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Add notes for 2019-01-04
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@ -68,4 +68,230 @@ $ sudo docker rm dspacedb
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$ 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
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$ 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
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```
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```
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- 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
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- After logging in via XMLUI and clicking the Listings and Reports link from the sidebar it redirects me to a JSPUI login page
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- If I log in again there the Listings and Reports work... hmm.
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- The JSPUI application—which Listings and Reports depends upon—also does not load, though the error is perhaps unrelated:
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```
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2019-01-03 14:45:21,727 INFO org.dspace.browse.BrowseEngine @ anonymous:session_id=9471D72242DAA05BCC87734FE3C66EA6:ip_addr=127.0.0.1:browse_mini:
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2019-01-03 14:45:21,971 INFO org.dspace.app.webui.discovery.DiscoverUtility @ facets for scope, null: 23
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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
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-- Method: GET
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-- Parameters were:
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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]
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at org.apache.jasper.compiler.DefaultErrorHandler.jspError(DefaultErrorHandler.java:41)
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at org.apache.jasper.compiler.ErrorDispatcher.dispatch(ErrorDispatcher.java:291)
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at org.apache.jasper.compiler.ErrorDispatcher.jspError(ErrorDispatcher.java:97)
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at org.apache.jasper.compiler.Parser.processIncludeDirective(Parser.java:347)
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at org.apache.jasper.compiler.Parser.parseIncludeDirective(Parser.java:380)
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at org.apache.jasper.compiler.Parser.parseDirective(Parser.java:481)
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at org.apache.jasper.compiler.Parser.parseElements(Parser.java:1445)
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at org.apache.jasper.compiler.Parser.parseBody(Parser.java:1683)
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at org.apache.jasper.compiler.Parser.parseOptionalBody(Parser.java:1016)
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at org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1291)
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at org.apache.jasper.compiler.Parser.parseElements(Parser.java:1470)
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at org.apache.jasper.compiler.Parser.parse(Parser.java:144)
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at org.apache.jasper.compiler.ParserController.doParse(ParserController.java:244)
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at org.apache.jasper.compiler.ParserController.parse(ParserController.java:105)
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at org.apache.jasper.compiler.Compiler.generateJava(Compiler.java:202)
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at org.apache.jasper.compiler.Compiler.compile(Compiler.java:373)
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at org.apache.jasper.compiler.Compiler.compile(Compiler.java:350)
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at org.apache.jasper.compiler.Compiler.compile(Compiler.java:334)
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at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:595)
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at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:399)
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at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
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at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
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at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
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at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
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at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:728)
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at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:470)
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at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:395)
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at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:316)
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at org.dspace.app.webui.util.JSPManager.showJSP(JSPManager.java:60)
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at org.apache.jsp.index_jsp._jspService(index_jsp.java:191)
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at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
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at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
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at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:476)
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at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
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at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
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at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
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at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
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at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
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at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
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at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
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at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
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at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
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at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
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at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:234)
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at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
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at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
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at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
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at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
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at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
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at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)
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at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)
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at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
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at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
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at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
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at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
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at java.lang.Thread.run(Thread.java:748)
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```
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- 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.
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- 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...
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- I didn't see that cookie being set on Tomcat 8.5.37
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- I sent a message to the dspace-tech mailing list to ask
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## 2019-01-04
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- 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:
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```
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# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "03/Jan/2019:1(7|8|9)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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189 207.46.13.192
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217 31.6.77.23
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340 66.249.70.29
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349 40.77.167.86
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417 34.218.226.147
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630 207.46.13.173
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710 35.237.175.180
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790 40.77.167.87
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1776 66.249.70.27
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2099 54.70.40.11
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```
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- I'm thinking about trying to validate our `dc.subject` terms against [AGROVOC webservices](http://aims.fao.org/agrovoc/webservices)
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- There seem to be a few APIs and the documentation is kinda confusing, but I found this REST endpoint that does work well, for example searching for `SOIL`:
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```
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$ http http://agrovoc.uniroma2.it/agrovoc/rest/v1/search?query=SOIL&lang=en
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HTTP/1.1 200 OK
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Access-Control-Allow-Origin: *
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Connection: Keep-Alive
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Content-Length: 493
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Content-Type: application/json; charset=utf-8
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Date: Fri, 04 Jan 2019 13:44:27 GMT
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Keep-Alive: timeout=5, max=100
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Server: Apache
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Strict-Transport-Security: max-age=63072000; includeSubdomains
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Vary: Accept
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X-Content-Type-Options: nosniff
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X-Frame-Options: ALLOW-FROM http://aims.fao.org
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{
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"@context": {
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"@language": "en",
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"altLabel": "skos:altLabel",
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"hiddenLabel": "skos:hiddenLabel",
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"isothes": "http://purl.org/iso25964/skos-thes#",
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"onki": "http://schema.onki.fi/onki#",
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"prefLabel": "skos:prefLabel",
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"results": {
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"@container": "@list",
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"@id": "onki:results"
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},
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"skos": "http://www.w3.org/2004/02/skos/core#",
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"type": "@type",
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"uri": "@id"
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},
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"results": [
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{
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"lang": "en",
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"prefLabel": "soil",
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"type": [
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"skos:Concept"
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],
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"uri": "http://aims.fao.org/aos/agrovoc/c_7156",
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"vocab": "agrovoc"
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}
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],
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"uri": ""
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}
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```
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- The API does not appear to be case sensitive (searches for `SOIL` and `soil` return the same thing)
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- I'm a bit confused that there's no obvious return code or status when a term is not found, for example `SOILS`:
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```
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HTTP/1.1 200 OK
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Access-Control-Allow-Origin: *
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Connection: Keep-Alive
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Content-Length: 367
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Content-Type: application/json; charset=utf-8
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Date: Fri, 04 Jan 2019 13:48:31 GMT
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Keep-Alive: timeout=5, max=100
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Server: Apache
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Strict-Transport-Security: max-age=63072000; includeSubdomains
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Vary: Accept
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X-Content-Type-Options: nosniff
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X-Frame-Options: ALLOW-FROM http://aims.fao.org
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{
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"@context": {
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"@language": "en",
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"altLabel": "skos:altLabel",
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"hiddenLabel": "skos:hiddenLabel",
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"isothes": "http://purl.org/iso25964/skos-thes#",
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"onki": "http://schema.onki.fi/onki#",
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"prefLabel": "skos:prefLabel",
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"results": {
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"@container": "@list",
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"@id": "onki:results"
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},
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"skos": "http://www.w3.org/2004/02/skos/core#",
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"type": "@type",
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"uri": "@id"
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},
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"results": [],
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"uri": ""
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}
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```
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- I guess the `results` object will just be empty...
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- Another way would be to try with SPARQL, perhaps using the Python 2.7 [sparql-client](https://pypi.org/project/sparql-client/):
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```
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$ python2.7 -m virtualenv /tmp/sparql
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$ . /tmp/sparql/bin/activate
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$ pip install sparql-client ipython
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$ ipython
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In [10]: import sparql
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In [11]: s = sparql.Service("http://agrovoc.uniroma2.it:3030/agrovoc/sparql", "utf-8", "GET")
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In [12]: statement=('PREFIX skos: <http://www.w3.org/2004/02/skos/core#> '
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...: 'SELECT '
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...: '?label '
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...: 'WHERE { '
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...: '{ ?concept skos:altLabel ?label . } UNION { ?concept skos:prefLabel ?label . } '
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...: 'FILTER regex(str(?label), "^fish", "i") . '
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...: '} LIMIT 10')
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In [13]: result = s.query(statement)
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In [14]: for row in result.fetchone():
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...: print(row)
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...:
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(<Literal "fish catching"@en>,)
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(<Literal "fish harvesting"@en>,)
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(<Literal "fish meat"@en>,)
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(<Literal "fish roe"@en>,)
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(<Literal "fish conversion"@en>,)
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(<Literal "fisheries catches (composition)"@en>,)
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(<Literal "fishtail palm"@en>,)
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(<Literal "fishflies"@en>,)
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(<Literal "fishery biology"@en>,)
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(<Literal "fish production"@en>,)
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```
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- The SPARQL query comes from my notes in [2017-08]({{< relref "2017-08.md" >}})
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<!-- vim: set sw=2 ts=2: -->
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<!-- vim: set sw=2 ts=2: -->
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@ -27,7 +27,7 @@ I don’t see anything interesting in the web server logs around that time t
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" />
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" />
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<meta property="og:type" content="article" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-01/" /><meta property="article:published_time" content="2019-01-02T09:48:30+02:00"/>
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-01/" /><meta property="article:published_time" content="2019-01-02T09:48:30+02:00"/>
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<meta property="article:modified_time" content="2019-01-02T20:52:39+02:00"/>
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<meta property="article:modified_time" content="2019-01-03T11:52:26+02:00"/>
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||||||
|
|
||||||
<meta name="twitter:card" content="summary"/>
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<meta name="twitter:card" content="summary"/>
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||||||
<meta name="twitter:title" content="January, 2019"/>
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<meta name="twitter:title" content="January, 2019"/>
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@ -60,9 +60,9 @@ I don’t see anything interesting in the web server logs around that time t
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"@type": "BlogPosting",
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"@type": "BlogPosting",
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||||||
"headline": "January, 2019",
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"headline": "January, 2019",
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||||||
"url": "https://alanorth.github.io/cgspace-notes/2019-01/",
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"url": "https://alanorth.github.io/cgspace-notes/2019-01/",
|
||||||
"wordCount": "312",
|
"wordCount": "1098",
|
||||||
"datePublished": "2019-01-02T09:48:30+02:00",
|
"datePublished": "2019-01-02T09:48:30+02:00",
|
||||||
"dateModified": "2019-01-02T20:52:39+02:00",
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"dateModified": "2019-01-03T11:52:26+02:00",
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"author": {
|
"author": {
|
||||||
"@type": "Person",
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"@type": "Person",
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||||||
"name": "Alan Orth"
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"name": "Alan Orth"
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@ -197,6 +197,247 @@ $ sudo docker rm dspacedb
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$ 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
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$ 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
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</code></pre>
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</code></pre>
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<ul>
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|
<li>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
|
||||||
|
|
||||||
|
<ul>
|
||||||
|
<li>After logging in via XMLUI and clicking the Listings and Reports link from the sidebar it redirects me to a JSPUI login page</li>
|
||||||
|
<li>If I log in again there the Listings and Reports work… hmm.</li>
|
||||||
|
</ul></li>
|
||||||
|
<li>The JSPUI application—which Listings and Reports depends upon—also does not load, though the error is perhaps unrelated:</li>
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||||||
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</ul>
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||||||
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|
||||||
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<pre><code>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)
|
||||||
|
</code></pre>
|
||||||
|
|
||||||
|
<ul>
|
||||||
|
<li>I notice that I get different JSESSIONID cookies for <code>/</code> (XMLUI) and <code>/jspui</code> (JSPUI) on Tomcat 8.5.37, I wonder if it’s the same on Tomcat 7.0.92… yes I do.</li>
|
||||||
|
<li>Hmm, on Tomcat 7.0.92 I see that I get a <code>dspace.current.user.id</code> session cookie after logging into XMLUI, and then when I browse to JSPUI I am still logged in…
|
||||||
|
|
||||||
|
<ul>
|
||||||
|
<li>I didn’t see that cookie being set on Tomcat 8.5.37</li>
|
||||||
|
</ul></li>
|
||||||
|
<li>I sent a message to the dspace-tech mailing list to ask</li>
|
||||||
|
</ul>
|
||||||
|
|
||||||
|
<h2 id="2019-01-04">2019-01-04</h2>
|
||||||
|
|
||||||
|
<ul>
|
||||||
|
<li>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:</li>
|
||||||
|
</ul>
|
||||||
|
|
||||||
|
<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "03/Jan/2019:1(7|8|9)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
|
||||||
|
189 207.46.13.192
|
||||||
|
217 31.6.77.23
|
||||||
|
340 66.249.70.29
|
||||||
|
349 40.77.167.86
|
||||||
|
417 34.218.226.147
|
||||||
|
630 207.46.13.173
|
||||||
|
710 35.237.175.180
|
||||||
|
790 40.77.167.87
|
||||||
|
1776 66.249.70.27
|
||||||
|
2099 54.70.40.11
|
||||||
|
</code></pre>
|
||||||
|
|
||||||
|
<ul>
|
||||||
|
<li>I’m thinking about trying to validate our <code>dc.subject</code> terms against <a href="http://aims.fao.org/agrovoc/webservices">AGROVOC webservices</a></li>
|
||||||
|
<li>There seem to be a few APIs and the documentation is kinda confusing, but I found this REST endpoint that does work well, for example searching for <code>SOIL</code>:</li>
|
||||||
|
</ul>
|
||||||
|
|
||||||
|
<pre><code>$ 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": ""
|
||||||
|
}
|
||||||
|
</code></pre>
|
||||||
|
|
||||||
|
<ul>
|
||||||
|
<li>The API does not appear to be case sensitive (searches for <code>SOIL</code> and <code>soil</code> return the same thing)</li>
|
||||||
|
<li>I’m a bit confused that there’s no obvious return code or status when a term is not found, for example <code>SOILS</code>:</li>
|
||||||
|
</ul>
|
||||||
|
|
||||||
|
<pre><code>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": ""
|
||||||
|
}
|
||||||
|
</code></pre>
|
||||||
|
|
||||||
|
<ul>
|
||||||
|
<li>I guess the <code>results</code> object will just be empty…</li>
|
||||||
|
<li>Another way would be to try with SPARQL, perhaps using the Python 2.7 <a href="https://pypi.org/project/sparql-client/">sparql-client</a>:</li>
|
||||||
|
</ul>
|
||||||
|
|
||||||
|
<pre><code>$ 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>,)
|
||||||
|
</code></pre>
|
||||||
|
|
||||||
|
<ul>
|
||||||
|
<li>The SPARQL query comes from my notes in <a href="/cgspace-notes/2017-08/">2017-08</a></li>
|
||||||
|
</ul>
|
||||||
|
|
||||||
<!-- vim: set sw=2 ts=2: -->
|
<!-- vim: set sw=2 ts=2: -->
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
@ -43,7 +43,7 @@ Disallow: /cgspace-notes/2015-12/
|
|||||||
Disallow: /cgspace-notes/2015-11/
|
Disallow: /cgspace-notes/2015-11/
|
||||||
Disallow: /cgspace-notes/
|
Disallow: /cgspace-notes/
|
||||||
Disallow: /cgspace-notes/categories/
|
Disallow: /cgspace-notes/categories/
|
||||||
Disallow: /cgspace-notes/categories/notes/
|
|
||||||
Disallow: /cgspace-notes/tags/notes/
|
Disallow: /cgspace-notes/tags/notes/
|
||||||
|
Disallow: /cgspace-notes/categories/notes/
|
||||||
Disallow: /cgspace-notes/posts/
|
Disallow: /cgspace-notes/posts/
|
||||||
Disallow: /cgspace-notes/tags/
|
Disallow: /cgspace-notes/tags/
|
||||||
|
|||||||
@ -4,7 +4,7 @@
|
|||||||
|
|
||||||
<url>
|
<url>
|
||||||
<loc>https://alanorth.github.io/cgspace-notes/2019-01/</loc>
|
<loc>https://alanorth.github.io/cgspace-notes/2019-01/</loc>
|
||||||
<lastmod>2019-01-02T20:52:39+02:00</lastmod>
|
<lastmod>2019-01-03T11:52:26+02:00</lastmod>
|
||||||
</url>
|
</url>
|
||||||
|
|
||||||
<url>
|
<url>
|
||||||
@ -204,7 +204,7 @@
|
|||||||
|
|
||||||
<url>
|
<url>
|
||||||
<loc>https://alanorth.github.io/cgspace-notes/</loc>
|
<loc>https://alanorth.github.io/cgspace-notes/</loc>
|
||||||
<lastmod>2019-01-02T20:52:39+02:00</lastmod>
|
<lastmod>2019-01-03T11:52:26+02:00</lastmod>
|
||||||
<priority>0</priority>
|
<priority>0</priority>
|
||||||
</url>
|
</url>
|
||||||
|
|
||||||
@ -213,27 +213,27 @@
|
|||||||
<priority>0</priority>
|
<priority>0</priority>
|
||||||
</url>
|
</url>
|
||||||
|
|
||||||
|
<url>
|
||||||
|
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
|
||||||
|
<lastmod>2019-01-03T11:52:26+02:00</lastmod>
|
||||||
|
<priority>0</priority>
|
||||||
|
</url>
|
||||||
|
|
||||||
<url>
|
<url>
|
||||||
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
|
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
|
||||||
<lastmod>2018-03-09T22:10:33+02:00</lastmod>
|
<lastmod>2018-03-09T22:10:33+02:00</lastmod>
|
||||||
<priority>0</priority>
|
<priority>0</priority>
|
||||||
</url>
|
</url>
|
||||||
|
|
||||||
<url>
|
|
||||||
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
|
|
||||||
<lastmod>2019-01-02T20:52:39+02:00</lastmod>
|
|
||||||
<priority>0</priority>
|
|
||||||
</url>
|
|
||||||
|
|
||||||
<url>
|
<url>
|
||||||
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
|
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
|
||||||
<lastmod>2019-01-02T20:52:39+02:00</lastmod>
|
<lastmod>2019-01-03T11:52:26+02:00</lastmod>
|
||||||
<priority>0</priority>
|
<priority>0</priority>
|
||||||
</url>
|
</url>
|
||||||
|
|
||||||
<url>
|
<url>
|
||||||
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
|
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
|
||||||
<lastmod>2019-01-02T20:52:39+02:00</lastmod>
|
<lastmod>2019-01-03T11:52:26+02:00</lastmod>
|
||||||
<priority>0</priority>
|
<priority>0</priority>
|
||||||
</url>
|
</url>
|
||||||
|
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user