cgspace-notes/content/posts/2019-11.md

---
title: "November, 2019"
date: 2019-11-04T12:20:30+02:00
author: "Alan Orth"
categories: ["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
```

<!--more-->

- The types of requests in the access logs are (by lazily extracting the sixth field in the nginx log)

```
# zcat --force /var/log/nginx/*access.log.*.gz | grep -E "[0-9]{1,2}/Oct/2019" | awk '{print $6}' | sed 's/"//' | sort | uniq -c | sort -n
      1 PUT
      8 PROPFIND
    283 OPTIONS
  30102 POST
  46581 HEAD
4594967 GET
```

- Two very active IPs are 34.224.4.16 and 34.234.204.152, which made over 360,000 requests in October:

```
# zcat --force /var/log/nginx/*access.log.*.gz | grep -E "[0-9]{1,2}/Oct/2019" | grep -c -E '(34\.224\.4\.16|34\.234\.204\.152)'
365288
```

- Their user agent is one I've never seen before:

```
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_1) AppleWebKit/600.2.5 (KHTML, like Gecko) Version/8.0.2 Safari/600.2.5 (Amazonbot/0.1; +https://developer.amazon.com/support/amazonbot)
```

- Most of them seem to be to community or collection discover and browse results pages like `/handle/10568/103/discover`:

# zcat --force /var/log/nginx/*access.log.*.gz | grep -E "[0-9]{1,2}/Oct/2019" | grep Amazonbot | grep -o -E "GET /(bitstream|discover|handle)" | sort | uniq -c
   6566 GET /bitstream
 351928 GET /handle
# zcat --force /var/log/nginx/*access.log.*.gz | grep -E "[0-9]{1,2}/Oct/2019" | grep Amazonbot | grep -E "GET /(bitstream|discover|handle)" | grep -c discover
214209
# zcat --force /var/log/nginx/*access.log.*.gz | grep -E "[0-9]{1,2}/Oct/2019" | grep Amazonbot | grep -E "GET /(bitstream|discover|handle)" | grep -c browse
86874
```

- As far as I can tell, none of their requests are counted in the Solr statistics:

```
$ http --print b 'http://localhost:8081/solr/statistics/select?q=(ip%3A34.224.4.16+OR+ip%3A34.234.204.152)&rows=0&wt=json&indent=true'
```

- Still, those requests are CPU intensive so I will add their user agent to the "badbots" rate limiting in nginx to reduce the impact on server load
- After deploying it I checked by setting my user agent to Amazonbot and making a few requests (which were denied with HTTP 503):

```
$ http --print Hh 'https://dspacetest.cgiar.org/handle/10568/1/discover' User-Agent:"Amazonbot/0.1"
```

- On the topic of spiders, I have been wanting to update DSpace's default list of spiders in `config/spiders/agents`, perhaps by dropping a new list in from [Atmire's COUNTER-Robots](https://github.com/atmire/COUNTER-Robots) project
  - First I checked for a user agent that is in COUNTER-Robots, but NOT in the current `dspace/config/spiders/example` list
  - Then I made some item and bitstream requests on DSpace Test using that user agent:

```
$ http --print Hh 'https://dspacetest.cgiar.org/handle/10568/105487' User-Agent:"iskanie"
$ http --print Hh 'https://dspacetest.cgiar.org/handle/10568/105487' User-Agent:"iskanie"
$ http --print Hh 'https://dspacetest.cgiar.org/bitstream/handle/10568/105487/csl_Crane_oct2019.pptx?sequence=1&isAllowed=y' User-Agent:"iskanie"
```

- A bit later I checked Solr and found three requests from my IP with that user agent this month:

```
$ http --print b 'http://localhost:8081/solr/statistics/select?q=ip:73.178.9.24+AND+userAgent:iskanie&fq=dateYearMonth%3A2019-11&rows=0'
<?xml version="1.0" encoding="UTF-8"?>
<response>
<lst name="responseHeader"><int name="status">0</int><int name="QTime">1</int><lst name="params"><str name="q">ip:73.178.9.24 AND userAgent:iskanie</str><str name="fq">dateYearMonth:2019-11</str><str name="rows">0</str></lst></lst><result name="response" numFound="3" start="0"></result>
</response>
```

- Now I want to make similar requests with a user agent that is included in DSpace's current user agent list:

```
$ http --print Hh 'https://dspacetest.cgiar.org/handle/10568/105487' User-Agent:"celestial"
$ http --print Hh 'https://dspacetest.cgiar.org/handle/10568/105487' User-Agent:"celestial"
$ http --print Hh 'https://dspacetest.cgiar.org/bitstream/handle/10568/105487/csl_Crane_oct2019.pptx?sequence=1&isAllowed=y' User-Agent:"celestial"
```

- After twenty minutes I didn't see any requests in Solr, so I assume they did not get logged because they matched a bot list...
  - What's strange is that the Solr spider agent configuration in `dspace/config/modules/solr-statistics.cfg` points to a file that doesn't exist...

```
spider.agentregex.regexfile = ${dspace.dir}/config/spiders/Bots-2013-03.txt
```

- Apparently that is part of Atmire's CUA, despite being in a standard DSpace configuration file...
- I tried with some other garbage user agents like "fuuuualan" and they were visible in Solr
  - Now I want to try adding "iskanie" and "fuuuualan" to the list of spider regexes in `dspace/config/spiders/example` and then try to use DSpace's "mark spiders" feature to change them to "isBot:true" in Solr
  - I restarted Tomcat and ran `dspace stats-util -m` and it did some stuff for awhile, but I still don't see any items in Solr with `isBot:true`
  - According to `dspace-api/src/main/java/org/dspace/statistics/util/SpiderDetector.java` the patterns for user agents are loaded from any file in the `config/spiders/agents` directory
  - I downloaded the COUNTER-Robots list to DSpace Test and overwrote the example file, then ran `dspace stats-util -m` and still there were no new items marked as being bots in Solr, so I think there is still something wrong
  - Jesus, the code in `./dspace-api/src/main/java/org/dspace/statistics/util/StatisticsClient.java` says that `stats-util -m` marks spider requests by their IPs, not by their user agents... WTF:

```
else if (line.hasOption('m'))
{
    SolrLogger.markRobotsByIP();
}
```

- WTF again, there is actually a function called `markRobotByUserAgent()` that is never called anywhere!
  - It appears to be unimplemented...
  - I sent a message to the dspace-tech mailing list to ask if I should file an issue

## 2019-11-05

- I added "alanfuu2" to the example spiders file, restarted Tomcat, then made two requests to DSpace Test:

```
$ http --print Hh 'https://dspacetest.cgiar.org/handle/10568/105487' User-Agent:"alanfuuu1"
$ http --print Hh 'https://dspacetest.cgiar.org/handle/10568/105487' User-Agent:"alanfuuu2"
```

- After committing the changes in Solr I saw one request for "alanfuu1" and no requests for "alanfuu2":

```
$ http --print b 'http://localhost:8081/solr/statistics/update?commit=true'
$ http --print b 'http://localhost:8081/solr/statistics/select?q=userAgent:alanfuuu1&fq=dateYearMonth%3A2019-11' | xmllint --format - | grep numFound
  <result name="response" numFound="1" start="0">
$ http --print b 'http://localhost:8081/solr/statistics/select?q=userAgent:alanfuuu2&fq=dateYearMonth%3A2019-11' | xmllint --format - | grep numFound
  <result name="response" numFound="0" start="0"/>
```

- So basically it seems like a win to update the example file with the latest one from Atmire's COUNTER-Robots list
  - Even though the "mark by user agent" function is not working (see email to dspace-tech mailing list) DSpace will still not log Solr events from these user agents
- I'm curious how the special character matching is in Solr, so I will test two requests: one with "www.gnip.com" which is in the spider list, and one with "www.gnyp.com" which isn't:

```
$ http --print Hh 'https://dspacetest.cgiar.org/handle/10568/105487' User-Agent:"www.gnip.com"
$ http --print Hh 'https://dspacetest.cgiar.org/handle/10568/105487' User-Agent:"www.gnyp.com"
```

- Then commit changes to Solr so we don't have to wait:

```
$ http --print b 'http://localhost:8081/solr/statistics/update?commit=true'
$ http --print b 'http://localhost:8081/solr/statistics/select?q=userAgent:www.gnip.com&fq=dateYearMonth%3A2019-11' | xmllint --format - | grep numFound 
  <result name="response" numFound="0" start="0"/>
$ http --print b 'http://localhost:8081/solr/statistics/select?q=userAgent:www.gnyp.com&fq=dateYearMonth%3A2019-11' | xmllint --format - | grep numFound
  <result name="response" numFound="1" start="0">
```

- So the blocking seems to be working because "www\.gnip\.com" is one of the new patterns added to the spiders file...

## 2019-11-07

- CCAFS finally confirmed that they do indeed need the confusing new project tag that looks like a duplicate
  - They had proposed a batch of new tags in 2019-09 and we never merged them due to this uncertainty
  - I have now merged the changes in to the `5_x-prod` branch ([#432](https://github.com/ilri/DSpace/pull/432))
- I am reconsidering the move of `cg.identifier.dataurl` to `cg.hasMetadata` in CG Core v2
  - The values of this field are mostly links to data sets on Dataverse and partner sites
  - I opened an [issue on GitHub](https://github.com/AgriculturalSemantics/cg-core/issues/10) to ask Marie-Angelique for clarification
- Looking into CGSpace statistics again
  - I searched for hits in Solr from the BUbiNG bot and found 63,000 in the `statistics-2018` core:

```
$ http --print b 'http://localhost:8081/solr/statistics-2018/select?facet=true&facet.field=ip&facet.mincount=1&type:0&q=userAgent:BUbiNG*' | xmllint --format - | grep numFound
  <result name="response" numFound="62944" start="0">
```

  - Similar for com.plumanalytics, Grammarly, and ltx71!

```
$ http --print b 'http://localhost:8081/solr/statistics-2018/select?facet=true&facet.field=ip&facet.mincount=1&type:0&q=userAgent:
*com.plumanalytics*' | xmllint --format - | grep numFound
  <result name="response" numFound="28256" start="0">
$ http --print b 'http://localhost:8081/solr/statistics-2018/select?facet=true&facet.field=ip&facet.mincount=1&type:0&q=userAgent:*Grammarly*' | xmllint --format - | grep numFound
  <result name="response" numFound="6288" start="0">
$ http --print b 'http://localhost:8081/solr/statistics-2018/select?facet=true&facet.field=ip&facet.mincount=1&type:0&q=userAgent:*ltx71*' | xmllint --format - | grep numFound
  <result name="response" numFound="105663" start="0">
```

- Deleting these seems to work, for example the 105,000 ltx71 records from 2018:

```
$ http --print b 'http://localhost:8081/solr/statistics-2018/update?stream.body=<delete><query>userAgent:*ltx71*</query><query>type:0</query></delete>&commit=true'
$ http --print b 'http://localhost:8081/solr/statistics-2018/select?facet=true&facet.field=ip&facet.mincount=1&type:0&q=userAgent:*ltx71*' | xmllint --format - | grep numFound
  <result name="response" numFound="0" start="0"/>
``` 

- I wrote a quick bash script to check all these user agents against the CGSpace Solr statistics cores
  - For years 2010 until 2019 there are 1.6 million hits from these spider user agents
  - For 2019 alone there are 740,000, over half of which come from Unpaywall!
  - Looking at the facets I see there were about 200,000 hits from Unpaywall in 2019-10:

```
$ curl -s 'http://localhost:8081/solr/statistics/select?facet=true&facet.field=dateYearMonth&facet.mincount=1&facet.offset=0&facet.limit=
12&q=userAgent:*Unpaywall*' | xmllint --format - | less
...
  <lst name="facet_counts">
    <lst name="facet_queries"/>
    <lst name="facet_fields">
      <lst name="dateYearMonth">
        <int name="2019-10">198624</int>
        <int name="2019-05">88422</int>
        <int name="2019-06">79911</int>
        <int name="2019-09">67065</int>
        <int name="2019-07">39026</int>
        <int name="2019-08">36889</int>
        <int name="2019-04">36512</int>
        <int name="2019-11">760</int>
      </lst>
    </lst>
```

- That answers Peter's question about why the stats jumped in October...

## 2019-11-08

- I saw a bunch of user agents that have the literal string `User-Agent` in their user agent HTTP header, for example:
  - `User-Agent: Drupal (+http://drupal.org/)`
  - `User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.64 Safari/537.31`
  - `User-Agent:Mozilla/5.0 (compatible; MSIE 10.0; Windows NT 6.1; WOW64; Trident/6.0) IKU/7.0.5.9226;IKUCID/IKU;`
  - `User-Agent: Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 5.1; 360SE)`
  - `User-Agent:User-Agent:Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 5.1; Trident/4.0; GTB7.5; .NET4.0C)IKU/6.7.6.12189;IKUCID/IKU;IKU/6.7.6.12189;IKUCID/IKU;`
  - `User-Agent:Mozilla/5.0 (compatible; MSIE 10.0; Windows NT 6.1; WOW64; Trident/6.0) IKU/7.0.5.9226;IKUCID/IKU;`
- I filed [an issue](https://github.com/atmire/COUNTER-Robots/issues/27) on the COUNTER-Robots project to see if they agree to add `User-Agent:` to the list of robot user agents

## 2019-11-09

- Deploy the latest `5_x-prod` branch on CGSpace (linode19)
  - This includes the updated CCAFS phase II project tags and the updated spider user agents
- Run all system updates on CGSpace and reboot the server
  - After rebooting it seems that all Solr statistics cores came back up fine...
- I did some work to clean up my bot processing script and removed about 2 million hits from the statistics cores on CGSpace
  - The script is called `check-spider-hits.sh`
  - After a bunch of tests and checks I ran it for each statistics shard like so:

```
$ for shard in statistics statistics-2018 statistics-2017 statistics-2016 statistics-2015 stat
istics-2014 statistics-2013 statistics-2012 statistics-2011 statistics-2010; do ./check-spider-hits.sh -s $shard -p yes; done
```

- Open a [pull request](https://github.com/atmire/COUNTER-Robots/pull/28) against COUNTER-Robots to remove unnecessary escaping of dashes

## 2019-11-12

- Udana and Chandima emailed me to ask why [one of their WLE items](https://hdl.handle.net/10568/81236) that is mapped from IWMI only shows up in the IWMI "department" on the Altmetric dashboard
  - A [search in the IWMI department shows the item](https://www.altmetric.com/explorer/outputs?department_id%5B%5D=CGSpace%3Agroup%3Acom_10568_16814&q=Towards%20sustainable%20sanitation%20management)
  - A [search in the WLE department shows no results](https://www.altmetric.com/explorer/outputs?department_id%5B%5D=CGSpace%3Agroup%3Acom_10568_34494&q=Towards%20sustainable%20sanitation%20management)
  - I emailed Altmetric support to ask for help
- Also, while analysing this, I looked through some of the other top WLE items and fixed some metadata issues (adding `dc.rights`, fixing DOIs, adding ISSNs, etc) and noticed one issue with [an item](https://hdl.handle.net/10568/97087) that has an Altmetric score for its Handle (lower) despite it having a correct DOI (with a higher score)
  - I tweeted the Handle to see if the score would get linked once Altmetric noticed it

## 2019-11-13

- The [item with a low Altmetric score for its Handle](https://hdl.handle.net/10568/97087) that I tweeted yesterday still hasn't linked with the DOI's score
  - I tweeted it again with the Handle and the DOI
- Testing modifying some of the COUNTER-Robots patterns to use `[0-9]` instead of `\d` digit character type, as Solr's regex search can't use those

```
$ http --print Hh 'https://dspacetest.cgiar.org/handle/10568/105487' User-Agent:"Scrapoo/1"
$ http "http://localhost:8081/solr/statistics/update?commit=true"
$ http "http://localhost:8081/solr/statistics/select?q=userAgent:Scrapoo*" | xmllint --format - | grep numFound
  <result name="response" numFound="1" start="0">
$ http "http://localhost:8081/solr/statistics/select?q=userAgent:/Scrapoo\/[0-9]/" | xmllint --format - | grep numFound
  <result name="response" numFound="1" start="0">
```

- Nice, so searching with regex in Solr with `//` syntax works for those digits!
- I realized that it's easier to search Solr from curl via POST using this syntax:

```
$ curl -s "http://localhost:8081/solr/statistics/select" -d "q=userAgent:*Scrapoo*&rows=0")
```

- If the parameters include something like "[0-9]" then curl interprets it as a range and will make ten requests
  - You can disable this using the `-g` option, but there are other benefits to searching with POST, for example it seems that I have less issues with escaping special parameters when using Solr's regex search:

```
$ curl -s 'http://localhost:8081/solr/statistics/select' -d 'q=userAgent:/Postgenomic(\s|\+)v2/&rows=2'
```

- I updated the `check-spider-hits.sh` script to use the POST syntax, and I'm evaluating the feasability of including the regex search patterns from the spider agent file, as I had been filtering them out due to differences in PCRE and Solr regex syntax and issues with shell handling

## 2019-11-14

- IWMI sent a few new ORCID identifiers for us to add to our controlled vocabulary
- I will merge them with our existing list and then resolve their names using my `resolve-orcids.py` script:

```
$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/iwmi-orcids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2019-11-14-combined-orcids.txt
$ ./resolve-orcids.py -i /tmp/2019-11-14-combined-orcids.txt -o /tmp/2019-11-14-combined-names.txt -d
# sort names, copy to cg-creator-id.xml, add XML formatting, and then format with tidy (preserving accents)
$ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml
```

- I created a [pull request](https://github.com/ilri/DSpace/pull/437) and merged them into the `5_x-prod` branch
  - I will deploy them to CGSpace in the next few days
- Greatly improve my `check-spider-hits.sh` script to handle regular expressions in the spider agents patterns file
  - This allows me to detect and purge many more hits from the Solr statistics core
  - I've tested it quite a bit on DSpace Test, but I need to do a little more before I feel comfortable running the new code on CGSpace's Solr cores

## 2019-11-15

- Run the new version of `check-spider-hits.sh` on CGSpace's Solr statistics cores one by one, starting from the oldest just in case something goes wrong
- But then I noticed that some (all?) of the hits weren't actually getting purged, all of which were using regular expressions like:
  - `MetaURI[\+\s]API\/[0-9]\.[0-9]`
  - `FDM(\s|\+)[0-9]`
  - `Goldfire(\s|\+)Server`
  - `^Mozilla\/4\.0\+\(compatible;\)$`
  - `^Mozilla\/4\.0\+\(compatible;\+ICS\)$`
  - `^Mozilla\/4\.5\+\[en]\+\(Win98;\+I\)$`
- Upon closer inspection, the plus signs seem to be getting misinterpreted somehow in the delete, but not in the select!
- Plus signs are special in regular expressions, URLs, and Solr's Lucene query parser, so I'm actually not sure where the issue is
  - I tried to do URL encoding of the +, double escaping, etc... but nothing worked 
  - I'm going to ignore regular expressions that have pluses for now
- I think I might also have to ignore patterns that have percent signs, like `^\%?default\%?$`
- After I added the ignores and did some more testing I finally ran the `check-spider-hits.sh` on all CGSpace Solr statistics cores and these are the number of hits purged from each core:
  - statistics-2010: 113
  - statistics-2011: 7235
  - statistics-2012: 0
  - statistics-2013: 0
  - statistics-2014: 316
  - statistics-2015: 16809
  - statistics-2016: 41732
  - statistics-2017: 39207
  - statistics-2018: 295546
  - statistics: 1043373
- That's 1.4 million hits in addition to the 2 million I purged earlier this week...
- For posterity, the major contributors to the hits on the statistics core were:
  - Purging 812429 hits from curl\/ in statistics
  - Purging 48206 hits from facebookexternalhit\/ in statistics
  - Purging 72004 hits from PHP\/ in statistics
  - Purging 76072 hits from Yeti\/[0-9] in statistics
- Most of the curl hits were from CIAT in mid-2019, where they were using [GuzzleHttp](https://guzzle3.readthedocs.io/http-client/client.html) from PHP, which uses something like this for its user agent:

```
Guzzle/<Guzzle_Version> curl/<curl_version> PHP/<PHP_VERSION>
```

- Run system updates on DSpace Test and reboot the server

<!-- vim: set sw=2 ts=2: -->