- IPT - lists.gbif.org

IPT v2.0.4 released
by Kyle Braak [GBIF] 18 Oct '12

18 Oct '12

Dear IPT users, The GBIF Secretariat is pleased to announce that a new release of the Integrated Publishing Toolkit (IPT v2.0.4) is now available for download here. Since the last version was released in November 2011, the growing user community has been actively reporting enhancement requests and minor bugs. A total of 108 issues were addressed in IPT version 2.0.4; 38 Defects, 35 Enhancements, 7 Other, 5 Patches, 18 Won't fix, 4 Duplicates, and 1 that was considered as Invalid. These are detailed in the issue tracking system. A few notable improvements to the User Interface include: Translation into Traditional Chinese Clearer setup pages aimed at preventing users from installing the IPT in the test mode unwittingly Improved user friendliness, done by adding more context help and better navigation between pages A couple of new features added in this release are: Resource migration: allows an IPT resource to replace the registration of an existing DiGIR, BioCASE, or TAPIR resource in the GBRDS [instructions] Creating a resource from an archived resource folder: allows a resource to be transferred between 2 IPTs including all its source files and mappings [instructions] As always, we’d like to give special thanks to the volunteer translators for their time and efforts: Nicolas Noé (Belgian Biodiversity Platform, Belgium) - French TaiBIF, Taiwan - Traditional Chinese Laura Roldan Gomez, Dairo Escobar, and Daniel Amariles, (Colombian Biodiversity Information System (SiB)) - Spanish Another couple of special mentions are owed to Peter Desmet and Laura Russell who provided an exceptional amount of feedback and suggestions. We highly recommend previous versions to be updated. Updating an IPT 2.0.x installation can be done in 3 simple steps: Replace the previous .war file with the latest edition Backup the existing data directory Reuse the existing data directory during setup New users should follow the installation guidelines in the IPT User Manual that has been updated for this version. A Spanish version of the IPT User Manual is also available now thanks to the volunteers from SiB. Thank you once again for using the IPT, and we hope you enjoy the latest version. With kind regards, Kyle, on behalf of the IPT development team and the GBIF Secretariat

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FW: IPT Zip File Upload - Not Successful
by Palanisamy, Giri 14 Oct '12

14 Oct '12

Hi, Can you please help us solve the following issues? Derek is using the USGS IPT installation at http://bison.ornl.gov/ipt (Version 2.0.2-r3306) Thanks! Giri From: Derek Masaki The zip file upload to the IPT was not successful. I was able to zip the csv to an acceptable size and added it to the resource, however the file appears unreadable. See screen capture below [cid:part1.05060404.05000600@usgs.gov] -- From: Derek Masaki Subject: IPT Max File Size Limit Hello, Ran into this error in attempting upload of MARIS - screenshot image below. This is a 1million record dataset. The file size limit on the IPT appears to be set at 100mb. I'm going to run compression to create a zip archive as it appears that IPT may be able to handle a zip file. Is there any way to increase the file size limit? Thanks, -derek [cid:image001.png@01CDA863.F439CDB0] -- Derek Masaki U.S. Geological Survey Biological Data Manager - Core Science Analytics and Synthesis Geospatial Liaison - National Geospatial Program 310 W Kaahumanu Ave, Kahului HI 96732 Ph 808-358-2497 dmasaki(a)usgs.gov<mailto:dmasaki@usgs.gov>

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Classloader leak in IPT
by Derek Broughton 01 Oct '12

01 Oct '12

I'm running IPT in Tomcat and experiencing PermGen memory errors. >From the Tomcat Manager, I can use "Find Leaks", and as suspected get: "The following web applications were stopped (reloaded, undeployed), but their classes from previous runs are still loaded in memory, thus causing a memory leak (use a profiler to confirm): /ipt" http://frankkieviet.blogspot.ca/2006/10/classloader-leaks-dreaded-permgen-s… does a pretty good job of explaining _why_ this happens. Unfortunately, I can't seem to find part two which is supposed to tell me how to go about fixing it. His blog also only deals with memory leaks on redeployment, but this is happening any time IPT is running for a while, so IPT is leaking in ordinary use, rather than just at context initialization. I'm going to try to find what's happening with a profiler, but I'm new to this... Tomcat Version 6.0.35 JVM Version Sun 1.6.0_24-b07 Linux 2.6.24-28-generic amd64 -- derek

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Updating registration of vocabularies results in startup warning
by DESMET, Peter 12 Sep '12

12 Sep '12

Hi, I just updated the registration of the vocabularies on http://ipt.inbo.be, which resulted in an error I don't understand. Can anyone help? Thanks, Peter The issue is recorded at: http://code.google.com/p/gbif-providertoolkit/issues/detail?id=913 What steps will reproduce the problem? 1. Browsed to the http://ipt.inbo.be<http://ipt.inbo.be/> administration panel > Core Types and Extensions 2. Updated the registration of the 9 vocabularies 3. This resulted in an error, which reads in the log file as: WARN Updating IPT instance throught GBIF Registry WARN Vocabulary URI http://rs.gbif.org/vocabulary/gbif/agentRole exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/gbif/agent_role.xml WARN Cant parse local vocabulary file org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId. at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1234) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:525) ... 4. A yellow warning is shown across the top of every page, even for not logged-in users: "IPT startup warnings, please see logs!" What version of the provider software are you using? The version should be displayed in the footer of any page. Version 2.0.3-r3672<http://code.google.com/p/gbif-providertoolkit/source/detail?r=3672> * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document.

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JDBC Connection to MS Access
by Dan Lear 10 Sep '12

10 Sep '12

Hi, I want to connect to a MS Access database to pull-in Source Data. But get the following error: Couldnt create new external datasource connection with JDBC Class=sun.jdbc.odbc.JdbcOdbcDriver, URL=jdbc:odbc:SMSGMR, user=. Error: [unixODBC][Driver Manager]Data source name not found, and no default driver specified I have a local System DSN set up, but presumably need to bridge between ODBC and JDBC, so is this a problem that is fixed by editing jdbc.properties as detailed here: http://code.google.com/p/gbif-providertoolkit/wiki/IPT2DatabaseConnection If not, can anyone enlighten me as to how to connect to an MS Access table? Thanks Dan

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Experience installing IPT on Ubuntu w/ Tomcat
by Derek Broughton 05 Aug '12

05 Aug '12

I just thought I'd share my experience installing IPT into a Tomcat (5.5 - but experience suggests 6 or 7 wouldn't have helped) installed from Ubuntu packages. In a nutshell: don't try it! Ubuntu's packages (and I imagine Debian or any Debian-based system, though I haven't confirmed that) block the normal logging available from the stock Apache versions of Tomcat. What logging there is, gets diverted to the system log (where it is both poorly formatted - no newlines - and truncated). More logging becomes available if you edit 03catalina.policy: // These permissions apply to JULI grant codeBase "file:${catalina.home}/bin/tomcat-juli.jar" { permission java.security.AllPermission; }; but in itself that isn't enough to get logging for IPT, and the IPT install fails, but is unable to log the cause of the failure (which I think is the inability to write to the log, but never managed to prove). The simple solution is to: - download Tomcat 6 from Apache (http://tomcat.apache.org/download-60.cgi - the tar.gz Binary version), - untar it anywhere (I put it in /opt), - optionally create a symbolic link from /opt/tomcat to the /opt/apache-tomcat* directory you have just created - stop your existing tomcat , - copy all .war files from /var/lib/tomcat*/webapps to the /opt/tomcat/webapps (you may want to copy the subdirectories from there too, if you have applications that store data in them) - start your new server with /opt/tomcat/bin/startup.sh (setting the environment variable JAVA_OPTS first, with any values that must be passed - for instance, our GeoServer app requires "-D GEOSERVER_DATA_DIR=/opt/geoserver/data") Don't forget to replace /etc/init.d/tomcat* with an appropriate script to start/stop the new tomcat using /opt/tomcat/bin/startup.sh & shutdown.sh -- derek broughton Pointerstop Consulting (for OBIS Canada)

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Running IPT in Netbeans for Debugging
by Sarfaraz Ahmed Soomro 13 Jun '12

13 Jun '12

Hi I am new to IPT and I want to be able to run IPT using Netbeans and the attached Tomcat Server with Netbeans. Right now if I do Run Project in Netbeans it gives the error "Deployment error: No archive for deployment" If I do "Clean and Build Project" it would just startup the Jetty server that's bundled with IPT. Is it possible to be able to run IPT with the attached Tomcat server instance in Netbeans so I can do debugging on the code as well. Thanks, Sarfaraz

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Re: [IPT] CentOS IPT Install
by Laura Russell 05 Apr '12

05 Apr '12

Hi Tim and Burke, Yes still having issues. Tried Kyle's suggestion on Friday. Didn't work, but did cause a connection refused error in Apache. I just read Burke's suggestion below and my our IT admin here at KU just suggested the same thing. Going to recommend to Field IT. Stan Blum also indicated that he had issues with CentOS 5 and Tomcat 5 and went with fresh installs on a virtual server and Tomcat 6. Can't do a fresh system install in this situation, but might be able to update to Tomcat 6. Going to investigate the SELinux policy settings first. I'll keep the list posted as to the resolution. Thanks. Laura Russell VertNet Programmer Biodiversity Institute University of Kansas Dyche Hall 1345 Jayhawk Blvd., Room 606 Lawrence, KS 66045 Phone: 785.864.4681 Fax: 785.864.5335 Email: larussell(a)vertnet.org Email: larussell(a)ku.edu Google Chat: larussell(a)vertnet.org Skype: laura.anne.russell URL: http://www.vertnet.org VertNet Portals: MaNIS: http://www.manisnet.org HerpNET: http://www.herpnet.org ORNIS: http://www.ornisnet.org FishNet2: http://www.fishnet2.net From: "Burke Chih-Jen Ko [GBIF]" <bko(a)gbif.org> Date: Mon, 26 Mar 2012 11:38:55 +0200 To: Laura Russell <larussell(a)vertnet.org> Cc: "Tim Robertson [GBIF]" <trobertson(a)gbif.org> Subject: Re: [IPT] CentOS IPT Install Hi Laura, Perhaps you would also want to check the SELINUX policy settings on the CentOS box. I happened to similar situations when every setting is honoured and it turns out the SELINUX add another layer of filtering communications of the linux box. Cheers, Burke On Mar 26, 2012, at 9:10 AM, Tim Robertson [GBIF] wrote: > Hi Laura > > After our Skype session, is this still an issue? > > For the benefit of the list: We found that using the terminal the machine > could not open connections to itself on port 8080. We found this using curl > > Cheers, > Tim > > > > On Mar 23, 2012, at 5:57 PM, Laura Russell wrote: > >> I'm having difficulty with a CentOS IPT Install that I'm doing for the Field >> Museum (in Chicago, I'm remote to their server from Kansas). The Field IT >> staff enabled their Tomcat on the server. And I've deployed the IPT. >> Permissions on the iptdata folder seem to be okay as it created all the >> folders and extension files in the first step. >> >> They are running >> CentOS 5.2 >> Tomcat 5.5.23 >> Java 1.6 >> >> I'm getting the following error when trying to complete the second setup page >> on the IPT. >> >> "The Base URL does not point to an IPT installation that is accessible from >> this computer." >> >> The URL is accessible outside of the firewall. I've also tried it with the >> IP address and get the same error. >> >> I chatted with Tim Robertson a bit yesterday and I've had the Field IT staff >> check that the port is open for both incoming and outgoing connections. They >> do not think their firewall is the issue so I'm looking at other >> possibilities. >> >> I've attached the Catalina.out file and the IPT Admin and Debug logs. >> >> Any assistance is appreciated. >> >> Thanks. >> >> >> Laura Russell >> VertNet Programmer >> Biodiversity Institute >> University of Kansas >> Dyche Hall >> 1345 Jayhawk Blvd., Room 606 >> Lawrence, KS 66045 >> >> Phone: 785.864.4681 >> Fax: 785.864.5335 >> >> Email: larussell(a)vertnet.org >> Email: larussell(a)ku.edu >> Google Chat: larussell(a)vertnet.org >> Skype: laura.anne.russell >> >> URL: http://www.vertnet.org <http://www.vertnet.org/> >> >> VertNet Portals: >> MaNIS: http://www.manisnet.org <http://www.manisnet.org/> >> HerpNET: http://www.herpnet.org <http://www.herpnet.org/> >> ORNIS: http://www.ornisnet.org <http://www.ornisnet.org/> >> FishNet2: http://www.fishnet2.net <http://www.fishnet2.net/> >> >> <FieldIPTerrors.zip>_______________________________________________ >> IPT mailing list >> IPT(a)lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt > > _______________________________________________ > IPT mailing list > IPT(a)lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt

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CentOS IPT Install
by Laura Russell 26 Mar '12

26 Mar '12

I'm having difficulty with a CentOS IPT Install that I'm doing for the Field Museum (in Chicago, I'm remote to their server from Kansas). The Field IT staff enabled their Tomcat on the server. And I've deployed the IPT. Permissions on the iptdata folder seem to be okay as it created all the folders and extension files in the first step. They are running CentOS 5.2 Tomcat 5.5.23 Java 1.6 I'm getting the following error when trying to complete the second setup page on the IPT. "The Base URL does not point to an IPT installation that is accessible from this computer." The URL is accessible outside of the firewall. I've also tried it with the IP address and get the same error. I chatted with Tim Robertson a bit yesterday and I've had the Field IT staff check that the port is open for both incoming and outgoing connections. They do not think their firewall is the issue so I'm looking at other possibilities. I've attached the Catalina.out file and the IPT Admin and Debug logs. Any assistance is appreciated. Thanks. Laura Russell VertNet Programmer Biodiversity Institute University of Kansas Dyche Hall 1345 Jayhawk Blvd., Room 606 Lawrence, KS 66045 Phone: 785.864.4681 Fax: 785.864.5335 Email: larussell(a)vertnet.org Email: larussell(a)ku.edu Google Chat: larussell(a)vertnet.org Skype: laura.anne.russell URL: http://www.vertnet.org VertNet Portals: MaNIS: http://www.manisnet.org HerpNET: http://www.herpnet.org ORNIS: http://www.ornisnet.org FishNet2: http://www.fishnet2.net

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All space-characters in metadata are replaced to plus-character
by Tero Mononen 10 Mar '12

10 Mar '12

Hi We have used this IPT-setup without any problems till now. System: Version 2.0.2-r3306 Apache Tomcat/6.0.24 JVM 1.6.0_29-b1 Problem: All space-characters in metadata are replaced to plus-character. For example title "foo bar car" is saved as "foo+bar+car". It affects in every text field in metadata. If I include at least one plus-char in a text value, it prevents the space replacement. For example "foo bar car+dar" is saved as it is. I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? Best Regards, Tero Mononen -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park Länsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ Tero Mononen, Analyst Programmer tero.mononen(a)uef.fi<mailto:juha.lehtonen@uef.fi> +358-50-5631788

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