November, 2017

Thu Nov 02, 2017 by Alan Orth in Notes

2017-11-01

The CORE developers responded to say they are looking into their bot not respecting our robots.txt

2017-11-02

Today there have been no hits by CORE and no alerts from Linode (coincidence?)

# grep -c "CORE" /var/log/nginx/access.log
0

Generate list of authors on CGSpace for Peter to go through and correct:

dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701

Abenet asked if it would be possible to generate a report of items in Listing and Reports that had “International Fund for Agricultural Development” as the only investor
I opened a ticket with Atmire to ask if this was possible: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=540
Work on making the thumbnails in the item view clickable
Basically, once you read the METS XML for an item it becomes easy to trace the structure to find the bitstream link

//mets:fileSec/mets:fileGrp[@USE='CONTENT']/mets:file/mets:FLocat[@LOCTYPE='URL']/@xlink:href

METS XML is available for all items with this pattern: /metadata/handle/10568/95947/mets.xml
I whipped up a quick hack to print a clickable link with this URL on the thumbnail but it needs to check a few corner cases, like when there is a thumbnail but no content bitstream!
Help proof fifty-three CIAT records for Sisay: https://dspacetest.cgiar.org/handle/10568/95895
A handful of issues with cg.place using format like “Lima, PE” instead of “Lima, Peru”
Also, some dates like with completely invalid format like “2010- 06” and “2011-3-28”
I also collapsed some consecutive whitespace on a handful of fields

2017-11-03

Atmire got back to us to say that they estimate it will take two days of labor to implement the change to Listings and Reports
I said I’d ask Abenet if she wants that feature

2017-11-04

I finished looking through Sisay’s CIAT records for the “Alianzas de Aprendizaje” data
I corrected about half of the authors to standardize them
Linode emailed this morning to say that the CPU usage was high again, this time at 6:14AM
It’s the first time in a few days that this has happened
I had a look to see what was going on, but it isn’t the CORE bot:

# awk '{print $1}' /var/log/nginx/access.log | sort -n | uniq -c | sort -h | tail
    306 68.180.229.31
    323 61.148.244.116
    414 66.249.66.91
    507 40.77.167.16
    618 157.55.39.161
    652 207.46.13.103
    666 157.55.39.254
   1173 104.196.152.243
   1737 66.249.66.90
  23101 138.201.52.218

138.201.52.218 is from some Hetzner server, and I see it making 40,000 requests yesterday too, but none before that:

# zgrep -c 138.201.52.218 /var/log/nginx/access.log*
/var/log/nginx/access.log:24403
/var/log/nginx/access.log.1:45958
/var/log/nginx/access.log.2.gz:0
/var/log/nginx/access.log.3.gz:0
/var/log/nginx/access.log.4.gz:0
/var/log/nginx/access.log.5.gz:0
/var/log/nginx/access.log.6.gz:0

It’s clearly a bot as it’s making tens of thousands of requests, but it’s using a “normal” user agent:

Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2227.0 Safari/537.36

For now I don’t know what this user is!

2017-11-05

Peter asked if I could fix the appearance of “International Livestock Research Institute” in the author lookup during item submission
It looks to be just an issue with the user interface expecting authors to have both a first and last name:

Author lookup Add author

But in the database the authors are correct (none with weird , / characters):

dspace=# select distinct text_value, authority, confidence from metadatavalue value where resource_type_id=2 and metadata_field_id=3 and text_value like 'International Livestock Research Institute%';
                 text_value                 |              authority               | confidence 
--------------------------------------------+--------------------------------------+------------
 International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c |          0
 International Livestock Research Institute | f4db1627-47cd-4699-b394-bab7eba6dadc |          0
 International Livestock Research Institute |                                      |         -1
 International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c |        600
 International Livestock Research Institute | f4db1627-47cd-4699-b394-bab7eba6dadc |         -1
 International Livestock Research Institute |                                      |        600
 International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c |         -1
 International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c |        500
(8 rows)

So I’m not sure if this is just a graphical glitch or if editors have to edit this metadata field prior to approval
Looking at monitoring Tomcat’s JVM heap with Prometheus, it looks like we need to use JMX + jmx_exporter
This guide shows how to enable JMX in Tomcat by modifying CATALINA_OPTS
I was able to successfully connect to my local Tomcat with jconsole!

2017-11-07

CGSpace when down and up a few times this morning, first around 3AM, then around 7
Tsega had to restart Tomcat 7 to fix it temporarily
I will start by looking at bot usage (access.log.1 includes usage until 6AM today):

# cat /var/log/nginx/access.log.1 | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
    619 65.49.68.184
    840 65.49.68.199
    924 66.249.66.91
   1131 68.180.229.254
   1583 66.249.66.90
   1953 207.46.13.103
   1999 207.46.13.80
   2021 157.55.39.161
   2034 207.46.13.36
   4681 104.196.152.243

104.196.152.243 seems to be a top scraper for a few weeks now:

# zgrep -c 104.196.152.243 /var/log/nginx/access.log*
/var/log/nginx/access.log:336
/var/log/nginx/access.log.1:4681
/var/log/nginx/access.log.2.gz:3531
/var/log/nginx/access.log.3.gz:3532
/var/log/nginx/access.log.4.gz:5786
/var/log/nginx/access.log.5.gz:8542
/var/log/nginx/access.log.6.gz:6988
/var/log/nginx/access.log.7.gz:7517
/var/log/nginx/access.log.8.gz:7211
/var/log/nginx/access.log.9.gz:2763

This user is responsible for hundreds and sometimes thousands of Tomcat sessions:

$ grep 104.196.152.243 dspace.log.2017-11-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
954
$ grep 104.196.152.243 dspace.log.2017-11-03 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
6199
$ grep 104.196.152.243 dspace.log.2017-11-01 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
7051

The worst thing is that this user never specifies a user agent string so we can’t lump it in with the other bots using the Tomcat Session Crawler Manager Valve
They don’t request dynamic URLs like “/discover” but they seem to be fetching handles from XMLUI instead of REST (and some with //handle, note the regex below):

# grep -c 104.196.152.243 /var/log/nginx/access.log.1
4681
# grep 104.196.152.243 /var/log/nginx/access.log.1 | grep -c -P 'GET //?handle'
4618

I just realized that ciat.cgiar.org points to 104.196.152.243, so I should contact Leroy from CIAT to see if we can change their scraping behavior
The next IP (207.46.13.36) seem to be Microsoft’s bingbot, but all its requests specify the “bingbot” user agent and there are no requests for dynamic URLs that are forbidden, like “/discover”:

$ grep -c 207.46.13.36 /var/log/nginx/access.log.1 
2034
# grep 207.46.13.36 /var/log/nginx/access.log.1 | grep -c "GET /discover"
0

The next IP (157.55.39.161) also seems to be bingbot, and none of its requests are for URLs forbidden by robots.txt either:

# grep 157.55.39.161 /var/log/nginx/access.log.1 | grep -c "GET /discover"
0

The next few seem to be bingbot as well, and they declare a proper user agent and do not request dynamic URLs like “/discover”:

# grep -c -E '207.46.13.[0-9]{2,3}' /var/log/nginx/access.log.1 
5997
# grep -E '207.46.13.[0-9]{2,3}' /var/log/nginx/access.log.1 | grep -c "bingbot"
5988
# grep -E '207.46.13.[0-9]{2,3}' /var/log/nginx/access.log.1 | grep -c "GET /discover"
0

The next few seem to be Googlebot, and they declare a proper user agent and do not request dynamic URLs like “/discover”:

# grep -c -E '66.249.66.[0-9]{2,3}' /var/log/nginx/access.log.1 
3048
# grep -E '66.249.66.[0-9]{2,3}' /var/log/nginx/access.log.1 | grep -c Google
3048
# grep -E '66.249.66.[0-9]{2,3}' /var/log/nginx/access.log.1 | grep -c "GET /discover"
0

The next seems to be Yahoo, which declares a proper user agent and does not request dynamic URLs like “/discover”:

# grep -c 68.180.229.254 /var/log/nginx/access.log.1 
1131
# grep  68.180.229.254 /var/log/nginx/access.log.1 | grep -c "GET /discover"
0

The last of the top ten IPs seems to be some bot with a weird user agent, but they are not behaving too well:

# grep -c -E '65.49.68.[0-9]{3}' /var/log/nginx/access.log.1 
2950
# grep -E '65.49.68.[0-9]{3}' /var/log/nginx/access.log.1 | grep -c "GET /discover"
330

Their user agents vary, ie:
- Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/61.0.3163.100 Safari/537.36
- Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.97 Safari/537.11
- Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 6.1; WOW64; Trident/7.0; SLCC2; .NET CLR 2.0.50727; .NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC 6.0; .NET4.0C; .NET4.0E)
I’ll just keep an eye on that one for now, as it only made a few hundred requests to dynamic discovery URLs
While it’s not in the top ten, Baidu is one bot that seems to not give a fuck:

# grep -c Baiduspider /var/log/nginx/access.log.1
8068
# grep Baiduspider /var/log/nginx/access.log.1 | grep -c -E "GET /(browse|discover)"
1431

According to their documentation their bot respects robots.txt, but I don’t see this being the case
I think I will end up blocking Baidu as well…
Next is for me to look and see what was happening specifically at 3AM and 7AM when the server crashed
I should look in nginx access.log, rest.log, oai.log, and DSpace’s dspace.log.2017-11-07
Here are the top IPs making requests to XMLUI from 2–8 AM:

# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E '07/Nov/2017:0[2-8]' | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
    279 66.249.66.91
    373 65.49.68.199
    446 68.180.229.254
    470 104.196.152.243
    470 197.210.168.174
    598 207.46.13.103
    603 157.55.39.161
    637 207.46.13.80
    703 207.46.13.36
    724 66.249.66.90

Of those, most are Google, Bing, Yahoo, etc, except 63.143.42.244 and 63.143.42.242 which are Uptime Robot
Here are the top IPs making requests to REST from 2–8 AM:

# cat /var/log/nginx/rest.log /var/log/nginx/rest.log.1 | grep -E '07/Nov/2017:0[2-8]' | awk '{print $1}' | sort -n | uniq -c | sort -h | tail                                                                        
      8 207.241.229.237
     10 66.249.66.90
     16 104.196.152.243
     25 41.60.238.61
     26 157.55.39.161
     27 207.46.13.103
     27 207.46.13.80
     31 207.46.13.36
   1498 50.116.102.77

The OAI requests during that same time period are nothing to worry about:

# cat /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E '07/Nov/2017:0[2-8]' | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
      1 66.249.66.92
      4 66.249.66.90
      6 68.180.229.254

The top IPs from dspace.log during the 2–8 AM period:

$ grep -E '2017-11-07 0[2-8]' dspace.log.2017-11-07 | grep -o -E 'ip_addr=[0-9.]+' | sort -n | uniq -c | sort -h | tail
    143 ip_addr=213.55.99.121
    181 ip_addr=66.249.66.91
    223 ip_addr=157.55.39.161
    248 ip_addr=207.46.13.80
    251 ip_addr=207.46.13.103
    291 ip_addr=207.46.13.36
    297 ip_addr=197.210.168.174
    312 ip_addr=65.49.68.199
    462 ip_addr=104.196.152.243
    488 ip_addr=66.249.66.90

These aren’t actually very interesting, as the top few are Google, CIAT, Bingbot, and a few other unknown scrapers
The number of requests isn’t even that high to be honest
As I was looking at these logs I noticed another heavy user (124.17.34.59) that was not active during this time period, but made many requests today alone:

# zgrep -c 124.17.34.59 /var/log/nginx/access.log*
/var/log/nginx/access.log:22581
/var/log/nginx/access.log.1:0
/var/log/nginx/access.log.2.gz:14
/var/log/nginx/access.log.3.gz:0
/var/log/nginx/access.log.4.gz:0
/var/log/nginx/access.log.5.gz:3
/var/log/nginx/access.log.6.gz:0
/var/log/nginx/access.log.7.gz:0
/var/log/nginx/access.log.8.gz:0
/var/log/nginx/access.log.9.gz:1

The whois data shows the IP is from China, but the user agent doesn’t really give any clues:

# grep 124.17.34.59 /var/log/nginx/access.log | awk -F'" ' '{print $3}' | sort | uniq -c | sort -h
    210 "Mozilla/5.0 (Windows NT 10.0; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/61.0.3163.100 Safari/537.36"
  22610 "Mozilla/5.0 (compatible; MSIE 9.0; Windows NT 6.2; Win64; x64; Trident/7.0; LCTE)"

A Google search for “LCTE bot” doesn’t return anything interesting, but this Stack Overflow discussion references the lack of information
So basically after a few hours of looking at the log files I am not closer to understanding what is going on!
I do know that we want to block Baidu, though, as it does not respect robots.txt
And as we speak Linode alerted that the outbound traffic rate is very high for the past two hours (about 12–14 hours)
At least for now it seems to be that new Chinese IP (124.17.34.59):

# grep -E "07/Nov/2017:1[234]:" /var/log/nginx/access.log | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
    198 207.46.13.103
    203 207.46.13.80
    205 207.46.13.36
    218 157.55.39.161
    249 45.5.184.221
    258 45.5.187.130
    386 66.249.66.90
    410 197.210.168.174
   1896 104.196.152.243
  11005 124.17.34.59

Seems 124.17.34.59 are really downloading all our PDFs, compared to the next top active IPs during this time!

# grep -E "07/Nov/2017:1[234]:" /var/log/nginx/access.log | grep 124.17.34.59 | grep -c pdf
5948
# grep -E "07/Nov/2017:1[234]:" /var/log/nginx/access.log | grep 104.196.152.243 | grep -c pdf
0

About CIAT, I think I need to encourage them to specify a user agent string for their requests, because they are not reuising their Tomcat session and they are creating thousands of sessions per day
All CIAT requests vs unique ones:

$ grep -Io -E 'session_id=[A-Z0-9]{32}:ip_addr=104.196.152.243' dspace.log.2017-11-07 | wc -l
3506
$ grep -Io -E 'session_id=[A-Z0-9]{32}:ip_addr=104.196.152.243' dspace.log.2017-11-07 | sort | uniq | wc -l
3506

I emailed CIAT about the session issue, user agent issue, and told them they should not scrape the HTML contents of communities, instead using the REST API
About Baidu, I found a link to their robots.txt tester tool
It seems like our robots.txt file is valid, and they claim to recognize that URLs like /discover should be forbidden (不允许, aka “not allowed”):

Baidu robots.txt tester

But they literally just made this request today:

180.76.15.136 - - [07/Nov/2017:06:25:11 +0000] "GET /discover?filtertype_0=crpsubject&filter_relational_operator_0=equals&filter_0=WATER%2C+LAND+AND+ECOSYSTEMS&filtertype=subject&filter_relational_operator=equals&filter=WATER+RESOURCES HTTP/1.1" 200 82265 "-" "Mozilla/5.0 (compatible; Baiduspider/2.0; +http://www.baidu.com/search/spider.html)"

Along with another thousand or so requests to URLs that are forbidden in robots.txt today alone:

# grep -c Baiduspider /var/log/nginx/access.log
3806
# grep Baiduspider /var/log/nginx/access.log | grep -c -E "GET /(browse|discover|search-filter)"
1085

I will think about blocking their IPs but they have 164 of them!

# grep "Baiduspider/2.0" /var/log/nginx/access.log | awk '{print $1}' | sort -n | uniq | wc -l
164

2017-11-08

Linode sent several alerts last night about CPU usage and outbound traffic rate at 6:13PM
Linode sent another alert about CPU usage in the morning at 6:12AM
Jesus, the new Chinese IP (124.17.34.59) has downloaded 22,000 PDFs in the last 24 hours:

# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E "0[78]/Nov/2017:" | grep 124.17.34.59 | grep -c pdf
22510

This is about 20,000 Tomcat sessions:

$ cat dspace.log.2017-11-07 dspace.log.2017-11-08 | grep -Io -E 'session_id=[A-Z0-9]{32}:ip_addr=124.17.34.59' | sort | uniq | wc -l
20733

I’m getting really sick of this
Sisay re-uploaded the CIAT records that I had already corrected earlier this week, erasing all my corrections
I had to re-correct all the publishers, places, names, dates, etc and apply the changes on DSpace Test