- IPT - lists.gbif.org

"Error Publishing Resource" message
by David Remsen (GBIF) 27 Jan '12

27 Jan '12

I have a validated DarwinCore Archive that I imported into the IPT. http://ipt.gbif.org/manage/resource.do?r=neembucu2 When I press the Publish button to publish the resource I get an error message that simply reads "Error publishing resource:" with no additional information. This file is intended to be published by Pensoft on their IPT instance which gives the same error. Any ideas? David R ---------------------------------------------------------------------------- David Remsen, Senior Programme Officer Electronic Catalog of Names of Known Organisms Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321472 Fax: +45-35321480 Mobile +45 28751472 Skype: dremsen ----------------------------------------------------------------------------

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IPT 2.0.3 is available for download
by Kyle Braak (GBIF) 03 Nov '11

03 Nov '11

Dear IPT users, The GBIF Secretariat is pleased to announce that a new release of the Integrated Publishing Toolkit (IPT v2.0.3) is now available for download here. The IPT version 2.0.3 addresses 76 reported issues from the previous version, and includes translations into French and Spanish. We’d like to give special thanks to all the volunteer translators for their time and efforts: (French translators) Nicolas Noe, Louis Reymondin, and Michael Akbaraly (Spanish translators) Daniel Amariles, Angela M. Suarez, Pere Roca Ristol, Arturo H. Ariño, and Héctor Fabio Tobón R. Another special mention is owed to Peter Desmet who has spent time simplifying how to customize the style of the IPT, as explained in his article Customizing the IPT. We would like to recommend that users of previous versions update to benefit from this new functionality and bug fixing. Updating an IPT 2.0.x installation involves the following steps: 1. Replace the previous .war file with the latest edition 2. Backup the existing data directory 3. Reuse the existing data directory during setup 4. Press the “Publish all resources” button on the Administration page after initial setup is complete (this may take some time depending on the size and number of resources your IPT hosts) New users should follow the installation guidelines in the IPT User Manual that has been updated for this version. 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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Tomcat 7 documentation for IPT wiki
by Laura Russell 27 Oct '11

27 Oct '11

In reference to the wiki page (http://code.google.com/p/gbif-providertoolkit/wiki/IPTServerPreparation), stating that Tomcat 7 doesn't work, I'm sending a link to the screenshots I took when I installed Tomcat 7 on Win7-64 on June 14, 2011 so they can be added to the wiki if you want since Tomcat 7 does at least work in the Win7-64 configuration. http://129.237.201.204/Tomcat7_Win7-64_Screens.zip There are 17 screen shots. I think the only I did not capture was editing the tomcat-users.xml file. I used the tomcat web manager to deploy the ipt.war file. Also including a link to the Tomcat7 IPT instance if you want to take a look. This instance is my test instance that I use to demonstrate IPT to institutions that we are considering hosting on our live VertNet IPT. http://129.237.201.204:8080/ipt/ Let me know if you have any questions or need additional details. 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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Looking for JAR file that is responsible for DwC-A creation.
by Aaron Low 20 Oct '11

20 Oct '11

Hi, I'm a developer working on the BDRS - http://code.google.com/p/ala-citizenscience/. I'm in the process of adding the ability to export observations of species as a darwin core archive. I've been perusing your code files at http://repository.gbif.org hoping to find a jar file that I can leverage some of the functionality of the IPT without having to run whole application. To achieve this I would like to include one (or more) of the org.gbif jars as a dependency in our maven build. Unfortunately, I can't seem to find the jar that constructs a new archive. Could someone please point me in the right direction? If the functionality I'm looking for doesn't exist, that would be great for me to know as well. Thanks for your time, Regards, Aaron Low Gaia Resources p +61 8 9227 7309 w www.gaiaresources.com.au e aaron.low(a)gaiaresources.com.au

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Fwd: RE: BushBlitz GBIF data entry
by info＠pensoft.net 06 Oct '11

06 Oct '11

A question from one of the most enthusiastic users of IPT (files are attached): At last I am writing you to say that I have sent the data for the Brueelia paper in IPT. Herewith I am sending the files generated after my submission, the zip file (dwca) with the xml and txt files, and one rtf with a summary of our project. The only concern about the this is that two of our columns were not recognized during the Darwin Core mapping, look the message: "No mapped columns The following columns of the source are not assigned to the properties of this mapping: occurrenceID, verbatimLabel." I double checked throughout the "Darwin Core Terms: A quick reference guide" and was unable to find these headings over there. Anyways, I think that our data base is small but still pretty complete and useful. If you have some idea for how to inlude these columns, it will be great. The quick class and information provide by Torsten Dikow was fundamental for this stuff be done and published in IPT. He was pretty nice and very patient with us while teaching how to handle these IPT tools. Michel P. Valim Skype me in mpvalim MSN me in mpvalim(a)hotmail.com > Date: Thu, 1 Sep 2011 12:49:23 +0300 > From: info(a)pensoft.net > To: jweckstein(a)fieldmuseum.org > CC: mpvalim(a)hotmail.com; preprint(a)pensoft.net > Subject: Re: BushBlitz GBIF data entry > > Dear Jason, > > Good to hear that. Today your final proofs will be posted, please > confirm so that the paper to be published next week. > > It makes sense to upload the data beforehand and to publish it along > with the paper as supplementary Darwin Core Archive file (with the > appropriate legend). You can easily download DwC-A once you upload the > data and fill in the metadata (or at least the most important of them). > > Then the localities in your paper will be published as data along with > the publication itself. We still have time to do that. DOI and details > can be added to the IPT after publication. > > Best regards, > Lyubo > > > > On 31.8.2011 г. 23:23 ч., Jason Weckstein wrote: > > Hi Lyubomir, > > > > Torsten Dikow just finished walking us through using IPT... so we are > > more or less ready with our files. We will just wait for the final > > paper to come out for the doi number etc. > > > > Thanks for your help with this. > > > > Sincerely, > > > > Jason > > > > On Tue, Aug 30, 2011 at 7:27 AM, info(a)pensoft.net<info(a)pensoft.net> wrote: > >> Hi Jason and Michel, > >> > >> I wonder how the trials with IPT are going? Please find attached sample > >> files created by another user, that have been successfully uploaded. > >> > >> Once uploaded, you may play with the metadata elements, with creating DwC > >> archive file from your dataset and also exporting the metadata into a "data > >> paper"manuscript (not really needed for your particular dataset). Please do > >> not hesitate to contact Teodor (preprint(a)pensoft.net) in case of questions. > >> > >> Best regards, > >> Lyubomir > > > > > > > -- > 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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IPT 2.0 and GeoServer
by Antony.Tomasovic＠csiro.au 14 Sep '11

14 Sep '11

Hi Folks, I am new to IPT. Reading through the doco I see reference to GeoServer. Can someone advise whether GeoServer install is required for IPT 2.0 or it was only required for IPT 1.0. Thanks, Antony Antony Tomasovic Technical Specialist (Software Services) CSIRO IM&T CSIRO

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Simple Images Extension
by Aurelio Sanabria 09 Sep '11

09 Sep '11

Hello, I was wondering, ¿why is that there is no "rightHolder" field on the Simple Images extension? Is there a 'formal' way to add this field? I need to share some images but, I need to specify "Who" is giving the images under "license". -- Best regards, Aurelio Sanabria http://informatics.inbio.ac.cr

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Re: [IPT] GBIF Case 1773: UTF8
by Burke Chih-Jen Ko (GBIF) 08 Sep '11

08 Sep '11

And have you tried Tim's suggestion? Could you try issuing \s command in the mysql client shell to show it's character set settings? That would show information like this: Connection id: 37141 Current database: Current user: root@localhost SSL: Not in use Current pager: stdout Using outfile: '' Using delimiter: ; Server version: 5.1.56 Source distribution Protocol version: 10 Connection: Localhost via UNIX socket Server characterset: utf8 Db characterset: utf8 Client characterset: utf8 Conn. characterset: utf8 UNIX socket: /var/lib/mysql/mysql.sock Uptime: 41 days 22 hours 43 min 50 sec Threads: 1 Questions: 597738 Slow queries: 20 Opens: 2328 Flush tables: 1 Open tables: 64 Queries per second avg: 0.164 -------------- which contains character set settings. Cheers, Burke On Aug 12, 2011, at 2:30 PM, Mickael Graf wrote: > That's possible. But the very same data is displayed correctly with TapirLink. > > Yes, you can copy to the mailing list later. > > Cheers, > Mickaël > ________________________________________ > From: Burke Chih-Jen Ko (GBIF) [bko(a)gbif.org] > Sent: Friday, August 12, 2011 2:08 PM > To: Mickael Graf > Cc: helpdesk(a)gbif.org > Subject: Re: GBIF Case 1773: UTF8 > > Hi Mickael, > > I can see in the script the accented characters are already wrong. If you generate the script from sql client, perhaps the problem is on the DB side? > > For the script I see now I am sure the IPT won't read it correctly if the source is already "NÃ¤rke". > > Would you mind I copy the thread to the IPT mailing list later? > > Burke > > On Aug 12, 2011, at 1:51 PM, Mickael Graf wrote: > >> Hi Burke, >> >> >> I am using a view. Here come some scripts for checking the data/IPT. >> >> The statement in IPT is then simply 'select * from rcDwCIPT'. >> >> Cheers, >> Mickaël >> >> ________________________________________ >> From: Burke Chih-Jen Ko (GBIF) [bko(a)gbif.org] >> Sent: Thursday, August 11, 2011 9:24 AM >> To: Mickael Graf >> Cc: helpdesk(a)gbif.org >> Subject: GBIF Case 1773: UTF8 >> >> Hi Mickaël, >> >> Do you use SQL view or text file as the source for IPT? May I have some sample records to test and reproduce your issue? >> >> Thanks! >> >> Burke >> >> On Aug 10, 2011, at 4:25 PM, Mickael Graf wrote: >> >>> Hi, >>> >>> >>> I am testing IPT 2 and NRM RingedBirds is the guinea pig. >>> >>> Well, I have some issue with the encoding because, while swedish characters work fine with TapirLink (see http://www.gbif.se/tapir/tapir_client.php, choose NRM-RingedBirds and make an inventory over StateProvince), it's a mess with IPT, both as a preview and as a zipped file. For instance 'Närke' is displayed as 'NÃ¤rke'. This happens regardless of the character encoding chosen under /source.do. The original data is UTF8, but then I don't know if any settings in tomcat need to be changed. >>> >>> Do you have some knowledge about this issue? I am very bad at java, so I don't know where to look (and issue 418 doesn't help). >>> >>> >>> Cheers, >>> Mickaël >> >> <View_RC_DwC_IPT.sql><rc_test.sql> > >

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Re: [IPT] System requirements for IPT
by Tim Robertson (GBIF) 26 Aug '11

26 Aug '11

Dear Massimo > Thank you for the quick reply! You are very welcome. > Yes there will be for the moment a single DBMS with 2 big databases > (1.2 GB and 800 MB respectively). > We would like to create a single hub for the synchronization of > several other databases in future (someone will be really huge). > Which configuration can you suggest us? I don't anticipate any special configuration is needed. Tomcat likes around 128MB of memory and you'll of course need enough disk space. > Would it be possible to create a test environment with you for > testing the sync from our server? Sure. If you get the resources mapped, we can verify that they are indexable. Cheers, Tim > Thank you, > Massimo > > > From: Tim Robertson (GBIF) [mailto:trobertson@gbif.org] > Sent: Friday, August 26, 2011 16:50 > To: Buonaiuto, Massimo (Bioversity) > Cc: ipt(a)lists.gbif.org > Subject: Re: [IPT] System requirements for IPT > > Dear Massimo > > You are likely to be the first person to really use *large* datasets > in the IPT, although we have put several 10s of millions of records > in a test environment. > The IPT has been carefully designed to use a low memory footprint. > To start with, I would recommend 128MB for Tomcat, and enough disk > space to hold your output archives. There are no particular > requirements other than disk space for larger datasets. > > Will the input be sourced from a database? > > Best wishes, > Tim > > > On Aug 26, 2011, at 4:46 PM, Buonaiuto, Massimo (Bioversity) wrote: > > > Dear IPT staff, > > My name is Massimo Buonaiuto, Multimedia Web Specialist at > Bioversity International. > > I am very interested in installing locally the IPT for the > synchronization of some datasets we have with GBIF. > > At the moment we plan to synchronize about 5 GB and I would like to > receive suggestions and best practices for a correct and > successfully installation in-house. > > > Thank you and kind regards, > > Massimo > > _______________________________________________ > IPT mailing list > IPT(a)lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt >

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System requirements for IPT
by Buonaiuto, Massimo (Bioversity) 26 Aug '11

26 Aug '11

Dear IPT staff, My name is Massimo Buonaiuto, Multimedia Web Specialist at Bioversity International. I am very interested in installing locally the IPT for the synchronization of some datasets we have with GBIF. At the moment we plan to synchronize about 5 GB and I would like to receive suggestions and best practices for a correct and successfully installation in-house. Thank you and kind regards, Massimo

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