cgspace-notes/content/posts/2020-01.md

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2020-01-06 10:14:44 +01:00
---
title: "January, 2020"
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date: 2020-01-06T10:48:30+02:00
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author: "Alan Orth"
categories: ["Notes"]
---
2020-01-07 11:24:29 +01:00
## 2020-01-06
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- Open [a ticket](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=706) with Atmire to request a quote for the upgrade to DSpace 6
- Last week Altmetric responded about the [item](https://hdl.handle.net/10568/97087) that had a lower score than than its DOI
- The score is now linked to the DOI
- Another [item](https://handle.hdl.net/10568/91278) that had the same problem in 2019 has now also linked to the score for its DOI
- Another [item](https://hdl.handle.net/10568/81236) that had the same problem in 2019 has also been fixed
2020-01-07 11:24:29 +01:00
## 2020-01-07
- Peter Ballantyne highlighted one more WLE [item](https://hdl.handle.net/10568/101286) that is missing the Altmetric score that its DOI has
- The DOI has a score of 259, but the Handle has no score at all
- I [tweeted](https://twitter.com/mralanorth/status/1214471427157626881) the CGSpace repository link
2020-01-08 14:33:56 +01:00
<!--more-->
## 2020-01-08
- Export a list of authors from CGSpace for Peter Ballantyne to look through and correct:
```
dspace=# \COPY (SELECT DISTINCT text_value as "dc.contributor.author", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 3 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-01-08-authors.csv WITH CSV HEADER;
COPY 68790
```
- As I always have encoding issues with files Peter sends, I tried to convert it to some Windows encoding, but got an error:
```
$ iconv -f utf-8 -t windows-1252 /tmp/2020-01-08-authors.csv -o /tmp/2020-01-08-authors-windows.csv
iconv: illegal input sequence at position 104779
```
- According to [this trick](https://www.datafix.com.au/BASHing/2018-09-13.html) the troublesome character is on line 5227:
```
$ awk 'END {print NR": "$0}' /tmp/2020-01-08-authors-windows.csv
5227: "Oue
$ sed -n '5227p' /tmp/2020-01-08-authors.csv | xxd -c1
00000000: 22 "
00000001: 4f O
00000002: 75 u
00000003: 65 e
00000004: cc .
00000005: 81 .
00000006: 64 d
00000007: 72 r
```
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- ~~According to the blog post linked above the troublesome character is probably the "High Octect Preset" (81)~~, which vim identifies (using `ga` on the character) as:
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```
<e> 101, Hex 65, Octal 145 < ́> 769, Hex 0301, Octal 1401
```
- If I understand the situation correctly it sounds like this means that the character is not actually encoded as UTF-8, so it's stored incorrectly in the database...
- Other encodings like `windows-1251` and `windows-1257` also fail on different characters like "ž" and "é" that _are_ legitimate UTF-8 characters
- Then there is the issue of Russian, Chinese, etc characters, which are simply not representable in any of those encodings
- I think the solution is to upload it to Google Docs, or just send it to him and deal with each case manually in the corrections he sends me
- Re-deploy DSpace Test (linode19) with a fresh snapshot of the CGSpace database and assetstore, and using the `5_x-prod` (no CG Core v2) branch
2020-01-14 19:40:41 +01:00
## 2020-01-14
- I checked the yearly Solr statistics sharding cron job that should have run on 2020-01 on CGSpace (linode18) and saw that there was an error
- I manually ran it on the server as the DSpace user and it said "Moving: 51633080 into core statistics-2019"
- After a few hours it died with the same error that I had seen in the log from the first run:
```
Exception: Read timed out
java.net.SocketTimeoutException: Read timed out
```
- I am not sure how I will fix that shard...
- I discovered a very interesting tool called [ftfy](https://github.com/LuminosoInsight/python-ftfy) that attempts to fix errors in UTF-8
- I'm curious to start checking input files with this to see what it highlights
- I ran it on the authors file from last week and it converted characters like those with Spanish accents from multi-byte sequences (I don't know what it's called?) to digraphs (é→é), which vim identifies as:
- `<e> 101, Hex 65, Octal 145 < ́> 769, Hex 0301, Octal 1401`
- `<é> 233, Hex 00e9, Oct 351, Digr e'`
- Ah hah! We need to be [normalizing characters into their canonical forms](https://withblue.ink/2019/03/11/why-you-need-to-normalize-unicode-strings.html)!
- In Python 3.8 we can even [check if the string is normalized using the `unicodedata` library](https://docs.python.org/3/library/unicodedata.html):
```
In [7]: unicodedata.is_normalized('NFC', 'é')
Out[7]: False
In [8]: unicodedata.is_normalized('NFC', 'é')
Out[8]: True
```
2020-01-15 12:51:35 +01:00
## 2020-01-15
- I added support for Unicode normalization to my [csv-metadata-quality](https://github.com/ilri/csv-metadata-quality) tool in [v0.4.0](https://github.com/ilri/csv-metadata-quality/releases/tag/v0.4.0)
- Generate ILRI and Bioversity subject lists for Elizabeth Arnaud from Bioversity:
```
dspace=# \COPY (SELECT DISTINCT text_value as "cg.subject.ilri", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 203 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-01-15-ilri-subjects.csv WITH CSV HEADER;
COPY 144
dspace=# \COPY (SELECT DISTINCT text_value as "cg.subject.bioversity", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 120 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-01-15-bioversity-subjects.csv WITH CSV HEADER;
COPY 1325
```
- She will be meeting with FAO and will look over the terms to see if they can add some to AGROVOC
- I noticed a few errors in the ILRI subjects so I fixed them locally and on CGSpace (linode18) using my `fix-metadata.py` script:
```
$ ./fix-metadata-values.py -i 2020-01-15-fix-8-ilri-subjects.csv -db dspace -u dspace -p 'fuuu' -f cg.subject.ilri -m 203 -t correct -d
```
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