- IPT - lists.gbif.org

Re: [IPT] IPT Digest, Vol 28, Issue 1
by Deependra Tandukar 02 Jun '11

02 Jun '11

HI, good news that new version is available? But what are the new in the IPT 2.02.? Best regards, Deependra -----Original Message----- From: ipt-bounces(a)lists.gbif.org [mailto:ipt-bounces@lists.gbif.org] On Behalf Of ipt-request(a)lists.gbif.org Sent: Thursday, June 02, 2011 3:45 PM To: ipt(a)lists.gbif.org Subject: IPT Digest, Vol 28, Issue 1 Send IPT mailing list submissions to ipt(a)lists.gbif.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gbif.org/mailman/listinfo/ipt or, via email, send a message with subject or body 'help' to ipt-request(a)lists.gbif.org You can reach the person managing the list at ipt-owner(a)lists.gbif.org When replying, please edit your Subject line so it is more specific than "Re: Contents of IPT digest..." Today's Topics: 1. IPT 2.0.2 is available for download (Kyle Braak (GBIF)) 2. VASCAN metadata can now be downloaded as RTF (Peter Desmet) 3. Re: VASCAN metadata can now be downloaded as RTF (info(a)pensoft.net) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Jun 2011 14:42:20 +0200 From: "Kyle Braak (GBIF)" <kbraak(a)gbif.org> Subject: [IPT] IPT 2.0.2 is available for download To: ipt(a)lists.gbif.org Message-ID: <32FA1495-F355-49AA-8D46-025CDFD95102(a)gbif.org> Content-Type: text/plain; charset="us-ascii" Dear IPT users, The GBIF Secretariat is pleased to announce that a new release of the Integrated Publishing Toolkit (IPT v2.0.2) is now available for download from http://code.google.com/p/gbif-providertoolkit/. The IPT version 2.0.2 addresses 44 reported issues (http://tinyurl.com/gbif-ipt-202 ) from the previous version, and introduces a new Rich Text Format (RTF) export for dataset metadata. The RTF view of the metadata is designed to allow IPT users to submit data papers to journals such as Pensoft Zookeys, for peer review and publishing. More information on the data paper concept can be found on http://www.gbif.org/communications/news-and-events/showsingle/article/new-i… . Users of previous versions of the IPT may choose to update to benefit from this new functionality and bug fixing. Updating an IPT 2.0.x installation involves simply replacing the previous .war file with the latest edition, and reusing the existing data directory. Please remember that it is good practice to keep backups of the data directory, and we advise that you make a backup before performing an update. New users should follow the installation guidelines in the IPT documentation (http://code.google.com/p/gbif-providertoolkit/wiki/IPT2ManualNotes ). Thank you once again for all your help in testing and contributing to the IPT! With best regards, Kyle, on behalf of the IPT development team and the GBIF Secretariat

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Re: [IPT] [Fwd: RE: Training Sessions]
by Tim Robertson (GBIF) 02 Jun '11

02 Jun '11

Dear Raj, This error occurs because the machine the IPT is being installed on cannot make outgoing connections. I see the error is saying it cannot talk to the GBIF registry. The IPT administrator will need to investigate if there are ports closed or firewall restrictions stopping this from happening. On Linux the best way to ensure it is possible is to open a terminal and type "curl http://gbrds.gbif.org" There is also no need to install Geoserver for the IPT 2.0.x although there should not be an issue if you so wish to. I would suggest not to do so during training though as it might complicate things unnecessarily. Please can ensure all issues are sent to the to the IPT users list (ipt(a)lists.gbif.org ) which you will have to subscribe to if not already? There are more people on the list that can help diagnose potential issues, and quicker normally than I can alone. I hope this helps, Tim On Jun 2, 2011, at 3:08 PM, Raj K. Sood (GBIF) wrote: > Dear Tim, > > Kindly see the email below. Our partner at WII India has tried to > install > new version of IPT and encountered some problems as listed in their > email. > Screen shots of error msg are also attached herewith. > I also encountered error msg at point 5 and 6 of the following email. > > This is for your information and will keep you posted of any other > issues > that may come up while working with the new version of IPT. > > Thanks and take care, > > Best regards, > > > Raj Sood > GBIF Secretariat > E-mail: rsood(a)gbif.org > URL: www.gbif.org > ---------------------------- Original Message > ---------------------------- > Subject: RE: Training Sessions > From: "Dinesh Singh Pundir" <dspundir(a)wii.gov.in> > Date: Thu, June 2, 2011 9:32 am > To: "'Raj K. Sood $GBIF$'" <rsood(a)gbif.org> > Cc: vchavan(a)gbif.org > gautam(a)wii.gov.in > dspundir(a)gmail.com > -------------------------------------------------------------------------- > > Dear Mr. Raj, > > As suggested I downloaded the latest IPT version(ipt-2.0.2.war) and > tried to > install on the test machine. > > Following steps were followed > > 1. Installed java(jre-6u25-windows-i586), apache (apache- > tomcat-6.0.32) > and copied ipt.war and geoserver files in apache webapps directory. > 2. Run localhost:8080/ipt on the firefox browser. > 3. In IPT Setup-I (directory path as c:\iptdata was given) > 4. In IPT Setup-II (gave email, firstname, lastname, password etc. > under base url it automatically took path as http://DSPUNDIR:8080/ > ipt but it > showed error when I clicked on Save. > 5. Then I changed to base url to http://localhost:8080/ipt and clicked > on save. Then it directed to error screen (As shown in pdf attachment) > 6. In proxy URL I tried both by leaving it blank and next time I have > our Institute proxy server setting as http://192.168.201.254:8080 > Then it > directed to error screen (As shown in pdf attachment) > 7. After step 5 it showed error screen(pdf file) which I am attaching > you for your information and action. I am also sending you the log > screen in > pdf file. > > Kindly guide. > > Regards > > Dinesh Singh Pundir > > > > > > > <untitled-1.2><logs.pdf><IPT 2 Setup Error.pdf>

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VASCAN metadata can now be downloaded as RTF
by Peter Desmet 02 Jun '11

02 Jun '11

Hi all, I was intrigued by GBIF's announcement regarding publishing biodiversity data (http://bit.ly/m8hR6U) so I updated our IPT (http://ipt.canadensys.net) to 2.0.2 and republished our dataset (http://ipt.canadensys.net/resource.do?r=vascan) Users can now export the Database of Vascular Plants of Canada metadata as RTF (http://ipt.canadensys.net/rtf.do?r=vascan) and we could even submit this as a data paper to a Pensoft journal. Really cool and very easy! Good job IPT team! Peter PS: When I find some time, I'm going to dig a bit deeper in the RTF file and see how the EML->RTF transition went. -- Peter Desmet Biodiversity Informatics Manager / Directeur de l'informatique de la biodiversité Biodiversity Centre / Centre sur la biodiversité de l'Université de Montréal Canadensys - www.canadensys.net Institut de recherche en biologie végétale Université de Montréal 4101 rue Sherbrooke est Montréal, Québec, H1X2B2 Canada Télé / Phone: 514-343-6111 #82354 Télécopie / Fax: 514-343-2288 Email: peter.desmet(a)umontreal.ca / peter.desmet.cubc(a)gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet

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IPT 2.0.2 is available for download
by Kyle Braak (GBIF) 01 Jun '11

01 Jun '11

Dear IPT users, The GBIF Secretariat is pleased to announce that a new release of the Integrated Publishing Toolkit (IPT v2.0.2) is now available for download from http://code.google.com/p/gbif-providertoolkit/. The IPT version 2.0.2 addresses 44 reported issues (http://tinyurl.com/gbif-ipt-202 ) from the previous version, and introduces a new Rich Text Format (RTF) export for dataset metadata. The RTF view of the metadata is designed to allow IPT users to submit data papers to journals such as Pensoft Zookeys, for peer review and publishing. More information on the data paper concept can be found on http://www.gbif.org/communications/news-and-events/showsingle/article/new-i… . Users of previous versions of the IPT may choose to update to benefit from this new functionality and bug fixing. Updating an IPT 2.0.x installation involves simply replacing the previous .war file with the latest edition, and reusing the existing data directory. Please remember that it is good practice to keep backups of the data directory, and we advise that you make a backup before performing an update. New users should follow the installation guidelines in the IPT documentation (http://code.google.com/p/gbif-providertoolkit/wiki/IPT2ManualNotes ). Thank you once again for all your help in testing and contributing to the IPT! With best regards, Kyle, on behalf of the IPT development team and the GBIF Secretariat

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How to configure IPT with Apache mod_proxy?
by janno jõgeva 31 May '11

31 May '11

Hello! I am quite new to this list so hello to everyone. Maybe I just missed something but here is my question. I am setting up an IPT node on our site. As IPT is not too much of a load it could run on a server that has other tasks as well. I have managed to set the IPT up and running via apache mod_proxy using jetty. I have daemonized it to a service on port 8080. The version I am using is ipt-2.0.2-SNAPSHOT-r3084. My ipt.properties is as follows: analytics.key= debug=false proxy= ipt.baseURL=http\://sitename.domain/ipt/ analytics.gbif=true defaultLocale=en and apache configured as: ... ProxyPass /ipt/ http://localhost:8080/ ProxyPassReverse /ipt/ http://localhost:8080/ ProxyPassReverseCookiePath /ipt / ProxyPreserveHost On ... Alias /ipt "/opt/ipt/webapp" <Directory "/opt/ipt/webapp"> ... My problem - the IPT runs fine - I can make changes for example in source data SQL configuration part. but whenever the application(IPT) has to call sitename.domain/ipt/admin/user.do it calls sitename.domain/admin/user.do instead and understandably fails. My question - is there a good documentation source for the ipt.properties file? If not then could you tell me what is the "proxy" configuration parameter for? Hope that the explanation is detailed enough. PS. IMHO a configuration file should have documentation for each and every parameter written inside the file. It would help a lot. Best wishes, Janno Jõgeva University of Tartu Natural History Museum

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Dwc Germplasm extension
by Jonas Nordling 23 May '11

23 May '11

Hi all When doing an installation of the new IPT2 on Tomcat 7 last week at the Vavilov Institute, we found that the DarwinCore Germplasm extension was not available for installation. Is it only in the dev reg? Jonas Nordling, NordGen

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About extensions
by Aurelio Sanabria 16 May '11

16 May '11

Hello, I check the Google code site and my installation of the IPT, and I can't found any way to install a new custom non-gbif extension. ¿Is there a way to do it or will be a way to do it? ¿where can i get the format of the extensions if I want to write my own extensions? -- Saludos, Aurelio Sanabria http://informatics.inbio.ac.cr

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How to register external usesr for locally installed IPT nodes
by info＠pensoft.net 26 Apr '11

26 Apr '11

Dear Tim, In our Data Publishing Guidelines we intend to point out http://ipt.pensoft.net as a venue for our authors to upload their datasets. Will there be a possibility to register/login in each locally installed IPT individually? Or, the user should register/login to the GBIF IPT and then use that account? The background of my question is: what kind of instruction in this respect should we address to our authors who want to publish data through IPT? Best regards, Lyubo -- Dr Lyubomir Penev Managing Director Pensoft Publishers 13a Geo Milev Street 1111 Sofia, Bulgaria Tel +359-2-8704281 Fax +359-2-8704282 www.pensoft.net www.pensoft.net/journals/zookeys www.pensoft.net/journals/phytokeys info(a)pensoft.net

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Security Exposures
by Bruce Wilson 20 Apr '11

20 Apr '11

I have installed the IPT on a Windows 2003 server (at http://science.uvu.edu:8080/ipt/) Recently, a security evaluation was made, and here are the medium-severity weaknesses found, all of which I think are attributable to Tomcat/Apache. What should I be doing to resolve these? I typically use automatic updates to keep things current, and don't normally install software that requires hands-on maintenance, so I'm unsure if an update of the Apache or Tomcat software might break the ITP app. Or even if an update will fix the holes. I think the security certificate errors are Tomcat also, because I didn't install any in Windows, but I'm not certain. # PLUGIN NAME 2 SSL Certificate signed with an unknown Certificate Authority 2 SSL Certificate with Wrong Hostname 2 SSL Certificate Expiry 1 Apache Tomcat < 6.0.32 / 7.0.8 NIO Connector Denial of Service 1 Apache Tomcat 6.0.x < 6.0.30 Multiple Vulnerabilities 1 Apache Tomcat 6.x < 6.0.30 / 7.x < 7.0.5 Multiple XSS Bruce Wilson Department of Chemistry | Mail Stop 179 | UVU | 800 W University Parkway, Orem UT 84058 (801)863-7138 | bruce.wilson(a)uvu.edu | http://science.uvu.edu/wilson

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permission settings for IPT data directory
by Burke Chih-Jen Ko (GBIF) 20 Apr '11

20 Apr '11

Dear IPT list members, For people who sets up Tomcat & IPT on UNIX servers (Linux, BSDs), when there is something not working, and it seems you've followed the manual properly, sometimes it could be the permission that plagues. But, what permission settings are right for IPT data directory? It depends on the user that is designated to run Tomcat. In your shell, type $ ps waux | grep tomcat should reveal who is running Tomcat. So assuming the user is "tomcatuser," and user "tomcatuser" belongs to group "tomcatgroup," and the ownership of the IPT data directory (and it's child folders and files) should be tomcatuser:tomcatgroup Then, with mod 0775 of the IPT data directory, both of the tomcatuser and tomcatgroup have write permission, some issues about IPT settings or using the existing IPT directory will be resolved. As to how the system assigns which user to run Tomcat, it is actually depended on whether Tomcat is set up as a daemon and used a non-root user, or, it's actually you firing up the ./startup.sh so Tomcat is running as the user you used to log in. Either way the IPT data directory should be owned by the user which runs Tomcat, so settings and modifications can be saved. Hope this helps people who have troubles getting IPT behaves properly. Cheers, Burke Informatics Liaison GBIF Secretariat Tel: +45 35 32 15 11 Fax: +45 35 32 14 80 E-mail: bko(a)gbif.org Skype: burkeker http://community.gbif.org/pg/profile/burkeker

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