alanorth/csv-metadata-quality
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156 Commits

Author SHA1 Message Date
Alan Orth
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
Alan Orth
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
Alan Orth
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
Alan Orth
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
Alan Orth
280a99c8a8
Sort imports with isort 
See: https://sourcery.ai/blog/python-best-practices/
 2019-08-29 01:15:04 +03:00
Alan Orth
d97dcd19db
Format with black 2019-08-29 01:10:39 +03:00
Alan Orth
c354a3687c
Release version 0.2.2 2019-08-28 00:10:17 +03:00
Alan Orth
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
Alan Orth
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
Alan Orth
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
Alan Orth
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
Alan Orth
7255bf4707
Version 0.2.1 2019-08-11 10:39:39 +03:00
Alan Orth
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
Alan Orth
13d5221378
csv_metadata_quality/check.py: Fix test for False 2019-08-10 23:52:53 +03:00
Alan Orth
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
Alan Orth
5ff584a8d7
Version 0.2.0 2019-08-09 01:39:51 +03:00
Alan Orth
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
Alan Orth
8772bdec51
csv_metadata_quality/app.py: Explicitly exit with success 2019-08-04 09:10:37 +03:00
Alan Orth
6d4ecd75aa
csv_metadata_quality/app.py: Close files before exit 2019-08-04 09:10:19 +03:00
Alan Orth
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
Alan Orth
85ae7bdc5a
Increment version to 0.1.0 2019-08-02 00:12:47 +03:00
Alan Orth
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
Alan Orth
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
Alan Orth
576b3a3638
csv_metadata_quality/__main__.py: Fix spacing 
Identified by flake8.
 2019-08-01 23:28:16 +03:00
Alan Orth
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
Alan Orth
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
Alan Orth
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
Alan Orth
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
Alan Orth
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
Alan Orth
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
Alan Orth
1e444cf040
Add fix for duplicate metadata values 2019-07-29 18:05:03 +03:00
Alan Orth
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
Alan Orth
50ae4e17f2
csv_metadata_quality/fix.py: Fix indent 2019-07-29 17:14:48 +03:00
Alan Orth
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
Alan Orth
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
Alan Orth
d73f7b54b1
csv_metadata_quality/app.py: Improve comments 2019-07-29 16:24:35 +03:00
Alan Orth
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
Alan Orth
7b5db1f5d9
csv_metadata_quality/app.py: Remove erroneous comment 2019-07-29 16:15:25 +03:00
Alan Orth
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
Alan Orth
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
Alan Orth
87b1997051
Fix whitespace errors found by flake8 2019-07-28 17:47:28 +03:00
Alan Orth
aadb3117eb
csv_metadata_quality/app.py: Remove unused test input files 2019-07-28 17:45:05 +03:00
Alan Orth
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
Alan Orth
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
Alan Orth
e2bb2d4df9
Main function should be "main()" 2019-07-27 23:09:16 +03:00
Alan Orth
c47c064a13
Make output less debuggy 2019-07-27 09:21:13 +03:00
Alan Orth
2b41f9416b
csv_metadata_quality/fix.py: Remove extra newline 2019-07-27 01:29:22 +03:00
Alan Orth
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
Alan Orth
18f26c343d
csv_metadata_quality/app.py: Fix path to test.csv 2019-07-27 00:25:30 +03:00
Alan Orth
84c3b17678
csv_metadata_quality/app.py: Add comment 2019-07-26 23:49:13 +03:00
Alan Orth
aaf3537ba4
Add check for invalid multi-value separators 2019-07-26 23:48:24 +03:00
Alan Orth
02f9d8a736
csv_metadata_quality/check.py: Add check for missing isbn values 2019-07-26 23:45:18 +03:00
Alan Orth
dfd961d720
Bring test.csv into project 2019-07-26 23:14:37 +03:00
Alan Orth
e160b17fb0
Add ISSN and ISBN checks using python-stdnum 2019-07-26 23:14:10 +03:00
Alan Orth
30a4b0005f
csv_metadata_quality/fix.py: Remove test function 2019-07-26 22:56:40 +03:00
Alan Orth
232d28e13e
Refactor as package with subpackages 
This makes it cleaner for introducing checks, fixes, tests, docs,
and tests in the future. Currently can be run like this:

  python -m csv_metadata_quality

CSV input and output paths are still hard coded.

See: https://dev.to/codemouse92/dead-simple-python-project-structure-and-imports-38c6
 2019-07-26 22:11:10 +03:00