cgspace-notes/content/post/2017-12.md

---
title: "December, 2017"
date: 2017-12-01T13:53:54+03:00
author: "Alan Orth"
tags: ["Notes"]
---

## 2017-12-01

- Uptime Robot noticed that CGSpace went down
- The logs say "Timeout waiting for idle object"
- PostgreSQL activity says there are 115 connections currently
- The list of connections to XMLUI and REST API for today:

<!--more-->

```
# cat /var/log/nginx/rest.log  /var/log/nginx/rest.log.1  /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -E "1/Dec/2017" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
    763 2.86.122.76
    907 207.46.13.94
   1018 157.55.39.206
   1021 157.55.39.235
   1407 66.249.66.70
   1411 104.196.152.243
   1503 50.116.102.77
   1805 66.249.66.90
   4007 70.32.83.92
   6061 45.5.184.196
```

- The number of DSpace sessions isn't even that high:

```
$ cat /home/cgspace.cgiar.org/log/dspace.log.2017-12-01 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
5815
```

- Connections in the last two hours:

```
# cat /var/log/nginx/rest.log  /var/log/nginx/rest.log.1  /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -E "1/Dec/2017:(09|10)" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail                                                      
     78 93.160.60.22
    101 40.77.167.122
    113 66.249.66.70
    129 157.55.39.206
    130 157.55.39.235
    135 40.77.167.58
    164 68.180.229.254
    177 87.100.118.220
    188 66.249.66.90
    314 2.86.122.76
```

- What the fuck is going on?
- I've never seen this 2.86.122.76 before, it has made quite a few unique Tomcat sessions today:

```
$ grep 2.86.122.76 /home/cgspace.cgiar.org/log/dspace.log.2017-12-01 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
822
```

- Appears to be some new bot:

```
2.86.122.76 - - [01/Dec/2017:09:02:53 +0000] "GET /handle/10568/78444?show=full HTTP/1.1" 200 29307 "-" "Mozilla/3.0 (compatible; Indy Library)"
```

- I restarted Tomcat and everything came back up
- I can add Indy Library to the Tomcat crawler session manager valve but it would be nice if I could simply remap the useragent in nginx
- I will also add 'Drupal' to the Tomcat crawler session manager valve because there are Drupals out there harvesting and they should be considered as bots

```
# cat /var/log/nginx/rest.log  /var/log/nginx/rest.log.1  /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -E "1/Dec/2017" | grep Drupal | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
      3 54.75.205.145
      6 70.32.83.92
     14 2a01:7e00::f03c:91ff:fe18:7396
     46 2001:4b99:1:1:216:3eff:fe2c:dc6c
    319 2001:4b99:1:1:216:3eff:fe76:205b
```

## 2017-12-03

- Linode alerted that CGSpace's load was 327.5% from 6 to 8 AM again

## 2017-12-04

- Linode alerted that CGSpace's load was 255.5% from 8 to 10 AM again
- I looked at the Munin stats on DSpace Test (linode02) again to see how the PostgreSQL tweaks from a few weeks ago were holding up:

![DSpace Test PostgreSQL connections month](/cgspace-notes/2017/12/postgres-connections-month.png)

- The results look fantastic! So the `random_page_cost` tweak is massively important for informing the PostgreSQL scheduler that there is no "cost" to accessing random pages, as we're on an SSD!
- I guess we could probably even reduce the PostgreSQL connections in DSpace / PostgreSQL after using this
- Run system updates on DSpace Test (linode02) and reboot it
- I'm going to enable the PostgreSQL `random_page_cost` tweak on CGSpace
- For reference, here is the past month's connections:

![CGSpace PostgreSQL connections month](/cgspace-notes/2017/12/postgres-connections-month-cgspace.png)

## 2017-12-05

- Linode alerted again that the CPU usage on CGSpace was high this morning from 8 to 10 AM
- CORE updated the entry for CGSpace on their index: https://core.ac.uk/search?q=repositories.id:(1016)&fullTextOnly=false
- Linode alerted again that the CPU usage on CGSpace was high this evening from 8 to 10 PM

## 2017-12-06

- Linode alerted again that the CPU usage on CGSpace was high this morning from 6 to 8 AM
- Uptime Robot alerted that the server went down and up around 8:53 this morning
- Uptime Robot alerted that CGSpace was down and up again a few minutes later
- I don't see any errors in the DSpace logs but I see in nginx's access.log that UptimeRobot was returned with HTTP 499 status (Client Closed Request)
- Looking at the REST API logs I see some new client IP I haven't noticed before:

```
# cat /var/log/nginx/rest.log /var/log/nginx/rest.log.1 | grep -E "6/Dec/2017" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
     18 95.108.181.88
     19 68.180.229.254
     30 207.46.13.151
     33 207.46.13.110
     38 40.77.167.20
     41 157.55.39.223
     82 104.196.152.243
   1529 50.116.102.77
   4005 70.32.83.92
   6045 45.5.184.196
```

- 50.116.102.77 is apparently in the US on websitewelcome.com

## 2017-12-07

- Uptime Robot reported a few times today that CGSpace was down and then up
- At one point Tsega restarted Tomcat
- I never got any alerts about high load from Linode though...
- I looked just now and see that there are 121 PostgreSQL connections!
- The top users right now are:

```
# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -E "7/Dec/2017" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail 
    838 40.77.167.11
    939 66.249.66.223
   1149 66.249.66.206
   1316 207.46.13.110
   1322 207.46.13.151
   1323 2001:da8:203:2224:c912:1106:d94f:9189
   1414 157.55.39.223
   2378 104.196.152.243
   2662 66.249.66.219
   5110 124.17.34.60
```

- We've never seen 124.17.34.60 yet, but it's really hammering us!
- Apparently it is from China, and here is one of its user agents:

```
Mozilla/5.0 (compatible; MSIE 9.0; Windows NT 6.2; Win64; x64; Trident/7.0; LCTE)
```

- It is responsible for 4,500 Tomcat sessions today alone:

```
$ grep 124.17.34.60 /home/cgspace.cgiar.org/log/dspace.log.2017-12-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
4574
```

- I've adjusted the nginx IP mapping that I set up last month to account for 124.17.34.60 and 124.17.34.59 using a regex, as it's the same bot on the same subnet
- I was running the DSpace cleanup task manually and it hit an error:

```
$ /home/cgspace.cgiar.org/bin/dspace cleanup -v
...
Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
  Detail: Key (bitstream_id)=(144666) is still referenced from table "bundle".
```

- The solution is like I discovered in [2017-04](/cgspace-notes/2017-04), to set the `primary_bitstream_id` to null:

```
dspace=# update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (144666);
UPDATE 1
```

## 2017-12-13

- Linode alerted that CGSpace was using high CPU from 10:13 to 12:13 this morning

## 2017-12-16

- Re-work the XMLUI base theme to allow child themes to override the header logo's image and link destination: [#349](https://github.com/ilri/DSpace/pull/349)
- This required a little bit of work to restructure the XSL templates
- Optimize PNG and SVG image assets in the CGIAR base theme using pngquant and svgo: [#350](https://github.com/ilri/DSpace/pull/350)

## 2017-12-17

- Reboot DSpace Test to get new Linode Linux kernel
- Looking at CCAFS bulk import for Magdalena Haman (she originally sent them in November but some of the thumbnails were missing and dates were messed up so she resent them now)
- A few issues with the data and thumbnails:
  - Her thumbnail files all use capital JPG so I had to rename them to lowercase: `rename -fc *.JPG`
  - thumbnail20.jpg is 1.7MB so I have to resize it
  - I also had to add the .jpg to the thumbnail string in the CSV
  - The thumbnail11.jpg is missing
  - The dates are in super long ISO8601 format (from Excel?) like `2016-02-07T00:00:00Z` so I converted them to simpler forms in GREL: `value.toString("yyyy-MM-dd")`
  - I trimmed the whitespaces in a few fields but it wasn't many
  - Rename her thumbnail column to filename, and format it so SAFBuilder adds the files to the thumbnail bundle with this GREL in OpenRefine: `value + "__bundle:THUMBNAIL"`
  - Rename dc.identifier.status and dc.identifier.url columns to cg.identifier.status and cg.identifier.url
  - Item 4 has weird characters in citation, ie: Nagoya et de Trait
  - Some author names need normalization, ie: `Aggarwal, Pramod` and `Aggarwal, Pramod K.`
  - Something weird going on with duplicate authors that have the same text value, like `Berto, Jayson C.` and `Balmeo, Katherine P.`
  - I will send her feedback on some author names like UNEP and ICRISAT and ask her for the missing thumbnail11.jpg
- I did a test import of the data locally after building with SAFBuilder but for some reason I had to specify the collection (even though the collections were specified in the `collection` field)

```
$ JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8" ~/dspace/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/89338 --source /Users/aorth/Downloads/2016\ bulk\ upload\ thumbnails/SimpleArchiveFormat --mapfile=/tmp/ccafs.map &> /tmp/ccafs.log
```