f552448330d0b52d5f24c91a322ea4a15ef22629740f3761c",
@ -345,18 +496,38 @@
],
"version": "==1.12.0"
},
"sqlalchemy": {
"hashes": [
"sha256:2f8ff566a4d3a92246d367f2e9cd6ed3edeef670dcd6dda6dfdc9efed88bcd80"
],
"version": "==1.3.8"
},
"termcolor": {
"hashes": [
"sha256:1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b"
],
"version": "==1.1.0"
},
"text-unidecode": {
"hashes": [
"sha256:1311f10e8b895935241623731c2ba64f4c455287888b18189350b67134a822e8",
"sha256:bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93"
],
"version": "==1.3"
},
"toml": {
"hashes": [
"sha256:229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c",
"sha256:235682dd292d5899d361a811df37e04a8828a5b1da3115886b73cf81ebc9100e"
],
"version": "==0.10.0"
},
"traitlets": {
"hashes": [
"sha256:9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835",
"sha256:c6cb5e6f57c5a9bdaa40fa71ce7b4af30298fbab9ece9815b5d995ab6217c7d9"
"sha256:262089114405f22f4833be96b31e143ab906d7764a22c04c71fee0bbda4787ba",
"sha256:6ad5b30dacd5e2424c46cc94a0aeab990d98ae17d181acea2cc4272ac3409fca"
],
"version": "==4.3.2"
"version": "==4.3.3.dev0"
},
"wcwidth": {
"hashes": [
@ -365,12 +536,20 @@
],
"version": "==0.1.7"
},
"xlrd": {
"hashes": [
"sha256:546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2",
"sha256:e551fb498759fa3a5384a94ccd4c3c02eb7c00ea424426e212ac0c57be9dfbde"
],
"index": "pypi",
"version": "==1.2.0"
},
"zipp": {
"hashes": [
"sha256:4970c3758f4e89a7857a973b1e2a5d75bcdc47794442f2e2dd4fe8e0466e809a",
"sha256:8a5712cfd3bb4248015eb3b0b3c54a5f6ee3f2425963ef2a0125b8bc40aafaec"
"sha256:3718b1cbcd963c7d4c5511a8240812904164b7f381b647143a89d3b98f9bcd8e",
"sha256:f06903e9f1f43b12d371004b4ac7b06ab39a44adc747266928ae6debfa7b3335"
],
"version": "==0.5.2"
"version": "==0.6.0"
}
}
}

View File

@ -1,12 +1,13 @@
# CSV Metadata Quality [![Build Status](https://travis-ci.org/ilri/csv-metadata-quality.svg?branch=master)](https://travis-ci.org/ilri/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.
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.
## 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`
@ -69,6 +70,18 @@ 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
@ -79,7 +92,6 @@ Invalid AGROVOC (cg.coverage.country): KENYAA
- 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 check for author names with incorrect spacing after commas, ie "Orth,Alan S."
- Add tests for application invocation, ie `tests/test_app.py`?
## License

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

@ -1,21 +1,53 @@
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.add_argument('--exclude-fields', '-x', help='Comma-separated list of fields to skip, for example: dc.contributor.author,dc.identifier.citation')
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
@ -34,17 +66,17 @@ 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(','):
for exclude in args.exclude_fields.split(","):
if column == exclude and skip is False:
skip = True
if skip:
print(f'Skipping {column}')
print(f"Skipping {column}")
continue
@ -58,7 +90,7 @@ def run(argv):
# 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).*$', column)
match = re.match(r"^.*?(author|citation).*$", column)
if match is not None:
df[column] = df[column].apply(fix.comma_space, field_name=column)
@ -83,34 +115,52 @@ def run(argv):
# 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, 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

@ -18,10 +18,10 @@ 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
@ -43,10 +43,10 @@ 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
@ -64,13 +64,13 @@ def separators(field):
return
# Try to split multi-value field on "||" separator
for value in field.split('||'):
for value in field.split("||"):
# After splitting, see if there are any remaining "|" characters
match = re.findall(r'^.*?\|.*$', value)
match = re.findall(r"^.*?\|.*$", value)
if match:
print(f'Invalid multi-value separator: {field}')
print(f"Invalid multi-value separator: {field}")
return field
@ -88,22 +88,22 @@ def date(field, field_name):
from datetime import datetime
if pd.isna(field):
print(f'Missing date ({field_name}).')
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_name}): {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 +111,7 @@ def date(field, field_name):
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 +119,11 @@ def date(field, field_name):
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_name}): {field}')
print(f"Invalid date ({field_name}): {field}")
return field
@ -140,7 +140,7 @@ 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
@ -156,14 +156,16 @@ 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.
"""
@ -177,22 +179,22 @@ 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
@ -220,12 +222,16 @@ def agrovoc(field, field_name):
return
# Try to split multi-value field on "||" separator
for value in field.split('||'):
request_url = f'http://agrovoc.uniroma2.it/agrovoc/rest/v1/agrovoc/search?query={value}'
for value in field.split("||"):
request_url = (
f"http://agrovoc.uniroma2.it/agrovoc/rest/v1/agrovoc/search?query={value}"
)
# enable transparent request cache with thirty days expiry
expire_after = timedelta(days=30)
requests_cache.install_cache('agrovoc-response-cache', expire_after=expire_after)
requests_cache.install_cache(
"agrovoc-response-cache", expire_after=expire_after
)
request = requests.get(request_url)
@ -236,8 +242,8 @@ def agrovoc(field, field_name):
data = request.json()
# check if there are any results
if len(data['results']) == 0:
print(f'Invalid AGROVOC ({field_name}): {value}')
if len(data["results"]) == 0:
print(f"Invalid AGROVOC ({field_name}): {value}")
return field
@ -260,10 +266,18 @@ 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:
@ -272,7 +286,7 @@ 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:
@ -282,6 +296,6 @@ 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

@ -1,6 +1,7 @@
import pandas as pd
import re
import pandas as pd
def whitespace(field):
"""Fix whitespace issues.
@ -16,23 +17,23 @@ 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: {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
@ -48,21 +49,21 @@ def separators(field):
values = list()
# Try to split multi-value field on "||" separator
for value in field.split('||'):
for value in field.split("||"):
# 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: {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 +74,10 @@ 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.
"""
@ -86,36 +87,36 @@ 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
@ -128,7 +129,7 @@ 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 +140,10 @@ 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: {value}")
# Create a new field consisting of all values joined with "||"
new_field = '||'.join(new_values)
new_field = "||".join(new_values)
return new_field
@ -169,11 +170,11 @@ 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
@ -193,10 +194,10 @@ def comma_space(field, field_name):
return
# Check for comma followed by a word character
match = re.findall(r',\w', field)
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)
print(f"Adding space after comma ({field_name}): {field}")
field = re.sub(r",(\w)", r", \1", field)
return field

View File

@ -1 +1 @@
VERSION = '0.2.2'
VERSION = "0.3.1"

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
@ -24,3 +24,5 @@ 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,,,

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
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

View File

@ -1,21 +1,39 @@
-i https://pypi.org/simple
agate-dbf==0.2.1
agate-excel==0.2.3
agate-sql==0.5.4
agate==1.6.1
appdirs==1.4.3
atomicwrites==1.3.0
attrs==19.1.0
babel==2.7.0
backcall==0.1.0
black==19.3b0
click==7.0
csvkit==1.0.4
dbfread==2.0.7
decorator==4.4.0
entrypoints==0.3
et-xmlfile==1.0.1
flake8==3.7.8
importlib-metadata==0.19
future==0.17.1
importlib-metadata==0.23 ; python_version < '3.8'
ipython-genutils==0.2.0
ipython==7.7.0
jedi==0.14.1
ipython==7.8.0
isodate==0.6.0
isort==4.3.21
jdcal==1.4.1
jedi==0.15.1
leather==0.3.3
mccabe==0.6.1
more-itertools==7.2.0
packaging==19.1
openpyxl==3.0.0
packaging==19.2
parsedatetime==2.4
parso==0.5.1
pexpect==4.7.0 ; sys_platform != 'win32'
pickleshare==0.7.5
pluggy==0.12.0
pluggy==0.13.0
prompt-toolkit==2.0.9
ptyprocess==0.6.0
py==1.8.0
@ -24,9 +42,16 @@ pyflakes==2.1.1
pygments==2.4.2
pyparsing==2.4.2
pytest-clarity==0.2.0a1
pytest==5.0.1
pytest==5.1.3
python-slugify==3.0.4
pytimeparse==1.1.8
pytz==2019.2
six==1.12.0
sqlalchemy==1.3.8
termcolor==1.1.0
traitlets==4.3.2
text-unidecode==1.3
toml==0.10.0
traitlets==4.3.3.dev0
wcwidth==0.1.7
zipp==0.5.2
xlrd==1.2.0
zipp==0.6.0

View File

@ -1,16 +1,17 @@
-i https://pypi.org/simple
-e .
certifi==2019.6.16
certifi==2019.9.11
chardet==3.0.4
idna==2.8
numpy==1.17.0
pandas==0.25.0
pycountry==19.7.15
langid==1.1.6
numpy==1.17.2
pandas==0.25.1
pycountry==19.8.18
python-dateutil==2.8.0
python-stdnum==1.11
pytz==2019.2
requests-cache==0.5.0
requests-cache==0.5.2
requests==2.22.0
six==1.12.0
urllib3==1.25.3
urllib3==1.25.6
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

@ -8,12 +8,13 @@ install_requires = [
'python-stdnum',
'requests',
'requests-cache',
'pycountry'
'pycountry',
'langid'
]
setuptools.setup(
name="csv-metadata-quality",
version="0.2.2",
version="0.3.1",
author="Alan Orth",
author_email="aorth@mjanja.ch",
description="A simple, but opinionated CSV quality checking and fixing pipeline for CSVs in the DSpace ecosystem.",

View File

@ -1,21 +1,23 @@
import csv_metadata_quality.check as check
import csv_metadata_quality.experimental as experimental
import pandas as pd
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 +25,20 @@ 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)
@ -44,20 +46,20 @@ 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)
captured = capsys.readouterr()
assert captured.out == f'Invalid multi-value separator: {value}\n'
assert captured.out == f"Invalid multi-value separator: {value}\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)
@ -65,50 +67,50 @@ def test_check_valid_separators():
def test_check_missing_date(capsys):
'''Test checking missing date.'''
"""Test checking missing date."""
value = None
field_name = 'dc.date.issued'
field_name = "dc.date.issued"
check.date(value, field_name)
captured = capsys.readouterr()
assert captured.out == f'Missing date ({field_name}).\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"
field_name = 'dc.date.issued'
field_name = "dc.date.issued"
check.date(value, field_name)
captured = capsys.readouterr()
assert captured.out == f'Multiple dates not allowed ({field_name}): {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"
field_name = 'dc.date.issued'
field_name = "dc.date.issued"
check.date(value, field_name)
captured = capsys.readouterr()
assert captured.out == f'Invalid date ({field_name}): {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"
field_name = 'dc.date.issued'
field_name = "dc.date.issued"
result = check.date(value, field_name)
@ -116,22 +118,22 @@ def test_check_valid_date():
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)
@ -139,65 +141,65 @@ 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)
@ -205,21 +207,89 @@ 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

@ -2,67 +2,67 @@ 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'
assert fix.whitespace(value) == "Alan"
def test_fix_trailing_whitespace():
'''Test fixing trailing whitespace.'''
"""Test fixing trailing whitespace."""
value = 'Alan '
value = "Alan "
assert fix.whitespace(value) == 'Alan'
assert fix.whitespace(value) == "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'
assert fix.whitespace(value) == "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'
assert fix.separators(value) == "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'
assert fix.duplicates(value) == "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.'''
"""Test adding space after comma."""
value = 'Orth,Alan S.'
value = "Orth,Alan S."
field_name = 'dc.contributor.author'
field_name = "dc.contributor.author"
assert fix.comma_space(value, field_name) == 'Orth, Alan S.'
assert fix.comma_space(value, field_name) == "Orth, Alan S."