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Commit Graph

154 Commits

Author SHA1 Message Date
3b40a68279
Add check for title in citation
This checks if the item title exists in the citation. If it is not
present it could just be missing, or could have minor differences
in the whitespace, accents, etc.
2021-12-05 15:52:42 +02:00
999cc65097
csv_metadata_quality/app.py: adjust mojibake check
If unsafe fixes (-u) are enabled then we don't need to do the check
first before actually fixing them. Doing the check first creates e-
tra output that needs to be reviewed by the user.
2021-12-05 15:18:35 +02:00
787fa9e8d9
Add field name to fix.newlines output 2021-10-08 14:36:43 +03:00
8a27fb2589
Add check for missing DOIs
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Sometimes an editor includes a DOI in the citation field, but does
not add a standalone DOI field.
2021-10-06 21:25:39 +03:00
6ba16d5d4c
csv_metadata_quality/check.py: Fix duplicate checker
Fix the incorrect type field regex, and improve the title regex to
consider dcterms.title and dc.title (along with the DSpace language
variants like dc.title[en_US]), but ignore dc.title.alternative.

See: https://regex101.com/r/I4m06F/1
2021-10-06 19:32:40 +03:00
54ab869297
csv_metadata_quality/experimental.py: Adjust citation match
We need to match both of these citation fields:

- dc.identifier.citation
- dcterms.bibliographicCitation
2021-10-06 16:13:10 +03:00
4e2eab68b0
Update requests-cache
Apparently we were stuck on an older version of requests-cache due
to the fact that we were using the caret, which will never update
the left-most (major) version. Upstream requests-cache is currently
version 0.6.4, and there seems to have been some changes to the API.
2021-07-06 15:24:39 +03:00
a8fe623f4c
csv_metadata_quality/check.py: Remove unnecessary pass
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LGTM warned that these pass statements are not necessary.

See: https://lgtm.com/rules/910088/
2021-04-20 08:20:13 +03:00
bd8943f36a
csv_metadata_quality/app.py: Don't crash if fields are missing
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We don't need to crash if someone feeds us a CSV file that is miss-
ing commont DSpace fields like title, type, and subject.
2021-03-21 19:47:29 +02:00
cfe09f7126
Add SPDX short license identifier to all Python files
See: https://spdx.github.io/spdx-spec/appendix-V-using-SPDX-short-identifiers-in-source-files/
2021-03-19 16:04:40 +02:00
8eddb76aab
Bump version to 0.4.8-dev
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2021-03-19 11:53:56 +02:00
898bb412c3
Add checks and unsafe fixes for mojibake
This detects whether text has likely been encoded in one encoding
and decoded in another, perhaps multiple times. This often results
in display of "mojibake" characters.

For example, a file encoded in UTF-8 is opened as CP-1252 (Windows
Latin codepage) in Microsoft Excel, and saved again as UTF-8. You
will see strings like this in the resulting file:

    - CIAT Publicaçao
    - CIAT Publicación

The correct version of these in UTF-8 would be:

    - CIAT Publicaçao
    - CIAT Publicación

I use a code snippet from Martijn Pieters on StackOverflow to de-
tect whether a string is "weird" as determined by the excellent
"fixes text for you" (ftfy) Python library, then check if a weird
string encodes as CP-1252 or not. If so, I can try to fix it.

See: https://stackoverflow.com/questions/29071995/identify-garbage-unicode-string-using-python
2021-03-19 10:22:21 +02:00
f816e17fe7
Version 0.4.7
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2021-03-17 10:00:34 +02:00
9f2dc0a0f5
Add support for detecting duplicate items
This uses the title, type, and date issued as a sort of "key" when
determining if an item already exists in the data set.
2021-03-17 09:53:07 +02:00
14010896a5
csv_metadata_quality/experimental.py: Move all imports to top of file
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PEP8 recommends keeping imports at the top of the file. Also, I had
to re-work the issn/isbn so they didn't conflict with the functions
in check.py (flake8 warned about them being redefined).

Imports sorted with isort.

See: https://www.python.org/dev/peps/pep-0008/#imports
2021-03-16 16:13:34 +02:00
ab3af2ec62
csv_metadata_quality/check.py: Reformat with black 2021-03-16 16:12:33 +02:00
330a7b7b9c
Don't unnecessarily rewrite DataFrames for checks
By using df[column] = df[column].apply(check...) we were re-writing
the DataFrame every time we returned from a check. We don't actuall
y need to return a value at all, as the point of checks is to print
a warning to the screen. In Python a "return" statement without a v
ariable returns None.

I haven't measured the impact of this, but I assume it will mean we
are faster and use less memory.
2021-03-16 16:04:19 +02:00
10612cf891
Remove checks for invalid multi-value separators
Now that I no longer treat the fix for these as "unsafe" I don't a
ctually need to check for them—I can just fix them when I see them.
2021-03-14 21:01:21 +02:00
c9c277f8df
csv_metadata_quality/app.py: Update help text
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Use DCTERMS fields where possible.
2021-03-14 10:52:58 +02:00
0e9176f0a6
csv_metadata_quality/check.py: requests cache
Allow overriding the directory for the requests cache. In the case
of csv-metadata-quality-web, which currently runs on Google's App
Engine, we can only write to /tmp.
2021-03-14 09:07:35 +02:00
1008acf35e
Always fix invalid multi-value separators
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This is no longer class-ified as "unsafe" as I have yet to see a
case where this was intentional, and it always causes issues when
you import the data in a DSpace repository.
2021-03-13 12:59:45 +02:00
fa84cfa440
Bump version to 0.4.6-dev 2021-03-11 22:44:36 +02:00
1554cfd5c9
Version 0.4.6 2021-03-11 12:14:54 +02:00
a0ea829f5c
csv_metadata_quality/fix.py: Fixes should be green 2021-03-11 11:47:24 +02:00
d88ea56488
csv_metadata_quality/check.py: Move all imports to top of file
PEP8 recommends keeping imports at the top of the file. Also, I had
to re-work the issn/isbn so they didn't conflict with the functions
in check.py (flake8 warned about them being redefined).

Imports sorted with isort.

See: https://www.python.org/dev/peps/pep-0008/#imports
2021-03-11 10:52:20 +02:00
6e4b0e5c1b
Add validation of SPDX license identifiers
Currently this only checks the dcterms.license field and the result
will only be a warning.
2021-03-11 10:33:16 +02:00
202bda862a
Bump version to 0.4.5
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2021-03-04 21:38:10 +02:00
dd2cfae047
csv_metadata_quality/app.py: Match dcterms.issued for dates
We used to only check fields that had "date" in their name because
we were using DSpace's default dc.date.* fields. Now we are using
dcterms.issued so I will add that one as well.
2021-02-28 15:11:06 +02:00
d76e72532a
Move unreleased changes to v0.4.4
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2021-02-21 13:25:22 +02:00
a7fc5a246c
Colorize output
Some checks failed
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Messages will be colorized:

- Red for errors
- Yellow for warnings or information
- Green for fixes
2021-02-21 13:01:25 +02:00
de92f32ab6
csv_metadata_quality/check.py: More date formats
We should also allow ISO 8601 extended in combined date and time
format. DSpace does not have a problem with dates in this format
and I have found some metadata that uses this date format.

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

See: https://en.wikipedia.org/wiki/ISO_8601
2021-02-04 21:39:14 +02:00
cbf94490f2
Version 0.4.3 2021-01-26 15:22:40 +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
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
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
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
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
0b2d211455
Version 0.4.1 2020-01-15 12:19:42 +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
705127fd28
Version 0.4.0 2020-01-15 11:44:56 +02:00
87181bc7b8
Run black, isort, and flake8. 2020-01-15 11:41:31 +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
efdc3a841a
Version 0.3.1 2019-10-01 17:11:13 +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
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
e15c98cccb
Move unreleased changes to v0.3.0 2019-09-26 14:06:31 +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
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
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
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
280a99c8a8
Sort imports with isort
See: https://sourcery.ai/blog/python-best-practices/
2019-08-29 01:15:04 +03:00
d97dcd19db
Format with black 2019-08-29 01:10:39 +03:00
c354a3687c
Release version 0.2.2 2019-08-28 00:10:17 +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
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
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
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
7255bf4707
Version 0.2.1 2019-08-11 10:39:39 +03:00
232ff99898
csv_metadata_quality/fix.py: Add more unneccessary Unicode fixes
Add a check for soft hyphens (U+00AD). In one sample CSV I have a
normal hyphen followed by a soft hyphen in an ISBN. This causes the
ISBN validation to fail.
2019-08-11 00:07:21 +03:00
13d5221378
csv_metadata_quality/check.py: Fix test for False 2019-08-10 23:52:53 +03:00
9ce7dc6716
Add check for uncommon filenames
Generally we want people to upload documents in accessible formats
like PDF, Word, Excel, and PowerPoint. This check warns if a file
is using an uncommon extension.
2019-08-10 23:41:16 +03:00
5ff584a8d7
Version 0.2.0 2019-08-09 01:39:51 +03:00
62fea95087
Improve suspicious character detection
Now it will print just the part of the metadata value that contains
the suspicious character (up to 80 characters, so we don't make the
line break on terminals that use 80 character width by default).

Also, print the name of the field in which the metadata value is so
that it is easier for the user to locate.
2019-08-09 01:25:40 +03:00
8772bdec51
csv_metadata_quality/app.py: Explicitly exit with success 2019-08-04 09:10:37 +03:00
6d4ecd75aa
csv_metadata_quality/app.py: Close files before exit 2019-08-04 09:10:19 +03:00
f4e7fd73f5
csv_metadata_quality/app.py: Handle Ctrl-C
Instead of printing an ugly two-page stack trace.
2019-08-03 21:11:57 +03:00
85ae7bdc5a
Increment version to 0.1.0 2019-08-02 00:12:47 +03:00
0561300ebe
Add option to print version with --version or -V
I guess `-v` is more commonly used for "verbose" so I will use the
short option of `-V` for version.
2019-08-02 00:09:54 +03:00
bf876a046a
Rework AGROVOC validation
AGROVOC validation is now disabled by default, but can be enabled
on a field-by-field basis. For example, countries and regions are
also present in AGROVOC. Fields with these values can be enabled
using the new `--agrovoc-fields` option.

I reworked the script output to show the field name when printing
an invalid term so that the user knows in which field the term is.
2019-08-01 23:51:58 +03:00
576b3a3638
csv_metadata_quality/__main__.py: Fix spacing
Identified by flake8.
2019-08-01 23:28:16 +03:00
9100efdf50
Re-work as a proper standalone Python package
Add a setup.py so that installation is easier and a standalone CLI
script called csv-metadata-quality is provided. Now the user only
needs to run this from a virtual environment inside the project
directory:

    $ pip install .

Eventually I could publish this on PyPi when I settle on a more
appropriate package name.

See: https://packaging.python.org/tutorials/packaging-projects/
See: https://chriswarrick.com/blog/2014/09/15/python-apps-the-right-way-entry_points-and-scripts/
2019-07-31 17:34:36 +03:00
40d5f7d81b
Add support for removing newlines
This was tricky because of the nature of newlines. In actuality we
are removing Unix line feeds here (U+000A) because Windows carriage
returns are actually already removed by the string stripping in the
whitespace fix.

Creating the test case in Vim was difficult because I couldn't fig-
ure out how to manually enter a line feed character. In the end I
used a search and replace on a known pattern like "ALAN", replacing
it with \r. Neither entering the Unicode code point (U+000A) direc-
tly or typing an "Enter" character after ^V worked. Grrr.
2019-07-30 20:05:12 +03:00
3c798fb504
Use pycountry instead of iso-639 for languages
The latter is a fork that hasn't been updated since 2016 and the
original still seems to be well maintained, with recent database
updates as well as tests for Python 3.7.

Also, pycountry supports ISO 3166-2 (administrative zones), which
we could eventually use for sub regions.
2019-07-30 16:39:26 +03:00
4e3511cd55
csv_metadata_quality/check.py: Fix AGROVOC lookup
We actually only need to see if there are more than zero matches
because a term like "Nigeria" will match in English, Spanish, etc,
whereas terms that *really* don't match will have zero results.
2019-07-30 14:51:44 +03:00
1f65a28307
Add support for validating subjects against AGROVOC
Checks values in the dc.subject or dcterms.subject field against the
AGROVOC REST API hosted by FAO. Code borrowed from agrovoc-lookup.py.

See: http://agrovoc.uniroma2.it/agrovoc/agrovoc/en/
See: https://github.com/ilri/DSpace/blob/5_x-prod/agrovoc-lookup.py
2019-07-30 00:30:31 +03:00
a36454a3ac
Add support for validating languages
Will validate against ISO 639-2 or ISO 639-3 depending on how long
the language field is. Otherwise will return that the language is
invalid.

Does not currently have any support for generic values like "Other".
2019-07-29 18:59:42 +03:00
1e444cf040
Add fix for duplicate metadata values 2019-07-29 18:05:03 +03:00
d7888d59a8
csv_metadata_quality/check.py: Return date even if it is invalid
Otherwise it is missing from the final CSV and then we can't even
fix it. :)
2019-07-29 17:40:14 +03:00
50ae4e17f2
csv_metadata_quality/fix.py: Fix indent 2019-07-29 17:14:48 +03:00
fa4fa3491b
Add check for "suspicious" characters
These standalone characters often indicate issues with encoding or
copy/paste in languages with accents like French and Spanish. For
example: foreˆt should be forêt.

It is not possible to fix these issues automatically, but this will
print a warning so you can notify the owner of the data.
2019-07-29 17:08:49 +03:00
8047a57cc5
Add support for fixing "unnecessary" Unicode
These are things like non-breaking spaces, "replacement" characters,
etc that add nothing to the metadata and often cause errors during
parsing or displaying in a UI.
2019-07-29 16:38:10 +03:00
d73f7b54b1
csv_metadata_quality/app.py: Improve comments 2019-07-29 16:24:35 +03:00
42920e9c7c
Test Python regular expression matches directly
Match objects always have a boolean value of True.

See: https://docs.python.org/3.7/library/re.html
2019-07-29 16:16:30 +03:00
7b5db1f5d9
csv_metadata_quality/app.py: Remove erroneous comment 2019-07-29 16:15:25 +03:00
40e77db713
Add "unsafe fixes" runtime option
In this case it fixes occurences of invalid multi-value separators.
DSpace uses "||" to separate multiple values in one field, but our
editors sometimes give us files with mistakes like "|". We can fix
these to be correct multi-value separators if we are sure that the
metadata is not actually using "|" for some legitimate purpose.
2019-07-28 22:53:39 +03:00
a93b5b31c5
Add support for command line arguments
Currently only supports specifying input and output files with -i
and -o. Eventually I'll add more options like dry run, debug, and
maybe things like forcing unsafe fixes.
2019-07-28 20:31:57 +03:00
87b1997051
Fix whitespace errors found by flake8 2019-07-28 17:47:28 +03:00
aadb3117eb
csv_metadata_quality/app.py: Remove unused test input files 2019-07-28 17:45:05 +03:00
e88d35ace3
csv_metadata_quality/app.py: Use regex in column match
Check for a column that has "issn" or "isbn" in the name rather
than by its explicit name, as the column is dc.identifier.issn now,
but will be cg.issn in the future if CG Core v2 happens.
2019-07-28 17:27:20 +03:00
196bb434fa
Add date validation
I'm only concerned with validating issue dates here. In DSpace they
are generally always YYYY, YYY-MM, or YYYY-MM-DD (though in theory
they could be any valid ISO8601 format).

This also checks for cases where the date is missing and where the
metadata has specified multiple dates like "1990||1991", as this is
valid, but there is no practical value for it in our system.
2019-07-28 16:11:36 +03:00
e2bb2d4df9
Main function should be "main()" 2019-07-27 23:09:16 +03:00
c47c064a13
Make output less debuggy 2019-07-27 09:21:13 +03:00
2b41f9416b
csv_metadata_quality/fix.py: Remove extra newline 2019-07-27 01:29:22 +03:00
3cf9f9452b
csv_metadata_quality/check.py: Always return field
We always need to return the field back so apply doesn't set it to
null when creating the new data frame.
2019-07-27 01:28:08 +03:00
18f26c343d
csv_metadata_quality/app.py: Fix path to test.csv 2019-07-27 00:25:30 +03:00
84c3b17678
csv_metadata_quality/app.py: Add comment 2019-07-26 23:49:13 +03:00
aaf3537ba4
Add check for invalid multi-value separators 2019-07-26 23:48:24 +03:00
02f9d8a736
csv_metadata_quality/check.py: Add check for missing isbn values 2019-07-26 23:45:18 +03:00