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.
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.
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
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.
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
continuous-integration/drone/push Build is passingDetails
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
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.
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.
continuous-integration/drone/push Build is passingDetails
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.
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
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.
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
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||"
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.
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
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".
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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".
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.
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.
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.
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.
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.
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.
Alan Orth