## January, 2020

Mon Jan 06, 2020 by Alan Orth in Notes

## 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

Read more →

## December, 2019

Sun Dec 01, 2019 by Alan Orth in Notes

## 2019-12-01

- Upgrade CGSpace (linode18) to Ubuntu 18.04:
  - Check any packages that have residual configs and purge them:
  - # dpkg -l | grep -E ‘^rc’ | awk ‘{print $2}’ | xargs dpkg -P
  - Make sure all packages are up to date and the package manager is up to date, then reboot:

    # apt update && apt full-upgrade
    # apt-get autoremove && apt-get autoclean
    # dpkg -C
    # reboot

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## November, 2019

Mon Nov 04, 2019 by Alan Orth in Notes

## 2019-11-04

- Peter noticed that there were 5.2 million hits on CGSpace in 2019-10 according to the Atmire usage statistics
  - I looked in the nginx logs and see 4.6 million in the access logs, and 1.2 million in the API logs:

    # zcat --force /var/log/nginx/*access.log.*.gz | grep -cE "[0-9]{1,2}/Oct/2019"
    4671942
    # zcat --force /var/log/nginx/{rest,oai,statistics}.log.*.gz | grep -cE "[0-9]{1,2}/Oct/2019"
    1277694

- So 4.6 million from XMLUI and another 1.2 million from API requests
- Let’s see how many of the REST API requests were for bitstreams (because they are counted in Solr stats):

    # zcat --force /var/log/nginx/rest.log.*.gz | grep -c -E "[0-9]{1,2}/Oct/2019"
    1183456
    # zcat --force /var/log/nginx/rest.log.*.gz | grep -E "[0-9]{1,2}/Oct/2019" | grep -c -E "/rest/bitstreams"
    106781

Read more →

## October, 2019

Tue Oct 01, 2019 by Alan Orth in Notes

2019-10-01 Udana from IWMI asked me for a CSV export of their community on CGSpace I exported it, but a quick run through the csv-metadata-quality tool shows that there are some low-hanging fruits we can fix before I send him the data I will limit the scope to the titles, regions, subregions, and river basins for now to manually fix some non-breaking spaces (U+00A0) there that would otherwise be removed by the csv-metadata-quality script’s “unneccesary Unicode” fix: $ csvcut -c 'id,dc. Read more →

## September, 2019

Sun Sep 01, 2019 by Alan Orth in Notes

## 2019-09-01

- Linode emailed to say that CGSpace (linode18) had a high rate of outbound traffic for several hours this morning
- Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:

    # zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E "01/Sep/2019:0" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
        440 17.58.101.255
        441 157.55.39.101
        485 207.46.13.43
        728 169.60.128.125
        730 207.46.13.108
        758 157.55.39.9
        808 66.160.140.179
        814 207.46.13.212
       2472 163.172.71.23
       6092 3.94.211.189
    # zcat --force /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E "01/Sep/2019:0" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
         33 2a01:7e00::f03c:91ff:fe16:fcb
         57 3.83.192.124
         57 3.87.77.25
         57 54.82.1.8
        822 2a01:9cc0:47:1:1a:4:0:2
       1223 45.5.184.72
       1633 172.104.229.92
       5112 205.186.128.185
       7249 2a01:7e00::f03c:91ff:fe18:7396
       9124 45.5.186.2

Read more →

## August, 2019

Sat Aug 03, 2019 by Alan Orth in Notes

## 2019-08-03

- Look at Bioversity’s latest migration CSV and now I see that Francesco has cleaned up the extra columns and the newline at the end of the file, but many of the column headers have an extra space in the name…

## 2019-08-04

- Deploy ORCID identifier updates requested by Bioversity to CGSpace
- Run system updates on CGSpace (linode18) and reboot it
  - Before updating it I checked Solr and verified that all statistics cores were loaded properly…
  - After rebooting, all statistics cores were loaded… wow, that’s lucky.
- Run system updates on DSpace Test (linode19) and reboot it

Read more →

## July, 2019

Mon Jul 01, 2019 by Alan Orth in Notes

## 2019-07-01

- Create an “AfricaRice books and book chapters” collection on CGSpace for AfricaRice
- Last month Sisay asked why the following “most popular” statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
  - DSpace Test
  - CGSpace
- Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community

Read more →

## June, 2019

Sun Jun 02, 2019 by Alan Orth in Notes

## 2019-06-02

- Merge the Solr filterCache and XMLUI ISI journal changes to the `5_x-prod` branch and deploy on CGSpace
- Run system updates on CGSpace (linode18) and reboot it

## 2019-06-03

- Skype with Marie-Angélique and Abenet about CG Core v2

Read more →

## May, 2019

Wed May 01, 2019 by Alan Orth in Notes

## 2019-05-01

- Help CCAFS with regenerating some item thumbnails after they uploaded new PDFs to some items on CGSpace
- A user on the dspace-tech mailing list offered some suggestions for troubleshooting the problem with the inability to delete certain items
  - Apparently if the item is in the `workflowitem` table it is submitted to a workflow
  - And if it is in the `workspaceitem` table it is in the pre-submitted state
- The item seems to be in a pre-submitted state, so I tried to delete it from there:

    dspace=# DELETE FROM workspaceitem WHERE item_id=74648;
    DELETE 1

- But after this I tried to delete the item from the XMLUI and it is still present…

Read more →

## April, 2019

Mon Apr 01, 2019 by Alan Orth in Notes

## 2019-04-01

- Meeting with AgroKnow to discuss CGSpace, ILRI data, AReS, GARDIAN, etc
  - They asked if we had plans to enable RDF support in CGSpace
- There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today
  - I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!

    # cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep 'Spore-192-EN-web.pdf' | grep -E '(18.196.196.108|18.195.78.144|18.195.218.6)' | awk '{print $9}' | sort | uniq -c | sort -n | tail -n 5
       4432 200

- In the last two weeks there have been 47,000 downloads of this same exact PDF by these three IP addresses
- Apply country and region corrections and deletions on DSpace Test and CGSpace:

    $ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-9-countries.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.country -m 228 -t ACTION -d
    $ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.region -m 231 -t action -d
    $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p 'fuuu' -m 228 -f cg.coverage.country -d
    $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p 'fuuu' -m 231 -f cg.coverage.region -d

Read more →