- IPT - lists.gbif.org

Problem with setenv.sh
by Peter Desmet 05 Feb '09

05 Feb '09

Hi all, I wanted to increase the memory of Tomcat, so I copied the setenv.sh Tim provided to the bin directory, but this breaks Tomcat (http://localhost:8080/ can not be found). Removing the file and restarting Tomcat fixes the problem. I also discovered some warnings in Terminal when I want to ./shutdown.sh Tomcat, which weren't there before. Are there other ways to increase the memory, and how can I check how much memory is allocated to Tomcat? I use apache-tomcat-6.0.18 on Mac OS X (10.5.6) with 4GB SDRAM. The setenv.sh file contains Tim's: export JAVA_OPTS="-server -XX:+UseParallelGC -Xmx2048m -XX:MaxPermSize=1024m -Xms1024m -Djava.awt.headless=true" Peter -- Peter Desmet Biodiversity Informatics Manager / Directeur de l'informatique de la biodiversité Montréal Biodiversity Centre / Centre sur la biodiversité de Montréal Institut de recherche en biologie végétale Université de Montréal 4101, rue Sherbrooke est Montréal, Québec, H1X 2B2 Canada Télé / Phone: 514-872-5249 Télécopie / Fax: 514-872-9406 Email: peter.desmet.cubc(a)gmail.com

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IPT for Mac OSX
by Markus Döring (GBIF) 05 Feb '09

05 Feb '09

Dear all, to make life easier for macintosh users I have adapted the geoserver installer to run the IPT: http://dl.getdropbox.com/u/457027/ipt-1.0b.3.dmg It is a regular Mac application that uses Jetty to host geoserver and the IPT locally. You can start/stop the server with a single click. This is not intended for serious production use, in that case Tomcat is still recommended and you will need to have a continously running server. But it should come handy for people to try and play with the IPT. Markus

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IPT beta available
by Markus Döring (GBIF) 05 Feb '09

05 Feb '09

+++ Welcome to IPT 1.0 beta +++ GBIF is happy to announce the first public beta version of the GBIF Integrated Publishing Toolkit. We have been working for quite a while on this software and finally reached a stage where we want to engage early users to get feedback. The IPT allows to host and share species occurrence or taxonomic checklist datasets based on an extendible darwin core as well as pure metadata descriptions for biological resources, whether they have been digitised or not. You can find further information on the project homepage: http://code.google.com/p/gbif-providertoolkit/ We are providing a public live demo installation at GBIF for anyone to try out. To gain access to most of the functionality you will have to register as a new user and ask me or Tim to assign you additional "manager" rights. http://ipt.gbif.org His voice may not be that of Morgan Freeman, but Tim has done a great job recording some screen casts to get you started. Before getting angry about the still missing user manual (which is being worked on and will be ready for the final release) please watch this movie first: ftp://ftp.gbif.org/projects/ipt/tutorial/beta/9minuteDemo.mov If you prefer to install the IPT yourself you can find basic instructions on the project site and you should also watch Tim playing with Tomcat: http://code.google.com/p/gbif-providertoolkit/wiki/Installation ftp://ftp.gbif.org/projects/ipt/tutorial/beta/installIPT.mov We'd like to thank any beta testers already. Your testing will help us improve the software and provide new ideas that we will try to incorporate in future releases. Please consider the following guidelines when testing: - if you run into any bugs, report them as issues in google code, which is linked at the bottom of every IPT page. - if you have any questions whatsoever, please post them on this mailing list instead of contacting us individually. This helps others facing the same problems. For the proper user manual and other documentation like screen casts we are always seeking help too. There is even some funding available for people willing to spend more time. In any of those case please get in touch with our training officer Alberto Gonzalez-Talavan: atalavan(a)gbif.org Thanks for your interest. I can't wait to get flooded with bug reports ;) Markus -- Markus Döring Bioinformatics Software Engineer GBIF Secretariat mdoering(a)gbif.org

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Re: [IPT] IPT beta available
by Tim Robertson 05 Feb '09

05 Feb '09

Hi all, I am in a meeting so must be quick, but here is the configuration file. The important thing is to increase the maximum memory. To achieve this is different on each operating system. Somehow you will set -Xmx1G If you have difficulties with this, please announce to the list with your operating system, and tomcat version and we can help. Thanks, Tim On 4 Feb 2009, at 17:49, Peter Desmet wrote: > Markus, Tim, > > I just posted your message on our Canadensys mailing list, so I hope > you do get flooded with bug reports. :-) > > Tim, your screencast mentions a setenv.sh, for creating a larger > memory for Tomcat. Could you put some more details and an example-file > on website's documentation section? > > If you like, I could contribute to the documentation. My IT-skills are > basic, but I think I could help updating the text or explaining > something in a less techy way. If you want to include me in the wiki, > my gmail address is: peter.desmet.cubc(a)gmail.com. > > Cheers, > > > Peter > > > > On Wed, Feb 4, 2009 at 10:22 AM, Markus Döring (GBIF) <mdoering(a)gbif.org > > wrote: >> +++ Welcome to IPT 1.0 beta +++ >> >> GBIF is happy to announce the first public beta version of the GBIF >> Integrated Publishing Toolkit. We have been working for quite a while >> on this software and finally reached a stage where we want to engage >> early users to get feedback. The IPT allows to host and share species >> occurrence or taxonomic checklist datasets based on an extendible >> darwin core as well as pure metadata descriptions for biological >> resources, whether they have been digitised or not. You can find >> further information on the project homepage: http://code.google.com/p/gbif-providertoolkit/ >> >> >> We are providing a public live demo installation at GBIF for anyone >> to >> try out. To gain access to most of the functionality you will have to >> register as a new user and ask me or Tim to assign you additional >> "manager" rights. >> http://ipt.gbif.org >> >> His voice may not be that of Morgan Freeman, but Tim has done a great >> job recording some screen casts to get you started. Before getting >> angry about the still missing user manual (which is being worked on >> and will be ready for the final release) please watch this movie >> first: >> ftp://ftp.gbif.org/projects/ipt/tutorial/beta/9minuteDemo.mov >> >> >> If you prefer to install the IPT yourself you can find basic >> instructions on the project site and you should also watch Tim >> playing >> with Tomcat: >> http://code.google.com/p/gbif-providertoolkit/wiki/Installation >> ftp://ftp.gbif.org/projects/ipt/tutorial/beta/installIPT.mov >> >> >> >> We'd like to thank any beta testers already. Your testing will help >> us >> improve the software and provide new ideas that we will try to >> incorporate in future releases. Please consider the following >> guidelines when testing: >> - if you run into any bugs, report them as issues in google code, >> which is linked at the bottom of every IPT page. >> - if you have any questions whatsoever, please post them on this >> mailing list instead of contacting us individually. This helps others >> facing the same problems. >> >> For the proper user manual and other documentation like screen casts >> we are always seeking help too. There is even some funding available >> for people willing to spend more time. In any of those case please >> get >> in touch with our training officer Alberto Gonzalez-Talavan: atalavan(a)gbif.org >> >> >> Thanks for your interest. >> I can't wait to get flooded with bug reports ;) >> >> Markus >> >> >> >> -- >> Markus Döring >> Bioinformatics Software Engineer >> GBIF Secretariat >> mdoering(a)gbif.org >> >> >> >> >> >> >> _______________________________________________ >> IPT mailing list >> IPT(a)lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt >> > > > > -- > Peter Desmet > Biodiversity Informatics Manager / Directeur de l'informatique de la > biodiversité > Montréal Biodiversity Centre / Centre sur la biodiversité de Montréal > > Institut de recherche en biologie végétale > Université de Montréal > 4101, rue Sherbrooke est > Montréal, Québec, H1X 2B2 > Canada > > Télé / Phone: 514-872-5249 > Télécopie / Fax: 514-872-9406 > Email: peter.desmet.cubc(a)gmail.com >

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How to become admin?
by Peter Desmet 03 Feb '09

03 Feb '09

Hi everyone, I managed to get IPT running on my local machine (http://localhost:8080/ipt-1.0beta/). How can I assign myself admin rights to get access to the admin webinterface? Thanks, Peter -- Peter Desmet Biodiversity Informatics Manager / Directeur de l'informatique de la biodiversité Montréal Biodiversity Centre / Centre sur la biodiversité de Montréal Institut de recherche en biologie végétale Université de Montréal 4101, rue Sherbrooke est Montréal, Québec, H1X 2B2 Canada Télé / Phone: 514-872-5249 Télécopie / Fax: 514-872-9406 Email: peter.desmet.cubc(a)gmail.com

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Resource configuration for new resource
by Peter Desmet 02 Feb '09

02 Feb '09

Hi, I added a new resource to my IPT and I could fill out all the metadata, but I don't see how I can add my source-file. If I check default resources (Pontaurus & Euro+Med), I do see Resource Configuration in the menu on the right (with Source Data, Data Transformation, Property Mappings, Cache, Validation). Am I missing something, or is this feature not available yet for newly added resources? Peter -- Peter Desmet Biodiversity Informatics Manager / Directeur de l'informatique de la biodiversité Montréal Biodiversity Centre / Centre sur la biodiversité de Montréal Institut de recherche en biologie végétale Université de Montréal 4101, rue Sherbrooke est Montréal, Québec, H1X 2B2 Canada Télé / Phone: 514-872-5249 Télécopie / Fax: 514-872-9406 Email: peter.desmet.cubc(a)gmail.com

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