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

---
title: "January, 2020"
date: 2020-01-06T10:48:30+02:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2020-01-06

- 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

- 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

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## 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
```

- ~~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:

```
<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

- 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

- 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
```

## 2020-01-16

- Extract a list of CIAT subjects from CGSpace for Elizabeth Arnaud from Bioversity:

```
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;
COPY 35
```

- Start examining the 175 IITA records that Bosede originally sent in October, 2019 (201907.xls)
  - We had delayed processing them because DSpace Test (linode19) was testing CG Core v2 implementation for the last few months
  - Sisay uploaded the records to DSpace Test as [IITA_201907_Jan13](https://dspacetest.cgiar.org/handle/10568/106567)
  - 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
  - I corrected one invalid AGROVOC subject
  - Validate and normalize affiliations against our 2019-04 list using reconcile-csv and OpenRefine:
    - `$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id`
    - 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)`

## 2020-01-20

- Last week Atmire sent a quotation for the DSpace 6 upgrade that I had requested a few weeks ago
  - I forwarded it to Peter et al for their comment
  - We decided that we should probably buy enough credits to cover the upgrade and have 100 remaining for future development
- Visit CodeObia to discuss the next phase of AReS development

## 2020-01-21

- Create two accounts on CGSpace for CTA users
- Marie-Angelique finally responded to some of the pull requests I made on the CG Core v2 repository last month:
  - Merged: [HTML syntax fixes](https://github.com/AgriculturalSemantics/cg-core/pull/16)
  - Merged: [Add LICENSE file](https://github.com/AgriculturalSemantics/cg-core/pull/17)
  - Merged: [Build main.css using npm build](https://github.com/AgriculturalSemantics/cg-core/pull/18)
  - Approved a [wider scope for `cg.peer-reviewed`](https://github.com/AgriculturalSemantics/cg-core/issues/14) (renaming the field and using non-boolean values), but there is more discussion needed
- I opened a new [pull request](https://github.com/AgriculturalSemantics/cg-core/pull/24) on the cg-core repository validate and fix the formatting of the HTML files
- Create more issues for OpenRXV:
  - Based on Peter's feedback on the [text for labels and tooltips](https://github.com/ilri/OpenRXV/issues/33)
  - Based on Peter's feedback for the [export icon](https://github.com/ilri/OpenRXV/issues/35)
  - Based on Peter's feedback for the [sort options](https://github.com/ilri/OpenRXV/issues/31)
  - Based on Abenet's feedback that [PDF and Word exports are not working](https://github.com/ilri/OpenRXV/issues/34)

## 2020-01-22

- I tried to create a MaxMind account so I can download the GeoLite2-City database with a license key, but their server refuses to accept me:

```
Sorry, we were not able to create your account. Please ensure that you are using an email that is not disposable, and that you are not connecting via a proxy or VPN.
```

- They started [limiting public access to the database in December, 2019 due to GDPR and CCPA](https://blog.maxmind.com/2019/12/18/significant-changes-to-accessing-and-using-geolite2-databases/)
  - This will be a problem in the future (see [DS-4409](https://jira.lyrasis.org/browse/DS-4409))

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