CGSpace Notes

Documenting day-to-day work on the CGSpace repository.

January, 2019

by Alan Orth in  

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
  • 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
  • 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:
$ 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

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

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 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:
$ 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