2020-01-06
- Open a ticket with Atmire to request a quote for the upgrade to DSpace 6
- Last week Altmetric responded about the item that had a lower score than than its DOI
- The score is now linked to the DOI
- Another item that had the same problem in 2019 has now also linked to the score for its DOI
- Another item that had the same problem in 2019 has also been fixed
2020-01-07
- Peter Ballantyne highlighted one more WLE item 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 the CGSpace repository link
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 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 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!
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 tool in 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
- 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)