--- title: "April, 2019" date: 2019-04-01T09:00:43+03:00 author: "Alan Orth" tags: ["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 ``` ## 2019-04-02 - CTA says the Amazon IPs are AWS gateways for real user traffic - I was trying to add Felix Shaw's account back to the Administrators group on DSpace Test, but I couldn't find his name in the user search of the groups page - If I searched for "Felix" or "Shaw" I saw other matches, included one for his personal email address! - I ended up finding him via searching for his email address ## 2019-04-03 - Maria from Bioversity emailed me a list of new ORCID identifiers for their researchers so I will add them to our controlled vocabulary - First I need to extract the ones that are unique from their list compared to our existing one: ``` $ cat dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/bioversity.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u > /tmp/2019-04-03-orcid-ids.txt ``` - We currently have 1177 unique ORCID identifiers, and this brings our total to 1237! - Next I will resolve all their names using my `resolve-orcids.py` script: ``` $ ./resolve-orcids.py -i /tmp/2019-04-03-orcid-ids.txt -o 2019-04-03-orcid-ids.txt -d ``` - After that I added the XML formatting, formatted the file with tidy, and sorted the names in vim - One user's name has changed so I will update those using my `fix-metadata-values.py` script: ``` $ ./fix-metadata-values.py -i 2019-04-03-update-orcids.csv -db dspace -u dspace -p 'fuuu' -f cg.creator.id -m 240 -t correct -d ``` - I created a pull request and merged the changes to the 5_x-prod branch ([#417](https://github.com/ilri/DSpace/pull/417)) - A few days ago I noticed some weird update process for the statistics-2018 Solr core and I see it's still going: ``` 2019-04-03 16:34:02,262 INFO org.dspace.statistics.SolrLogger @ Updating : 1754500/21701 docs in http://localhost:8081/solr//statistics-2018 ``` - Interestingly, there are 5666 occurences, and they are mostly for the 2018 core: ``` $ grep 'org.dspace.statistics.SolrLogger @ Updating' /home/cgspace.cgiar.org/log/dspace.log.2019-04-03 | awk '{print $11}' | sort | uniq -c 1 3 http://localhost:8081/solr//statistics-2017 5662 http://localhost:8081/solr//statistics-2018 ``` - I will have to keep an eye on it because nothing should be updating 2018 stats in 2019... ## 2019-04-05 - Uptime Robot reported that CGSpace (linode18) went down tonight - I see there are lots of PostgreSQL connections: ``` $ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c 5 dspaceApi 10 dspaceCli 250 dspaceWeb ``` - I still see those weird messages about updating the statistics-2018 Solr core: ``` 2019-04-05 21:06:53,770 INFO org.dspace.statistics.SolrLogger @ Updating : 2444600/21697 docs in http://localhost:8081/solr//statistics-2018 ``` - Looking at `iostat 1 10` I also see some CPU steal has come back, and I can confirm it by looking at the Munin graphs: ![CPU usage week](/cgspace-notes/2019/04/cpu-week.png) - The other thing visible there is that the past few days the load has spiked to 500% and I don't think it's a coincidence that the Solr updating thing is happening... - I ran all system updates and rebooted the server - The load was lower on the server after reboot, but Solr didn't come back up properly according to the Solr Admin UI: ``` statistics-2017: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher ``` - I restarted it again and all the Solr cores came up properly... ## 2019-04-06 - Udana asked why item [10568/91278](https://cgspace.cgiar.org/handle/10568/91278) didn't have an Altmetric badge on CGSpace, but on the [WLE website](https://wle.cgiar.org/food-and-agricultural-innovation-pathways-prosperity) it does - I looked and saw that the WLE website is using the Altmetric score associated with the DOI, and that the Handle has no score at all - I tweeted the item and I assume this will link the Handle with the DOI in the system - Twenty minutes later I see the same Altmetric score (9) on CGSpace - Linode sent an alert that there was high CPU usage this morning on CGSpace (linode18) and these were the top IPs in the webserver access logs around the time: ``` # zcat --force /var/log/nginx/{access,error,library-access}.log /var/log/nginx/{access,error,library-access}.log.1 | grep -E "06/Apr/2019:(06|07|08|09)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 222 18.195.78.144 245 207.46.13.58 303 207.46.13.194 328 66.249.79.33 564 207.46.13.210 566 66.249.79.62 575 40.77.167.66 1803 66.249.79.59 2834 2a01:4f8:140:3192::2 9623 45.5.184.72 # zcat --force /var/log/nginx/{rest,oai}.log /var/log/nginx/{rest,oai}.log.1 | grep -E "06/Apr/2019:(06|07|08|09)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 31 66.249.79.62 41 207.46.13.210 42 40.77.167.66 54 42.113.50.219 132 66.249.79.59 785 2001:41d0:d:1990:: 1164 45.5.184.72 2014 50.116.102.77 4267 45.5.186.2 4893 205.186.128.185 ``` - `45.5.184.72` is in Colombia so it's probably CIAT, and I see they are indeed trying to get crawl the Discover pages on CIAT's datasets collection: ``` GET /handle/10568/72970/discover?filtertype_0=type&filtertype_1=author&filter_relational_operator_1=contains&filter_relational_operator_0=equals&filter_1=&filter_0=Dataset&filtertype=dateIssued&filter_relational_operator=equals&filter=2014 ``` - Their user agent is the one I added to the badbots list in nginx last week: "GuzzleHttp/6.3.3 curl/7.47.0 PHP/7.0.30-0ubuntu0.16.04.1" - They made 22,000 requests to Discover on this collection today alone (and it's only 11AM): ``` # cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep "06/Apr/2019" | grep 45.5.184.72 | grep -oE '/handle/[0-9]+/[0-9]+/discover' | sort | uniq -c 22077 /handle/10568/72970/discover ``` - Yesterday they made 43,000 requests and we actually blocked most of them: ``` # zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep "05/Apr/2019" | grep 45.5.184.72 | grep -oE '/handle/[0-9]+/[0-9]+/discover' | sort | uniq -c 43631 /handle/10568/72970/discover # zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep "05/Apr/2019" | grep 45.5.184.72 | grep -E '/handle/[0-9]+/[0-9]+/discover' | awk '{print $9}' | sort | uniq -c 142 200 43489 503 ``` - I need to find a contact at CIAT to tell them to use the REST API rather than crawling Discover - Maria from Bioversity recommended that we use the phrase "AGROVOC subject" instead of "Subject" in Listings and Reports - I made a pull request to update this and merged it to the `5_x-prod` branch ([#418](https://github.com/ilri/DSpace/pull/418))