PubMan 7 7

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

Core Infrastructure

• 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

• 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

• 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

• Take indexing stylesheets from wildfly branch, not from trunk:
  • https://subversion.mpdl.mpg.de/repos/common/wildfly_migration/common_services/framework_access/src/main/resources/

PubMan Properties

• 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

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

PubMan Wildfly

• 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"/>

eSciDoc-OAI-Provider

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

Publication Management

Flexible Extensible Digital Object Repository Architecture

Open Source and Most Widely Used Web Server

Open source Java EE-based application server

Enterprise Archive File Formate

Portable Document Format

Uniform Resource Locator

Enhanced Scientific Documentation

Open Source Library for Creating pdf Files in Java

Portable Document Format

Filename Extension for Text Files

Central European Summer Time

Enterprise Archive File Formate

Unicode Transformation Format

Control of Named Entities