- IPT - lists.gbif.org

Happy new year and two questions
by Michel Kapel 02 Jan '14

02 Jan '14

Happy new year everybody. I have two questions here. 1. I am searching for DarwinCore element "verbatim_scientific_name" is this available somewhere? 2. I have a need for a non DarwinCore field namely "WaterBodyType" with values such as (RIVER|LAKE|ESTUARY|SEA|...) I have looked but it does not seem to exist in DarwinCore. WaterBody does exist but this refers to the name of the water body such as "Nile river" or "Ganges river" or just "Amazon" . I want something that just specifies the type. Would it be possible to define such a field and add it to the mapping interface? Thanks in advance for any info. Michel K.

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use of extensions; how can duplication of rows be avoided?
by "Dröge, Gabriele" 02 Jan '14

02 Jan '14

Dear all, I have a general question on Darwin Core and the use of Darwin Core extensions. E.g. I want to use the Occurrence Core and Simple Images with a mysql database. Problem: Only a few of my occurrences have images. The Darwin Core Archive creates a large images file with all occurrence IDs and only a few have also Image urls. But I did expect a file with the image urls only (so much shorter) and all occurrences (with or without image) in the occurrences file. The same problem appears for the identification extension the other way round (duplication of occurrence rows for multiple identifications) and every other extension I've tested... But I am a bit confused how this can be done with only one big sql query (with some left joins). Do I have to use multiple resources to use multiple sql queries? Or is this a problem/bug of IPT? Best, Gabi

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Conflict "Darwin Core Sample Extension" and "Darwin Core Sample Core"
by "Dröge, Gabriele" 23 Oct '13

23 Oct '13

Dear all, I have another question concerning IPT and the Darwin Core extensions. For my test mapping I am using the Occurrences Core. Using the "Darwin Core Sample Extension" works in principal but unfortunately it is changed to "Darwin Core Sample Core" today (and can therefore not be used). Due to the similar name there seems to be a technical conflict. Could you please check this? Best, Gabi

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IPT bug -> MySQL
by "Dröge, Gabriele" 17 Oct '13

17 Oct '13

Dear all, I've downloaded the latest IPT version 2.0.5-r4398 and tried to map my data. I want to use a MySQL database, but there seems to be a bug in IPT concerning MySQL. IPT is not able to handle the SQL statement even though it is correct (tested on the MySQL server directly) Log file says: 1. Error in SQL (there is definitely no error in the sql statement) 2. IPT expects one more column than the sql statement queries for (unclear why) 3. IPT can't handle datetime (unclear why) A CSV file and a connection to a MS SQL Server did work. Preview looks like this: [cid:image001.jpg@01CECB47.70BB6950] It would be great if someone could fix those bugs. Thanks in advance! Best wishes, Gabi ----------------------------------------------------------------- Gabriele Droege Coordinator - DNA Bank Network Global Genome Biodiversity Network (GGBN) Berlin-Dahlem DNA Bank Deputy Women's Officer ZE BGBM Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität Berlin Koenigin-Luise-Str. 6-8 14195 Berlin Germany +49 30 838 50 139 www.dnabank-network.org<http://www.dnabank-network.org> www.ggbn.org<http://www.ggbn.org> www.bgbm.org<http://www.bgbm.org>

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mapping to the wrong datatypes
by BROSENS, Dimitri 02 Oct '13

02 Oct '13

* modified is mapped to values with the wrong data type. * eventDate is mapped to values with the wrong data type. * individualCount is mapped to values with the wrong data type. Dear, Here, we have chosen the wrong data type on purpose. For the terms eventDate and modified, the reason is that we sometimes have very vague dates. (ex: Winter 1921) and for individualCount we would like to use "unknown". (As the field is empty in the original data) Would this create any problems during the indexing? Can we just leave it like that? In the standard it is not specified which type the data has to be... only "best practices". Kind regards, Dimi * * * * * * * * * * * * * 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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IPT behind firewall [SEC=UNCLASSIFIED]
by Miles Jordan 02 Oct '13

02 Oct '13

Hello, I've been trying to set up IPT from behind a corporate firewall, however it doesn't let me access the resources from http://gbrdsdev.gbif.org. I've tried putting a valid proxy in the proxy URL parameter (although I don't think that's what it's for) and also tried starting tomcat with standard JVM http.proxy parameters, which should work, but it looks like it's just ignoring them. Other apps on the same tomcat server do pick them up. I'd appreciate some guidance because I'm still using DiGIR and would like to switch but this is holding me back. Cheers, Miles Jordan [P]+61 3 6232 3486 Australian Antarctic Data Centre | Australian Antarctic Division Dept. of Sustainability, Environment, Water, Population and Communities ___________________________________________________________________________ Australian Antarctic Division - Commonwealth of Australia IMPORTANT: This transmission is intended for the addressee only. If you are not the intended recipient, you are notified that use or dissemination of this communication is strictly prohibited by Commonwealth law. If you have received this transmission in error, please notify the sender immediately by e-mail or by telephoning +61 3 6232 3209 and DELETE the message. Visit our web site at http://www.antarctica.gov.au/ ___________________________________________________________________________

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Security update
by Kyle Braak [GBIF] 25 Sep '13

25 Sep '13

Dear IPT users, This is an important message. IPT administrators should update their IPTs to the new version which has a security update and was released yesterday: https://code.google.com/p/gbif-providertoolkit/ The security update fixes critical vulnerabilities that have been discovered in the Apache Struts web framework, which the IPT uses. According to this article, these Struts vulnerabilities allow hackers to break into a server. It goes on to say that hackers are actively exploiting these vulnerabilities. Simple instructions on how to update your IPT are below. If you don't have time to update your IPT immediately, I would advise you to take it offline until you can. You can refer to this article, which describes how to determine if you have been attacked. Please email the IPT list directly for more help upgrading your installation. Sincerely, Kyle, on behalf of the IPT development team and the GBIF Secretariat Instructions how to update IPT in Tomcat: Please download: https://gbif-providertoolkit.googlecode.com/files/ipt-2.0.5-security-update… Backup IPT data directory somewhere safe Remove ipt.war from $tomcat/webapps/ (some seconds later, the deployed /ipt folder should automatically delete) Once ipt.war and /ipt have been removed from /webapps - stop Tomcat Add new version to /webapps renaming it from ipt-2.0.5-security-update-1.war to ipt.war Start Tomcat In a browser open the application (if it doesn't appear at first, try restarting Tomcat once more). When prompted for IPT data directory, enter same location as existing IPT data directory Press continue, hopefully installation succeeds.

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IPT v2.0.5 released
by Kyle Braak 23 May '13

23 May '13

Dear IPT users, The GBIF Secretariat is pleased to announce that a new release of the Integrated Publishing Toolkit (IPT v2.0.5) is now available for download here. For information about how to upgrade your installation, you can check out the Release Notes. To find out how v2.0.5 compares to previous versions, you can check out the latest post on the GBIF Developer Blog. New users should follow the installation guidelines in the IPT User Manual that has been updated for this version. 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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IPT 2.0.4 Test Mode to Production mode
by Michel Kapel 28 Feb '13

28 Feb '13

Hello. I am looking at the version 2.0.4 of IPT and preparing for an upgrade from a 2.0.3 version. Everything looks OK to me. I have managed to customize the look and feel a little so the look fits the environment. Before I deploy there is still something I am unsure of. Switching from test mode to production mode ... With the previous version switching the "debug" value in the ipt.properties file was enough (I had problems doing so through the interface but doing it "by hand" worked fine). 2.0.4 seems to require something else linked with registration ??? in inc/menu.ftl [#if !cfg.devMode() && cfg.getRegistryType()=='PRODUCTION'] where does cfg.getRegistryType() come from ?? some property in the ipt.properties or rather the new registration.xml file ? I take it there must be some way to change this through the web interface but I would welcome the description of changes in the files themselves. Regards to all of you Michel K.

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Re: [IPT] IPT Workbook - LINK
by Francis Strobbe 12 Feb '13

12 Feb '13

Hello Kyle, Thanks a lot for the IPT Workbook notification! It could perhaps be useful for others to add a link, where to find the workbook and sample datasets: http://community.gbif.org/pg/file/read/13559/ipt-worskshop-2011-workbook or https://code.google.com/p/gbif-providertoolkit/ Best regards, Francis

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