52 Commits

Author	SHA1	Message	Date
Alan Orth	7cc49b500d	Use licenses.json from SPDX instead of spdx-license-list ... spdx-license-list has been deprecated[1] and already has outdated information compared to recent SPDX data releases. Now I use the JSON license data directly from SPDX[2] (currently version 3.19). The JSON file is loaded from the package's data directory using Python 3's stdlib functions from importlib[3], though we now need Python 3.9 as a minimum for importlib.resources.files[4]. Also note that the data directory is not properly packaged via setuptools, so this only works for local installs, and not via versions published to pypi, for example (I'm currently not doing this anyways). If I want to publish this in the future I will need to modify setup.py/pyproject.toml to include the data files. [1] https://gitlab.com/uniqx/spdx-license-list [2] https://github.com/spdx/license-list-data/blob/main/json/licenses.json [3] https://copdips.com/2022/09/adding-data-files-to-python-package-with-setup-py.html [4] https://docs.python.org/3/library/importlib.resources.html#importlib.resources.files	2022-12-13 10:39:17 +03:00
Alan Orth	051777bcec	Ignore subregion field for missing region checks ... Due to a sloppy regex I was sometimes matching the subregion field when checking for missing UN M.49 regions in the region field.	2022-12-07 23:18:47 +01:00
Alan Orth	141b2e1da3	csv_metadata_quality/check.py: update region output ... Add the country to the message about missing regions. This makes it easier to see which country is triggering the missing region error, and helps in case of debugging possible mistakes in the data coming from the country_converter library.	2022-11-28 17:40:27 +03:00
Alan Orth	040e56fc76	Improve exclude function ... When a user explicitly requests that a field be excluded with -x we skip that field in most checks. Up until now that did not include the item-based checks using a transposed dataframe because we don't know the metadata field names (labels) until we iterate over them. Now the excludes are respected for item-based checks.	2022-09-02 15:59:22 +03:00
Alan Orth	117c6ca85d	csv_metadata_quality/check.py: missing region fixes ... Port over the recent fixes and logic improvements to regions from fix.py.	2022-09-01 16:38:35 +03:00
Alan Orth	a7727b8431	Add support for dropping invalid AGROVOC terms ... Requires --agrovoc-fields <field.name> to do the actual validation, and -d to drop invalid ones.	2021-12-23 12:43:55 +02:00
Alan Orth	ccc2a73456	Add check for countries without matching regions ... If we have country "Kenya" we should have region "Eastern Africa" according to the UN M.49 geolocation scheme.	2021-12-08 15:02:20 +02:00
Alan Orth	4d5696c4cb	csv_metadata_quality/check.py: update title in citation check ... Initialize the titles and citations before the for loop so we can access them later. This makes it easier to check if the item actua- lly has a citation.	2021-12-05 16:21:44 +02:00
Alan Orth	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
Alan Orth	8a27fb2589	Add check for missing DOIs ... 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
Alan Orth	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
Alan Orth	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
Alan Orth	a8fe623f4c	csv_metadata_quality/check.py: Remove unnecessary pass ... LGTM warned that these pass statements are not necessary. See: https://lgtm.com/rules/910088/	2021-04-20 08:20:13 +03:00
Alan Orth	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
Alan Orth	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
Alan Orth	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
Alan Orth	ab3af2ec62	csv_metadata_quality/check.py: Reformat with black	2021-03-16 16:12:33 +02:00
Alan Orth	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
Alan Orth	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
Alan Orth	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
Alan Orth	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
Alan Orth	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
Alan Orth	a7fc5a246c	Colorize output ... Messages will be colorized: - Red for errors - Yellow for warnings or information - Green for fixes	2021-02-21 13:01:25 +02:00
Alan Orth	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
Alan Orth	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
Alan Orth	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
Alan Orth	431e6331c8	csv_metadata_quality/check.py: Format with black	2020-07-06 14:10:19 +03:00
Alan Orth	2a1566af62	csv_metadata_quality/check.py: Parameterize AGROVOC request	2020-07-06 13:44:46 +03:00
Alan Orth	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
Alan Orth	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
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	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	d97dcd19db	Format with black	2019-08-29 01:10:39 +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	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	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	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	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	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	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	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	87b1997051	Fix whitespace errors found by flake8	2019-07-28 17:47:28 +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	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	aaf3537ba4	Add check for invalid multi-value separators	2019-07-26 23:48:24 +03:00