- IPT - lists.gbif.org

Re: [IPT] IPT Documentation
by Mergen Patricia 17 Mar '09

17 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 11 Mar '09

11 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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Re: [IPT] User Manager
by Holetschek, Jörg 11 Mar '09

11 Mar '09

Hi again, seems I can't edit the "Source Data" settings for a SQL datasource. After entering connection URL and database user with empty password, I get Sapperlott! java.lang.NullPointerException at org.apache.struts2.views.jsp.ComponentTagSupport.doStartTag(ComponentTagSupport.java:50) at org.apache.jsp._404_jsp._jspx_meth_s_005ftext_005f0(_404_jsp.java:186) at org.apache.jsp._404_jsp._jspx_meth_c_005fset_005f1(_404_jsp.java:158) at org.apache.jsp._404_jsp._jspService(_404_jsp.java:101) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70) at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:337) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266) at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:630) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:438) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:374) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:302) at org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:424) at org.apache.catalina.core.StandardHostValve.status(StandardHostValve.java:343) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:144) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:286) at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190) at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283) at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:767) at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:697) at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:889) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:690) at java.lang.Thread.run(Thread.java:619) Jörg -----Ursprüngliche Nachricht----- Von: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Gesendet: Mittwoch, 11. März 2009 15:28 An: Holetschek, Jörg Cc: Tim Robertson (GBIF); ipt(a)lists.gbif.org Betreff: Re: User Manager I am working on that, Jörg, just today! Its because I switched javascript frameworks...to assign different roles for users right now you can only do this in the database, I am sorry. But will be fixed this week! m On Mar 11, 2009, at 15:17, Holetschek, Jörg wrote: > Hi Tim & Markus, > > it's not possible in our installation to edit any user. There's an > error in the underlying link is > http://de.mirror.gbif.org/ipteditUser.html?id=5&from=list > > Is there something I can do about it? > > > Cheers, > Jörg > > -----Ursprüngliche Nachricht----- > Von: ipt-bounces(a)lists.gbif.org [mailto:ipt-bounces@lists.gbif.org]Im > Auftrag von Tim Robertson (GBIF) > Gesendet: Donnerstag, 26. Februar 2009 21:00 > An: Mihail-Constantin Carausu > Cc: ipt(a)lists.gbif.org > Betreff: Re: [IPT] Beta update > > > Thank you very much. > > I suggest starting with 0.5million, and then 1 million and then 3 > million. > I will be surprised if this works without some bug fixing. > > You may just use http://ipt.gbif.org rather than installation. > > Thanks Mihail, help with tests like this is greatly appreciated. > > Tim > > >> Dear Tim >> >> I can volunteer for uploading up to 3 million records if you want. >> The >> only problem is I have not installed yet the IPT software on our >> servers >> (sorry) because I didn't get the time, yet. But I will definitely >> try to >> do the installation tomorrow and the upload too. >> >> Best wishes >> Mihail >> >> ---------------------------- >> Mihail Carausu >> MSc.Eng., Informatics Manager >> Danish Biodiversity Information Facility (DanBIF) >> c/o Zoological Museum >> University of Copenhagen >> Universitetsparken 15 >> DK-2100 Copenhagen Ø >> >> Tel.: (+45) 3532 1063 >> Mobil:(+45) 2618 3636 >> email:mccarausu@zmuc.ku.dk >> web: http://www.DanBIF.dk >> ....oooO.............. >> ....(....)....Oooo.... >> .....)../. ...(....)... >> .....(_/.......)../...... >> .............. (_/....... >> -------------------------------------------- >> >> >> -----Original Message----- >> From: ipt-bounces(a)lists.gbif.org [mailto:ipt- >> bounces(a)lists.gbif.org] On >> Behalf Of Tim Robertson >> Sent: 26. februar 2009 16:26 >> To: ipt(a)lists.gbif.org >> Subject: [IPT] Beta update >> >> Dear All, >> >> A new version has just been deployed, and all user accounts have been >> kept intact, but you will notice significant changes, and we hope >> improvements. >> Please use the http://code.google.com/p/gbif-providertoolkit/issues/ >> list to track and input issues. >> >> If there is a volunteer wishing to test an upload of a large dataset >> (500,000+ records) it would be very much appreciated if you could >> report back on the experience. >> >> Thanks for all your feedback, >> >> Best wishes, >> >> Tim >> >> _______________________________________________ >> IPT mailing list >> IPT(a)lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt >> >> > > > ____________________________________________________________ > Tim Robertson > Systems Architect > Global Biodiversity Information Facility Secretariat (GBIF) > Universitetsparken 15, 2100 Copenhagen Ø, Denmark > http://www.gbif.org > trobertson(a)gbif.org > Phone: +45 35 32 14 87 (Office) > Fax: +45 35 32 14 80 > ____________________________________________________________ > > _______________________________________________ > IPT mailing list > IPT(a)lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt >

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User Manager
by Holetschek, Jörg 11 Mar '09

11 Mar '09

Hi Tim & Markus, it's not possible in our installation to edit any user. There's an error in the underlying link is http://de.mirror.gbif.org/ipteditUser.html?id=5&from=list Is there something I can do about it? Cheers, Jörg -----Ursprüngliche Nachricht----- Von: ipt-bounces(a)lists.gbif.org [mailto:ipt-bounces@lists.gbif.org]Im Auftrag von Tim Robertson (GBIF) Gesendet: Donnerstag, 26. Februar 2009 21:00 An: Mihail-Constantin Carausu Cc: ipt(a)lists.gbif.org Betreff: Re: [IPT] Beta update Thank you very much. I suggest starting with 0.5million, and then 1 million and then 3 million. I will be surprised if this works without some bug fixing. You may just use http://ipt.gbif.org rather than installation. Thanks Mihail, help with tests like this is greatly appreciated. Tim > Dear Tim > > I can volunteer for uploading up to 3 million records if you want. The > only problem is I have not installed yet the IPT software on our servers > (sorry) because I didn't get the time, yet. But I will definitely try to > do the installation tomorrow and the upload too. > > Best wishes > Mihail > > ---------------------------- > Mihail Carausu > MSc.Eng., Informatics Manager > Danish Biodiversity Information Facility (DanBIF) > c/o Zoological Museum > University of Copenhagen > Universitetsparken 15 > DK-2100 Copenhagen Ø > > Tel.: (+45) 3532 1063 > Mobil:(+45) 2618 3636 > email:mccarausu@zmuc.ku.dk > web: http://www.DanBIF.dk > ....oooO.............. > ....(....)....Oooo.... > .....)../. ...(....)... > .....(_/.......)../...... > .............. (_/....... > -------------------------------------------- > > > -----Original Message----- > From: ipt-bounces(a)lists.gbif.org [mailto:ipt-bounces@lists.gbif.org] On > Behalf Of Tim Robertson > Sent: 26. februar 2009 16:26 > To: ipt(a)lists.gbif.org > Subject: [IPT] Beta update > > Dear All, > > A new version has just been deployed, and all user accounts have been > kept intact, but you will notice significant changes, and we hope > improvements. > Please use the http://code.google.com/p/gbif-providertoolkit/issues/ > list to track and input issues. > > If there is a volunteer wishing to test an upload of a large dataset > (500,000+ records) it would be very much appreciated if you could > report back on the experience. > > Thanks for all your feedback, > > Best wishes, > > Tim > > _______________________________________________ > IPT mailing list > IPT(a)lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > > ____________________________________________________________ Tim Robertson Systems Architect Global Biodiversity Information Facility Secretariat (GBIF) Universitetsparken 15, 2100 Copenhagen Ø, Denmark http://www.gbif.org trobertson(a)gbif.org Phone: +45 35 32 14 87 (Office) Fax: +45 35 32 14 80 ____________________________________________________________ _______________________________________________ IPT mailing list IPT(a)lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

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Re: [IPT] Beta update
by Holetschek, Jörg 05 Mar '09

05 Mar '09

Hi Markus, I already setup our our google maps api. The domains are not also setup correctly (see screenshot). http://de.mirror.gbif.org:8080/ipt Anything else I can try? Jörg -----Ursprüngliche Nachricht----- Von: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Gesendet: Donnerstag, 5. März 2009 11:46 An: Holetschek, Jörg Cc: Tim Robertson (GBIF); ipt(a)lists.gbif.org; Kelbert, Patricia Betreff: Re: AW: AW: AW: AW: [IPT] Beta update Jörg, this seems to be a local IP address, doesnt work from here. For the maps to work you need to make sure the IPT & geoserver host domains are all correctly configured in the settings. If they use localhost you can only access them from that very machine. when looking at http://de.mirror.gbif.org/ipt/resources.html this seems to work. you just have to use your google maps api key for de.mirror.gbif.org to get rid of the map error message. Markus On Mar 5, 2009, at 11:40, Holetschek, Jörg wrote: > Hi Markus, > > thanks... looks better this time... but no maps yet: > http://192.168.2.251:8080/ipt/resources.html > > Attached the log with some error messages at the end... > > > Cheers, > Jörg > > -----Ursprüngliche Nachricht----- > Von: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] > Gesendet: Mittwoch, 4. März 2009 18:00 > An: Holetschek, Jörg > Cc: Tim Robertson (GBIF); ipt(a)lists.gbif.org; Kelbert, Patricia > Betreff: Re: AW: AW: AW: [IPT] Beta update > > > Jörg, > I have just uploaded a new ipt version 1.0b.7. Would you mind to > replace your existing one with this, including geoserver? > Especially the geoserver plugin is updated to do taxonomic and > regional nested searches for occurrences in maps. Also for > configuration there shouuld not be the need anymore to visit the > geoserver UI. From within the IPT admin configuration you can now > update the geoserver settings, which writes the current IPT data > directory into geoservers config files. > > As before IPT and the geoserver bundle are preconfigured to work when > dropped into tomcat on port 8080. > > http://code.google.com/p/gbif-providertoolkit/downloads/list?can=3&q=&colsp… > > Markus > > > > On Mar 4, 2009, at 11:41, Holetschek, Jörg wrote: > >> Hi Markus, >> >> I've set the data directory in the geoserver configuration (see >> screenshot), but to no avail :/ >> >> After restarting tomcat, the IPT application didn't work anymore - >> like yesterday. And in case it will work in an hour or so (like >> yesterday), there's a lot of errors in the log - is that still a >> configuration problem? I've set the path to the IPT data folder in >> geoserver, that shouldn't be the problem anymore... >> >> Jörg >> >> -----Ursprüngliche Nachricht----- >> Von: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] >> Gesendet: Dienstag, 3. März 2009 20:45 >> An: Holetschek, Jörg >> Cc: Tim Robertson (GBIF); ipt(a)lists.gbif.org >> Betreff: Re: AW: AW: [IPT] Beta update >> >> >> this looks like a configuration problem. It cant find the IPTs H2 >> database. >> Ive seen that in your installation geoserver doesnt automatically >> find >> the IPT data directory. >> You need to set the IPT data directory manually in the geoserver >> config interface config->data->IPT datasource >> use the full absolute file path to your data dir, by default >> PATH_TO_TOMCAT/webapps/ipt/data >> >> Markus >> >> >> On Mar 3, 2009, at 18:25, Holetschek, Jörg wrote: >> >>> Hmm... I didn't change anything! But I like that sort of magic... >>> just wait until it works :) >>> >>> Just found out one of the menu entries doesn't work... is this a >>> problem of our installation? >>> http://de.mirror.gbif.org/ipt/admin/activeDatasources.html >>> >>> The maps do not get rendered by geoserver correctly, I found a "bad >>> SQL grammar" error in the log (see attachement). Is this a bug or a >>> configuration problem? >>> >>> >>> Cheers from Berlin, >>> Jörg >>> >>> -----Ursprüngliche Nachricht----- >>> Von: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] >>> Gesendet: Dienstag, 3. März 2009 15:45 >>> An: Holetschek, Jörg >>> Cc: Tim Robertson (GBIF); ipt(a)lists.gbif.org >>> Betreff: Re: AW: [IPT] Beta update >>> >>> >>> hmm, there are a couple of errors in the log, but the site seems to >>> work fine: >>> http://de.mirror.gbif.org/ipt >>> >>> apart from the geoserver maps, I have to admit. >>> I have changed your IPT & Geoserver settings to reflect the domain >>> de.mirror.gbif.org, but that didnt solve the problem. >>> As I have completely replaced the openlayers maps with flash based >>> google maps in the latest trunk, do you mind to test the latest >>> version? >>> >>> I will upload a 1.0b.6 war in a few minutes. >>> thanks for trying, Jörg. >>> Markus >>> >>> >>> >>> >>> On Mar 3, 2009, at 13:10, Holetschek, Jörg wrote: >>> >>>> sorry.. little bit scatterbrained today! >>>> here are the logs... >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: Holetschek, Jörg >>>> Gesendet: Dienstag, 3. März 2009 13:04 >>>> An: '"Markus Döring (GBIF)"'; Tim Robertson (GBIF) >>>> Cc: ipt(a)lists.gbif.org; Kelbert, Patricia; Roepert, Dominik >>>> Betreff: AW: [IPT] Beta update >>>> >>>> >>>> Hi Markus, >>>> >>>> I'm trying to install the latest IPT on our server. It worked fine, >>>> but after installing the geoserveer application, th IPT doesn't >>>> work >>>> anymore :/ >>>> >>>> Attached the logs... do you have an idea? >>>> Using Tomcat 6.0.16 on Red Hat 3.4.3-22. >>>> >>>> >>>> Cheers, >>>> Jörg >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: ipt-bounces(a)lists.gbif.org [mailto:ipt- >>>> bounces(a)lists.gbif.org]Im >>>> Auftrag von "Markus Döring (GBIF)" >>>> Gesendet: Freitag, 27. Februar 2009 10:36 >>>> An: Tim Robertson (GBIF) >>>> Cc: Mihail-Constantin Carausu; ipt(a)lists.gbif.org >>>> Betreff: Re: [IPT] Beta update >>>> >>>> >>>> it would also be nice if someone could test the SQL based upload, >>>> which requires a local installation. >>>> If there is help needed with the installation, just post to this >>>> list >>>> please. >>>> >>>> Markus >>>> >>>> >>>> On Feb 26, 2009, at 8:59 PM, Tim Robertson (GBIF) wrote: >>>> >>>>> Thank you very much. >>>>> >>>>> I suggest starting with 0.5million, and then 1 million and then 3 >>>>> million. >>>>> I will be surprised if this works without some bug fixing. >>>>> >>>>> You may just use http://ipt.gbif.org rather than installation. >>>>> >>>>> Thanks Mihail, help with tests like this is greatly appreciated. >>>>> >>>>> Tim >>>>> >>>>> >>>>>> Dear Tim >>>>>> >>>>>> I can volunteer for uploading up to 3 million records if you >>>>>> want. >>>>>> The >>>>>> only problem is I have not installed yet the IPT software on our >>>>>> servers >>>>>> (sorry) because I didn't get the time, yet. But I will definitely >>>>>> try to >>>>>> do the installation tomorrow and the upload too. >>>>>> >>>>>> Best wishes >>>>>> Mihail >>>>>> >>>>>> ---------------------------- >>>>>> Mihail Carausu >>>>>> MSc.Eng., Informatics Manager >>>>>> Danish Biodiversity Information Facility (DanBIF) >>>>>> c/o Zoological Museum >>>>>> University of Copenhagen >>>>>> Universitetsparken 15 >>>>>> DK-2100 Copenhagen Ø >>>>>> >>>>>> Tel.: (+45) 3532 1063 >>>>>> Mobil:(+45) 2618 3636 >>>>>> email:mccarausu@zmuc.ku.dk >>>>>> web: http://www.DanBIF.dk >>>>>> ....oooO.............. >>>>>> ....(....)....Oooo.... >>>>>> .....)../. ...(....)... >>>>>> .....(_/.......)../...... >>>>>> .............. (_/....... >>>>>> -------------------------------------------- >>>>>> >>>>>> >>>>>> -----Original Message----- >>>>>> From: ipt-bounces(a)lists.gbif.org [mailto:ipt- >>>>>> bounces(a)lists.gbif.org] On >>>>>> Behalf Of Tim Robertson >>>>>> Sent: 26. februar 2009 16:26 >>>>>> To: ipt(a)lists.gbif.org >>>>>> Subject: [IPT] Beta update >>>>>> >>>>>> Dear All, >>>>>> >>>>>> A new version has just been deployed, and all user accounts have >>>>>> been >>>>>> kept intact, but you will notice significant changes, and we hope >>>>>> improvements. >>>>>> Please use the http://code.google.com/p/gbif-providertoolkit/ >>>>>> issues/ >>>>>> list to track and input issues. >>>>>> >>>>>> If there is a volunteer wishing to test an upload of a large >>>>>> dataset >>>>>> (500,000+ records) it would be very much appreciated if you could >>>>>> report back on the experience. >>>>>> >>>>>> Thanks for all your feedback, >>>>>> >>>>>> Best wishes, >>>>>> >>>>>> Tim >>>>>> >>>>>> _______________________________________________ >>>>>> IPT mailing list >>>>>> IPT(a)lists.gbif.org >>>>>> http://lists.gbif.org/mailman/listinfo/ipt >>>>>> >>>>>> >>>>> >>>>> >>>>> ____________________________________________________________ >>>>> Tim Robertson >>>>> Systems Architect >>>>> Global Biodiversity Information Facility Secretariat (GBIF) >>>>> Universitetsparken 15, 2100 Copenhagen Ø, Denmark >>>>> http://www.gbif.org >>>>> trobertson(a)gbif.org >>>>> Phone: +45 35 32 14 87 (Office) >>>>> Fax: +45 35 32 14 80 >>>>> ____________________________________________________________ >>>>> >>>>> _______________________________________________ >>>>> IPT mailing list >>>>> IPT(a)lists.gbif.org >>>>> http://lists.gbif.org/mailman/listinfo/ipt >>>>> >>>> >>>> _______________________________________________ >>>> IPT mailing list >>>> IPT(a)lists.gbif.org >>>> http://lists.gbif.org/mailman/listinfo/ipt >>>> <logs.zip> >>> >>> <catalina.out> >> >> <GeoServer Feature Datensatz Editor.png><localhost.2009-03-04.log> > > <catalina.out>

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Re: [IPT] Beta update
by Holetschek, Jörg 05 Mar '09

05 Mar '09

Hi Markus, thanks... looks better this time... but no maps yet: http://192.168.2.251:8080/ipt/resources.html Attached the log with some error messages at the end... Cheers, Jörg -----Ursprüngliche Nachricht----- Von: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Gesendet: Mittwoch, 4. März 2009 18:00 An: Holetschek, Jörg Cc: Tim Robertson (GBIF); ipt(a)lists.gbif.org; Kelbert, Patricia Betreff: Re: AW: AW: AW: [IPT] Beta update Jörg, I have just uploaded a new ipt version 1.0b.7. Would you mind to replace your existing one with this, including geoserver? Especially the geoserver plugin is updated to do taxonomic and regional nested searches for occurrences in maps. Also for configuration there shouuld not be the need anymore to visit the geoserver UI. From within the IPT admin configuration you can now update the geoserver settings, which writes the current IPT data directory into geoservers config files. As before IPT and the geoserver bundle are preconfigured to work when dropped into tomcat on port 8080. http://code.google.com/p/gbif-providertoolkit/downloads/list?can=3&q=&colsp… Markus On Mar 4, 2009, at 11:41, Holetschek, Jörg wrote: > Hi Markus, > > I've set the data directory in the geoserver configuration (see > screenshot), but to no avail :/ > > After restarting tomcat, the IPT application didn't work anymore - > like yesterday. And in case it will work in an hour or so (like > yesterday), there's a lot of errors in the log - is that still a > configuration problem? I've set the path to the IPT data folder in > geoserver, that shouldn't be the problem anymore... > > Jörg > > -----Ursprüngliche Nachricht----- > Von: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] > Gesendet: Dienstag, 3. März 2009 20:45 > An: Holetschek, Jörg > Cc: Tim Robertson (GBIF); ipt(a)lists.gbif.org > Betreff: Re: AW: AW: [IPT] Beta update > > > this looks like a configuration problem. It cant find the IPTs H2 > database. > Ive seen that in your installation geoserver doesnt automatically find > the IPT data directory. > You need to set the IPT data directory manually in the geoserver > config interface config->data->IPT datasource > use the full absolute file path to your data dir, by default > PATH_TO_TOMCAT/webapps/ipt/data > > Markus > > > On Mar 3, 2009, at 18:25, Holetschek, Jörg wrote: > >> Hmm... I didn't change anything! But I like that sort of magic... >> just wait until it works :) >> >> Just found out one of the menu entries doesn't work... is this a >> problem of our installation? >> http://de.mirror.gbif.org/ipt/admin/activeDatasources.html >> >> The maps do not get rendered by geoserver correctly, I found a "bad >> SQL grammar" error in the log (see attachement). Is this a bug or a >> configuration problem? >> >> >> Cheers from Berlin, >> Jörg >> >> -----Ursprüngliche Nachricht----- >> Von: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] >> Gesendet: Dienstag, 3. März 2009 15:45 >> An: Holetschek, Jörg >> Cc: Tim Robertson (GBIF); ipt(a)lists.gbif.org >> Betreff: Re: AW: [IPT] Beta update >> >> >> hmm, there are a couple of errors in the log, but the site seems to >> work fine: >> http://de.mirror.gbif.org/ipt >> >> apart from the geoserver maps, I have to admit. >> I have changed your IPT & Geoserver settings to reflect the domain >> de.mirror.gbif.org, but that didnt solve the problem. >> As I have completely replaced the openlayers maps with flash based >> google maps in the latest trunk, do you mind to test the latest >> version? >> >> I will upload a 1.0b.6 war in a few minutes. >> thanks for trying, Jörg. >> Markus >> >> >> >> >> On Mar 3, 2009, at 13:10, Holetschek, Jörg wrote: >> >>> sorry.. little bit scatterbrained today! >>> here are the logs... >>> >>> -----Ursprüngliche Nachricht----- >>> Von: Holetschek, Jörg >>> Gesendet: Dienstag, 3. März 2009 13:04 >>> An: '"Markus Döring (GBIF)"'; Tim Robertson (GBIF) >>> Cc: ipt(a)lists.gbif.org; Kelbert, Patricia; Roepert, Dominik >>> Betreff: AW: [IPT] Beta update >>> >>> >>> Hi Markus, >>> >>> I'm trying to install the latest IPT on our server. It worked fine, >>> but after installing the geoserveer application, th IPT doesn't work >>> anymore :/ >>> >>> Attached the logs... do you have an idea? >>> Using Tomcat 6.0.16 on Red Hat 3.4.3-22. >>> >>> >>> Cheers, >>> Jörg >>> >>> -----Ursprüngliche Nachricht----- >>> Von: ipt-bounces(a)lists.gbif.org [mailto:ipt- >>> bounces(a)lists.gbif.org]Im >>> Auftrag von "Markus Döring (GBIF)" >>> Gesendet: Freitag, 27. Februar 2009 10:36 >>> An: Tim Robertson (GBIF) >>> Cc: Mihail-Constantin Carausu; ipt(a)lists.gbif.org >>> Betreff: Re: [IPT] Beta update >>> >>> >>> it would also be nice if someone could test the SQL based upload, >>> which requires a local installation. >>> If there is help needed with the installation, just post to this >>> list >>> please. >>> >>> Markus >>> >>> >>> On Feb 26, 2009, at 8:59 PM, Tim Robertson (GBIF) wrote: >>> >>>> Thank you very much. >>>> >>>> I suggest starting with 0.5million, and then 1 million and then 3 >>>> million. >>>> I will be surprised if this works without some bug fixing. >>>> >>>> You may just use http://ipt.gbif.org rather than installation. >>>> >>>> Thanks Mihail, help with tests like this is greatly appreciated. >>>> >>>> Tim >>>> >>>> >>>>> Dear Tim >>>>> >>>>> I can volunteer for uploading up to 3 million records if you want. >>>>> The >>>>> only problem is I have not installed yet the IPT software on our >>>>> servers >>>>> (sorry) because I didn't get the time, yet. But I will definitely >>>>> try to >>>>> do the installation tomorrow and the upload too. >>>>> >>>>> Best wishes >>>>> Mihail >>>>> >>>>> ---------------------------- >>>>> Mihail Carausu >>>>> MSc.Eng., Informatics Manager >>>>> Danish Biodiversity Information Facility (DanBIF) >>>>> c/o Zoological Museum >>>>> University of Copenhagen >>>>> Universitetsparken 15 >>>>> DK-2100 Copenhagen Ø >>>>> >>>>> Tel.: (+45) 3532 1063 >>>>> Mobil:(+45) 2618 3636 >>>>> email:mccarausu@zmuc.ku.dk >>>>> web: http://www.DanBIF.dk >>>>> ....oooO.............. >>>>> ....(....)....Oooo.... >>>>> .....)../. ...(....)... >>>>> .....(_/.......)../...... >>>>> .............. (_/....... >>>>> -------------------------------------------- >>>>> >>>>> >>>>> -----Original Message----- >>>>> From: ipt-bounces(a)lists.gbif.org [mailto:ipt- >>>>> bounces(a)lists.gbif.org] On >>>>> Behalf Of Tim Robertson >>>>> Sent: 26. februar 2009 16:26 >>>>> To: ipt(a)lists.gbif.org >>>>> Subject: [IPT] Beta update >>>>> >>>>> Dear All, >>>>> >>>>> A new version has just been deployed, and all user accounts have >>>>> been >>>>> kept intact, but you will notice significant changes, and we hope >>>>> improvements. >>>>> Please use the http://code.google.com/p/gbif-providertoolkit/ >>>>> issues/ >>>>> list to track and input issues. >>>>> >>>>> If there is a volunteer wishing to test an upload of a large >>>>> dataset >>>>> (500,000+ records) it would be very much appreciated if you could >>>>> report back on the experience. >>>>> >>>>> Thanks for all your feedback, >>>>> >>>>> Best wishes, >>>>> >>>>> Tim >>>>> >>>>> _______________________________________________ >>>>> IPT mailing list >>>>> IPT(a)lists.gbif.org >>>>> http://lists.gbif.org/mailman/listinfo/ipt >>>>> >>>>> >>>> >>>> >>>> ____________________________________________________________ >>>> Tim Robertson >>>> Systems Architect >>>> Global Biodiversity Information Facility Secretariat (GBIF) >>>> Universitetsparken 15, 2100 Copenhagen Ø, Denmark >>>> http://www.gbif.org >>>> trobertson(a)gbif.org >>>> Phone: +45 35 32 14 87 (Office) >>>> Fax: +45 35 32 14 80 >>>> ____________________________________________________________ >>>> >>>> _______________________________________________ >>>> IPT mailing list >>>> IPT(a)lists.gbif.org >>>> http://lists.gbif.org/mailman/listinfo/ipt >>>> >>> >>> _______________________________________________ >>> IPT mailing list >>> IPT(a)lists.gbif.org >>> http://lists.gbif.org/mailman/listinfo/ipt >>> <logs.zip> >> >> <catalina.out> > > <GeoServer Feature Datensatz Editor.png><localhost.2009-03-04.log>

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Re: [IPT] Beta update
by Holetschek, Jörg 04 Mar '09

04 Mar '09

Hi Markus, I've set the data directory in the geoserver configuration (see screenshot), but to no avail :/ After restarting tomcat, the IPT application didn't work anymore - like yesterday. And in case it will work in an hour or so (like yesterday), there's a lot of errors in the log - is that still a configuration problem? I've set the path to the IPT data folder in geoserver, that shouldn't be the problem anymore... Jörg -----Ursprüngliche Nachricht----- Von: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Gesendet: Dienstag, 3. März 2009 20:45 An: Holetschek, Jörg Cc: Tim Robertson (GBIF); ipt(a)lists.gbif.org Betreff: Re: AW: AW: [IPT] Beta update this looks like a configuration problem. It cant find the IPTs H2 database. Ive seen that in your installation geoserver doesnt automatically find the IPT data directory. You need to set the IPT data directory manually in the geoserver config interface config->data->IPT datasource use the full absolute file path to your data dir, by default PATH_TO_TOMCAT/webapps/ipt/data Markus On Mar 3, 2009, at 18:25, Holetschek, Jörg wrote: > Hmm... I didn't change anything! But I like that sort of magic... > just wait until it works :) > > Just found out one of the menu entries doesn't work... is this a > problem of our installation? > http://de.mirror.gbif.org/ipt/admin/activeDatasources.html > > The maps do not get rendered by geoserver correctly, I found a "bad > SQL grammar" error in the log (see attachement). Is this a bug or a > configuration problem? > > > Cheers from Berlin, > Jörg > > -----Ursprüngliche Nachricht----- > Von: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] > Gesendet: Dienstag, 3. März 2009 15:45 > An: Holetschek, Jörg > Cc: Tim Robertson (GBIF); ipt(a)lists.gbif.org > Betreff: Re: AW: [IPT] Beta update > > > hmm, there are a couple of errors in the log, but the site seems to > work fine: > http://de.mirror.gbif.org/ipt > > apart from the geoserver maps, I have to admit. > I have changed your IPT & Geoserver settings to reflect the domain > de.mirror.gbif.org, but that didnt solve the problem. > As I have completely replaced the openlayers maps with flash based > google maps in the latest trunk, do you mind to test the latest > version? > > I will upload a 1.0b.6 war in a few minutes. > thanks for trying, Jörg. > Markus > > > > > On Mar 3, 2009, at 13:10, Holetschek, Jörg wrote: > >> sorry.. little bit scatterbrained today! >> here are the logs... >> >> -----Ursprüngliche Nachricht----- >> Von: Holetschek, Jörg >> Gesendet: Dienstag, 3. März 2009 13:04 >> An: '"Markus Döring (GBIF)"'; Tim Robertson (GBIF) >> Cc: ipt(a)lists.gbif.org; Kelbert, Patricia; Roepert, Dominik >> Betreff: AW: [IPT] Beta update >> >> >> Hi Markus, >> >> I'm trying to install the latest IPT on our server. It worked fine, >> but after installing the geoserveer application, th IPT doesn't work >> anymore :/ >> >> Attached the logs... do you have an idea? >> Using Tomcat 6.0.16 on Red Hat 3.4.3-22. >> >> >> Cheers, >> Jörg >> >> -----Ursprüngliche Nachricht----- >> Von: ipt-bounces(a)lists.gbif.org [mailto:ipt-bounces@lists.gbif.org]Im >> Auftrag von "Markus Döring (GBIF)" >> Gesendet: Freitag, 27. Februar 2009 10:36 >> An: Tim Robertson (GBIF) >> Cc: Mihail-Constantin Carausu; ipt(a)lists.gbif.org >> Betreff: Re: [IPT] Beta update >> >> >> it would also be nice if someone could test the SQL based upload, >> which requires a local installation. >> If there is help needed with the installation, just post to this list >> please. >> >> Markus >> >> >> On Feb 26, 2009, at 8:59 PM, Tim Robertson (GBIF) wrote: >> >>> Thank you very much. >>> >>> I suggest starting with 0.5million, and then 1 million and then 3 >>> million. >>> I will be surprised if this works without some bug fixing. >>> >>> You may just use http://ipt.gbif.org rather than installation. >>> >>> Thanks Mihail, help with tests like this is greatly appreciated. >>> >>> Tim >>> >>> >>>> Dear Tim >>>> >>>> I can volunteer for uploading up to 3 million records if you want. >>>> The >>>> only problem is I have not installed yet the IPT software on our >>>> servers >>>> (sorry) because I didn't get the time, yet. But I will definitely >>>> try to >>>> do the installation tomorrow and the upload too. >>>> >>>> Best wishes >>>> Mihail >>>> >>>> ---------------------------- >>>> Mihail Carausu >>>> MSc.Eng., Informatics Manager >>>> Danish Biodiversity Information Facility (DanBIF) >>>> c/o Zoological Museum >>>> University of Copenhagen >>>> Universitetsparken 15 >>>> DK-2100 Copenhagen Ø >>>> >>>> Tel.: (+45) 3532 1063 >>>> Mobil:(+45) 2618 3636 >>>> email:mccarausu@zmuc.ku.dk >>>> web: http://www.DanBIF.dk >>>> ....oooO.............. >>>> ....(....)....Oooo.... >>>> .....)../. ...(....)... >>>> .....(_/.......)../...... >>>> .............. (_/....... >>>> -------------------------------------------- >>>> >>>> >>>> -----Original Message----- >>>> From: ipt-bounces(a)lists.gbif.org [mailto:ipt- >>>> bounces(a)lists.gbif.org] On >>>> Behalf Of Tim Robertson >>>> Sent: 26. februar 2009 16:26 >>>> To: ipt(a)lists.gbif.org >>>> Subject: [IPT] Beta update >>>> >>>> Dear All, >>>> >>>> A new version has just been deployed, and all user accounts have >>>> been >>>> kept intact, but you will notice significant changes, and we hope >>>> improvements. >>>> Please use the http://code.google.com/p/gbif-providertoolkit/ >>>> issues/ >>>> list to track and input issues. >>>> >>>> If there is a volunteer wishing to test an upload of a large >>>> dataset >>>> (500,000+ records) it would be very much appreciated if you could >>>> report back on the experience. >>>> >>>> Thanks for all your feedback, >>>> >>>> Best wishes, >>>> >>>> Tim >>>> >>>> _______________________________________________ >>>> IPT mailing list >>>> IPT(a)lists.gbif.org >>>> http://lists.gbif.org/mailman/listinfo/ipt >>>> >>>> >>> >>> >>> ____________________________________________________________ >>> Tim Robertson >>> Systems Architect >>> Global Biodiversity Information Facility Secretariat (GBIF) >>> Universitetsparken 15, 2100 Copenhagen Ø, Denmark >>> http://www.gbif.org >>> trobertson(a)gbif.org >>> Phone: +45 35 32 14 87 (Office) >>> Fax: +45 35 32 14 80 >>> ____________________________________________________________ >>> >>> _______________________________________________ >>> IPT mailing list >>> IPT(a)lists.gbif.org >>> http://lists.gbif.org/mailman/listinfo/ipt >>> >> >> _______________________________________________ >> IPT mailing list >> IPT(a)lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt >> <logs.zip> > > <catalina.out>

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Re: [IPT] Beta update
by Holetschek, Jörg 03 Mar '09

03 Mar '09

Hmm... I didn't change anything! But I like that sort of magic... just wait until it works :) Just found out one of the menu entries doesn't work... is this a problem of our installation? http://de.mirror.gbif.org/ipt/admin/activeDatasources.html The maps do not get rendered by geoserver correctly, I found a "bad SQL grammar" error in the log (see attachement). Is this a bug or a configuration problem? Cheers from Berlin, Jörg -----Ursprüngliche Nachricht----- Von: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] Gesendet: Dienstag, 3. März 2009 15:45 An: Holetschek, Jörg Cc: Tim Robertson (GBIF); ipt(a)lists.gbif.org Betreff: Re: AW: [IPT] Beta update hmm, there are a couple of errors in the log, but the site seems to work fine: http://de.mirror.gbif.org/ipt apart from the geoserver maps, I have to admit. I have changed your IPT & Geoserver settings to reflect the domain de.mirror.gbif.org, but that didnt solve the problem. As I have completely replaced the openlayers maps with flash based google maps in the latest trunk, do you mind to test the latest version? I will upload a 1.0b.6 war in a few minutes. thanks for trying, Jörg. Markus On Mar 3, 2009, at 13:10, Holetschek, Jörg wrote: > sorry.. little bit scatterbrained today! > here are the logs... > > -----Ursprüngliche Nachricht----- > Von: Holetschek, Jörg > Gesendet: Dienstag, 3. März 2009 13:04 > An: '"Markus Döring (GBIF)"'; Tim Robertson (GBIF) > Cc: ipt(a)lists.gbif.org; Kelbert, Patricia; Roepert, Dominik > Betreff: AW: [IPT] Beta update > > > Hi Markus, > > I'm trying to install the latest IPT on our server. It worked fine, > but after installing the geoserveer application, th IPT doesn't work > anymore :/ > > Attached the logs... do you have an idea? > Using Tomcat 6.0.16 on Red Hat 3.4.3-22. > > > Cheers, > Jörg > > -----Ursprüngliche Nachricht----- > Von: ipt-bounces(a)lists.gbif.org [mailto:ipt-bounces@lists.gbif.org]Im > Auftrag von "Markus Döring (GBIF)" > Gesendet: Freitag, 27. Februar 2009 10:36 > An: Tim Robertson (GBIF) > Cc: Mihail-Constantin Carausu; ipt(a)lists.gbif.org > Betreff: Re: [IPT] Beta update > > > it would also be nice if someone could test the SQL based upload, > which requires a local installation. > If there is help needed with the installation, just post to this list > please. > > Markus > > > On Feb 26, 2009, at 8:59 PM, Tim Robertson (GBIF) wrote: > >> Thank you very much. >> >> I suggest starting with 0.5million, and then 1 million and then 3 >> million. >> I will be surprised if this works without some bug fixing. >> >> You may just use http://ipt.gbif.org rather than installation. >> >> Thanks Mihail, help with tests like this is greatly appreciated. >> >> Tim >> >> >>> Dear Tim >>> >>> I can volunteer for uploading up to 3 million records if you want. >>> The >>> only problem is I have not installed yet the IPT software on our >>> servers >>> (sorry) because I didn't get the time, yet. But I will definitely >>> try to >>> do the installation tomorrow and the upload too. >>> >>> Best wishes >>> Mihail >>> >>> ---------------------------- >>> Mihail Carausu >>> MSc.Eng., Informatics Manager >>> Danish Biodiversity Information Facility (DanBIF) >>> c/o Zoological Museum >>> University of Copenhagen >>> Universitetsparken 15 >>> DK-2100 Copenhagen Ø >>> >>> Tel.: (+45) 3532 1063 >>> Mobil:(+45) 2618 3636 >>> email:mccarausu@zmuc.ku.dk >>> web: http://www.DanBIF.dk >>> ....oooO.............. >>> ....(....)....Oooo.... >>> .....)../. ...(....)... >>> .....(_/.......)../...... >>> .............. (_/....... >>> -------------------------------------------- >>> >>> >>> -----Original Message----- >>> From: ipt-bounces(a)lists.gbif.org [mailto:ipt- >>> bounces(a)lists.gbif.org] On >>> Behalf Of Tim Robertson >>> Sent: 26. februar 2009 16:26 >>> To: ipt(a)lists.gbif.org >>> Subject: [IPT] Beta update >>> >>> Dear All, >>> >>> A new version has just been deployed, and all user accounts have >>> been >>> kept intact, but you will notice significant changes, and we hope >>> improvements. >>> Please use the http://code.google.com/p/gbif-providertoolkit/issues/ >>> list to track and input issues. >>> >>> If there is a volunteer wishing to test an upload of a large dataset >>> (500,000+ records) it would be very much appreciated if you could >>> report back on the experience. >>> >>> Thanks for all your feedback, >>> >>> Best wishes, >>> >>> Tim >>> >>> _______________________________________________ >>> IPT mailing list >>> IPT(a)lists.gbif.org >>> http://lists.gbif.org/mailman/listinfo/ipt >>> >>> >> >> >> ____________________________________________________________ >> Tim Robertson >> Systems Architect >> Global Biodiversity Information Facility Secretariat (GBIF) >> Universitetsparken 15, 2100 Copenhagen Ø, Denmark >> http://www.gbif.org >> trobertson(a)gbif.org >> Phone: +45 35 32 14 87 (Office) >> Fax: +45 35 32 14 80 >> ____________________________________________________________ >> >> _______________________________________________ >> IPT mailing list >> IPT(a)lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt >> > > _______________________________________________ > IPT mailing list > IPT(a)lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > <logs.zip>

2 1