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---
title: "January, 2019"
date: 2019-01-02T09:48:30+02:00
author: "Alan Orth"
tags: ["Notes"]
---
## 2019-01-02
- Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning
- I don't see anything interesting in the web server logs around that time though:
```
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
92 40.77.167.4
99 210.7.29.100
120 38.126.157.45
177 35.237.175.180
177 40.77.167.32
216 66.249.75.219
225 18.203.76.93
261 46.101.86.248
357 207.46.13.1
903 54.70.40.11
```
<!--more-->
- Analyzing the types of requests made by the top few IPs during that time:
```
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | grep 54.70.40.11 | grep -o -E "(bitstream|discover|handle)" | sort | uniq -c
30 bitstream
534 discover
352 handle
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | grep 207.46.13.1 | grep -o -E "(bitstream|discover|handle)" | sort | uniq -c
194 bitstream
345 handle
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | grep 46.101.86.248 | grep -o -E "(bitstream|discover|handle)" | sort | uniq -c
261 handle
```
- It's not clear to me what was causing the outbound traffic spike
- Oh nice! The once-per-year cron job for rotating the Solr statistics actually worked now (for the first time ever!):
```
Moving: 81742 into core statistics-2010
Moving: 1837285 into core statistics-2011
Moving: 3764612 into core statistics-2012
Moving: 4557946 into core statistics-2013
Moving: 5483684 into core statistics-2014
Moving: 2941736 into core statistics-2015
Moving: 5926070 into core statistics-2016
Moving: 10562554 into core statistics-2017
Moving: 18497180 into core statistics-2018
```
- This could by why the outbound traffic rate was high, due to the S3 backup that run at 3:30AM...
- Run all system updates on DSpace Test (linode19) and reboot the server
## 2019-01-03
- Update local Docker image for DSpace PostgreSQL, re-using the existing data volume:
```
$ sudo docker pull postgres:9.6-alpine
$ sudo docker rm dspacedb
$ sudo docker run --name dspacedb -v /home/aorth/.local/lib/containers/volumes/dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
```
- Testing DSpace 5.9 with Tomcat 8.5.37 on my local machine and I see that Atmire's Listings and Reports still doesn't work
- After logging in via XMLUI and clicking the Listings and Reports link from the sidebar it redirects me to a JSPUI login page
- If I log in again there the Listings and Reports work... hmm.
- The JSPUI application—which Listings and Reports depends upon—also does not load, though the error is perhaps unrelated:
```
2019-01-03 14:45:21,727 INFO org.dspace.browse.BrowseEngine @ anonymous:session_id=9471D72242DAA05BCC87734FE3C66EA6:ip_addr=127.0.0.1:browse_mini:
2019-01-03 14:45:21,971 INFO org.dspace.app.webui.discovery.DiscoverUtility @ facets for scope, null: 23
2019-01-03 14:45:22,115 WARN org.dspace.app.webui.servlet.InternalErrorServlet @ :session_id=9471D72242DAA05BCC87734FE3C66EA6:internal_error:-- URL Was: http://localhost:8080/jspui/internal-error
-- Method: GET
-- Parameters were:
org.apache.jasper.JasperException: /home.jsp (line: [214], column: [1]) /discovery/static-tagcloud-facet.jsp (line: [57], column: [8]) No tag [tagcloud] defined in tag library imported with prefix [dspace]
at org.apache.jasper.compiler.DefaultErrorHandler.jspError(DefaultErrorHandler.java:41)
at org.apache.jasper.compiler.ErrorDispatcher.dispatch(ErrorDispatcher.java:291)
at org.apache.jasper.compiler.ErrorDispatcher.jspError(ErrorDispatcher.java:97)
at org.apache.jasper.compiler.Parser.processIncludeDirective(Parser.java:347)
at org.apache.jasper.compiler.Parser.parseIncludeDirective(Parser.java:380)
at org.apache.jasper.compiler.Parser.parseDirective(Parser.java:481)
at org.apache.jasper.compiler.Parser.parseElements(Parser.java:1445)
at org.apache.jasper.compiler.Parser.parseBody(Parser.java:1683)
at org.apache.jasper.compiler.Parser.parseOptionalBody(Parser.java:1016)
at org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1291)
at org.apache.jasper.compiler.Parser.parseElements(Parser.java:1470)
at org.apache.jasper.compiler.Parser.parse(Parser.java:144)
at org.apache.jasper.compiler.ParserController.doParse(ParserController.java:244)
at org.apache.jasper.compiler.ParserController.parse(ParserController.java:105)
at org.apache.jasper.compiler.Compiler.generateJava(Compiler.java:202)
at org.apache.jasper.compiler.Compiler.compile(Compiler.java:373)
at org.apache.jasper.compiler.Compiler.compile(Compiler.java:350)
at org.apache.jasper.compiler.Compiler.compile(Compiler.java:334)
at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:595)
at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:399)
at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:728)
at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:470)
at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:395)
at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:316)
at org.dspace.app.webui.util.JSPManager.showJSP(JSPManager.java:60)
at org.apache.jsp.index_jsp._jspService(index_jsp.java:191)
at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:476)
at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:234)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
```
- I notice that I get different JSESSIONID cookies for `/` (XMLUI) and `/jspui` (JSPUI) on Tomcat 8.5.37, I wonder if it's the same on Tomcat 7.0.92... yes I do.
- Hmm, on Tomcat 7.0.92 I see that I get a `dspace.current.user.id` session cookie after logging into XMLUI, and then when I browse to JSPUI I am still logged in...
- I didn't see that cookie being set on Tomcat 8.5.37
- I sent a message to the dspace-tech mailing list to ask
## 2019-01-04
- Linode sent a message last night that CGSpace (linode18) had high CPU usage, but I don't see anything around that time in the web server logs:
```
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "03/Jan/2019:1(7|8|9)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
189 207.46.13.192
217 31.6.77.23
340 66.249.70.29
349 40.77.167.86
417 34.218.226.147
630 207.46.13.173
710 35.237.175.180
790 40.77.167.87
1776 66.249.70.27
2099 54.70.40.11
```
- I'm thinking about trying to validate our `dc.subject` terms against [AGROVOC webservices](http://aims.fao.org/agrovoc/webservices)
- There seem to be a few APIs and the documentation is kinda confusing, but I found this REST endpoint that does work well, for example searching for `SOIL`:
```
$ http http://agrovoc.uniroma2.it/agrovoc/rest/v1/search?query=SOIL&lang=en
HTTP/1.1 200 OK
Access-Control-Allow-Origin: *
Connection: Keep-Alive
Content-Length: 493
Content-Type: application/json; charset=utf-8
Date: Fri, 04 Jan 2019 13:44:27 GMT
Keep-Alive: timeout=5, max=100
Server: Apache
Strict-Transport-Security: max-age=63072000; includeSubdomains
Vary: Accept
X-Content-Type-Options: nosniff
X-Frame-Options: ALLOW-FROM http://aims.fao.org
{
"@context": {
"@language": "en",
"altLabel": "skos:altLabel",
"hiddenLabel": "skos:hiddenLabel",
"isothes": "http://purl.org/iso25964/skos-thes#",
"onki": "http://schema.onki.fi/onki#",
"prefLabel": "skos:prefLabel",
"results": {
"@container": "@list",
"@id": "onki:results"
},
"skos": "http://www.w3.org/2004/02/skos/core#",
"type": "@type",
"uri": "@id"
},
"results": [
{
"lang": "en",
"prefLabel": "soil",
"type": [
"skos:Concept"
],
"uri": "http://aims.fao.org/aos/agrovoc/c_7156",
"vocab": "agrovoc"
}
],
"uri": ""
}
```
- The API does not appear to be case sensitive (searches for `SOIL` and `soil` return the same thing)
- I'm a bit confused that there's no obvious return code or status when a term is not found, for example `SOILS`:
```
HTTP/1.1 200 OK
Access-Control-Allow-Origin: *
Connection: Keep-Alive
Content-Length: 367
Content-Type: application/json; charset=utf-8
Date: Fri, 04 Jan 2019 13:48:31 GMT
Keep-Alive: timeout=5, max=100
Server: Apache
Strict-Transport-Security: max-age=63072000; includeSubdomains
Vary: Accept
X-Content-Type-Options: nosniff
X-Frame-Options: ALLOW-FROM http://aims.fao.org
{
"@context": {
"@language": "en",
"altLabel": "skos:altLabel",
"hiddenLabel": "skos:hiddenLabel",
"isothes": "http://purl.org/iso25964/skos-thes#",
"onki": "http://schema.onki.fi/onki#",
"prefLabel": "skos:prefLabel",
"results": {
"@container": "@list",
"@id": "onki:results"
},
"skos": "http://www.w3.org/2004/02/skos/core#",
"type": "@type",
"uri": "@id"
},
"results": [],
"uri": ""
}
```
- I guess the `results` object will just be empty...
- Another way would be to try with SPARQL, perhaps using the Python 2.7 [sparql-client](https://pypi.org/project/sparql-client/):
```
$ python2.7 -m virtualenv /tmp/sparql
$ . /tmp/sparql/bin/activate
$ pip install sparql-client ipython
$ ipython
In [10]: import sparql
In [11]: s = sparql.Service("http://agrovoc.uniroma2.it:3030/agrovoc/sparql", "utf-8", "GET")
In [12]: statement=('PREFIX skos: <http://www.w3.org/2004/02/skos/core#> '
...: 'SELECT '
...: '?label '
...: 'WHERE { '
...: '{ ?concept skos:altLabel ?label . } UNION { ?concept skos:prefLabel ?label . } '
...: 'FILTER regex(str(?label), "^fish", "i") . '
...: '} LIMIT 10')
In [13]: result = s.query(statement)
In [14]: for row in result.fetchone():
...: print(row)
...:
(<Literal "fish catching"@en>,)
(<Literal "fish harvesting"@en>,)
(<Literal "fish meat"@en>,)
(<Literal "fish roe"@en>,)
(<Literal "fish conversion"@en>,)
(<Literal "fisheries catches (composition)"@en>,)
(<Literal "fishtail palm"@en>,)
(<Literal "fishflies"@en>,)
(<Literal "fishery biology"@en>,)
(<Literal "fish production"@en>,)
```
- The SPARQL query comes from my notes in [2017-08]({{< relref "2017-08.md" >}})
## 2019-01-06
- I built a clean DSpace 5.8 installation from the upstream `dspace-5.8` tag and the issue with the XMLUI/JSPUI login is still there with Tomcat 8.5.37
- If I log into XMLUI and then nagivate to JSPUI I need to log in again
- XMLUI does not set the `dspace.current.user.id` session cookie in Tomcat 8.5.37 for some reason
- I sent an update to the dspace-tech mailing list to ask for more help troubleshooting
## 2019-01-07
- I built a clean DSpace 6.3 installation from the upstream `dspace-6.3` tag and the issue with the XMLUI/JSPUI login is still there with Tomcat 8.5.37
- If I log into XMLUI and then nagivate to JSPUI I need to log in again
- XMLUI does not set the `dspace.current.user.id` session cookie in Tomcat 8.5.37 for some reason
- I sent an update to the dspace-tech mailing list to ask for more help troubleshooting
## 2019-01-08
- Tim Donohue responded to my thread about the cookies on the dspace-tech mailing list
- He suspects it's a change of behavior in Tomcat 8.5, and indeed I see a mention of new cookie processing in the [Tomcat 8.5 migration guide](https://tomcat.apache.org/migration-85.html#Cookies)
- I tried to switch my XMLUI and JSPUI contexts to use the `LegacyCookieProcessor`, but it didn't seem to help
- I [filed DS-4140 on the DSpace issue tracker](https://jira.duraspace.org/browse/DS-4140)
## 2019-01-11
- Tezira wrote to say she has stopped receiving the `DSpace Submission Approved and Archived` emails from CGSpace as of January 2nd
- I told her that I haven't done anything to disable it lately, but that I would check
- Bizu also says she hasn't received them lately
## 2019-01-14
- Day one of CGSpace AReS meeting in Amman
## 2019-01-15
- Day two of CGSpace AReS meeting in Amman
- Discuss possibly extending the [dspace-statistics-api](https://github.com/ilri/dspace-statistics-api) to make community and collection statistics available
- Discuss new "final" CG Core document and some changes that we'll need to do on CGSpace and other repositories
- We agreed to try to stick to pure Dublin Core where possible, then use fields that exist in standard DSpace, and use "cg" namespace for everything else
- Major changes are to move `dc.contributor.author` to `dc.creator` (which MELSpace and WorldFish are already using in their DSpace repositories)
- I am testing the speed of the WorldFish DSpace repository's REST API and it's five to ten times faster than CGSpace as I tested in [2018-10]({{< relref "2018-10.md" >}}):
```
$ time http --print h 'https://digitalarchive.worldfishcenter.org/rest/items?expand=metadata,bitstreams,parentCommunityList&limit=100&offset=0'
0.16s user 0.03s system 3% cpu 5.185 total
0.17s user 0.02s system 2% cpu 7.123 total
0.18s user 0.02s system 6% cpu 3.047 total
```
- In other news, Linode sent a mail last night that the CPU load on CGSpace (linode18) was high, here are the top IPs in the logs around those few hours:
```
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "14/Jan/2019:(17|18|19|20)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
157 31.6.77.23
192 54.70.40.11
202 66.249.64.157
207 40.77.167.204
220 157.55.39.140
326 197.156.105.116
385 207.46.13.158
1211 35.237.175.180
1830 66.249.64.155
2482 45.5.186.2
```
## 2019-01-16
- Day three of CGSpace AReS meeting in Amman
- We discussed CG Core 2.0 metadata and decided some action points
- We discussed branding of AReS tool
- Notes from our CG Core 2.0 metadata discussion:
- Not Dublin Core:
- dc.subtype
- dc.peer-reviewed
- Dublin Core, possible action for CGSpace:
- dc.description:
- We use dc.description.abstract, dc.description (Notes), dc.description.version (Peer review status), dc.description.sponsorship (Funder)
- Maybe move abstract to dc.description
- Maybe notes moves to cg.description.notes???
- Maybe move dc.description.version to cg.peer-reviewed or cg.peer-review-status???
- Move dc.description.sponsorship to cg.contributor.donor???
- dc.subject:
- Wait for guidance, evaluate technical implications (Google indexing, OAI, etc)
- Move dc.contributor.author to dc.creator
- dc.contributor Project
- Recommend against creating new fields for all projects
- We use collections projects/themes/etc
- dc.contributor Project Lead Center
- MELSpace uses cg.contributor.project-lead-institute (institute is more generic than center)
- Maybe we use?
- dc.contributor Partner
- Wait for guidance
- MELSpace uses cg.contibutor.center (?)
- dc.contributor Donor
- Use cg.contributor.donor
- dc.date
- Wait for guidance, maybe move dc.date.issued?
- dc.date.accessioned and dc.date.available are automatic in DSpace
- dc.language
- Move dc.language.iso to dc.language
- dc.identifier
- Move cg.identifier.url to dc.identifier
- dc.identifier bibliographicCitation
- dc.identifier.citation should move to dc.bibliographicCitation
- dc.description.notes
- Wait for guidance, maybe move to cg.description.notes ???
- dc.relation
- Maybe move cg.link.reference
- Perhaps consolodate cg.link.audio etc there...?
- dc.relation.isPartOf
- Move dc.relation.ispartofseries to dc.relation.isPartOf
- dc.audience
- Move cg.targetaudience to dc.audience
- Something happened to the Solr usage statistics on CGSpace
- I looked on the server and the Solr cores are there (56GB!), and I don't see any obvious errors in dmesg or anything
- I see that the server hasn't been rebooted in 26 days so I rebooted it
- After reboot the Solr stats are still messed up in the Atmire Usage Stats module, it only shows 2019-01!
![Solr stats fucked up](/cgspace-notes/2019/01/solr-stats-incorrect.png)
- In the Solr admin UI I see the following error:
```
statistics-2018: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher
```
- Looking in the Solr log I see this:
```
2019-01-16 13:37:55,395 ERROR org.apache.solr.core.CoreContainer @ Error creating core [statistics-2018]: Error opening new searcher
org.apache.solr.common.SolrException: Error opening new searcher
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:873)
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:646)
at org.apache.solr.core.CoreContainer.create(CoreContainer.java:491)
at org.apache.solr.core.CoreContainer.create(CoreContainer.java:466)
at org.apache.solr.handler.admin.CoreAdminHandler.handleCreateAction(CoreAdminHandler.java:575)
at org.apache.solr.handler.admin.CoreAdminHandler.handleRequestInternal(CoreAdminHandler.java:199)
at org.apache.solr.handler.admin.CoreAdminHandler.handleRequestBody(CoreAdminHandler.java:188)
at org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:135)
at org.apache.solr.servlet.SolrDispatchFilter.handleAdminRequest(SolrDispatchFilter.java:729)
at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:258)
at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:207)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.solr.filters.LocalHostRestrictionFilter.doFilter(LocalHostRestrictionFilter.java:50)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:221)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:180)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:436)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1078)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.solr.common.SolrException: Error opening new searcher
at org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1565)
at org.apache.solr.core.SolrCore.getSearcher(SolrCore.java:1677)
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:845)
... 31 more
Caused by: org.apache.lucene.store.LockObtainFailedException: Lock obtain timed out: NativeFSLock@/home/cgspace.cgiar.org/solr/statistics-2018/data/index/write.lock
at org.apache.lucene.store.Lock.obtain(Lock.java:89)
at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:753)
at org.apache.solr.update.SolrIndexWriter.<init>(SolrIndexWriter.java:77)
at org.apache.solr.update.SolrIndexWriter.create(SolrIndexWriter.java:64)
at org.apache.solr.update.DefaultSolrCoreState.createMainIndexWriter(DefaultSolrCoreState.java:279)
at org.apache.solr.update.DefaultSolrCoreState.getIndexWriter(DefaultSolrCoreState.java:111)
at org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1528)
... 33 more
2019-01-16 13:37:55,401 ERROR org.apache.solr.core.SolrCore @ org.apache.solr.common.SolrException: Error CREATEing SolrCore 'statistics-2018': Unable to create core [statistics-2018] Caused by: Lock obtain timed out: NativeFSLock@/home/cgspace.cgiar.org/solr/statistics-2018/data/index/write.lock
at org.apache.solr.handler.admin.CoreAdminHandler.handleCreateAction(CoreAdminHandler.java:613)
at org.apache.solr.handler.admin.CoreAdminHandler.handleRequestInternal(CoreAdminHandler.java:199)
at org.apache.solr.handler.admin.CoreAdminHandler.handleRequestBody(CoreAdminHandler.java:188)
at org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:135)
at org.apache.solr.servlet.SolrDispatchFilter.handleAdminRequest(SolrDispatchFilter.java:729)
at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:258)
at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:207)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.solr.filters.LocalHostRestrictionFilter.doFilter(LocalHostRestrictionFilter.java:50)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:221)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:180)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:436)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1078)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.solr.common.SolrException: Unable to create core [statistics-2018]
at org.apache.solr.core.CoreContainer.create(CoreContainer.java:507)
at org.apache.solr.core.CoreContainer.create(CoreContainer.java:466)
at org.apache.solr.handler.admin.CoreAdminHandler.handleCreateAction(CoreAdminHandler.java:575)
... 27 more
Caused by: org.apache.solr.common.SolrException: Error opening new searcher
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:873)
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:646)
at org.apache.solr.core.CoreContainer.create(CoreContainer.java:491)
... 29 more
Caused by: org.apache.solr.common.SolrException: Error opening new searcher
at org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1565)
at org.apache.solr.core.SolrCore.getSearcher(SolrCore.java:1677)
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:845)
... 31 more
Caused by: org.apache.lucene.store.LockObtainFailedException: Lock obtain timed out: NativeFSLock@/home/cgspace.cgiar.org/solr/statistics-2018/data/index/write.lock
at org.apache.lucene.store.Lock.obtain(Lock.java:89)
at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:753)
at org.apache.solr.update.SolrIndexWriter.<init>(SolrIndexWriter.java:77)
at org.apache.solr.update.SolrIndexWriter.create(SolrIndexWriter.java:64)
at org.apache.solr.update.DefaultSolrCoreState.createMainIndexWriter(DefaultSolrCoreState.java:279)
at org.apache.solr.update.DefaultSolrCoreState.getIndexWriter(DefaultSolrCoreState.java:111)
at org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1528)
... 33 more
```
- I found some threads on StackOverflow etc discussing this and several suggested increasing the address space for the shell with ulimit
- I added `ulimit -v unlimited` to the `/etc/default/tomcat7` and restarted Tomcat and now Solr is working again:
![Solr stats working](/cgspace-notes/2019/01/solr-stats-incorrect.png)
- Some StackOverflow discussions related to this:
- https://stackoverflow.com/questions/2895417/solrexception-internal-server-error/3035916#3035916
- https://stackoverflow.com/questions/11683850/how-much-memory-could-vm-use
- https://stackoverflow.com/questions/8892143/error-when-opening-a-lucene-index-map-failed/8893684#8893684
- Abenet was asking if the Atmire Usage Stats are correct because they are over 2 million the last few months...
- For 2019-01 alone the Usage Stats are already around 1.2 million
- I tried to look in the nginx logs to see how many raw requests there are so far this month and it's about 1.4 million:
```
# time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Jan/2019"
1442874
real 0m17.161s
user 0m16.205s
sys 0m2.396s
```
## 2019-01-17
- Send reminder to Atmire about purchasing the [MQM module](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=657)
- Trying to decide the solid action points for CGSpace on the CG Core 2.0 metadata...
- It's difficult to decide some of these because the current CG Core 2.0 document does not provide guidance or rationale (yet)!
- Also, there is not a good Dublin Core reference (or maybe I just don't understand?)
- Several authoritative documents on Dublin Core appear to be:
- [Dublin Core Metadata Element Set, Version 1.1: Reference Description](http://dublincore.org/documents/dces/)
- [DCMI Metadata Terms](http://www.dublincore.org/documents/dcmi-terms/)
- And what is the relationship between DC and DCTERMS?
- DSpace uses DCTERMS in the metadata it embeds in XMLUI item views!
- We really need to look at this more carefully and see the impacts that might be made from switching core fields like languages, abstract, authors, etc
- We can check WorldFish and MELSpace repositories to see what effects these changes have had on theirs because they have already adopted some of these changes...
- I think I understand the difference between DC and DCTERMS finally: DC is the original set of fifteen elements and DCTERMS is the newer version that was supposed to address much of the drawbacks of the original with regards to digital content
- We might be able to use some proper fields for citation, abstract, etc that are part of DCTERMS
- To make matters more confusing, there is also "qualified Dublin Core" that uses the original fifteen elements of legacy DC and qualifies them, like `dc.date.accessioned`
- According to Wikipedia [Qualified Dublin Core was superseded by DCTERMS in 2008](https://en.wikipedia.org/wiki/Dublin_Core)!
- So we should be trying to use DCTERMS where possible, unless it is some internal thing that might mess up DSpace (like dates)
- "Elements 1.1" means legacy DC
- Possible action list for CGSpace:
- dc.description.abstract → dcterms.abstract
- dc.description.version → cg.peer-reviewed (or cg.peer-review-status?)
- dc.description.sponsorship → cg.contributor.donor
- dc.contributor.author → dc.creator
- dc.language.iso → dcterms.language
- cg.identifier.url → dcterms.identifier
- dc.identifier.citation → dcterms.bibliographicCitation
- dc.relation.ispartofseries → dcterms.isPartOf
- cg.targetaudience → dcterms.audience
## 2019-01-19
- There's no official set of Dublin Core qualifiers so I can't tell if things like `dc.contributor.author` that are used by DSpace are official
- I found a great [presentation from 2015 by the Digital Repository of Ireland](https://www.dri.ie/sites/default/files/files/qualified-dublin-core-metadata-guidelines.pdf) that discusses using MARC Relator Terms with Dublin Core elements
- It seems that `dc.contributor.author` would be a supported term according to this [Library of Congress list](https://memory.loc.gov/diglib/loc.terms/relators/dc-contributor.html) linked from the [Dublin Core website](http://dublincore.org/usage/documents/relators/)
- The Library of Congress document specifically says:
These terms conform with the DCMI Abstract Model and may be used in DCMI application profiles. DCMI endorses their use with Dublin Core elements as indicated.
## 2019-01-20
- That's weird, I logged into DSpace Test (linode19) and it says it has been up for 213 days:
```
# w
04:46:14 up 213 days, 7:25, 4 users, load average: 1.94, 1.50, 1.35
```
- I've definitely rebooted it several times in the past few months... according to `journalctl -b` it was a few weeks ago on 2019-01-02
- I re-ran the Ansible DSpace tag, ran all system updates, and rebooted the host
- After rebooting I notice that the Linode kernel went down from 4.19.8 to 4.18.16...
- Atmire sent a quote on our [ticket about purchasing the Metadata Quality Module (MQM) for DSpace 5.8](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=657)
- Abenet asked me for an [OpenSearch query that could generate and RSS feed for items in the Livestock CRP](https://cgspace.cgiar.org/open-search/discover?query=crpsubject:Livestock&sort_by=3&order=DESC)
- According to my notes, `sort_by=3` is accession date (as configured in `dspace.cfg)
- The query currently shows 3023 items, but a [Discovery search for Livestock CRP only returns 858 items](https://cgspace.cgiar.org/discover?filtertype_1=crpsubject&filter_relational_operator_1=equals&filter_1=Livestock&submit_apply_filter=&query=)
- That query seems to return items tagged with `Livestock and Fish` CRP as well... hmm.
## 2019-01-21
- Investigating running Tomcat 7 on Ubuntu 18.04 with the tarball and a custom systemd package instead of waiting for our DSpace to get compatible with Ubuntu 18.04's Tomcat 8.5
- I could either run with a simple `tomcat7.service` like this:
```
[Unit]
Description=Apache Tomcat 7 Web Application Container
After=network.target
[Service]
Type=forking
ExecStart=/path/to/apache-tomcat-7.0.92/bin/startup.sh
ExecStop=/path/to/apache-tomcat-7.0.92/bin/shutdown.sh
User=aorth
Group=aorth
[Install]
WantedBy=multi-user.target
```
- Or try to use adapt a real systemd service like Arch Linux's:
```
[Unit]
Description=Tomcat 7 servlet container
After=network.target
[Service]
Type=forking
PIDFile=/var/run/tomcat7.pid
Environment=CATALINA_PID=/var/run/tomcat7.pid
Environment=TOMCAT_JAVA_HOME=/usr/lib/jvm/default-runtime
Environment=CATALINA_HOME=/usr/share/tomcat7
Environment=CATALINA_BASE=/usr/share/tomcat7
Environment=CATALINA_OPTS=
Environment=ERRFILE=SYSLOG
Environment=OUTFILE=SYSLOG
ExecStart=/usr/bin/jsvc \
-Dcatalina.home=${CATALINA_HOME} \
-Dcatalina.base=${CATALINA_BASE} \
-Djava.io.tmpdir=/var/tmp/tomcat7/temp \
-cp /usr/share/java/commons-daemon.jar:/usr/share/java/eclipse-ecj.jar:${CATALINA_HOME}/bin/bootstrap.jar:${CATALINA_HOME}/bin/tomcat-juli.jar \
-user tomcat7 \
-java-home ${TOMCAT_JAVA_HOME} \
-pidfile /var/run/tomcat7.pid \
-errfile ${ERRFILE} \
-outfile ${OUTFILE} \
$CATALINA_OPTS \
org.apache.catalina.startup.Bootstrap
ExecStop=/usr/bin/jsvc \
-pidfile /var/run/tomcat7.pid \
-stop \
org.apache.catalina.startup.Bootstrap
[Install]
WantedBy=multi-user.target
```
- I see that `jsvc` and `libcommons-daemon-java` are both available on Ubuntu so that should be easy to port
- We probably don't need Eclipse Java Bytecode Compiler (ecj)
- I tested Tomcat 7.0.92 on Arch Linux using the `tomcat7.service` with `jsvc` and it works... nice!
- I think I might manage this the same way I do the restic releases in the [Ansible infrastructure scripts](https://github.com/ilri/rmg-ansible-public), where I download a specific version and symlink to some generic location without the version number
- I verified that there is indeed an issue with sharded Solr statistics cores on DSpace, which will cause inaccurate results in the dspace-statistics-api:
```
$ http 'http://localhost:3000/solr/statistics/select?indent=on&rows=0&q=type:2+id:11576&fq=isBot:false&fq=statistics_type:view' | grep numFound
<result name="response" numFound="33" start="0">
$ http 'http://localhost:3000/solr/statistics-2018/select?indent=on&rows=0&q=type:2+id:11576&fq=isBot:false&fq=statistics_type:view' | grep numFound
<result name="response" numFound="241" start="0">
```
- I opened an issue on the GitHub issue tracker ([#10](https://github.com/ilri/dspace-statistics-api/issues/10))
- I don't think the [SolrClient library](https://solrclient.readthedocs.io/en/latest/) we are currently using supports these type of queries so we might have to just do raw queries with requests
<!-- vim: set sw=2 ts=2: -->
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