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140 lines
7.2 KiB
Markdown
140 lines
7.2 KiB
Markdown
---
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title: "January, 2020"
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date: 2020-01-06T10:48:30+02:00
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author: "Alan Orth"
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categories: ["Notes"]
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---
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## 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
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- Last week Altmetric responded about the [item](https://hdl.handle.net/10568/97087) that had a lower score than than its DOI
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- The score is now linked to the DOI
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- 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
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- Another [item](https://hdl.handle.net/10568/81236) that had the same problem in 2019 has also been fixed
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## 2020-01-07
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- Peter Ballantyne highlighted one more WLE [item](https://hdl.handle.net/10568/101286) that is missing the Altmetric score that its DOI has
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- The DOI has a score of 259, but the Handle has no score at all
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- I [tweeted](https://twitter.com/mralanorth/status/1214471427157626881) the CGSpace repository link
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<!--more-->
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## 2020-01-08
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- Export a list of authors from CGSpace for Peter Ballantyne to look through and correct:
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```
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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;
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COPY 68790
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```
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- As I always have encoding issues with files Peter sends, I tried to convert it to some Windows encoding, but got an error:
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```
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$ iconv -f utf-8 -t windows-1252 /tmp/2020-01-08-authors.csv -o /tmp/2020-01-08-authors-windows.csv
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iconv: illegal input sequence at position 104779
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```
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- According to [this trick](https://www.datafix.com.au/BASHing/2018-09-13.html) the troublesome character is on line 5227:
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```
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$ awk 'END {print NR": "$0}' /tmp/2020-01-08-authors-windows.csv
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5227: "Oue
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$ sed -n '5227p' /tmp/2020-01-08-authors.csv | xxd -c1
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00000000: 22 "
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00000001: 4f O
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00000002: 75 u
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00000003: 65 e
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00000004: cc .
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00000005: 81 .
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00000006: 64 d
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00000007: 72 r
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```
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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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```
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<e> 101, Hex 65, Octal 145 < ́> 769, Hex 0301, Octal 1401
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```
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- 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...
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- Other encodings like `windows-1251` and `windows-1257` also fail on different characters like "ž" and "é" that _are_ legitimate UTF-8 characters
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- Then there is the issue of Russian, Chinese, etc characters, which are simply not representable in any of those encodings
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- 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
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- 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
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## 2020-01-14
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- 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
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- I manually ran it on the server as the DSpace user and it said "Moving: 51633080 into core statistics-2019"
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- After a few hours it died with the same error that I had seen in the log from the first run:
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```
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Exception: Read timed out
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java.net.SocketTimeoutException: Read timed out
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```
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- I am not sure how I will fix that shard...
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- I discovered a very interesting tool called [ftfy](https://github.com/LuminosoInsight/python-ftfy) that attempts to fix errors in UTF-8
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- I'm curious to start checking input files with this to see what it highlights
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- 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:
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- `<e> 101, Hex 65, Octal 145 < ́> 769, Hex 0301, Octal 1401`
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- `<é> 233, Hex 00e9, Oct 351, Digr e'`
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- 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)!
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- 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):
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```
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In [7]: unicodedata.is_normalized('NFC', 'é')
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Out[7]: False
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In [8]: unicodedata.is_normalized('NFC', 'é')
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Out[8]: True
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```
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## 2020-01-15
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- 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)
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- Generate ILRI and Bioversity subject lists for Elizabeth Arnaud from Bioversity:
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```
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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;
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COPY 144
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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;
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COPY 1325
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```
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- She will be meeting with FAO and will look over the terms to see if they can add some to AGROVOC
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- I noticed a few errors in the ILRI subjects so I fixed them locally and on CGSpace (linode18) using my `fix-metadata.py` script:
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```
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$ ./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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```
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## 2020-01-16
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- Extract a list of CIAT subjects from CGSpace for Elizabeth Arnaud from Bioversity:
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```
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dspace=# \COPY (SELECT DISTINCT text_value as "cg.subject.ciat", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 122 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-01-16-ciat-subjects.csv WITH CSV HEADER;
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COPY 35
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```
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- Start examining the 175 IITA records that Bosede originally sent in October, 2019 (201907.xls)
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- We had delayed processing them because DSpace Test (linode19) was testing CG Core v2 implementation for the last few months
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- Sisay uploaded the records to DSpace Test as [IITA_201907_Jan13](https://dspacetest.cgiar.org/handle/10568/106567)
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- I started first with basic sanity checks using my csv-metadata-quality tool and found twenty-two items with extra whitespace, invalid multi-value separators, and duplicates, which means Sisay did not do any quality checking on the data
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- I corrected one invalid AGROVOC subject
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- Validate and normalize affiliations against our 2019-04 list using reconcile-csv and OpenRefine:
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- `$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id`
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- I always forget how to copy the reconciled values in OpenRefine, but you need to make a new colum and populate it using this GREL: `if(cell.recon.matched, cell.recon.match.name, value)`
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## 2020-01-20
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- Last week Atmire sent a quotation for the DSpace 6 upgrade that I had requested a few weeks ago
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- I forwarded it to Peter et al for their comment
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- Visit CodeObia to discuss the next phase of AReS development
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<!-- vim: set sw=2 ts=2: -->
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