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January, 2018 2018-01-02T08:35:54-08:00 Alan Orth
Notes

2018-01-02

  • Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time
  • I didn't get any load alerts from Linode and the REST and XMLUI logs don't show anything out of the ordinary
  • The nginx logs show HTTP 200s until 02/Jan/2018:11:27:17 +0000 when Uptime Robot got an HTTP 500
  • In dspace.log around that time I see many errors like "Client closed the connection before file download was complete"
  • And just before that I see this:
Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
  • Ah hah! So the pool was actually empty!
  • I need to increase that, let's try to bump it up from 50 to 75
  • After that one client got an HTTP 499 but then the rest were HTTP 200, so I don't know what the hell Uptime Robot saw
  • I notice this error quite a few times in dspace.log:
2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
  • And there are many of these errors every day for the past month:
$ grep -c "Error while searching for sidebar facets" dspace.log.*
dspace.log.2017-11-21:4
dspace.log.2017-11-22:1
dspace.log.2017-11-23:4
dspace.log.2017-11-24:11
dspace.log.2017-11-25:0
dspace.log.2017-11-26:1
dspace.log.2017-11-27:7
dspace.log.2017-11-28:21
dspace.log.2017-11-29:31
dspace.log.2017-11-30:15
dspace.log.2017-12-01:15
dspace.log.2017-12-02:20
dspace.log.2017-12-03:38
dspace.log.2017-12-04:65
dspace.log.2017-12-05:43
dspace.log.2017-12-06:72
dspace.log.2017-12-07:27
dspace.log.2017-12-08:15
dspace.log.2017-12-09:29
dspace.log.2017-12-10:35
dspace.log.2017-12-11:20
dspace.log.2017-12-12:44
dspace.log.2017-12-13:36
dspace.log.2017-12-14:59
dspace.log.2017-12-15:104
dspace.log.2017-12-16:53
dspace.log.2017-12-17:66
dspace.log.2017-12-18:83
dspace.log.2017-12-19:101
dspace.log.2017-12-20:74
dspace.log.2017-12-21:55
dspace.log.2017-12-22:66
dspace.log.2017-12-23:50
dspace.log.2017-12-24:85
dspace.log.2017-12-25:62
dspace.log.2017-12-26:49
dspace.log.2017-12-27:30
dspace.log.2017-12-28:54
dspace.log.2017-12-29:68
dspace.log.2017-12-30:89
dspace.log.2017-12-31:53
dspace.log.2018-01-01:45
dspace.log.2018-01-02:34
  • Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let's Encrypt if it's just a handful of domains

2018-01-03

  • I woke up to more up and down of CGSpace, this time UptimeRobot noticed a few rounds of up and down of a few minutes each and Linode also notified of high CPU load from 12 to 2 PM
  • Looks like I need to increase the database pool size again:
$ grep -c "Timeout: Pool empty." dspace.log.2018-01-*
dspace.log.2018-01-01:0
dspace.log.2018-01-02:1972
dspace.log.2018-01-03:1909
  • For some reason there were a lot of "active" connections last night:

CGSpace PostgreSQL connections

  • The active IPs in XMLUI 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 "3/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
    607 40.77.167.141
    611 2a00:23c3:8c94:7800:392c:a491:e796:9c50
    663 188.226.169.37
    759 157.55.39.245
    887 68.180.229.254
   1037 157.55.39.175
   1068 216.244.66.245
   1495 66.249.64.91
   1934 104.196.152.243
   2219 134.155.96.78
  • 134.155.96.78 appears to be at the University of Mannheim in Germany
  • They identify as: Mozilla/5.0 (compatible; heritrix/3.2.0 +http://ifm.uni-mannheim.de)
  • This appears to be the Internet Archive's open source bot
  • They seem to be re-using their Tomcat session so I don't need to do anything to them just yet:
$ grep 134.155.96.78 dspace.log.2018-01-03 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
2
  • The API logs show the normal users:
# cat /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E "3/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
     32 207.46.13.182
     38 40.77.167.132
     38 68.180.229.254
     43 66.249.64.91
     46 40.77.167.141
     49 157.55.39.245
     79 157.55.39.175
   1533 50.116.102.77
   4069 70.32.83.92
   9355 45.5.184.196
  • In other related news I see a sizeable amount of requests coming from python-requests
  • For example, just in the last day there were 1700!
# 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 -c python-requests
1773
  • But they come from hundreds of IPs, many of which are 54.x.x.x:
# 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 python-requests | awk '{print $1}' | sort -n | uniq -c | sort -h | tail -n 30
      9 54.144.87.92
      9 54.146.222.143
      9 54.146.249.249
      9 54.158.139.206
      9 54.161.235.224
      9 54.163.41.19
      9 54.163.4.51
      9 54.196.195.107
      9 54.198.89.134
      9 54.80.158.113
     10 54.198.171.98
     10 54.224.53.185
     10 54.226.55.207
     10 54.227.8.195
     10 54.242.234.189
     10 54.242.238.209
     10 54.80.100.66
     11 54.161.243.121
     11 54.205.154.178
     11 54.234.225.84
     11 54.87.23.173
     11 54.90.206.30
     12 54.196.127.62
     12 54.224.242.208
     12 54.226.199.163
     13 54.162.149.249
     13 54.211.182.255
     19 50.17.61.150
     21 54.211.119.107
    139 164.39.7.62
  • I have no idea what these are but they seem to be coming from Amazon...
  • I guess for now I just have to increase the database connection pool's max active
  • It's currently 75 and normally I'd just bump it by 25 but let me be a bit daring and push it by 50 to 125, because I used to see at least 121 connections in pg_stat_activity before when we were using the shitty default pooling

2018-01-04

  • CGSpace went down and up a bunch of times last night and ILRI staff were complaining a lot last night
  • The XMLUI logs show this activity:
# 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 "4/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
    968 197.211.63.81
    981 213.55.99.121
   1039 66.249.64.93
   1258 157.55.39.175
   1273 207.46.13.182
   1311 157.55.39.191
   1319 157.55.39.197
   1775 66.249.64.78
   2216 104.196.152.243
   3366 66.249.64.91
  • Again we ran out of PostgreSQL database connections, even after bumping the pool max active limit from 50 to 75 to 125 yesterday!
2018-01-04 07:36:08,089 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-256] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:125; busy:125; idle:0; lastwait:5000].
  • So for this week that is the number one problem!
$ grep -c "Timeout: Pool empty." dspace.log.2018-01-*
dspace.log.2018-01-01:0
dspace.log.2018-01-02:1972
dspace.log.2018-01-03:1909
dspace.log.2018-01-04:1559
  • I will just bump the connection limit to 300 because I'm fucking fed up with this shit
  • Once I get back to Amman I will have to try to create different database pools for different web applications, like recently discussed on the dspace-tech mailing list
  • Create accounts on CGSpace for two CTA staff km4ard@cta.int and bheenick@cta.int

2018-01-05

  • Peter said that CGSpac was down last night and Tsega restarted Tomcat
  • I don't see any alerts from Linode or UptimeRobot, and there are no PostgreSQL connection errors in the dspace logs for today:
$ grep -c "Timeout: Pool empty." dspace.log.2018-01-*
dspace.log.2018-01-01:0
dspace.log.2018-01-02:1972
dspace.log.2018-01-03:1909
dspace.log.2018-01-04:1559
dspace.log.2018-01-05:0
  • Daniel asked for help with their DAGRIS server (linode2328112) that has no disk space
  • I had a look and there is one Apache 2 log file that is 73GB, with lots of this:
[Fri Jan 05 09:31:22.965398 2018] [:error] [pid 9340] [client 213.55.99.121:64476] WARNING: Unable to find a match for "9-16-1-RV.doc" in "/home/files/journals/6//articles/9/". Skipping this file., referer: http://dagris.info/reviewtool/index.php/index/install/upgrade
  • I will delete the log file for now and tell Danny
  • Also, I'm still seeing a hundred or so of the "ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer" errors in dspace logs, I need to search the dspace-tech mailing list to see what the cause is
  • I will run a full Discovery reindex in the mean time to see if it's something wrong with the Discovery Solr core
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b

real    110m43.985s
user    15m24.960s
sys     3m14.890s

2018-01-06

  • I'm still seeing Solr errors in the DSpace logs even after the full reindex yesterday:
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1983+TO+1989]': Encountered " "]" "] "" at line 1, column 32.
  • I posted a message to the dspace-tech mailing list to see if anyone can help

2018-01-09

  • Advise Sisay about blank lines in some IITA records
  • Generate a list of author affiliations for Peter to clean up:
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 = 'affiliation') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/affiliations.csv with csv;
COPY 4515

2018-01-10

  • I looked to see what happened to this year's Solr statistics sharding task that should have run on 2018-01-01 and of course it failed:
Moving: 81742 into core statistics-2010
Exception: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2010
org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2010
        at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:566)
        at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
        at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
        at org.dspace.statistics.SolrLogger.shardSolrIndex(SourceFile:2243)
        at org.dspace.statistics.util.StatisticsClient.main(StatisticsClient.java:106)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:226)
        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
Caused by: org.apache.http.client.ClientProtocolException
        at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:867)
        at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
        at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
        at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
        at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:448)
        ... 10 more
Caused by: org.apache.http.client.NonRepeatableRequestException: Cannot retry request with a non-repeatable request entity.  The cause lists the reason the original request failed.
        at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:659)
        at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:487)
        at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:863)
        ... 14 more
Caused by: java.net.SocketException: Connection reset
        at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:115)
        at java.net.SocketOutputStream.write(SocketOutputStream.java:155)
        at org.apache.http.impl.io.AbstractSessionOutputBuffer.flushBuffer(AbstractSessionOutputBuffer.java:159)
        at org.apache.http.impl.io.AbstractSessionOutputBuffer.write(AbstractSessionOutputBuffer.java:179)
        at org.apache.http.impl.io.ChunkedOutputStream.flushCacheWithAppend(ChunkedOutputStream.java:124)
        at org.apache.http.impl.io.ChunkedOutputStream.write(ChunkedOutputStream.java:181)
        at org.apache.http.entity.InputStreamEntity.writeTo(InputStreamEntity.java:132)
        at org.apache.http.entity.HttpEntityWrapper.writeTo(HttpEntityWrapper.java:89)
        at org.apache.http.impl.client.EntityEnclosingRequestWrapper$EntityWrapper.writeTo(EntityEnclosingRequestWrapper.java:108)
        at org.apache.http.impl.entity.EntitySerializer.serialize(EntitySerializer.java:117)
        at org.apache.http.impl.AbstractHttpClientConnection.sendRequestEntity(AbstractHttpClientConnection.java:265)
        at org.apache.http.impl.conn.ManagedClientConnectionImpl.sendRequestEntity(ManagedClientConnectionImpl.java:203)
        at org.apache.http.protocol.HttpRequestExecutor.doSendRequest(HttpRequestExecutor.java:236)
        at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:121)
        at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:685)
        ... 16 more
  • DSpace Test has the same error but with creating the 2017 core:
Moving: 2243021 into core statistics-2017
Exception: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2017
org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2017
        at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:566)
        at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
        at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
        at org.dspace.statistics.SolrLogger.shardSolrIndex(SourceFile:2243)
        at org.dspace.statistics.util.StatisticsClient.main(StatisticsClient.java:106)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:226)
        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
Caused by: org.apache.http.client.ClientProtocolException
        at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:867)
        at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
        at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
        at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
        at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:448)
        ... 10 more

$ http 'http://localhost:3000/solr/statistics/select?q=owningColl%3A*&wt=json&indent=true' | grep numFound 
  "response":{"numFound":48476327,"start":0,"docs":[
$ http 'http://localhost:3000/solr/statistics/select?q=-owningColl%3A*&wt=json&indent=true' | grep numFound
  "response":{"numFound":34879872,"start":0,"docs":[
  • I tested the dspace stats-util -s process on my local machine and it failed the same way
  • It doesn't seem to be helpful, but the dspace log shows this:
2018-01-10 10:51:19,301 INFO  org.dspace.statistics.SolrLogger @ Created core with name: statistics-2016
2018-01-10 10:51:19,301 INFO  org.dspace.statistics.SolrLogger @ Moving: 3821 records into core statistics-2016

$ grep -c "Timeout: Pool empty." dspace.log.2018-01-10 
0
  • The XMLUI logs show quite a bit of activity today:
# 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 "10/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
    951 207.46.13.159
    954 157.55.39.123
   1217 95.108.181.88
   1503 104.196.152.243
   6455 70.36.107.50
  11412 70.36.107.190
  16730 70.36.107.49
  17386 2607:fa98:40:9:26b6:fdff:feff:1c96
  21566 2607:fa98:40:9:26b6:fdff:feff:195d
  45384 2607:fa98:40:9:26b6:fdff:feff:1888
  • The user agent for the top six or so IPs are all the same:
"Mozilla/5.0 (Windows NT 6.3; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/38.0.2125.111 Safari/537.36"
  • whois says they come from Perfect IP
  • I've never seen those top IPs before, but they have created 50,000 Tomcat sessions today:
$ grep -E '(2607:fa98:40:9:26b6:fdff:feff:1888|2607:fa98:40:9:26b6:fdff:feff:195d|2607:fa98:40:9:26b6:fdff:feff:1c96|70.36.107.49|70.36.107.190|70.36.107.50)' /home/cgspace.cgiar.org/log/dspace.log.2018-01-10 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l                                                                                                                                                                                                  
49096
  • Rather than blocking their IPs, I think I might just add their user agent to the "badbots" zone with Baidu, because they seem to be the only ones using that user agent:
# 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 "Mozilla/5.0 (Windows NT 6.3; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/38.0.2125.111 Safari
/537.36" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
   6796 70.36.107.50
  11870 70.36.107.190
  17323 70.36.107.49
  19204 2607:fa98:40:9:26b6:fdff:feff:1c96
  23401 2607:fa98:40:9:26b6:fdff:feff:195d 
  47875 2607:fa98:40:9:26b6:fdff:feff:1888
  • I added the user agent to nginx's badbots limit req zone but upon testing the config I got an error:
# nginx -t
nginx: [emerg] could not build map_hash, you should increase map_hash_bucket_size: 64
nginx: configuration file /etc/nginx/nginx.conf test failed

# cat /proc/cpuinfo | grep cache_alignment | head -n1
cache_alignment : 64
  • On our servers that is 64, so I increased this parameter to 128 and deployed the changes to nginx
  • Almost immediately the PostgreSQL connections dropped back down to 40 or so, and UptimeRobot said the site was back up
  • So that's interesting that we're not out of PostgreSQL connections (current pool maxActive is 300!) but the system is "down" to UptimeRobot and very slow to use
  • Linode continues to test mitigations for Meltdown and Spectre: https://blog.linode.com/2018/01/03/cpu-vulnerabilities-meltdown-spectre/
  • I rebooted DSpace Test to see if the kernel will be updated (currently Linux 4.14.12-x86_64-linode92)... nope.
  • It looks like Linode will reboot the KVM hosts later this week, though
  • Udana from WLE asked if we could give him permission to upload CSVs to CGSpace (which would require super admin access)
  • Citing concerns with metadata quality, I suggested adding him on DSpace Test first
  • I opened a ticket with Atmire to ask them about DSpace 5.8 compatibility: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560

2018-01-11

  • The PostgreSQL and firewall graphs from this week show clearly the load from the new bot from PerfectIP.net yesterday:

PostgreSQL load Firewall load

  • Linode rebooted DSpace Test and CGSpace for their host hypervisor kernel updates
  • Following up with the Solr sharding issue on the dspace-tech mailing list, I noticed this interesting snippet in the Tomcat localhost_access_log at the time of my sharding attempt on my test machine:
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/statistics/select?q=type%3A2+AND+id%3A1&wt=javabin&version=2 HTTP/1.1" 200 107
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/statistics/select?q=*%3A*&rows=0&facet=true&facet.range=time&facet.range.start=NOW%2FYEAR-18YEARS&facet.range.end=NOW%2FYEAR%2B0YEARS&facet.range.gap=%2B1YEAR&facet.mincount=1&wt=javabin&version=2 HTTP/1.1" 200 447
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/admin/cores?action=STATUS&core=statistics-2016&indexInfo=true&wt=javabin&version=2 HTTP/1.1" 200 76
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/admin/cores?action=CREATE&name=statistics-2016&instanceDir=statistics&dataDir=%2FUsers%2Faorth%2Fdspace%2Fsolr%2Fstatistics-2016%2Fdata&wt=javabin&version=2 HTTP/1.1" 200 63
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/statistics/select?csv.mv.separator=%7C&q=*%3A*&fq=time%3A%28%5B2016%5C-01%5C-01T00%5C%3A00%5C%3A00Z+TO+2017%5C-01%5C-01T00%5C%3A00%5C%3A00Z%5D+NOT+2017%5C-01%5C-01T00%5C%3A00%5C%3A00Z%29&rows=10000&wt=csv HTTP/1.1" 200 2137630
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/statistics/admin/luke?show=schema&wt=javabin&version=2 HTTP/1.1" 200 16253
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "POST /solr//statistics-2016/update/csv?commit=true&softCommit=false&waitSearcher=true&f.previousWorkflowStep.split=true&f.previousWorkflowStep.separator=%7C&f.previousWorkflowStep.encapsulator=%22&f.actingGroupId.split=true&f.actingGroupId.separator=%7C&f.actingGroupId.encapsulator=%22&f.containerCommunity.split=true&f.containerCommunity.separator=%7C&f.containerCommunity.encapsulator=%22&f.range.split=true&f.range.separator=%7C&f.range.encapsulator=%22&f.containerItem.split=true&f.containerItem.separator=%7C&f.containerItem.encapsulator=%22&f.p_communities_map.split=true&f.p_communities_map.separator=%7C&f.p_communities_map.encapsulator=%22&f.ngram_query_search.split=true&f.ngram_query_search.separator=%7C&f.ngram_query_search.encapsulator=%22&f.containerBitstream.split=true&f.containerBitstream.separator=%7C&f.containerBitstream.encapsulator=%22&f.owningItem.split=true&f.owningItem.separator=%7C&f.owningItem.encapsulator=%22&f.actingGroupParentId.split=true&f.actingGroupParentId.separator=%7C&f.actingGroupParentId.encapsulator=%22&f.text.split=true&f.text.separator=%7C&f.text.encapsulator=%22&f.simple_query_search.split=true&f.simple_query_search.separator=%7C&f.simple_query_search.encapsulator=%22&f.owningComm.split=true&f.owningComm.separator=%7C&f.owningComm.encapsulator=%22&f.owner.split=true&f.owner.separator=%7C&f.owner.encapsulator=%22&f.filterquery.split=true&f.filterquery.separator=%7C&f.filterquery.encapsulator=%22&f.p_group_map.split=true&f.p_group_map.separator=%7C&f.p_group_map.encapsulator=%22&f.actorMemberGroupId.split=true&f.actorMemberGroupId.separator=%7C&f.actorMemberGroupId.encapsulator=%22&f.bitstreamId.split=true&f.bitstreamId.separator=%7C&f.bitstreamId.encapsulator=%22&f.group_name.split=true&f.group_name.separator=%7C&f.group_name.encapsulator=%22&f.p_communities_name.split=true&f.p_communities_name.separator=%7C&f.p_communities_name.encapsulator=%22&f.query.split=true&f.query.separator=%7C&f.query.encapsulator=%22&f.workflowStep.split=true&f.workflowStep.separator=%7C&f.workflowStep.encapsulator=%22&f.containerCollection.split=true&f.containerCollection.separator=%7C&f.containerCollection.encapsulator=%22&f.complete_query_search.split=true&f.complete_query_search.separator=%7C&f.complete_query_search.encapsulator=%22&f.p_communities_id.split=true&f.p_communities_id.separator=%7C&f.p_communities_id.encapsulator=%22&f.rangeDescription.split=true&f.rangeDescription.separator=%7C&f.rangeDescription.encapsulator=%22&f.group_id.split=true&f.group_id.separator=%7C&f.group_id.encapsulator=%22&f.bundleName.split=true&f.bundleName.separator=%7C&f.bundleName.encapsulator=%22&f.ngram_simplequery_search.split=true&f.ngram_simplequery_search.separator=%7C&f.ngram_simplequery_search.encapsulator=%22&f.group_map.split=true&f.group_map.separator=%7C&f.group_map.encapsulator=%22&f.owningColl.split=true&f.owningColl.separator=%7C&f.owningColl.encapsulator=%22&f.p_group_id.split=true&f.p_group_id.separator=%7C&f.p_group_id.encapsulator=%22&f.p_group_name.split=true&f.p_group_name.separator=%7C&f.p_group_name.encapsulator=%22&wt=javabin&version=2 HTTP/1.1" 409 156
  • The new core is created but when DSpace attempts to POST to it there is an HTTP 409 error
  • This is apparently a common Solr error code that means "version conflict": http://yonik.com/solr/optimistic-concurrency/
  • Looks like that bot from the PerfectIP.net host ended up making about 450,000 requests to XMLUI alone yesterday:
# 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 "Mozilla/5.0 (Windows NT 6.3; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/38.0.2125.111 Safari/537.36" | grep "10/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
  21572 70.36.107.50
  30722 70.36.107.190
  34566 70.36.107.49
 101829 2607:fa98:40:9:26b6:fdff:feff:195d
 111535 2607:fa98:40:9:26b6:fdff:feff:1c96
 161797 2607:fa98:40:9:26b6:fdff:feff:1888
  • Wow, I just figured out how to set the application name of each database pool in the JNDI config of Tomcat's server.xml:
<Resource name="jdbc/dspaceWeb" auth="Container" type="javax.sql.DataSource"
          driverClassName="org.postgresql.Driver"
          url="jdbc:postgresql://localhost:5432/dspacetest?ApplicationName=dspaceWeb"
          username="dspace"
          password="dspace"
          initialSize='5'
          maxActive='75'
          maxIdle='15'
          minIdle='5'
          maxWait='5000'
          validationQuery='SELECT 1'
          testOnBorrow='true' />
  • So theoretically I could name each connection "xmlui" or "dspaceWeb" or something meaningful and it would show up in PostgreSQL's pg_stat_activity table!
  • This would be super helpful for figuring out where load was coming from (now I wonder if I could figure out how to graph this)
  • Also, I realized that the db.jndi parameter in dspace.cfg needs to match the name value in your applicaiton's context—not the global one
  • Ah hah! Also, I can name the default DSpace connection pool in dspace.cfg as well, like:
db.url = jdbc:postgresql://localhost:5432/dspacetest?ApplicationName=dspaceDefault
  • With that it is super easy to see where PostgreSQL connections are coming from in pg_stat_activity

2018-01-12

  • I'm looking at the DSpace 6.0 Install docs and notice they tweak the number of threads in their Tomcat connector:
<!-- Define a non-SSL HTTP/1.1 Connector on port 8080 -->
<Connector port="8080"
           maxThreads="150"
           minSpareThreads="25"
           maxSpareThreads="75"
           enableLookups="false"
           redirectPort="8443"
           acceptCount="100"
           connectionTimeout="20000"
           disableUploadTimeout="true"
           URIEncoding="UTF-8"/>
  • In Tomcat 8.5 the maxThreads defaults to 200 which is probably fine, but tweaking minSpareThreads could be good
  • I don't see a setting for maxSpareThreads in the docs so that might be an error
  • Looks like in Tomcat 8.5 the default URIEncoding for Connectors is UTF-8, so we don't need to specify that manually anymore: https://tomcat.apache.org/tomcat-8.5-doc/config/http.html
  • Ooh, I just the acceptorThreadCount setting (in Tomcat 7 and 8.5):
The number of threads to be used to accept connections. Increase this value on a multi CPU machine, although you would never really need more than 2. Also, with a lot of non keep alive connections, you might want to increase this value as well. Default value is 1.
  • That could be very interesting

2018-01-13

  • Still testing DSpace 6.2 on Tomcat 8.5.24
  • Catalina errors at Tomcat 8.5 startup:
13-Jan-2018 13:59:05.245 WARNING [main] org.apache.tomcat.dbcp.dbcp2.BasicDataSourceFactory.getObjectInstance Name = dspace6 Property maxActive is not used in DBCP2, use maxTotal instead. maxTotal default value is 8. You have set value of "35" for "maxActive" property, which is being ignored.
13-Jan-2018 13:59:05.245 WARNING [main] org.apache.tomcat.dbcp.dbcp2.BasicDataSourceFactory.getObjectInstance Name = dspace6 Property maxWait is not used in DBCP2 , use maxWaitMillis instead. maxWaitMillis default value is -1. You have set value of "5000" for "maxWait" property, which is being ignored.
  • I looked in my Tomcat 7.0.82 logs and I don't see anything about DBCP2 errors, so I guess this a Tomcat 8.0.x or 8.5.x thing
  • DBCP2 appears to be Tomcat 8.0.x and up according to the Tomcat 8.0 migration guide
  • I have updated our Ansible infrastructure scripts so that it will be ready whenever we switch to Tomcat 8 (probably with Ubuntu 18.04 later this year)
  • When I enable the ResourceLink in the ROOT.xml context I get the following error in the Tomcat localhost log:
13-Jan-2018 14:14:36.017 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.dspace.app.util.DSpaceWebappListener]
 java.lang.ExceptionInInitializerError
        at org.dspace.app.util.AbstractDSpaceWebapp.register(AbstractDSpaceWebapp.java:74)
        at org.dspace.app.util.DSpaceWebappListener.contextInitialized(DSpaceWebappListener.java:31)
        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
        at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:629)
        at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1839)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NullPointerException
        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:547)
        at org.dspace.core.Context.<clinit>(Context.java:103)
        ... 15 more
  • Interesting blog post benchmarking Tomcat JDBC vs Apache Commons DBCP2, with configuration snippets: http://www.tugay.biz/2016/07/tomcat-connection-pool-vs-apache.html
  • The Tomcat vs Apache pool thing is confusing, but apparently we're using Apache Commons DBCP2 because we don't specify factory="org.apache.tomcat.jdbc.pool.DataSourceFactory" in our global resource
  • So at least I know that I'm not looking for documentation or troubleshooting on the Tomcat JDBC pool!
  • I looked at pg_stat_activity during Tomcat's startup and I see that the pool created in server.xml is indeed connecting, just that nothing uses it
  • Also, the fallback connection parameters specified in local.cfg (not dspace.cfg) are used
  • Shit, this might actually be a DSpace error: https://jira.duraspace.org/browse/DS-3434
  • I'll comment on that issue

2018-01-14

  • Looking at the authors Peter had corrected
  • Some had multiple and he's corrected them by adding || in the correction column, but I can't process those this way so I will just have to flag them and do those manually later
  • Also, I can flag the values that have "DELETE"
  • Then I need to facet the correction column on isBlank(value) and not flagged

2018-01-15

  • Help Udana from IWMI export a CSV from DSpace Test so he can start trying a batch upload
  • I'm going to apply these ~130 corrections on CGSpace:
update metadatavalue set text_value='Formally Published' where resource_type_id=2 and metadata_field_id=214 and text_value like 'Formally published';
delete from metadatavalue where resource_type_id=2 and metadata_field_id=214 and text_value like 'NO';
update metadatavalue set text_value='en' where resource_type_id=2 and metadata_field_id=38 and text_value ~ '(En|English)';
update metadatavalue set text_value='fr' where resource_type_id=2 and metadata_field_id=38 and text_value ~ '(fre|frn|French)';
update metadatavalue set text_value='es' where resource_type_id=2 and metadata_field_id=38 and text_value ~ '(Spanish|spa)';
update metadatavalue set text_value='vi' where resource_type_id=2 and metadata_field_id=38 and text_value='Vietnamese';
update metadatavalue set text_value='ru' where resource_type_id=2 and metadata_field_id=38 and text_value='Ru';
update metadatavalue set text_value='in' where resource_type_id=2 and metadata_field_id=38 and text_value ~ '(IN|In)';
delete from metadatavalue where resource_type_id=2 and metadata_field_id=38 and text_value ~ '(dc.language.iso|CGIAR Challenge Program on Water and Food)';
  • Continue proofing Peter's author corrections that I started yesterday, faceting on non blank, non flagged, and briefly scrolling through the values of the corrections to find encoding errors for French and Spanish names

OpenRefine Authors

$ ./fix-metadata-values.py -i /tmp/2018-01-14-Authors-1300-Corrections.csv -f dc.contributor.author -t correct -m 3 -d dspace-u dspace -p 'fuuu'
  • In looking at some of the values to delete or check I found some metadata values that I could not resolve their handle via SQL:
dspace=# select * from metadatavalue where resource_type_id=2 and metadata_field_id=3 and text_value='Tarawali';
 metadata_value_id | resource_id | metadata_field_id | text_value | text_lang | place | authority | confidence | resource_type_id
-------------------+-------------+-------------------+------------+-----------+-------+-----------+------------+------------------
           2757936 |        4369 |                 3 | Tarawali   |           |     9 |           |        600 |                2
(1 row)

dspace=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id = '4369';
 handle
--------
(0 rows)
  • Even searching in the DSpace advanced search for author equals "Tarawali" produces nothing...
  • Otherwise, the DSpace 5 SQL Helper Functions provide ds5_item2itemhandle(), which is much easier than my long query above that I always have to go search for
  • For example, to find the Handle for an item that has the author "Erni":
dspace=# select * from metadatavalue where resource_type_id=2 and metadata_field_id=3 and text_value='Erni';
 metadata_value_id | resource_id | metadata_field_id | text_value | text_lang | place |              authority               | confidence | resource_type_id 
-------------------+-------------+-------------------+------------+-----------+-------+--------------------------------------+------------+------------------
           2612150 |       70308 |                 3 | Erni       |           |     9 | 3fe10c68-6773-49a7-89cc-63eb508723f2 |         -1 |                2
(1 row)
dspace=# select ds5_item2itemhandle(70308);
 ds5_item2itemhandle 
---------------------
 10568/68609
(1 row)
  • Next I apply the author deletions:
$ ./delete-metadata-values.py -i /tmp/2018-01-14-Authors-5-Deletions.csv -f dc.contributor.author -m 3 -d dspace -u dspace -p 'fuuu'
  • Now working on the affiliation corrections from Peter:
$ ./fix-metadata-values.py -i /tmp/2018-01-15-Affiliations-888-Corrections.csv -f cg.contributor.affiliation -t correct -m 211 -d dspace -u dspace -p 'fuuu'
$ ./delete-metadata-values.py -i /tmp/2018-01-15-Affiliations-11-Deletions.csv -f cg.contributor.affiliation -m 211 -d dspace -u dspace -p 'fuuu'
  • Now I made a new list of affiliations for Peter to look through:
dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where metadata_schema_id = 2 and element = 'contributor' and qualifier = 'affiliation') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/affiliations.csv with csv;
COPY 4552
  • Looking over the affiliations again I see dozens of CIAT ones with their affiliation formatted like: International Center for Tropical Agriculture (CIAT)
  • For example, this one is from just last month: https://cgspace.cgiar.org/handle/10568/89930
  • Our controlled vocabulary has this in the format without the abbreviation: International Center for Tropical Agriculture
  • So some submitters don't know to use the controlled vocabulary lookup