March 2009 - IPT - lists.gbif.org

IPT Documentation
by Arnaud Réveillon 02 Apr '09

02 Apr '09

Dear all, My name is Arnaud Réveillon and I have been appointed to write the documentation for the IPT. I am not new to the GBIF and biodiversity-related software as I worked during four years (2004-2008) for the Belgian focal point for the Convention on Biological Diversity, acting as tutor (mostly on databases, web applications, web pages editors, etc.) and as webmaster. During this period, I have been regularly in contact with members of several national GBIF nodes and am generally well aware of their work. I am not yet fully familiar with the IPT but hope to get up to speed in the next few days, with the help of the list. Please do not hesitate to let me know about your needs, the difficulties you are having with the IPT or anything that may be of interest regarding the documentation, which is scheduled to be ready on 16 April. Thank you, Arnaud Réveillon-

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IPT 1.0b.8 online
by Markus Döring (GBIF) 23 Mar '09

23 Mar '09

Dear all, a new pre relase of the IPT is available for testing. You can try it here as usual: * online demo http://ipt.gbif.org * a war archive for your own tomcat installation http://gbif-providertoolkit.googlecode.com/files/ipt-1.0b.8.war * a mac standalone version without any further dependecies ftp://ftp.gbif.org/projects/ipt/downloads/ipt-1.0b.8.dmg Many, many thanks for the valuable feedback we have received in the past weeks. There are still outstanding bugs, but the new release 1.0b. 8 fixes many of them. Work has been done to fix SQL source problems, to provide a better property mapping interface, to connect to the GBIF registry (a test registry is currently configured) and to update darwin core extensions and vocabularies for controlled terms from central sites. If you havent tried the new Flash based maps provided by Javier de la Torre, give it a go. If you encounter problems, please report them as usual in the issue tracker: http://code.google.com/p/gbif-providertoolkit/issues/list best wishes, Markus

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Re: [IPT] SQL datasource upload
by "Holetschek, Jörg" 18 Mar '09

18 Mar '09

Good idea, Tim! But no SELECT gets to the server... apparently only some preparations: SELECT @@MAX_PRECISION SET TRANSACTION ISOLATION LEVEL READ COMMITTED SET IMPLICIT_TRANSACTIONS OFF SET QUOTED_IDENTIFIER ON SET TEXTSIZE 2147483647 Cheers, Jörg -----Ursprüngliche Nachricht----- Von: Tim Robertson [mailto:trobertson@gbif.org] Gesendet: Mittwoch, 18. März 2009 11:06 An: =?ISO-8859-1?Q?=22Holetschek(a)ns.gbif.org; Holetschek, Jörg Cc: "Markus Döring (GBIF)"; ipt(a)lists.gbif.org Betreff: Re: [IPT] SQL datasource upload Hi Jörg I've looked through the code and it is not possible to switch on the SQL logging through configuration. I will change this for the next release so that the SQL is logged prior to execution for easier debug. Could you please check the SQLServer logs and report if the query reaches the DB? Cheers, Tim On 18 Mar 2009, at 10:48, Holetschek, Jörg wrote: > Hi Markus, > > I've tried to upload data from our SQL server database, after > creating one datasource and 11 mappings. > The upload takes only a second and ends up with 0 records uploaded, > even though I can't find an error in the logs... Is there something > I need to do first? > > INFO pool-1-thread-1-OccUploadTask.call(105) | Import preparation > took 78 ms > INFO pool-1-thread-1-OccUploadTask.uploadCore(225) | Starting upload > of core records for resource Desmids > INFO pool-1-thread-1-DarwinCoreManagerHibernate.removeAll(41) | > Removed 0 DarwinCores bound to resource Desmids > INFO pool-1-thread-1- > DarwinCoreManagerHibernate.flagAllAsDeleted(109) | 0 > org.gbif.provider.model.DarwinCore records of resource were flagged > as deleted. > INFO pool-1-thread-1-OccStatManagerHibernate.removeAll(41) | Removed > 0 OccStatByRegionAndTaxons bound to resource Desmids > INFO pool-1-thread-1-TreeNodeSupportHibernate.removeAll(85) | > Removed 0 taxons bound to resource Desmids > INFO pool-1-thread-1-TreeNodeSupportHibernate.removeAll(85) | > Removed 0 regions bound to resource Desmids > INFO pool-1-thread-1-AnnotationManagerHibernate.removeAll(133) | > Removed 2 annotations bound to resource Desmids > > > Cheers, > Jörg > _______________________________________________ > IPT mailing list > IPT(a)lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt >

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SQL datasource upload
by "Holetschek, Jörg" 18 Mar '09

18 Mar '09

Hi Markus, I've tried to upload data from our SQL server database, after creating one datasource and 11 mappings. The upload takes only a second and ends up with 0 records uploaded, even though I can't find an error in the logs... Is there something I need to do first? INFO pool-1-thread-1-OccUploadTask.call(105) | Import preparation took 78 ms INFO pool-1-thread-1-OccUploadTask.uploadCore(225) | Starting upload of core records for resource Desmids INFO pool-1-thread-1-DarwinCoreManagerHibernate.removeAll(41) | Removed 0 DarwinCores bound to resource Desmids INFO pool-1-thread-1-DarwinCoreManagerHibernate.flagAllAsDeleted(109) | 0 org.gbif.provider.model.DarwinCore records of resource were flagged as deleted. INFO pool-1-thread-1-OccStatManagerHibernate.removeAll(41) | Removed 0 OccStatByRegionAndTaxons bound to resource Desmids INFO pool-1-thread-1-TreeNodeSupportHibernate.removeAll(85) | Removed 0 taxons bound to resource Desmids INFO pool-1-thread-1-TreeNodeSupportHibernate.removeAll(85) | Removed 0 regions bound to resource Desmids INFO pool-1-thread-1-AnnotationManagerHibernate.removeAll(133) | Removed 2 annotations bound to resource Desmids Cheers, Jörg

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Re: [IPT] IPT 1.0b.8 online
by "Holetschek, Jörg" 18 Mar '09

18 Mar '09

Hi Markus et al, pressing the "publish" button for a data resource doesn't work like in the previous versions, I just get a never ending animation (see screenshot). Is that somehow connected to not being registered yet? Cheers, Jörg -----Ursprüngliche Nachricht----- Von: ipt-bounces(a)lists.gbif.org [mailto:ipt-bounces@lists.gbif.org]Im Auftrag von "Markus Döring (GBIF)" Gesendet: Mittwoch, 18. März 2009 09:20 An: Burke Chih-Jen Ko Cc: ipt(a)lists.gbif.org Betreff: Re: [IPT] IPT 1.0b.8 online Burke, you dont have to register,but you can if you like to try the registry integration. The registry connected is a test one until the real release, so you dont harm anyone, just go ahead and register anything you want. The functionality of the registry is still being updated, not all email notifications for example might work right now, in particular the resend password link (which you need to use an existing organisation without knowing its password). Once you have selected an existing or registered a new organisation, publishing a resource also registers it with GBIF and updates its metadata in the registry (not fully working in the current registry version). A resource therefore has 3 states: - private/draft: this is the default for new resources. Its neither registered nor should it be visible in the public portal part of the IPT - public/modified: the resource is intended to be public, its present in the IPT portal and if all goes well and your settings allow to, its also registered with GBIF. The resource metadata is modified though and differes from a) GBIFs registry metadata or b) the versioned EML document which is generated each time you press publish (actually also the geoserver WFS/WMS services have their own metadata which is out of date then too) - public/clean: same as above, but the metadata in the registry/ EML&geoserver should reflect your latest state Does this clarify the registry integration? Markus On Mar 18, 2009, at 3:59, Burke Chih-Jen Ko wrote: > Dear Markus, > > Thank GBIF team for this brilliant work! > > A question: > Now in Admin->settings->Organisation, > Must we register to test IPT? > In the publishing box, does the "private, not registered" mean the > same thing? > > Best regards, > Burke > > > Taiwan Biodiversity Information Facility, TaiBIF > Biodiversity Research Center, Academia Sinica > No. 128, Sec 2, Academia Rd., Nangang District > Taipei 115, Taiwan > Tel: +886+2+27899621 ext.220 > > _______________________________________________ IPT mailing list IPT(a)lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

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IPT on glassfish
by Esteban Mata 18 Mar '09

18 Mar '09

Hi everybody! I was trying to deploy the ipt.war on glassfish! ... I know probably it would be easier on Tomcat but i have glassfish already installed, so I have to know if is posible to run IPT on glassfish? Could someone help me?! Thanks.

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Re: [IPT] IPT Documentation
by Mergen Patricia 18 Mar '09

18 Mar '09

Hi Arnaud First of all congratulation for your new position! In the framework of mainly the project "Central Biodiversity Information Network" to be installed in Central Africa, we are currently testing a lot with the GBIF tool including already a bit the IPT portal. For the EDIT project, there are also training materials being compiled for the moment (more for the GIS part, which is also present in form of maps in the IPT tool.) My colleague Franck is currently in Africa to do some testing, but he has internet and can answers mails from time to time. We will be happy to collaborate with you and do not hesitate to contact us to know more about the ongoing projects and compare the available docs or those in preparation in near future so that we can help each other out at best. Best regards Patricia Patricia Mergen Project Manager Biodiversity Information and Cybertaxonomy Unit Royal Museum for Central Africa Leuvensesteenweg 13 B-3080 Tervuren Phone:+ 32 2 769 56 26 Fax: + 32 2 769 56 42 E-mail: patricia.mergen(a)africamuseum.be http://www.africamuseum.be/research/cooperation -----Original Message----- From: ipt-bounces(a)lists.gbif.org [mailto:ipt-bounces@lists.gbif.org] On Behalf Of Arnaud Réveillon Sent: mardi 17 mars 2009 15:44 To: ipt(a)lists.gbif.org Subject: [IPT] IPT Documentation Dear all, My name is Arnaud Réveillon and I have been appointed to write the documentation for the IPT. I am not new to the GBIF and biodiversity-related software as I worked during four years (2004-2008) for the Belgian focal point for the Convention on Biological Diversity, acting as tutor (mostly on databases, web applications, web pages editors, etc.) and as webmaster. During this period, I have been regularly in contact with members of several national GBIF nodes and am generally well aware of their work. I am not yet fully familiar with the IPT but hope to get up to speed in the next few days, with the help of the list. Please do not hesitate to let me know about your needs, the difficulties you are having with the IPT or anything that may be of interest regarding the documentation, which is scheduled to be ready on 16 April. Thank you, Arnaud Réveillon- _______________________________________________ IPT mailing list IPT(a)lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt ########################################### This message has been scanned by ICT - Africa Museum ________________________________________ 17/3/2009 - Filtered through antispam by ICT

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SQL Database connection
by Holetschek, Jörg 12 Mar '09

12 Mar '09

Hi Markus and Tim, I've just connected the IPT to our mySQL server. On the "property mappings" page there's a hint "There are no data sources configured. Please define at least one source first." What am I supposed to do? Isn't the mySQL database connection (jdbc:mysql://192.168.2.10/pontaurus) the data source? Cheers from Berlin, Jörg

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Re: [IPT] tomcat question
by H 12 Mar '09

12 Mar '09

Markus, all/ How can tomcat and/or the ipt be viewed from specific machines [ip addresses]? I've found tomcat 5.5 documentation [ http://tomcat.apache.org/tomcat-5.5-doc/manager-howto.html] but have yet to successfully open up the manager application. Also when trying to install Extensions like "ResourceRelationship" I'm getting a not so nice javax.servlet.... YIKES! Is this part of my instellation error? Thanks, HW Ikerd

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Selecting area in Geographic Coverage never take effect
by Burke Chih-Jen Ko 12 Mar '09

12 Mar '09

Hi Tim, I am not sure if these issues are correlated, so maybe it's good to write it together. I tried using the dataset, pontaurus.txt, to reproduce the same presentation as the default one. Let's say, the original is ponTaurus1 and the one I set up by choosing "new occurrence resource" is ponTaurus2. I can adjust the geographic coverage of ponTaurus1: 1. In geographic coverage page, re-select the area and save. 2. IPT then brings us to the taxonomic coverage page, if I click "publish" in this page, I get Yikes. Please see error1.txt as attached. 3. I then click the "previous page" bottom of the browser, navigate to basic resource page of ponTaurus1 4. Click "publish" in this page, then I can see the updated shape in the main "Explore" page. But I can't make selecting area take effect with ponTaurus2. Actually I can't do the same thing on any newly established resources. After I did the property mapping and uploaded to the cache, the server once became unresponsive when I clicked done. It stopped when loading(or calculating?) the occResource.html. Restart Tomcat I get messages in catalina.out said "Could not get JDBC Connection". See error3.txt as attached. 1. Choose ponTaurus2 in manage page, navigate to geographic coverage. 2. Select Area and save. IPT brings me to the taxonomic coverage. 3. Publish in the basic metadata page or not, when click back to the geographic coverage page, the map remains blank without any selection made. error2.txt is the new message of /Library/Tomcat/logs/catalina.out during the above operation. If I "publish all" or "republish" in the main Manage page, then when I click to the Explore page, I get another Yikes. Attached as error4.txt Because the Explore page is broken since the last action, I then restart Tomcat, the Explore page remains broken. You can visit http://informatics.biodiv.tw:8080/ipt/resources.html. Hope this make sense. I am using Safari 4b and the IPT1.0b7 is set up on a Mac OS X Server with the Tomcat 6.0.18 coming with the OS. Cheers, Chih-Jen (Burke) Taiwan Biodiversity Information Facility, TaiBIF Biodiversity Research Center, Academia Sinica No. 128, Sec 2, Academia Rd., Nangang District Taipei 115, Taiwan Tel: +886+2+27899621 ext.220

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