PubMan 7 7

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This page shall contain every change that is made during a qa release of the version mentioned above. If it's not here, it never happened!

PubMan 7.7 Release[edit]

Affected Servers[edit]

Prepare read only system[edit]

Fedora[edit]

Coreservice Apache[edit]

Coreservice JBoss[edit]

Core Infrastructure[edit]

  • copy jboss-log4j.xml from srv11 /home/siedersleben/escidoc-core-1.3.10-For-Release7.7 to JBOSS_HOME/server/default/conf
  • copy escidoc-core-1.3.10-SNAPSHOT-build72.ear, fedoragsearch.war, srw.war from /home/siedersleben/escidoc-core-1.3.10-For-Release7.7 to JBOSS_HOME/server/default/deploy
  • chown jboss:jboss ....

Core Properties[edit]

  • escidoc-core.properties: remove the pdf extractor properties from escidoc-core.properties and put the corresponding properties to fedoragsearch.properties (gs: Änderungen eingefügt auf srv11 unter escidoc-core.properties.release7.7.)
# true|false Defines what happenes if an Exception occurs while extracting the text from an pdf for indexing
# if set to true, Exception is ignored and object is indexed without the fulltext.
# if set to false, Exception is thrown and object is not indexed at all.
gsearch.ignoreTextExtractionErrors = true
# Location of the indexingStylesheet that generates the indexInformation-Document for gsearch-indexing.
# has to be an URL
# currently the eSciDoc-Core-Infrastructure provides 2 index-databases: escidoc_all and escidocou_all
# stylesheet-path-property for index escidoc_all is gsearch.escidoc.indexingStylesheet
# stylesheet-path-property for index escidoc_all is gsearch.escidocou.indexingStylesheet
#gsearch.escidoc.indexingStylesheet = http://escidoc1.escidoc.mpg.de/resources/searchIndexDefinition/mpdlEscidocXmlToLucene_1.2.xslt
gsearch.escidoc.indexingStylesheet = http://coreservice.mpdl.mpg.de/mpdlEscidocXmlToLucene.xslt
gsearch.escidocou.indexingStylesheet = 
# if pdfBox (internally used by gsearch to extract text from pdfs) is not working well for your pdfs,
# define command-line-command to custom pdf-text-extractor (has to get installed seperately)
# define command with full path, define inputfile with <inputfile> and outputfile with <outputfile>
#example: C:/Programme/xpdf-3.02pl2-win32/pdftotext -cfg C:/Programme/xpdf-3.02pl2-win32/xpdfrc <inputfile> <outputfile>
# gsearch.pdfTextExtractorCommand = /usr/bin/pdftotext -cfg /etc/xpdfrc <inputfile> <outputfile>
gsearch.pdfTextExtractorCommand = /usr/bin/java -classpath /usr/share/jboss/server/default/conf/pdf-extraction/classes:/usr/share/jboss/server/default/conf/pdf-extraction/lib/iText-5.0.6.jar de.mpg.escidoc.services.extraction.ExtractionChain <inputfile> <outputfile>
# Analyzer to use for indexing and search
lucene.analyzer = de.escidoc.sb.common.lucene.analyzer.EscidocAnalyzer
  • add new property for skipping reindex to escidoc-core.properties (gs: already in escidoc-core.properties.release7.7)
# Comma separated List of method names, where automatic indexing is skipped
escidoc-core.skip.notify.indexer.methods = assignObjectPid, assignVersionPid
  • fedoragsearch.properties: add the following properties to JBOSS_HOME/conf/search/config/fedoragsearch.properties: (gs: Änderungen eingefügt auf srv11 unter fedoragsearch.properties.release7.7.)
# if pdfBox (internally used by gsearch to extract text from pdfs) is not working well for your pdfs,
# use a command-line tool.
# If you want to use a command-line tool,
# define command-line-command to custom pdf-text-extractor (has to get installed seperately)
# define command with full path, define inputfile with <inputfile> and outputfile with <outputfile>
#example: C:/Programme/xpdf-3.02pl2-win32/pdftotext -cfg C:/Programme/xpdf-3.02pl2-win32/xpdfrc <inputfile> <outputfile>
fedoragsearch.pdfTextExtractorCommand=/usr/bin/java -classpath /usr/share/jboss/server/default/conf/pdf-extraction/classes:/usr/share/jboss/server/default/conf/pdf-extraction/lib/itextpdf-5.5.1.jar de.mpg.escidoc.services.extraction.ExtractionChain <inputfile> <outputfile>
# true|false Defines what happens if an Exception occurs while extracting the text from an pdf for indexing
# if set to true, Exception is ignored and object is indexed without the fulltext.
# if set to false, Exception is thrown and object is not indexed at all.
fedoragsearch.ignoreTextExtractionErrors=true
  • copy directory pdf-extraction and pdfbox-app-1.8.6.jar from /home/siedersleben/escidoc-core-1.3.10-For-Release7.7 to JBOSS_HOME/conf (gs: already done)

Core Index Properties[edit]

  • Reindex: set the following properties in $JBOSS_HOME/conf/search/config/index/escidoc_all/index.properties (remove comment sign)
 #Use this property for bulk index operations: the index is hold in memory until ramBufferSize is reached.
 #Make sure this property does not conflict with fgsindex.maxBufferedDocs.
 fgsindex.ramBufferSizeMb = 128
 # Use this property to minimize garbage collection during indexing. Be careful: index is not thread save when running in this mode.
 fgsindex.indexMode = 1
  • same for item_container_admin
  • set indexing to asynchron for item_container_admin during reindex in $JBOSS_HOME/conf/search/config/index/item_container_admin/index.object-types.properties
 Resource.Item.indexAsynchronous=true
  • check if pdf extraction works properly looking for log messages like the following in fedoragsearch.log (don't care about the WARN)
 WARN 2014-08-06 09:17:54,269 (TransformerToText)(http-0.0.0.0-8080-4) error while transforming pdf to text with external tool:
 Extracting PDF content ----------------------------------------
 Infile: /usr/share/jboss-4.2.3.GA/server/default/1407309473650.pdf
 Outfile: /usr/share/jboss-4.2.3.GA/server/default/1407309473650.txt
 Wed Aug 06 09:17:53 CEST 2014 -- started
 Extracting with xPDF
 Wed Aug 06 09:17:54 CEST 2014 -- finished successfully
 Extraction took 314
  • dont't forget to set back all these properties modified when reindex has finished

Core Lucene Index[edit]

PubMan EAR[edit]

PubMan Properties[edit]

  • escidoc.transformation.wos.stylesheet.filename=/usr/share/jboss/server/default/conf/transformation/transformations/otherFormats/xslt/wosxml2escidoc.xslt

& check if transformation exists

  • escidoc.framework_access.framework.url=http://localhost:8080 (instead of coreservice)
  • CHANGE: escidoc.pubman.favicon.url=/pubman/faces/javax.faces.resources/pubman_favicon_32_32.png
  • escidoc.dataaquisition.resources.fop.configuration (?)
  • escidoc.cone.modelsxml.path (?)
  • escidoc.transformation.edoc.stylesheet.filename (?)
  • escidoc.transformation.endnote.ice.stylesheet.filename
  • escidoc.transformation.endnote.stylesheet.filename (?)
  • escidoc.transformation.edoc.configuration.filename (?)
  • escidoc.transformation.escidoc2marcxml.stylesheet.filename (?)
  • escidoc.aa.public.key.file
  • escidoc.aa.private.key.file
  • escidoc.aa.config.file

PubMan Apache[edit]

  • Add ProxyPassReverse for /cone, /sword-app, /dataacquisition in Apache 2 config, if not done yet

PubMan Wildfly[edit]

  • Add pubman module, which should contain all properties and configuration files for PubMan:
    • Create directory WILDFLY_HOME/modules/pubman/main
    • Add a file called module.xml to this directory, containing the following xml
 <?xml version="1.0" encoding="UTF-8"?>
 <module xmlns="urn:jboss:module:1.1" name="pubman">
     <resources>
                 <resource-root path="."/>
     </resources>
 </module>
    • Add all necessary property files to this directory (pubman.properties, solution.properties, auth.properties, cone.properties, conf.xml, apache-fop-config.xml)
    • Make this module global by adding the following xml snippet to standalone.xml, subsystem urn:jboss:domain:ee
 <global-modules>
   <module name="pubman" slot="main"/>
 </global-modules>


  • Wildfly has a default maximum POST size of 10mb and a default POST parameter size of 1000, which is not convenient for large file uploads
    • Increase max-post and max-parameters size in standalone.xml, subsystem urn:jboss:domain:undertow by changing http-listener to (for e.g. 1024 mb)
 <http-listener name="default" socket-binding="http" max-post-size="1024000000" max-parameters="50000"/>

PubMan PidCache[edit]

eSciDoc-OAI-Provider[edit]

  • copy escidoc-oaiprovider.war from /home/walter

AA[edit]

Validation Database[edit]

Migration database[edit]

CoNE[edit]

eSciDoc Admin[edit]

Data Migration[edit]

PubMan Software Homepage[edit]

Miscellaneous[edit]