---
title: "June, 2021"
date: 2021-06-01T10:51:07+03:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2021-06-01

- IWMI notified me that AReS was down with an HTTP 502 error
  - Looking at UptimeRobot I see it has been down for 33 hours, but I never got a notification
  - I don't see anything in the Elasticsearch container logs, or the systemd journal on the host, but I notice that the `angular_nginx` container isn't running
  - I simply started it and AReS was running again:

<!--more-->

```console
$ docker-compose -f docker/docker-compose.yml start angular_nginx
```

- Margarita from CCAFS emailed me to say that workflow alerts haven't been working lately
  - I guess this is related to the SMTP issues last week
  - I had fixed the config, but didn't restart Tomcat so DSpace didn't load the new variables
  - I ran all system updates on CGSpace (linode18) and DSpace Test (linode26) and rebooted the servers

## 2021-06-03

- Meeting with AMCOW and IWMI to discuss AMCOW getting IWMI's content into the new AMCOW Knowledge Hub
  - At first we spent some time talking about DSpace communities/collections and the REST API, but then they said they actually prefer to send queries to sites on the fly and cache them in Redis for some time
  - That's when I thought they could perhaps use the OpenSearch, but I can't remember if it's possible to limit by community, or only collection...
  - Looking now, I see there is a "scope" parameter that can be used for community or collection, for example:

```
https://cgspace.cgiar.org/open-search/discover?query=subject:water%20scarcity&scope=10568/16814&order=DESC&rpp=100&sort_by=2&start=1
```

- That will sort by date issued (see: `webui.itemlist.sort-option.2` in dspace.cfg), give 100 results per page, and start on item 1
- Otherwise, another alternative would be to use the IWMI CSV that we are already exporting every week
- Fill out the *CGIAR-AGROVOC Task Group: Survey on the current CGIAR use of AGROVOC* survey on behalf of CGSpace

## 2021-06-06

- The Elasticsearch indexes are messed up so I dumped and re-created them correctly:

```console
curl -XDELETE 'http://localhost:9200/openrxv-items-final'
curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
curl -XPUT 'http://localhost:9200/openrxv-items-final'
curl -XPUT 'http://localhost:9200/openrxv-items-temp'
curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{"actions" : [{"add" : { "index" : "openrxv-items-final", "alias" : "openrxv-items"}}]}'
elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items-final --type=data --limit=1000
```

- Then I started a harvesting on AReS

## 2021-06-07

- The harvesting on AReS completed successfully
- Provide feedback to FAO on how we use AGROVOC for their "AGROVOC call for use cases"

## 2021-06-10

- Skype with Moayad to discuss AReS harvesting improvements
  - He will work on a plugin that reads the XML sitemap to get all item IDs and checks whether we have them or not

## 2021-06-14

- Dump and re-create indexes on AReS (as above) so I can do a harvest

## 2021-06-16

- Looking at the Solr statistics on CGSpace for last month I see many requests from hosts using seemingly normal Windows browser user agents, but using the MSN bot's DNS
  - For example, user agent `Mozilla/5.0 (compatible; MSIE 9.0; Windows NT 6.0; Trident/5.0;  Trident/5.0)` with DNS `msnbot-131-253-25-91.search.msn.com.`
  - I queried Solr for all hits using the MSN bot DNS (`dns:*msnbot* AND dns:*.msn.com.`) and found 457,706
  - I extracted their IPs using Solr's CSV format and ran them through my `resolve-addresses.py` script and found that they all belong to MICROSOFT-CORP-MSN-AS-BLOCK (AS8075)
  - Note that [Microsoft's docs say that reverse lookups on Bingbot IPs will always have "search.msn.com"](https://www.bing.com/webmasters/help/how-to-verify-bingbot-3905dc26) so it is safe to purge these as non-human traffic
  - I purged the hits with `ilri/check-spider-ip-hits.sh` (though I had to do it in 3 batches because I forgot to increase the `facet.limit` so I was only getting them 100 at a time)
- Moayad sent a pull request a few days ago to re-work the harvesting on OpenRXV
  - It will hopefully also fix the duplicate and missing items issues
  - I had a Skype with him to discuss
  - I got it running on podman-compose, but I had to fix the storage permissions on the Elasticsearch volume after the first time it tries (and fails) to run:

```console
$ podman unshare chown 1000:1000 /home/aorth/.local/share/containers/storage/volumes/docker_esData_7/_data
```

- The new OpenRXV harvesting method by Moayad uses pages of 10 items instead of 100 and it's much faster
  - I harvested 90,000+ items from DSpace Test in ~3 hours
  - There seem to be some issues with the health check step though, as I see it is requesting one restricted item 600,000+ times...

## 2021-06-17

- I ported my ilri/resolve-addresses.py script that uses IPAPI.co to use the local GeoIP2 databases
  - The new script is ilri/resolve-addresses-geoip2.py and it is much faster and works offline with no API rate limits
- Teams meeting with the CGIAR Metadata Working group to discuss CGSpace and open repositories and the way forward
- More work with Moayad on OpenRXV harvesting issues
  - Using a JSON export from elasticdump we debugged the duplicate checker plugin and found that there are indeed duplicates:

```console
$ grep -oE '"handle":"[[:digit:]]+/[[:digit:]]+"' openrxv-items_data.json | awk -F: '{print $2}' | wc -l
90459
$ grep -oE '"handle":"[[:digit:]]+/[[:digit:]]+"' openrxv-items_data.json | awk -F: '{print $2}' | sort | uniq | wc -l
90380
$ grep -oE '"handle":"[[:digit:]]+/[[:digit:]]+"' openrxv-items_data.json | awk -F: '{print $2}' | sort | uniq -c | sort -h
...
      2 "10568/99409"
      2 "10568/99410"
      2 "10568/99411"
      2 "10568/99516"
      3 "10568/102093"
      3 "10568/103524"
      3 "10568/106664"
      3 "10568/106940"
      3 "10568/107195"
      3 "10568/96546"
```

## 2021-06-20

- Udana asked me to update their IWMI subjects from `farmer managed irrigation systems` to `farmer-led irrigation`
  - First I extracted the IWMI community from CGSpace:

```console
$ dspace metadata-export -i 10568/16814 -f /tmp/2021-06-20-IWMI.csv
```

- Then I used `csvcut` to extract just the columns I needed and do the replacement into a new CSV:

```console
$ csvcut -c 'id,dcterms.subject[],dcterms.subject[en_US]' /tmp/2021-06-20-IWMI.csv | sed 's/farmer managed irrigation systems/farmer-led irrigation/' > /tmp/2021-06-20-IWMI-new-subjects.csv
```

- Then I uploaded the resulting CSV to CGSpace, updating 161 items
- Start a harvest on AReS
- I found [a bug](https://jira.lyrasis.org/browse/DS-1977) and [a patch](https://github.com/DSpace/DSpace/pull/2584) for the private items showing up in the DSpace sitemap bug
  - The fix is super simple, I should try to apply it

## 2021-06-21

- The AReS harvesting finished, but the indexes got messed up again
- I was looking at the JSON export I made yesterday and trying to understand the situation with duplicates
  - We have 90,000+ items, but only 85,000 unique:

```console
$ grep -E '"repo":"CGSpace"' openrxv-items_data.json | grep -oE '"handle":"[[:digit:]]+/[[:alnum:]]+"' | wc -l
90937
$ grep -E '"repo":"CGSpace"' openrxv-items_data.json | grep -oE '"handle":"[[:digit:]]+/[[:alnum:]]+"' | sort -u | wc -l
85709
```

- So those could be duplicates from the way we harvest pages, but they could also be from mappings...
  - Manually inspecting the duplicates where handles appear more than once:

```console
$ grep -E '"repo":"CGSpace"' openrxv-items_data.json | grep -oE '"handle":"[[:digit:]]+/[[:alnum:]]+"' | sort | uniq -c | sort -h
```

- Unfortunately I found no pattern:
  - Some appear twice in the Elasticsearch index, but appear in only one collection
  - Some appear twice in the Elasticsearch index, and appear in *two* collections
  - Some appear twice in the Elasticsearch index, but appear in three collections (!)
- So really we need to just check whether a handle exists before we insert it
- I tested the [pull request for DS-1977](https://github.com/DSpace/DSpace/pull/2584) that adjusts the sitemap generation code to exclude private items
  - It applies cleanly and seems to work, but we don't actually have any private items
  - The issue we are having with AReS hitting restricted items in the sitemap is that the items have restricted metadata, not that they are private
- Testing the [pull request for DS-4065](https://github.com/DSpace/DSpace/pull/2275) where the REST API's `/rest/items` endpoint is not aware of private items and returns an incorrect number of items
  - This is most easily seen by setting a low limit in `/rest/items`, making one of the items private, and requesting items again with the same limit
  - I confirmed the issue on the current DSpace 6 Demo:

```console
$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq length
5
$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq '.[].handle'
"10673/4"
"10673/3"
"10673/6"
"10673/5"
"10673/7"
# log into DSpace Demo XMLUI as admin and make one item private (for example 10673/6)
$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq length       
4
$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq '.[].handle' 
"10673/4"
"10673/3"
"10673/5"
"10673/7"
```

- I tested the pull request on DSpace Test and it works, so I left a note on GitHub and Jira
- Last week I noticed that the Gender Platform website is using "cgspace.cgiar.org" links for CGSpace, instead of handles
  - I emailed Fabio and Marianne to ask them to please use the Handle links
- I tested the [pull request for DS-4271](https://github.com/DSpace/DSpace/pull/2543) where Discovery filters of type "contains" don't work as expected when the user's search term has spaces
  - I tested with filter "farmer managed irrigation systems" on DSpace Test
  - Before the patch I got 293 results, and the few I checked didn't have the expected metadata value
  - After the patch I got 162 results, and all the items I checked had the exact metadata value I was expecting
- I tested a fresh harvest from my local AReS on DSpace Test with the DS-4065 REST API patch and here are my results:
  - 90459 in final from last harvesting
  - 90307 in temp after new harvest
  - 90327 in temp after start plugins
- The 90327 number seems closer to the "real" number of items on CGSpace...
  - Seems close, but not entirely correct yet:

```console
$ grep -oE '"handle":"[[:digit:]]+/[[:digit:]]+"' openrxv-items_data-local-ds-4065.json | wc -l
90327
$ grep -oE '"handle":"[[:digit:]]+/[[:digit:]]+"' openrxv-items_data-local-ds-4065.json | sort -u | wc -l
90317
```

## 2021-06-22

- Make a [pull request](https://github.com/atmire/COUNTER-Robots/pull/43) to the COUNTER-Robots project to add two new user agents: crusty and newspaper
  - These two bots have made ~3,000 requests on CGSpace
  - Then I added them to our local bot override in CGSpace (until the above pull request is merged) and ran my bot checking script:

```console
$ ./ilri/check-spider-hits.sh -f dspace/config/spiders/agents/ilri -p   
Purging 1339 hits from RI\/1\.0 in statistics
Purging 447 hits from crusty in statistics
Purging 3736 hits from newspaper in statistics

Total number of bot hits purged: 5522
```

- Surprised to see RI/1.0 in there because it's been in the override file for a while
- Looking at the 2021 statistics in Solr I see a few more suspicious user agents:
  - `PostmanRuntime/7.26.8`
  - `node-fetch/1.0 (+https://github.com/bitinn/node-fetch)`
  - `Photon/1.0`
  - `StatusCake_Pagespeed_indev`
  - `node-superagent/3.8.3`
  - `cortex/1.0`
- These bots account for ~42,000 hits in our statistics... I will just purge them and add them to our local override, but I can't be bothered to submit them to COUNTER-Robots since I'd have to look up the information for each one

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